@article {pmid39692564,
year = {2024},
author = {Sloan, DB and Broz, AK and Kuster, SA and Muthye, V and Peñafiel-Ayala, A and Marron, JR and Lavrov, DV and Brieba, LG},
title = {Expansion of the MutS gene family in plants.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koae277},
pmid = {39692564},
issn = {1532-298X},
abstract = {The widely distributed MutS gene family functions in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded this gene family in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Cyanobacterial-like MutS1 and MutS2 genes were ancestrally gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae). Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing a name, "plant MSH1" is not directly related to the MSH1 gene in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotes. There has been substantial progress in understanding the functions of plant MSH1 and MSH6 genes, but the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are mitochondrial and/or plastid-targeted, the expansion of this family has played a large role in shaping plant organelle genetics.},
}

@article {pmid39690351,
year = {2024},
author = {Ullah, H and Hassan, SHA and Yang, Q and Salama, ES and Liu, P and Li, X},
title = {Dynamic interaction of antibiotic resistance between plant microbiome and organic fertilizers: sources, dissemination, and health risks.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {1},
pages = {4},
pmid = {39690351},
issn = {1573-0972},
support = {lzujbky-2024-ey12//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Microbiota/drug effects ; *Fertilizers/analysis ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Plants/microbiology ; *Soil Microbiology ; *Bacteria/drug effects/genetics/classification ; *Manure/microbiology ; Gene Transfer, Horizontal ; Agriculture/methods ; Drug Resistance, Bacterial ; Sewage/microbiology ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Animals ; Soil/chemistry ; },
abstract = {Antibiotic resistance is a global health problem driven by the irrational use of antibiotics in different areas (such as agriculture, animal farming, and human healthcare). Sub-lethal concentrations of antibiotic residues impose selective pressure on environmental, plant-associated, and human microbiome leading to the emergence of antibiotic-resistant bacteria (ARB). This review summarizes all sources of antibiotic resistance in agricultural soils (including manure, sewage sludge, wastewater, hospitals/pharmaceutical industry, and bioinoculants). The factors (such as the physicochemical properties of soil, root exudates, concentration of antibiotic exposure, and heavy metals) that facilitate the transmission of resistance in plant microbiomes are discussed. Potential solutions for effective measures and control of antibiotic resistance in the environment are also hypothesized. Manure exhibits the highest antibiotics load, followed by hospital and municipal WW. Chlortetracycline, tetracycline, and sulfadiazine have the highest concentrations in the manure. Antibiotic resistance from organic fertilizers is transmitted to the plant microbiome via horizontal gene transfer (HGT). Plant microbiomes serve as transmission routes of ARB and ARGS to humans. The ingestion of ARB leads to human health risks (such as ineffectiveness of medication, increased morbidity, and mortality).},
}

*Microbiota/drug effects
*Fertilizers/analysis
Humans
*Anti-Bacterial Agents/pharmacology
*Plants/microbiology
*Soil Microbiology
*Bacteria/drug effects/genetics/classification
*Manure/microbiology
Gene Transfer, Horizontal
Agriculture/methods
Drug Resistance, Bacterial
Sewage/microbiology
Drug Resistance, Microbial/genetics
Wastewater/microbiology
Animals
Soil/chemistry

@article {pmid39689477,
year = {2024},
author = {Li, S and Wang, K and Wang, D and Wang, H and Zhao, H and Pu, J and Wang, K and Li, C},
title = {Distribution and environmental dissemination of antibiotic resistance genes in poultry farms and surrounding ecosystems.},
journal = {Poultry science},
volume = {104},
number = {1},
pages = {104665},
doi = {10.1016/j.psj.2024.104665},
pmid = {39689477},
issn = {1525-3171},
abstract = {Antibiotic resistance poses a significant threat to human and animal health worldwide, with farms serving as crucial reservoirs of Antibiotic Resistance Genes (ARGs) and Antibiotic-resistant bacteria. However, the distribution of ARGs in poultry farms and their transmission patterns in the environment remain poorly understood. This study collected samples of aerosol microorganisms, cloacal matter, soil, and vegetables from poultry farms and surrounding environments at three different distances. We used 16S rRNA gene sequencing and HT-qPCR to analyze the characteristics of aerosol microbial communities and the abundance of ARGs. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in cloacal samples, aerosol samples, and vegetable samples, while Proteobacteria Actinobacteriota and Acidobacteria dominated soil. Pseudomonas was dominant in cloacal samples at the genus level, whereas Fusobacterium was prevalent in soil. The diversity and richness of bacterial communities were more similar between cloacal samples than those observed between either sample type compared with soil. Our results showed that tetracycline and aminoglycoside ARG relative abundance was high across all sample types but significantly increased within feces/air compared to soils/vegetables. Association analysis revealed five potential host genera for ARG/MGE presence among various microbiota populations studied here. Our findings confirm that farms are important sources for the environmental dissemination of pathogens and ARGs.},
}

@article {pmid39686544,
year = {2024},
author = {Stott, C and Diop, A and Raymann, K and Bobay, LM},
title = {Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae256},
pmid = {39686544},
issn = {1537-1719},
abstract = {Microbial communities that maintain symbiotic relationships with animals evolve by adapting to the specific environmental niche provided by their host, yet understanding their patterns of speciation remains challenging. Whether bacterial speciation occurs primarily through allopatric or sympatric processes remains an open question. In addition, patterns of DNA transfers, which are pervasive in bacteria, are more constrained in a closed host-gut system. Eusocial bees have co-evolved with their specialized microbiota for over 85 million years, constituting a simple and valuable system to study the complex dynamics of host-associated microbial interactions. Here we studied the patterns of speciation and evolution of seven specialized gut bacteria from three clades of eusocial bee species: western honey bees, eastern honey bees and bumblebees. We conducted genomic analyses to infer species delineation relative to the patterns of homologous recombination (HR), and horizontal gene transfer (HGT). The studied bacteria presented various modes of evolution and speciation relative to their hosts, but some trends were consistent across all of them. We observed a clear interruption of homologous recombination between bacteria inhabiting different bee hosts, which is consistent with a mechanism of allopatric speciation, but we also identified interruptions of homologous recombination within hosts, suggesting recent or ongoing sympatric speciation. In contrast to HR, we observed that HGT events were not constrained by species borders. Overall, our findings show that in host-associated bacterial populations, patterns of HR and HGT have different impacts on speciation patterns, which are driven by both allopatric and sympatric speciation processes.},
}

@article {pmid39684674,
year = {2024},
author = {Wiśniewski, P and Chajęcka-Wierzchowska, W and Zadernowska, A},
title = {High-Pressure Processing Influences Antibiotic Resistance Gene Transfer in Listeria monocytogenes Isolated from Food and Processing Environments.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684674},
issn = {1422-0067},
support = {2018/29/B/NZ9/00645 (OPUS-15)//National Science Center/ ; },
mesh = {*Listeria monocytogenes/genetics/drug effects ; *Food Microbiology ; *Anti-Bacterial Agents/pharmacology ; Food Handling/methods ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Pressure ; Daucus carota/microbiology/genetics ; },
abstract = {The study aimed to assess the high-pressure processing (HPP) impact on antibiotic resistance gene transfer in L. monocytogenes from food and food processing environments, both in vitro (in microbiological medium) and in situ (in carrot juice), using the membrane filter method. Survival, recovery, and frequency of antibiotic resistance gene transfer analyses were performed by treating samples with HPP at different pressures (200 MPa and 400 MPa). The results showed that the higher pressure (400 MPa) had a significant effect on increasing the transfer frequency of genes such as fosX, encoding fosfomycin resistance, and tet_A1, tet_A3, tetC, responsible for tetracycline resistance, both in vitro and in situ. In contrast, the Lde gene (the gene encoding ciprofloxacin resistance) was not transferred under any conditions. In the food matrix (carrot juice), greater variability in results was observed, suggesting that food matrices may have a protective effect on bacteria and modify HPP efficacy. In general, an increase in MIC values for antibiotics was noted in transconjugants compared to donors. Genotypic analysis of transconjugants showed differences in genetic structure, especially after exposure to 400 MPa pressure, indicating genotypic changes induced by pressure stress. The study confirms the possibility of antibiotic resistance genes transfer in the food environment, even from strains showing initial susceptibility to antibiotics carrying so-called silent antibiotic resistance genes, highlighting the public health risk of the potential spread of antibiotic-resistant strains through the food chain. The findings suggest that high-pressure processing can increase and decrease the frequency of resistance gene transfer depending on the strain, antibiotic combination, and processing conditions.},
}

*Listeria monocytogenes/genetics/drug effects
*Food Microbiology
*Anti-Bacterial Agents/pharmacology
Food Handling/methods
Gene Transfer, Horizontal
Drug Resistance, Bacterial/genetics
Microbial Sensitivity Tests
Pressure
Daucus carota/microbiology/genetics

@article {pmid39671179,
year = {2024},
author = {Chen, X and Urban, JM and Wurlitzer, J and Wei, X and Han, J and E O'Connor, S and Rudolf, JD and Köllner, TG and Chen, F},
title = {Canonical terpene synthases in arthropods: Intraphylum gene transfer.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {51},
pages = {e2413007121},
doi = {10.1073/pnas.2413007121},
pmid = {39671179},
issn = {1091-6490},
mesh = {Animals ; *Alkyl and Aryl Transferases/genetics/metabolism ; *Gene Transfer, Horizontal ; *Arthropods/genetics/enzymology ; *Phylogeny ; Male ; Female ; Evolution, Molecular ; Terpenes/metabolism ; },
abstract = {Insects employ terpenoids for communication both within and between species. While terpene synthases derived from isoprenyl diphosphate synthase have been shown to catalyze terpenoid biosynthesis in some insects, canonical terpene synthases (TPS) commonly found in plants, fungi, and bacteria were previously unidentified in insects. This study reveals the presence of TPS genes in insects, likely originating via horizontal gene transfer from noninsect arthropods. By examining 361 insect genomes, we identified TPS genes in five species of the Sciaridae family (fungus gnats). Additionally, TPS genes were found in Collembola (springtails) and Acariformes (mites) among diverse noninsect arthropods. Selected TPS enzymes from Sciaridae, Collembola, and Acariformes display monoterpene, sesquiterpene, and/or diterpene synthase activities. Through comprehensive protein database search and phylogenetic analysis, the TPS genes in Sciaridae were found to be most closely related to those in Acariformes, suggesting transfer of TPS genes from Acariformes to Sciaridae. In the model Sciaridae Bradysia coprophila, all five TPS genes are most highly expressed in adult males, suggesting a sex- and developmental stage-specific role of their terpenoid products. The finding of TPS genes in insects and their possible evolutionary origin through intraphylum gene transfer within arthropods sheds light on metabolic innovation in insects.},
}

Animals
*Alkyl and Aryl Transferases/genetics/metabolism
*Gene Transfer, Horizontal
*Arthropods/genetics/enzymology
*Phylogeny
Male
Female
Evolution, Molecular
Terpenes/metabolism

@article {pmid39670763,
year = {2024},
author = {Dalia, TN and Dalia, AB},
title = {SbcB facilitates natural transformation in Vibrio cholerae in an exonuclease-independent manner.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0041924},
doi = {10.1128/jb.00419-24},
pmid = {39670763},
issn = {1098-5530},
abstract = {UNLABELLED: Natural transformation (NT) is a conserved mechanism of horizontal gene transfer in bacterial species. During this process, DNA is taken up into the cytoplasm where it can be integrated into the host genome by homologous recombination. We have previously shown that some cytoplasmic exonucleases inhibit NT by degrading ingested DNA prior to its successful recombination. However, one exonuclease, SbcB, counterintuitively promotes NT in Vibrio cholerae. Here, through a systematic analysis of the distinct steps of NT, we show that SbcB acts downstream of DNA uptake into the cytoplasm, but upstream of recombinational branch migration. Through mutational analysis, we show that SbcB promotes NT in a manner that does not rely on its exonuclease activity. Finally, we provide genetic evidence that SbcB directly interacts with the primary bacterial recombinase, RecA. Together, these data advance our molecular understanding of horizontal gene transfer in V. cholerae and reveal that SbcB promotes homologous recombination during NT in a manner that does not rely on its canonical exonuclease activity.

IMPORTANCE: Horizontal gene transfer by natural transformation contributes to the spread of antibiotic resistance and virulence factors in bacterial species. Here, we study how one protein, SbcB, helps facilitate this process in the facultative bacterial pathogen Vibrio cholerae. SbcB is a well-known for its exonuclease activity (i.e., the ability to degrade the ends of linear DNA). Through this study, we uncover that while SbcB is important for natural transformation, it does not facilitate this process using its exonuclease activity. Thus, this work helps further our understanding of the molecular events required for this conserved evolutionary process and uncovers a function for SbcB beyond its canonical exonuclease activity.},
}

@article {pmid39668116,
year = {2025},
author = {Fagerquist, CK and Shi, Y and Park, J},
title = {Colicin Immunity Proteins of Pathogenic Bacteria Detected by Antibiotic-Induced SOS Response, Plasmid Sequencing, MALDI-TOF-TOF Mass Spectrometry, and Top-Down Proteomic Analysis.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {39},
number = {5},
pages = {e9964},
doi = {10.1002/rcm.9964},
pmid = {39668116},
issn = {1097-0231},
support = {ARS project number 0500-00093-001-00-D//USDA-ARS/ ; USDA-ARS project numbers: 2030-42000-055-000-D//USDA-ARS/ ; 0500-00093-001-00-D//USDA-ARS/ ; 2030-42000-055-000-D//USDA-ARS/ ; },
mesh = {*Colicins/genetics/chemistry ; *Proteomics/methods ; *Plasmids/genetics ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Anti-Bacterial Agents/pharmacology ; *SOS Response, Genetics ; Escherichia coli Proteins/genetics ; Shiga-Toxigenic Escherichia coli/genetics ; Sequence Analysis, DNA ; },
abstract = {RATIONALE: Plasmids can play a major role in the survival of pathogenic bacteria. Plasmids are acquired through horizontal gene transfer resulting in their spread across various strains, species and genera of bacteria. Colicins are bacterial protein toxins expressed by plasmid genes and released against co-located bacterial competitors.

METHODS: Three Shiga toxin-producing E. coli (STEC), whose genomes were sequenced previously, were analyzed using a combination of antibiotic induction, MALDI-TOF-TOF mass spectrometry, top-down proteomic analysis, and small plasmid sequencing. Protein biomarkers were identified using in-house software that matches protein mass and fragment ions of backbone cleavage by the aspartic acid effect. Predicted in silico protein structures assisted in the interpretation of protein ion fragmentation.

RESULTS: In addition to proteomic identification of phage-encoded Shiga toxin, we were able to identify plasmid-encoded immunity proteins for colicin D and E3. The genes for these plasmid-encoded proteins were not found in the previous genomic sequencing. However, resequencing of these strains for small plasmids revealed the genes to be present on 7-8 kb sized plasmids. Upstream of the colicin/immunity genes was an inverted repeat of the SOS/LexA box that represses gene expression until antibiotic challenge.

CONCLUSIONS: Our top-down proteomic method demonstrates that it is possible to screen putative pathogenic bacteria (whose genomes have been sequenced in full, in part or not at all) for the presence of phage- and plasmid-encoded toxin and colicin genes under SOS control. Small plasmid sequencing confirmed the presence of colicin/immunity genes (and their regulatory control) suggested from induction and top-down proteomic analysis.},
}

*Colicins/genetics/chemistry
*Proteomics/methods
*Plasmids/genetics
*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
*Anti-Bacterial Agents/pharmacology
*SOS Response, Genetics
Escherichia coli Proteins/genetics
Shiga-Toxigenic Escherichia coli/genetics
Sequence Analysis, DNA

@article {pmid39667859,
year = {2025},
author = {Pham, VD and Gerlinsky, M and Lettrari, S and Gänzle, MG},
title = {Evolution and ecology of C30 carotenoid synthesis in Lactobacillaceae and application of pigmented lactobacilli in pasta production.},
journal = {Food microbiology},
volume = {127},
number = {},
pages = {104688},
doi = {10.1016/j.fm.2024.104688},
pmid = {39667859},
issn = {1095-9998},
mesh = {*Carotenoids/metabolism ; *Fermentation ; *Phylogeny ; *Flour/microbiology/analysis ; Lactobacillaceae/metabolism/genetics/classification/isolation & purification ; Triticum/microbiology ; Food Microbiology ; Pigmentation ; Bacterial Proteins/genetics/metabolism ; Color ; },
abstract = {Pasta is a staple food in many parts of the world. A bright yellow colour of pasta is preferred by consumers. However, the colour is easily degraded during pasta processing. In a sourdough used for pasta production, we identified the pigmented Fructilactobacillus spp. FUA 3913, which represents a novel species that remains to be described ,and carries genes for the carotenoid-producing enzymes CrtM and CrtN in its genome. HPLC and spectral analysis identified the carotenoid as 4,4'-diaponeurosporene which is also produced by other lactobacilli expressing CrtM and CrtN. The topology of the CrtM/N trees does not match the phylogeny of the organisms, indicating that the enzymes were acquired by horizontal gene transfer. Pigmentation is frequent in insect-associated lactobacilli and lactobacilli that are part of the phyllosphere. Pigmented heterofermentative lactobacilli may enhance the yellow colour of durum semolina pasta by two mechanisms, first, by producing carotenoids and second, by preventing lipoxygenase-mediated degradation of durum carotenoids during dough mixing and extrusion. The comparison of the influence of fermentation with the non-pigmented, homofermentative Lactiplantibacillus plantarum, the non-pigmented heterofermentative Fructilactobacillus sanfranciscensis and the pigmented, heterofermentative Fructilactobacillus spp. FUA3913 indicated that inhibition of lipid oxidation is more relevant for the colour of pasta. In summary, our study provides novel insights into the evolution of C30 carotenoid and ecology of lactobacilli, and documents the use of pigmented lactobacilli to enhance the yellow colour of fermented foods.},
}

*Carotenoids/metabolism
*Fermentation
*Phylogeny
*Flour/microbiology/analysis
Lactobacillaceae/metabolism/genetics/classification/isolation & purification
Triticum/microbiology
Food Microbiology
Pigmentation
Bacterial Proteins/genetics/metabolism
Color

@article {pmid39667662,
year = {2024},
author = {Sandmann, G},
title = {Origin and evolution of yeast carotenoid pathways.},
journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids},
volume = {1870},
number = {2},
pages = {159586},
doi = {10.1016/j.bbalip.2024.159586},
pmid = {39667662},
issn = {1879-2618},
abstract = {Carotenoid pathways exist in nature in all domains. Comparison of the genes involved and their distribution allowed the elucidation of the origin and evolution of carotenoid biosynthesis from an early common ancestor of prokaryotes to Bacteria and Archaea. From the latter domain, carotenogenic genes are inherited by fungi as the only phylum of Eukarya. Carotenoid biosynthesis in the algal-plant lineage emerged independently by endosymbiotic gene transfer from an engulfed carotenogenic cyanobacterium. The early set of carotenogenic genes included crtB of phytoene synthase, the desaturase gene crtI, and the lycopene cyclase gene crtYcd for the synthesis of β-carotene. This carotenoid is further metabolised either to zeaxanthin and retinal due to the presence of crtZ and ccd or elongated to a C50 carotenoids by the crtEb gene product. The diversified pathways, especially in bacteria and fungi, result from gene modifications altering the substrate and product specificities of the corresponding enzymes or from the acquisition of novel genes. This was highlighted in more detail for the carotenoid pathways in the red yeasts of Basidiomycota leading to torularhodin, 2'-plectaniaxanthin, and astaxanthin.},
}

@article {pmid39660924,
year = {2024},
author = {Christel, S and Carrell, AA and Hochanadel, LH and Villalobos Solis, MI and Abraham, PE and Jawdy, SS and Chaves, JE and Engle, NL and Berhane, T-K and Yao, T and Chen, J-G and Muchero, W and Tschaplinski, TJ and Cregger, MA and Michener, JK},
title = {Catabolic pathway acquisition by rhizosphere bacteria readily enables growth with a root exudate component but does not affect root colonization.},
journal = {mBio},
volume = {},
number = {},
pages = {e0301624},
doi = {10.1128/mbio.03016-24},
pmid = {39660924},
issn = {2150-7511},
abstract = {Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally simulated the consequences of one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol between rhizosphere isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to the existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferable but is selectively neutral under environmentally relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting because the selective benefits are small.IMPORTANCEHorizontal gene transfer (HGT) is a key process in microbial evolution, but the factors limiting HGT are poorly understood. Aside from the rather unique scenario of antibiotic resistance, the evolutionary benefits of pathway acquisition are still unclear. To experimentally test the effects of pathway acquisition, we transferred a pathway for catabolism of a plant-derived aromatic compound between soil bacteria isolated from the roots of poplar trees and determined the resulting phenotypic and fitness effects. We found that pathway acquisition allowed bacteria to grow using the plant-derived compound in the laboratory, but that this new phenotype did not provide an advantage when the bacteria were reinoculated onto plant roots. These results suggest that the benefits of pathway acquisition may be small when measured under ecologically-relevant conditions. From an engineering perspective, efforts to alter microbial community composition in situ by manipulating catabolic pathways or nutrient availability will be challenging when gaining access to a new niche does not provide a benefit.},
}

@article {pmid39660283,
year = {2024},
author = {Fang, L and Chen, R and Li, C and Sun, J and Liu, R and Shen, Y and Guo, X},
title = {The association between the genetic structures of commonly incompatible plasmids in Gram-negative bacteria, their distribution and the resistance genes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1472876},
pmid = {39660283},
issn = {2235-2988},
mesh = {*Plasmids/genetics ; *Gram-Negative Bacteria/genetics/drug effects ; *Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Incompatible plasmids play a crucial role in the horizontal transfer of antibiotic resistance in bacteria, particularly in Gram-negative bacteria, and have thus attracted considerable attention in the field of microbiological research. In the 1970s, these plasmids, housing an array of resistance genes and genetic elements, were predominantly discovered. They exhibit a broad presence in diverse host bacteria, showcasing diversity in geographic distribution and the spectrum of antibiotic resistance genes. The complex genetic structure of plasmids further accelerates the accumulation of resistance genes in Gram-negative bacteria. This article offers a comprehensive review encompassing the discovery process, host distribution, geographic prevalence, carried resistance genes, and the genetic structure of different types incompatible plasmids, including IncA, IncC, IncF, IncL, IncM, IncH, and IncP. It serves as a valuable reference for enhancing our understanding of the role of these different types of plasmids in bacterial evolution and the dissemination of antibiotic resistance.},
}

*Plasmids/genetics
*Gram-Negative Bacteria/genetics/drug effects
*Gene Transfer, Horizontal
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid39608506,
year = {2025},
author = {Chetri, S},
title = {Escherichia coli: An arduous voyage from commensal to Antibiotic-resistance.},
journal = {Microbial pathogenesis},
volume = {198},
number = {},
pages = {107173},
doi = {10.1016/j.micpath.2024.107173},
pmid = {39608506},
issn = {1096-1208},
mesh = {Humans ; *Virulence Factors/genetics ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli Infections/microbiology/drug therapy ; *Escherichia coli/genetics/drug effects/pathogenicity ; Animals ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome/drug effects ; Drug Resistance, Multiple, Bacterial/genetics ; Virulence/genetics ; Symbiosis ; },
abstract = {Escherichia coli (E. coli), a normal intestinal microbiota is one of the most common pathogen known for infecting urinary tract, wound, lungs, bone marrow, blood system and brain. Irrational and overuse of commercially available antibiotics is the most imperative reason behind the emergence of the life threatening infections caused due to antibiotic resistant pathogens. The World Health Organization (WHO) identified antimicrobial resistance (AMR) as one of the 10 biggest public health threats of our time. This harmless commensal can acquire a range of mobile genetic elements harbouring genes coding for virulence factors becoming highly versatile human pathogens causing severe intestinal and extra intestinal diseases. Although, E. coli has been the most widely studied micro-organism, it never ceases to astound us with its ability to open up new research avenues and reveal cutting-edge survival mechanisms in diverse environments that impact human and surrounding environment. This review aims to summarize and highlight persistent research gaps in the field, including: (i) the transfer of resistant genes among bacterial species in diverse environments, such as those associated with humans and animals; (ii) the development of resistance mechanisms against various classes of antibiotics, including quinolones, tetracyclines, etc., in addition to β-lactams; and (iii) the relationship between resistance and virulence factors for understanding how virulence factors and resistance interact to gain a better grasp of how resistance mechanisms impact an organism's capacity to spread illness and interact with the host's defences. Moreover, this review aims to offer a thorough overview, exploring the history and factors contributing to antimicrobial resistance (AMR), the different reported pathotypes, and their links to virulence in both humans and animals. It will also examine their prevalence in various contexts, including food, environmental, and clinical settings. The objective is to deliver a more informative and current analysis, highlighting the evolution from microbiota (historical context) to sophisticated diseases caused by highly successful pathogens. Developing more potent tactics to counteract antibiotic resistance in E. coli requires filling in these gaps. By bridging these gaps, we can strengthen our capacity to manage and prevent resistance, which will eventually enhance public health and patient outcomes.},
}

Humans
*Virulence Factors/genetics
*Anti-Bacterial Agents/pharmacology
*Escherichia coli Infections/microbiology/drug therapy
*Escherichia coli/genetics/drug effects/pathogenicity
Animals
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
Gastrointestinal Microbiome/drug effects
Drug Resistance, Multiple, Bacterial/genetics
Virulence/genetics
Symbiosis

@article {pmid39455017,
year = {2024},
author = {Zhou, Y and Yang, Y and Wu, C and Zhou, P and Gao, H and Wang, B and Zhao, H and Xu, Y and Yu, F},
title = {LuxS/AI-2 system facilitates the dissemination of antibiotic-resistant plasmids in Klebsiella pneumoniae.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {6},
pages = {107361},
doi = {10.1016/j.ijantimicag.2024.107361},
pmid = {39455017},
issn = {1872-7913},
mesh = {*Klebsiella pneumoniae/genetics/drug effects ; *Plasmids/genetics ; *Bacterial Proteins/genetics/metabolism ; *Carbon-Sulfur Lyases/genetics ; *Conjugation, Genetic ; *Quorum Sensing/genetics ; Homoserine/analogs & derivatives/metabolism ; Lactones/metabolism/pharmacology ; Gene Expression Regulation, Bacterial ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Plasmid conjugation is a central mechanism driving the dissemination of antibiotic resistance in Klebsiella pneumoniae. However, the conjugative operon requires specific stimuli for activation. Identifying signals and elucidating the underlying mechanisms is crucial in combating plasmid spread. This study uncovers a key mechanism promoting the dissemination of high-risk plasmids, including IncFII, IncX3, and IncX4 types, in K. pneumoniae. In this study, increased donor density significantly enhanced conjugation, and transcript levels of both conjugation and AI-2 quorum sensing genes were markedly upregulated. Mutating the luxS and lsrR genes in K. pneumoniae 1678 decreased plasmid conjugation efficiency in the 1678ΔluxS mutant, and significantly increased plasmid conjugation efficiency in the 1678ΔlsrR mutant. RT-qPCR and β-galactosidase assays showed that LsrR represses transcription of relaxosome and T4CP genes, whereas AI-2 (synthesised by LuxS) activates their expression. AlphaFold 3 docking models indicate that LsrR may bind directly to IncX plasmid relaxase promoters, inhibiting their expression. Adding external AI-2 signals revealed no effect on plasmid conjugation when LsrR was absent, confirming the dependence of AI-2 signals on LsrR repression. In conclusion, AI-2-mediated signalling enhances donor density effects on plasmid conjugation by de-repressing LsrR-mediated suppression.},
}

*Klebsiella pneumoniae/genetics/drug effects
*Plasmids/genetics
*Bacterial Proteins/genetics/metabolism
*Carbon-Sulfur Lyases/genetics
*Conjugation, Genetic
*Quorum Sensing/genetics
Homoserine/analogs & derivatives/metabolism
Lactones/metabolism/pharmacology
Gene Expression Regulation, Bacterial
Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology

@article {pmid39655960,
year = {2024},
author = {Tian, Q and Ye, H and Zhou, X and Wang, J and Zhang, L and Sun, W and Duan, C and Fan, M and Zhou, W and Bi, C and Ye, Q and Wong, A},
title = {Evaluating the health risk of probiotic supplements from the perspective of antimicrobial resistance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0001924},
doi = {10.1128/spectrum.00019-24},
pmid = {39655960},
issn = {2165-0497},
abstract = {UNLABELLED: Antimicrobial resistance remains a public health threat. Probiotics harboring antimicrobial resistant genes (ARGs) have, in recent years, been considered a potential health risk. Studies conducted on probiotics from increasingly popular health supplements have raised the possibility of transmitting ARGs to commensals in the human gut, concomitantly establishing a reservoir of ARGs and risking acquisition by opportunistic pathogens. Building on our previous study that reported multiple antibiotic resistance in probiotics of health supplements, in this research, we have attempted to detect their ARGs that may account for resistant phenotypes. ARGs responsible for tetracycline, macrolide, aminoglycoside, and glycopeptide resistance were prevalent in probiotics. Through laboratory adaptive evolution studies, we also show that streptomycin-adapted probiotics gained resistance to erythromycin, tetracycline, and doxycycline more effectively than non-adapted ones. When co-incubated with Enterococcus faecalis, Escherichia coli, or Staphylococcus aureus on Caco-2 and/or HCT-116 cells, streptomycin resistance was transferred from the adapted probiotics to generate transconjugants at frequencies comparable to or higher than that of other studies conducted through filter mating. Consistently, ARGs conferring resistance to streptomycin (aadA) and erythromycin [erm(B)-1] were detected in E. coli and S. aureus transconjugants, respectively, after co-incubation with streptomycin-adapted probiotics on Caco-2 cells. aadA and erm(B)-1 were both detected in E. faecalis transconjugant after the same co-incubation on HCT-116 cells. Our data and future comparative genomics and metagenomics studies conducted on animal models and in healthy, immunocompromised, and/or antibiotic-treated human cohorts will contribute to a more comprehensive understanding of probiotic consumption, application, and safety.

IMPORTANCE: Probiotics are becoming increasingly popular, with promising applications in food and medicine, but the risk of transferring ARGs to disease-causing bacteria has raised concerns. Our study detected ARGs in probiotics of health supplements conferring resistance to tetracycline, macrolide, aminoglycoside, and glycopeptide drugs. Streptomycin-adapted probiotics also gained resistance to other antibiotics more effectively than non-adapted ones. Importantly, we showed that streptomycin resistance could be transferred to other bacteria after co-incubation with probiotics on human intestinal cells. ARGs responsible for erythromycin and streptomycin resistance, which were initially absent in the recipient bacteria, were also detected in the transconjugants. Our data build the foundation for future studies that will be conducted on animal models and in humans and leveraging advanced metagenomics approaches to clarify the long-term health risk of probiotic consumption.},
}

@article {pmid39653497,
year = {2024},
author = {St Leger, RJ},
title = {The evolution of complex Metarhizium-insect-plant interactions.},
journal = {Fungal biology},
volume = {128},
number = {8 Pt B},
pages = {2513-2528},
doi = {10.1016/j.funbio.2024.01.001},
pmid = {39653497},
issn = {1878-6146},
mesh = {*Metarhizium/genetics/pathogenicity/physiology ; Animals ; *Insecta/microbiology ; *Plants/microbiology ; Gene Transfer, Horizontal ; Symbiosis ; Biological Evolution ; Host Specificity ; Host-Pathogen Interactions ; },
abstract = {Metarhizium species interact with plants, insects, and microbes within a diffuse coevolutionary framework that benefits soil health, biodiversity, and plant growth. The insect host ranges of these fungi vary greatly. Specialization to a narrow host range usually occurs in the tropics with its stable insect populations, and is characterized by the rapid evolution of existing protein sequences, sexual recombination, and small genomes. Host-generalists are associated with temperate regions and ephemeral insect populations. Their mutualistic plant-colonizing lifestyle increases survival when insects are rare, while facultative entomopathogenicity feeds both the fungi and plants when insects are common. Generalists have lost meiosis and associated genome defense mechanisms, enabling gene duplications to diversify functions related to plant colonization and host exploitation. Horizontal gene transfer events via transposons have also contributed to host range changes, while parasexuality combines beneficial mutations within individual clones of generalists. There is also a lot of genetic variation in insect populations and both pathogen virulence and insect immunity are linked with variations in stress responses. Thus, susceptibility to generalists can vary due to non-specific resistance to multiple stressors, multipurpose physical and chemical barriers, and heterogeneity in physiological and behavioral factors, such as sleep.},
}

*Metarhizium/genetics/pathogenicity/physiology
Animals
*Insecta/microbiology
*Plants/microbiology
Gene Transfer, Horizontal
Symbiosis
Biological Evolution
Host Specificity
Host-Pathogen Interactions

@article {pmid39647412,
year = {2024},
author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD},
title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.},
journal = {Environment international},
volume = {194},
number = {},
pages = {109155},
doi = {10.1016/j.envint.2024.109155},
pmid = {39647412},
issn = {1873-6750},
abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.},
}

@article {pmid39644844,
year = {2024},
author = {Liu, X and Fan, Q and Li, F and Wu, C and Yi, S and Lu, H and Wu, Y and Liu, Y and Tian, J},
title = {Assessing foodborne health risks from dietary exposure to antibiotic resistance genes and opportunistic pathogens in three types of vegetables: An in vitro simulation of gastrointestinal digestion.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136731},
doi = {10.1016/j.jhazmat.2024.136731},
pmid = {39644844},
issn = {1873-3336},
abstract = {Foodborne health risks posed by antibiotic resistant genes (ARGs) and pathogenic bacteria have garnered increasing global attention. However, the patterns of their propagation and reduction, as well as the resulting health risks in the human gastrointestinal tract, remain unknown. We employed leafy vegetables (water spinach), solanaceous vegetables (pepper), and root vegetables (radish) to investigate the propagation and reduction patterns of ARGs and pathogenic bacteria within an in vitro simulated digestion system. This system mimicked the soil-vegetable-stomach-small intestine (SVSTI) transmission chain. We found that kan, oqxA, and multidrug resistance genes were enriched by 1.10-fold, 11.2-fold, and 2.21-fold, respectively, along the transmission chain. The succession of bacterial communities and horizontal gene transfer mediated by intl1 were identified as the primary drivers of ARG accumulation. Notably, certain pathogenic bacteria (Bacillus cereus, Klebsiella pneumoniae) accumulated in the intestinal environment. According to our proposed health risk assessment system, Bacillus species, as potential ARG hosts, and multidrug ARGs are at a higher risk of exposure to intestinal environment through the transmission chain. Our findings highlight the significant health risks associated with the intake of ARGs and pathogenic bacteria carried by vegetables, emphasizing an urgent need to implement effective biological control measures in vegetable production and consumption.},
}

@article {pmid39642748,
year = {2024},
author = {Lin, H and Diarra, MS and Jia, G and Zhao, X},
title = {Detection of plasmids in Salmonella from poultry and investigating the potential horizontal transfer of antimicrobial resistance and virulence genes: PLASMID TRANSFER OF RESISTANCE AND VIRULENCE.},
journal = {Poultry science},
volume = {104},
number = {1},
pages = {104591},
doi = {10.1016/j.psj.2024.104591},
pmid = {39642748},
issn = {1525-3171},
abstract = {Antimicrobial resistance genes (ARGs) and virulence genes (VGs) have been widely reported in Salmonella which are major foodborne pathogens from poultry. This study assessed the replicon typing and conjugative ability of plasmids from poultry-derived Salmonella as well as ARGs and VGs carried by these plasmids using an in silico approach. Both PlasmidFinder 2.1 and VRprofile2 were employed to detect plasmids in Salmonella sequences downloaded from the National Center for Biotechnology Information (NCBI) Reference Sequences (RefSeq) database, and then oriTfinder was used to determine the conjugative ability of plasmids. The ARGs and VGs on plasmids were identified by both VRprofile2 and oriTfinder. The phenotypes of ARGs were predicted by ResFinder 4.1 and oriTfinder, while the phenotypes of virulence were predicted by oriTfinder and VRprofile2. We identified 183 plasmid sequences from 309 downloaded sequences. Among them, 77 (42.1 %) plasmids were conjugative, 25 (13.7 %) mobilizable, and 81 (44.3 %) non-mobilizable. Fifty-one plasmids (27.9 %) contained multi-replicons. One hundred and five plasmids carried 58 ARGs, belonging to 12 classes. The most prevalent ARG groups in plasmids were the aminoglycoside, β-lactam, sulfonamide, and tetracycline groups. In addition, 49 plasmids carried 36 different VGs belonging to 13 gene classes. The most prevalent VG groups were the adhesin, type III secretion system, and resistance to complement killing groups. The detected high percentage of conjugative plasmids and existence of many multiple replicons suggest possible high rates of plasmid-mediated horizontal gene transfer (HGT) events. Detection of previously unreported plasmid-borne VG (fdeC) from Salmonella in poultry calls for more vigilant monitoring.},
}

@article {pmid39535230,
year = {2024},
author = {van Westerhoven, AC and Dijkstra, J and Aznar Palop, JL and Wissink, K and Bell, J and Kema, GHJ and Seidl, MF},
title = {Frequent genetic exchanges revealed by a pan-mitogenome graph of a fungal plant pathogen.},
journal = {mBio},
volume = {15},
number = {12},
pages = {e0275824},
doi = {10.1128/mbio.02758-24},
pmid = {39535230},
issn = {2150-7511},
support = {AG-5797//Bill and Melinda Gates Foundation (GF)/ ; },
mesh = {*Genome, Mitochondrial/genetics ; *Fusarium/genetics/classification ; *Recombination, Genetic ; Evolution, Molecular ; Phylogeny ; Gene Transfer, Horizontal ; Genome, Fungal ; Plant Diseases/microbiology ; Genetic Variation ; },
abstract = {Mitochondria are present in almost all eukaryotic lineages. The mitochondrial genomes (mitogenomes) evolve separately from nuclear genomes, and they can therefore provide relevant insights into the evolution of their host species. Fusarium oxysporum is a major fungal plant pathogen that is assumed to reproduce clonally. However, horizontal chromosome transfer between strains can occur through heterokaryon formation, and recently, signs of sexual recombination have been observed. Similarly, signs of recombination in F. oxysporum mitogenomes challenged the prevailing assumption of clonal reproduction in this species. Here, we construct, to our knowledge, the first fungal pan-mitogenome graph of nearly 500 F. oxysporum mitogenome assemblies to uncover the variation and evolution. In general, the gene order of fungal mitogenomes is not well conserved, yet the mitogenome of F. oxysporum and related species are highly colinear. We observed two strikingly contrasting regions in the F. oxysporum pan-mitogenome, comprising a highly conserved core mitogenome and a long variable region (6-16 kb in size), of which we identified three distinct types. The pan-mitogenome graph reveals that only five intron insertions occurred in the core mitogenome and that the long variable regions drive the difference between mitogenomes. Moreover, we observed that their evolution is neither concurrent with the core mitogenome nor with the nuclear genome. Our large-scale analysis of long variable regions uncovers frequent recombination between mitogenomes, even between strains that belong to different taxonomic clades. This challenges the common assumption of incompatibility between genetically diverse F. oxysporum strains and provides new insights into the evolution of this fungal species.IMPORTANCEInsights into plant pathogen evolution is essential for the understanding and management of disease. Fusarium oxysporum is a major fungal pathogen that can infect many economically important crops. Pathogenicity can be transferred between strains by the horizontal transfer of pathogenicity chromosomes. The fungus has been thought to evolve clonally, yet recent evidence suggests active sexual recombination between related isolates, which could at least partially explain the horizontal transfer of pathogenicity chromosomes. By constructing a pan-genome graph of nearly 500 mitochondrial genomes, we describe the genetic variation of mitochondria in unprecedented detail and demonstrate frequent mitochondrial recombination. Importantly, recombination can occur between genetically diverse isolates from distinct taxonomic clades and thus can shed light on genetic exchange between fungal strains.},
}

*Genome, Mitochondrial/genetics
*Fusarium/genetics/classification
*Recombination, Genetic
Evolution, Molecular
Phylogeny
Gene Transfer, Horizontal
Genome, Fungal
Plant Diseases/microbiology
Genetic Variation

@article {pmid39642232,
year = {2024},
author = {Urquhart, AS and Gluck-Thaler, E and Vogan, AA},
title = {Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer.},
journal = {Science advances},
volume = {10},
number = {49},
pages = {eadp8738},
pmid = {39642232},
issn = {2375-2548},
mesh = {*Gene Transfer, Horizontal ; *DNA Transposable Elements/genetics ; *Evolution, Molecular ; Phylogeny ; Eukaryota/genetics ; Fungi/genetics ; Multigene Family ; Genome, Fungal ; },
abstract = {Horizontal gene transfer (HGT) disseminates genetic information between species and is a powerful mechanism of adaptation. Yet, we know little about its underlying drivers in eukaryotes. Giant Starship transposons have been implicated as agents of fungal HGT, providing an unprecedented opportunity to reveal the evolutionary parameters behind this process. Here, we characterize the ssf gene cluster, which contributes to formaldehyde resistance, and use it to demonstrate how mobile element evolution shapes fungal adaptation. We found that ssf clusters have been acquired by various distantly related Starships, which each exhibit multiple instances of horizontal transfer across fungal species (at least nine events, including between different taxonomic orders). Many ssf clusters have subsequently integrated into their host's genome, illustrating how Starships shape the evolutionary trajectory of fungal hosts beyond any single transfer. Our results demonstrate the key role Starships play in mediating rapid and repeated adaptation via HGT, elevating the importance of mobile element evolution in eukaryotic biology.},
}

*Gene Transfer, Horizontal
*DNA Transposable Elements/genetics
*Evolution, Molecular
Phylogeny
Eukaryota/genetics
Fungi/genetics
Multigene Family
Genome, Fungal

@article {pmid39642107,
year = {2024},
author = {Wingfield, BD and Wingfield, MJ},
title = {Gene transfer between fungal species triggers repeated coffee wilt disease outbreaks.},
journal = {PLoS biology},
volume = {22},
number = {12},
pages = {e3002901},
pmid = {39642107},
issn = {1545-7885},
mesh = {*Plant Diseases/microbiology ; *Gene Transfer, Horizontal ; *Disease Outbreaks ; Coffea/microbiology ; Coffee/microbiology ; DNA Transposable Elements/genetics ; },
abstract = {Two outbreaks of coffee wilt disease have devastated African coffee production. A PLOS Biology study suggests that horizontal gene transfer via large Starship transposons between 2 fungal species played a key role in the repeated emergence of the disease.},
}

*Plant Diseases/microbiology
*Gene Transfer, Horizontal
*Disease Outbreaks
Coffea/microbiology
Coffee/microbiology
DNA Transposable Elements/genetics

@article {pmid39642000,
year = {2024},
author = {Villavicencio, F and Albán, V and Satán, C and Quintana, H and Enríquez, W and Jaramillo, K and Flores, F and Arisqueta, L},
title = {Salmonella enterica Serovar Infantis KPC-2 Producer: First Isolate Reported in Ecuador.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {30},
number = {12},
pages = {502-508},
doi = {10.1089/mdr.2024.0072},
pmid = {39642000},
issn = {1931-8448},
mesh = {Ecuador ; *Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics ; *Salmonella enterica/drug effects/genetics ; Humans ; *Microbial Sensitivity Tests ; *Plasmids ; *Whole Genome Sequencing ; Serogroup ; Salmonella Infections/microbiology/drug therapy ; Gene Transfer, Horizontal ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Antimicrobial resistance is currently considered a public health threat. Carbapenems are antimicrobials for hospital use, and Enterobacterales resistant to these β-lactams have spread alarmingly in recent years, especially those that cause health care-associated infections. The blaKPC gene is considered one of the most important genetic determinants disseminated by plasmids, promoting horizontal gene transfer. This study describes, for the first time in Ecuador, and worldwide, the presence of a blaKPC-2 gene in an isolate of Salmonella enterica serovar Infantis from a clinical sample. Through whole-genome sequencing, we characterized the genetic determinants of antimicrobial resistance in this Salmonella ST-32 strain. Our results showed the presence of several resistance genes, including blaCTX-M-65, and a conjugative plasmid Kpn-WC17-007-03 that may be responsible for the horizontal transference of these resistance mechanisms.},
}

Ecuador
*Anti-Bacterial Agents/pharmacology
*beta-Lactamases/genetics
*Salmonella enterica/drug effects/genetics
Humans
*Microbial Sensitivity Tests
*Plasmids
*Whole Genome Sequencing
Serogroup
Salmonella Infections/microbiology/drug therapy
Gene Transfer, Horizontal
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid39640918,
year = {2024},
author = {Baede, VO and Jlassi, O and Lesiczka, PM and Younsi, H and Jansen, HJ and Dachraoui, K and Segobola, J and Ben Said, M and Veneman, WJ and Dirks, RP and Sprong, H and Zhioua, E},
title = {Similarities between Ixodes ricinus and Ixodes inopinatus genomes and horizontal gene transfer from their endosymbionts.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {6},
number = {},
pages = {100229},
pmid = {39640918},
issn = {2667-114X},
abstract = {The taxa Ixodes ricinus and Ixodes inopinatus are sympatric in Tunisia. The genetics underlying their morphological differences are unresolved. In this study, ticks collected in Jouza-Amdoun, Tunisia, were morphologically identified and sequenced using Oxford Nanopore Technologies. Three complete genome assemblies of I. inopinatus and three of I. ricinus with BUSCO scores of ∼98% were generated, including the reconstruction of mitochondrial genomes and separation of both alleles of the TRPA1, TROSPA and calreticulin genes. Deep sequencing allowed the first descriptions of complete bacterial genomes for "Candidatus Midichloria mitochondrii", Rickettsia helvetica and R. monacensis from North Africa, and the discovery of extensive integration of parts of the Spiroplasma ixodetis and "Ca. M. mitochondrii" into the nuclear genome of these ticks. Phylogenetic analyses of the mitochondrial genome, the nuclear genes, and symbionts showed differentiation between Tunisian and Dutch ticks, but high genetic similarities between Tunisian I. ricinus and I. inopinatus. Subtraction of the genome assemblies identified the presence of some unique sequences, which could not be confirmed when screening a larger batch of I. ricinus and I. inopinatus ticks using PCR. Our findings yield compelling evidence that I. inopinatus is genetically highly similar, if not identical, to sympatric I. ricinus. Defined morphological differences might be caused by extrinsic factors such as micro-climatic conditions or bloodmeal composition. Our findings support the existence of different lineages of I. ricinus as well of its symbionts/pathogens from geographically dispersed locations.},
}

@article {pmid39637834,
year = {2024},
author = {Peck, LD and Llewellyn, T and Bennetot, B and O'Donnell, S and Nowell, RW and Ryan, MJ and Flood, J and Rodríguez de la Vega, RC and Ropars, J and Giraud, T and Spanu, PD and Barraclough, TG},
title = {Horizontal transfers between fungal Fusarium species contributed to successive outbreaks of coffee wilt disease.},
journal = {PLoS biology},
volume = {22},
number = {12},
pages = {e3002480},
pmid = {39637834},
issn = {1545-7885},
mesh = {*Plant Diseases/microbiology ; *Fusarium/genetics/pathogenicity/isolation & purification ; *Gene Transfer, Horizontal ; *Coffea/microbiology/genetics ; *Genome, Fungal/genetics ; Phylogeny ; Disease Outbreaks ; Host Specificity ; },
abstract = {Outbreaks of fungal diseases have devastated plants and animals throughout history. Over the past century, the repeated emergence of coffee wilt disease caused by the fungal pathogen Fusarium xylarioides severely impacted coffee production across sub-Saharan Africa. To improve the disease management of such pathogens, it is crucial to understand their genetic structure and evolutionary potential. We compared the genomes of 13 historic strains spanning 6 decades and multiple disease outbreaks to investigate population structure and host specialisation. We found that F. xylarioides comprised at least 4 distinct lineages: 1 host-specific to Coffea arabica, 1 to C. canephora var. robusta, and 2 historic lineages isolated from various Coffea species. The presence/absence of large genomic regions across populations, the higher genetic similarities of these regions between species than expected based on genome-wide divergence and their locations in different loci in genomes across populations showed that horizontal transfers of effector genes from members of the F. oxysporum species complex contributed to host specificity. Multiple transfers into F. xylarioides populations matched different parts of the F. oxysporum mobile pathogenicity chromosome and were enriched in effector genes and transposons. Effector genes in this region and other carbohydrate-active enzymes important in the breakdown of plant cell walls were shown by transcriptomics to be highly expressed during infection of C. arabica by the fungal arabica strains. Widespread sharing of specific transposons between F. xylarioides and F. oxysporum, and the correspondence of a putative horizontally transferred regions to a Starship (large mobile element involved in horizontal gene transfers in fungi), reinforce the inference of horizontal transfers and suggest that mobile elements were involved. Our results support the hypothesis that horizontal gene transfers contributed to the repeated emergence of coffee wilt disease.},
}

*Plant Diseases/microbiology
*Fusarium/genetics/pathogenicity/isolation & purification
*Gene Transfer, Horizontal
*Coffea/microbiology/genetics
*Genome, Fungal/genetics
Phylogeny
Disease Outbreaks
Host Specificity

@article {pmid39637780,
year = {2024},
author = {Huang, C and Cui, M and Li, T and Zheng, C and Qiu, M and Shan, M and Li, B and Zhang, L and Yu, Y and Fang, H},
title = {Migration of fungicides, antibiotics and resistome in the soil-lettuce system.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136725},
doi = {10.1016/j.jhazmat.2024.136725},
pmid = {39637780},
issn = {1873-3336},
abstract = {The emergence and spread of antibiotic resistance genes (ARGs) have become a serious issue in global agricultural production. However, understanding how these ARGs spread across different spatial scales, especially when exposed to both pesticides and antibiotics, has remained a challenge. Here, metagenomic assembly and binning methodologies were used to determine the spread pathway of ARGs in the soil-lettuce system under individual and combined exposure of fungicides (carbendazim and pyraclostrobin) and antibiotics (chlortetracycline and ciprofloxacin). These agrochemicals not only facilitated the spread of ARGs from soil to lettuce but also significantly elevated the risk of developing multi-antibiotic resistance among bacteria, especially to some antibiotic types (i.e. sulfonamide, aminoglycoside, quinolone, and tetracycline). ARGs could be migrated through distinct pathways, including both vertical and horizontal gene transfer, with plasmids playing a crucial role in facilitating the horizontal gene transfer. These transfer pathways have enabled key pathogenic bacteria belonging to the genera Acinetobacter, Pseudomonas, and Pantoea to acquire resistance and remain recalcitrant, posing the potential risk to crop health and food safety. In summary, our findings highlighted that fungicide and antibiotic could drive upward migration of ARGs in the soil-lettuce system and reduced the quality safety of agricultural products.},
}

@article {pmid39636264,
year = {2024},
author = {Romanov, KA and O'Connor, TJ},
title = {Legionella pneumophila, a Rosetta stone to understanding bacterial pathogenesis.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0032424},
doi = {10.1128/jb.00324-24},
pmid = {39636264},
issn = {1098-5530},
abstract = {Legionella pneumophila is an environmentally acquired pathogen that causes respiratory disease in humans. While the discovery of L. pneumophila is relatively recent compared to other bacterial pathogens, over the past 50 years, L. pneumophila has emerged as a powerhouse for studying host-pathogen interactions. In its natural habitat of fresh water, L. pneumophila interacts with a diverse array of protozoan hosts and readily evolve to expand their host range. This has led to the accumulation of the most extensive arsenal of secreted virulence factors described for a bacterial pathogen and their ability to infect humans. Within amoebae and human alveolar macrophages, the bacteria replicate within specialized membrane-bound compartments, establishing L. pneumophila as a model for studying intracellular vacuolar pathogens. In contrast, the virulence factors required for intracellular replication are specifically tailored to individual host cells types, allowing the pathogen to adapt to variation between disparate niches. The broad host range of this pathogen, combined with the extensive diversity and genome plasticity across the Legionella genus, has thus established this bacterium as an archetype to interrogate pathogen evolution, functional genomics, and ecology. In this review, we highlight the features of Legionella that establish them as a versatile model organism, new paradigms in bacteriology and bacterial pathogenesis resulting from the study of Legionella, as well as current and future questions that will undoubtedly expand our understanding of the complex and intricate biology of the microbial world.},
}

@article {pmid39631624,
year = {2024},
author = {Chen, W and Li, Z and Zheng, J and Wang, D and Gao, S and Zhou, W and Shen, H and Zhang, Y and Cao, X},
title = {A Comprehensive Analysis of the Epidemiological and Genomic Characteristics of Global Serratia marcescens.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2024.11.013},
pmid = {39631624},
issn = {2213-7173},
abstract = {BACKGROUND: Serratia marcescens outbreaks present significant challenges in clinical treatment, necessitating a deeper understanding of its epidemiological and genomic traits.

OBJECTIVE: To analyze the epidemiological and genomic characteristics of S. marcescens at a global scale.

METHODS: High-quality genomes of S. marcescens were retrieved from NCBI and annotated using Prodigal. Antibiotic resistance genes (ARGs) were identified via Blastn, sequence types (STs) were determined with a proprietary tool, and phylogenetic analysis was conducted to explore evolutionary relationships.

RESULTS: The study analyzed genomes from 33 countries, with major contributions from the USA (27.8%), UK (15.3%), Italy (14.7%), and Japan (10.7%). Human clinical samples accounted for 73.5% of the isolates, primarily from blood (44.8%) and sputum (19.3%). Eleven ARGs were identified, with sde being the most prevalent. Carbapenemase genes included blaSME, blaKPC, and blaNDM-1, though co-occurrence in individual strains was absent. Novel ARGs, including armA, rmtC, and fosA7.2, were reported. Among 855 genomes with identified STs, ST366, ST367, ST365, and ST423 were most common. Phylogenetic analysis highlighted significant genetic diversity and distinct evolutionary lineages.

CONCLUSION: Temporal analysis showed a genome peak in 2019, underscoring the global prevalence and adaptability of S. marcescens. The distribution of ARGs across diverse STs emphasizes horizontal gene transfer as a key driver of resistance. Judicious antibiotic use is essential to mitigate further resistance.},
}

@article {pmid39631390,
year = {2024},
author = {Feyissa, BA and de Becker, EM and Salesse-Smith, CE and Zhang, J and Yates, TB and Xie, M and De, K and Gotarkar, D and Chen, MSS and Jawdy, SS and Carper, DL and Barry, K and Schmutz, J and Weston, DJ and Abraham, PE and Tsai, CJ and Morrell-Falvey, JL and Taylor, G and Chen, JG and Tuskan, GA and Long, SP and Burgess, SJ and Muchero, W},
title = {An orphan gene BOOSTER enhances photosynthetic efficiency and plant productivity.},
journal = {Developmental cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.devcel.2024.11.002},
pmid = {39631390},
issn = {1878-1551},
abstract = {Organelle-to-nucleus DNA transfer is an ongoing process playing an important role in the evolution of eukaryotic life. Here, genome-wide association studies (GWAS) of non-photochemical quenching parameters in 743 Populus trichocarpa accessions identified a nuclear-encoded genomic region associated with variation in photosynthesis under fluctuating light. The identified gene, BOOSTER (BSTR), comprises three exons, two with apparent endophytic origin and the third containing a large fragment of plastid-encoded Rubisco large subunit. Higher expression of BSTR facilitated anterograde signaling between nucleus and plastid, which corresponded to enhanced expression of Rubisco, increased photosynthesis, and up to 35% greater plant height and 88% biomass in poplar accessions under field conditions. Overexpression of BSTR in Populus tremula × P. alba achieved up to a 200% in plant height. Similarly, Arabidopsis plants heterologously expressing BSTR gained up to 200% in biomass and up to 50% increase in seed.},
}

@article {pmid39631158,
year = {2024},
author = {Wang, Y and Liu, X and Huang, C and Han, W and Gu, P and Jing, R and Yang, Q},
title = {Antibiotic resistance genes and virulence factors in the plastisphere in wastewater treatment plant effluent: Health risk quantification and driving mechanism interpretation.},
journal = {Water research},
volume = {271},
number = {},
pages = {122896},
doi = {10.1016/j.watres.2024.122896},
pmid = {39631158},
issn = {1879-2448},
abstract = {Microplastics (MPs) are ubiquitous in wastewater treatment plants (WWTPs) and provide a unique niche for the spread of pollutants. To date, risk assessments and driving mechanisms of pathogens, antibiotic resistance genes (ARGs), and virulence factors (VFs) in the plastisphere are still lacking. Here, the microbiota, ARGs, VFs, their potential health risks, and biologically driving mechanisms on polythene (PE), polyethylene terephthalate (PET), poly (butyleneadipate-co-terephthalate) and polylactic acid blends (PBAT/PLA), PLA MPs, and gravel in WWTP effluent were investigated. The results showed that plastisphere and gravel biofilm harbored more distinctive microorganisms, promoting the uniqueness of pathogens, ARGs, and VFs compared to WWTP effluent. The abundance of major pathogens, ARGs, and VFs in the plastisphere was 1.01-1.35 times higher than that in the effluent. The high health risk of ARGs (HRA) calculated by fully considering the abundance, clinical relevance, pathogenicity, accessibility and mobility, and the high proportion of resistance contigs with mobile genetic elements confirmed that the plastisphere posed the highest potential health risk. Candidatus Microthrix and Candidatus Promineifilum were the essential hosts of ARGs and VFs in the plastisphere and gravel biofilm, respectively. High metabolic activity such as amino acid metabolism and biosynthesis of secondary metabolites, and highly expressed key genes increased the synthesis of ARGs and VFs. The primary mechanisms driving ARG enrichment in the plastisphere were enhanced microbial metabolic activity, increased frequency of horizontal gene transfer, heightened antibiotic inactivation and efflux, and reduced cell permeability. This study provided new insights into the ARGs, VFs, and health risks of the plastisphere and emphasized the importance of strict control of wastewater discharge.},
}

@article {pmid39630207,
year = {2024},
author = {Markert, EX and Severe, L and Severe, K and Twing, KI and Ward, LM},
title = {Genomes of novel Serratia strains from suburban soil.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0086624},
doi = {10.1128/mra.00866-24},
pmid = {39630207},
issn = {2576-098X},
abstract = {Here, we present genomes of three strains of Serratia initially isolated from suburban soil-one strain of S. ureilytica and two strains of S. quinivorans-resistant to multiple classes of antibiotics. This expands the genomic sampling of a group relevant to the ecosystem and human health.},
}

@article {pmid39628168,
year = {2024},
author = {Gu, JY and Li, WY and Zhou, Y and Zhang, GS},
title = {[Environmental Pollution and Extraction Methods of Extracellular Antibiotic Resistance Genes in Water].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {12},
pages = {7041-7048},
doi = {10.13227/j.hjkx.202401087},
pmid = {39628168},
issn = {0250-3301},
mesh = {*Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Water Microbiology ; Anti-Bacterial Agents ; Genes, Bacterial ; China ; Environmental Monitoring ; Bacteria/genetics/isolation & purification/drug effects ; Gene Transfer, Horizontal ; },
abstract = {Antibiotics are widely used to treat diseases such as bacterial infections. However, the abuse of antibiotics has led to the spread of antibiotic resistant bacteria and intracellular and extracellular antibiotic resistance genes, making China one of the countries with the highest incidence of antibiotic resistance and thus threatening public health. Extracellular antibiotic resistance genes, as one of the novel environmental pollutants, could exist in water for a long time and could be transmitted between different bacteria through horizontal gene transfer, resulting in the spread of antibiotic resistance. At present, due to the limitation of enrichment and recovery methods, the in-depth studies of extracellular antibiotic resistance genes in water have been rarely reported. Thus, it is impossible to carry out effective supervision and risk assessments. Based on literature analysis and investigation, the pollution sources, current situations, and characteristics of extracellular antibiotic resistance genes in water are expounded. Meanwhile, the advantages and disadvantages of their enrichment and recovery methods are compared and analyzed and the enrichment and recovery methods are verified and discussed through practical cases. These provide theoretical reference for studies such as examining extracellular antibiotic resistance genes in water on their transmission and provide a technical basis for antibiotic resistance control and health risk assessments of extracellular antibiotic resistance genes.},
}

*Drug Resistance, Microbial/genetics
Drug Resistance, Bacterial/genetics
Water Microbiology
Anti-Bacterial Agents
Genes, Bacterial
China
Environmental Monitoring
Bacteria/genetics/isolation & purification/drug effects
Gene Transfer, Horizontal

@article {pmid39626640,
year = {2024},
author = {Magyar, LB and Ábrahám, E and Lipinszki, Z and Tarnopol, RL and Whiteman, NK and Varga, V and Hultmark, D and Andó, I and Cinege, G},
title = {Pore-forming toxin-like proteins in the anti-parasitoid immune response of Drosophila.},
journal = {Journal of innate immunity},
volume = {},
number = {},
pages = {1-24},
doi = {10.1159/000542583},
pmid = {39626640},
issn = {1662-8128},
abstract = {INTRODUCTION: Species of the ananassae subgroup of Drosophilidae are highly resistant to parasitoid wasp infections. We have previously shown that the genes encoding Cytolethal Distending Toxin B (CdtB) and the Apoptosis Inducing Protein of 56 kDa (AIP56) were horizontally transferred to these fly species from prokaryotes and are now instrumental in the anti-parasitoid immune defense of Drosophila ananassae. Here we describe a new family of genes, which encode proteins with Hemolysin E domains, heretofore only identified in prokaryotes. Hemolysin E proteins are pore-forming toxins, important virulence factors of bacteria.

METHODS: Bioinformatical, transcriptional and protein expressional studies were used.

RESULTS: The hemolysin E-like genes have a scattered distribution among the genomes of species belonging to several different monophyletic lineages in the family Drosophilidae. We detected structural homology with the bacterial Hemolysin E toxins and showed that the origin of the D. ananassae hemolysin E-like genes (hl1-38) is consistent with prokaryotic horizontal gene transfer. These genes encode humoral factors, secreted into the hemolymph by the fat body and hemocytes. Their expression is induced solely by parasitoid infection and the proteins bind to the developing parasitoids.

CONCLUSIONS: Hemolysin E-like proteins acquired by horizontal gene transfer and expressed by the primary immune organs may contribute to the elimination of parasitoids, as novel humoral factors in Drosophila innate immunity.},
}

@article {pmid39621811,
year = {2024},
author = {Wright, RCT and Wood, AJ and Bottery, MJ and Muddiman, KJ and Paterson, S and Harrison, E and Brockhurst, MA and Hall, JPJ},
title = {A chromosomal mutation is superior to a plasmid-encoded mutation for plasmid fitness cost compensation.},
journal = {PLoS biology},
volume = {22},
number = {12},
pages = {e3002926},
doi = {10.1371/journal.pbio.3002926},
pmid = {39621811},
issn = {1545-7885},
abstract = {Plasmids are important vectors of horizontal gene transfer in microbial communities but can impose a burden on the bacteria that carry them. Such plasmid fitness costs are thought to arise principally from conflicts between chromosomal- and plasmid-encoded molecular machineries, and thus can be ameliorated by compensatory mutations (CMs) that reduce or resolve the underlying causes. CMs can arise on plasmids (i.e., plaCM) or on chromosomes (i.e., chrCM), with contrasting predicted effects upon plasmid success and subsequent gene transfer because plaCM can also reduce fitness costs in plasmid recipients, whereas chrCM can potentially ameliorate multiple distinct plasmids. Here, we develop theory and a novel experimental system to directly compare the ecological effects of plaCM and chrCM that arose during evolution experiments between Pseudomonas fluorescens SBW25 and its sympatric mercury resistance megaplasmid pQBR57. We show that while plaCM was predicted to succeed under a broader range of parameters in mathematical models, chrCM dominated in our experiments, including conditions with numerous recipients, due to a more efficacious mechanism of compensation, and advantages arising from transmission of costly plasmids to competitors (plasmid "weaponisation"). We show analytically the presence of a mixed Rock-Paper-Scissors (RPS) regime for CMs, driven by trade-offs with horizontal transmission, that offers one possible explanation for the observed failure of plaCM to dominate even in competition against an uncompensated plasmid. Our results reveal broader implications of plasmid-bacterial evolution for plasmid ecology, demonstrating the importance of specific compensatory mutations for resistance gene spread. One consequence of the superiority of chrCM over plaCM is the likely emergence in microbial communities of compensated bacteria that can act as "hubs" for plasmid accumulation and dissemination.},
}

@article {pmid39621273,
year = {2025},
author = {Hancks, DC},
title = {An Evolutionary Framework Exploiting Virologs and Their Host Origins to Inform Poxvirus Protein Functions.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2860},
number = {},
pages = {257-272},
pmid = {39621273},
issn = {1940-6029},
mesh = {Humans ; *Poxviridae/genetics/physiology ; Animals ; *Viral Proteins/genetics/metabolism ; Host-Pathogen Interactions/genetics ; Evolution, Molecular ; Genome, Viral ; Poxviridae Infections/virology/veterinary ; Host Specificity/genetics ; Open Reading Frames/genetics ; },
abstract = {Poxviruses represent evolutionary successful infectious agents. As a family, poxviruses can infect a wide variety of species including humans, fish, and insects. While many other viruses are species-specific, an individual poxvirus species is often capable of infecting diverse hosts and cell types. For example, the prototypical poxvirus, vaccinia, is well known to infect numerous human cell types but can also infect cells from divergent hosts like frog neurons. Notably, poxvirus infections result in both detrimental human and animal diseases. The most infamous disease linked to a poxvirus is smallpox caused by variola virus. Poxviruses are large double-stranded DNA viruses, which uniquely replicate in the cytoplasm of cells. The model poxvirus genome encodes ~200 nonoverlapping protein-coding open reading frames (ORFs). Poxvirus gene products impact various biological processes like the production of virus particles, the host range of infectivity, and disease pathogenesis. In addition, poxviruses and their gene products have biomedical application with several species commonly engineered for use as vaccines and oncolytic virotherapy. Nevertheless, we still have an incomplete understanding of the functions associated with many poxvirus genes. In this chapter, we outline evolutionary insights that can complement ongoing studies of poxvirus gene functions and biology, which may serve to elucidate new molecular activities linked to this biomedically relevant class of viruses.},
}

Humans
*Poxviridae/genetics/physiology
Animals
*Viral Proteins/genetics/metabolism
Host-Pathogen Interactions/genetics
Evolution, Molecular
Genome, Viral
Poxviridae Infections/virology/veterinary
Host Specificity/genetics
Open Reading Frames/genetics

@article {pmid38806321,
year = {2024},
author = {Craske, MW and Wilson, JS and Fogg, PCM},
title = {Gene transfer agents: structural and functional properties of domesticated viruses.},
journal = {Trends in microbiology},
volume = {32},
number = {12},
pages = {1200-1211},
doi = {10.1016/j.tim.2024.05.002},
pmid = {38806321},
issn = {1878-4380},
mesh = {*Gene Transfer, Horizontal ; *Bacteriophages/genetics/physiology ; Rhodobacter capsulatus/virology/genetics/metabolism ; Archaea/virology/genetics ; Bacteria/virology/genetics/metabolism ; Evolution, Molecular ; DNA, Viral/genetics ; },
abstract = {Horizontal exchange of DNA between bacteria and archaea is prevalent and has major potential implications for genome evolution, plasticity, and population fitness. Several transfer mechanisms have been identified, including gene transfer agents (GTAs). GTAs are intricately regulated domesticated viruses that package host DNA into virus-like capsids and transfer this DNA throughout the bacterial community. Several important advances have recently been made in our understanding of these unusual particles. In this review, we highlight some of these findings, primarily for the model GTA produced by Rhodobacter capsulatus but also for newly identified GTA producers. We provide key insights into these important genetic elements, including the differences between GTAs from their ancestral bacteriophages, their regulation and control, and their elusive evolutionary function.},
}

*Gene Transfer, Horizontal
*Bacteriophages/genetics/physiology
Rhodobacter capsulatus/virology/genetics/metabolism
Archaea/virology/genetics
Bacteria/virology/genetics/metabolism
Evolution, Molecular
DNA, Viral/genetics

@article {pmid39617215,
year = {2024},
author = {Zuccarotto, A and Sollitto, M and Leclère, L and Panzella, L and Gerdol, M and Leone, S and Castellano, I},
title = {Molecular evolution of ovothiol biosynthesis in animal life reveals diversity of the natural antioxidant ovothiols in Cnidaria.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2024.11.037},
pmid = {39617215},
issn = {1873-4596},
abstract = {Sulfoxide synthase OvoA is the key enzyme involved in the biosynthesis of ovothiols (OSHs), secondary metabolites endowed with unique antioxidant properties. Understanding the evolution of such enzymes and the diversity of their metabolites should reveal fundamental mechanisms governing redox signaling and environmental adaptation. "Early-branching" animals such as Cnidaria display unique molecular diversity and symbiotic relationships responsible for the biosynthesis of natural products, however, they have been neglected in previous research on antioxidants and OSHs. In this work, we have integrated genome and transcriptome mining with biochemical analyses to study the evolution and diversification of OSHs biosynthesis in cnidarians. By tracing the history of the ovoA gene, we inferred its loss in the latest common ancestor of Medusozoa, followed by the acquisition of a unique ovoB/ovoA chimeric gene in Hydrozoa, likely through a horizontal gene transfer from dinoflagellate donors. While Anthozoa (corals and anemones), bearing canonical ovoA genes, produced a striking variety of OSHs (A, B, and C), the multifunctional enzyme in Hydrozoa was related to OSH B biosynthesis, as shown in Clytia hemisphaerica. Surprisingly, the ovoA-lacking jellyfish Aurelia aurita and Pelagia noctiluca also displayed OSHs, and we provided evidence of their incorporation from external sources. Finally, transcriptome mining revealed ovoA conserved expression pattern during larval development from Cnidaria to more evolved organisms and its regulation by external stimuli, such as UV exposure. The results of our study shed light on the origin and diversification of OSH biosynthesis in basal animals and highlight the importance of redox-active molecules from ancient metazoans as cnidarians to vertebrates.},
}

@article {pmid39615392,
year = {2024},
author = {Zhao, C and Suyamud, B and Yuan, Y and Ghosh, S and Xu, X and Hu, J},
title = {Effect of non-antibiotic factors on conjugative transfer of antibiotic resistance genes in aquaculture water.},
journal = {Journal of hazardous materials},
volume = {483},
number = {},
pages = {136701},
doi = {10.1016/j.jhazmat.2024.136701},
pmid = {39615392},
issn = {1873-3336},
abstract = {Aquaculture water with antibiotic resistance genes (ARGs) is escalating due to the horizontal gene transfer. Non-antibiotic stressors specifically found, including those from fishery feed and disinfectants, are potential co-selectors. However, the mechanisms underlying this process remains unclear. Intragenus and intergenus conjugative transfer systems of the antibiotic-resistant plasmid RP4 were established to examine conjugative transfer frequency under exposure to five widely used non-antibiotic factors in aquaculture water: iodine, oxolinic acid, NO2-N, NO3-N and H2O2 and four different recipient bacteria: E. coli HB101, Citrobacter portucalensis SG1, Vibrio harveyi and Vibrio alginolyticus. The study found that low concentrations of non-antibiotic factors significantly promoted conjugative transfer, whereas high concentrations inhibited it. Moreover, the conjugation transfer efficiencies were significantly different with different bacterial species within (E. coli HB101 ∼ 10[-3] %) or cross genera (C. portucalensis SG1 ∼10[-5] %, V. harveyi ∼1 %). Besides, excessive exposure concentrations inhibited the expression of related genes and the generation of reactive oxygen species (ROS). Regulation of multiple related genes and ROS-induced SOS responses are common primary mechanisms. However, the mechanisms of non-antibiotic factors differ from those of standard antibiotics, with direct changes in cell membrane permeability potentially playing a dominant role. Additionally, variations among non-antibiotic factors and the specific characteristics of bacterial species contribute to differences in conjugation mechanisms. Notably, this study found that non-antibiotic factors could increase the frequency of intergeneric conjugation beyond that of intrageneric conjugation. Furthermore, non-antibiotic factors influenced by multiple transport systems may raise the risk of unintended cross-resistance, significantly amplifying the potential for resistance gene spread. This study underscores the significance of non-antibiotic factors in the propagation of ARGs, highlighting their role in advancing aquaculture development and protecting human health.},
}

@article {pmid39611838,
year = {2024},
author = {Liu, F and Wang, S-H and Cheewangkoon, R and Zhao, R-L},
title = {Uneven distribution of prokaryote-derived horizontal gene transfer in fungi: a lifestyle-dependent phenomenon.},
journal = {mBio},
volume = {},
number = {},
pages = {e0285524},
doi = {10.1128/mbio.02855-24},
pmid = {39611838},
issn = {2150-7511},
abstract = {UNLABELLED: Horizontal gene transfer (HGT) in fungi is less understood despite its significance in prokaryotes. In this study, we systematically searched for HGT events in 829 representative fungal genomes. Using a combination of sequence similarity and phylogeny-based approaches, we detected 20,093 prokaryotic-derived transferred genes across 750 fungal genomes, via 8,815 distinct HGT events. Notably, our analysis revealed that eight lifestyle-related traits significantly influence HGT diversity in fungi. For instance, parasites exhibited the highest estimated number of HGT-acquired genes, followed by saprotrophs, with symbionts showing the lowest. HGT-acquired genes were predominantly associated with metabolism and cellular functions and underwent purifying selection. Moreover, horizontally transferred genes with introns have significantly higher expression levels compared to intron-lacking genes, suggesting a probable role of intron gains in the adaptation of HGT-acquired genes. Overall, our findings highlight the influence of lifestyle on HGT diversity in fungi and underscore the substantial contribution of HGT to fungal adaptation.

IMPORTANCE: This study sheds new light on the role of horizontal gene transfer (HGT) in fungi, an area that has remained relatively unexplored compared to its well-established prevalence in bacteria. By analyzing 829 fungal genomes, we identified over 20,000 genes that fungi acquired from prokaryotes, revealing the significant impact of HGT on fungal evolution. Our findings highlight that fungal lifestyle traits, such as being parasitic or saprotrophic, play a key role in determining the extent of HGT, with parasites showing the highest gene acquisition rates. We also uncovered unique patterns of HGT occurrence based on fungal morphology and reproduction. Importantly, genes with introns, which are more highly expressed, appear to play a crucial role in fungal adaptation. This research deepens our understanding of how HGT contributes to the metabolic diversity and ecological success of fungi, and it underscores the broader significance of gene transfer in shaping fungal evolution.},
}

@article {pmid39611587,
year = {2024},
author = {Sayid, R and van den Hurk, AWM and Rothschild-Rodriguez, D and Herrema, H and de Jonge, PA and Nobrega, FL},
title = {Characteristics of phage-plasmids and their impact on microbial communities.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20240014},
pmid = {39611587},
issn = {1744-1358},
support = {AUF 5188//Amsterdam University Fund/ ; PhD fellowship//Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers (ACS)/ ; //Bowel Research UK (BRUK)/ ; Aspasia premium (015.017.050)//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; BB/T008768/1//Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Black Futures Research Studentship//University of Southampton (University of Southampton UK)/ ; },
abstract = {Bacteria host various foreign genetic elements, most notably plasmids and bacteriophages (or phages). Historically, these two classes were seen as separate, but recent research has shown considerable interplay between them. Phage-plasmids (P-Ps) exhibit characteristics of both phages and plasmids, allowing them to exist extrachromosomally within bacterial hosts as plasmids, but also to infect and lyse bacteria as phages. This dual functionality enables P-Ps to utilize the modes of transmission of both phage and plasmids, facilitating the rapid dissemination of genetic material, including antibiotic resistance and virulence genes, throughout bacterial populations. Additionally, P-Ps have been found to encode toxin-antitoxin and CRISPR-Cas adaptive immune systems, which enhance bacterial survival under stress and provide immunity against other foreign genetic elements. Despite a growing body of literature on P-Ps, large gaps remain in our understanding of their ecological roles and environmental prevalence. This review aims to synthesise existing knowledge and identify research gaps on the impacts of P-Ps on microbial communities.},
}

@article {pmid39611041,
year = {2024},
author = {Liu, L and Lian, ZH and Lv, AP and Salam, N and Zhang, JC and Li, MM and Sun, WM and Tan, S and Luo, ZH and Gao, L and Yuan, Y and Ming, YZ and OuYang, YT and Li, YX and Liu, ZT and Hu, CJ and Chen, Y and Hua, ZS and Shu, WS and Hedlund, BP and Li, WJ and Jiao, JY},
title = {Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota.},
journal = {National science review},
volume = {11},
number = {11},
pages = {nwae378},
pmid = {39611041},
issn = {2053-714X},
abstract = {Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.},
}

@article {pmid39606649,
year = {2024},
author = {Qing, Y and Zou, Z and Jiang, G and Qin, L and Liu, K and Liu, Z},
title = {A global perspective on the abundance, diversity and mobility of antibiotic resistance genes in Escherichia coli.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1442159},
pmid = {39606649},
issn = {2297-1769},
abstract = {INTRODUCTION: Escherichia coli (E. coli), a ubiquitous opportunistic pathogen, poses a growing threat to human health due to the increasing prevalence of antibiotic resistance. However, a comprehensive understanding of the global distribution, diversity, and transmission of antibiotic resistance genes (ARGs) in E. coli remains lacking, hindering effective strategies to combat resistance.

METHODS: In this study, we analyzed 94,762 E. coli genome sequences obtained from the NCBI database using advanced bioinformatics tools. ARGs were identified by comparing sequences against a custom ARG database using BLAST. Mobile genetic element (MGE)-associated ARGs were identified by matching with ISfinder databases. Global distribution of ARGs was analyzed by clustering mobile ARG sequences with 99% genetic similarity.

RESULTS: Our analysis revealed that 50.51% of the E. coli genome sequences contained ARGs, totaling 301,317 identified ARG sequences. These ARGs were categorized into 12 major classes and 229 subtypes. Notably, ARGs associated with multi-drug resistance (MDR), β-lactams, macrolide-lincosamide-streptogramins (MLS), tetracyclines, and aminoglycosides were particularly abundant, with the subtypes mdtK, macB, and ampC being especially prevalent. Additionally, significant differences in ARG abundance and diversity were observed across countries, with higher diversity found in high-income nations. Furthermore, 9.28% of the ARG sequences were linked to MGEs, accounting for 98.25% of all ARG subtypes. Notably, 4.20% of mobile ARGs were identified in over 20 countries, with β-lactam and aminoglycoside ARGs being the most widespread.

DISCUSSION: This study provides a comprehensive overview of the global distribution and transmission of ARGs in E. coli. The high abundance of MDR and β-lactam-related ARGs, along with their widespread transmission across countries, highlights the urgent need for global surveillance and control measures. Furthermore, the strong association between ARGs and MGEs underscores the role of horizontal gene transfer in the spread of resistance. The observed variations in ARG diversity between countries suggest that socioeconomic factors, such as healthcare infrastructure and antibiotic usage patterns, significantly influence ARG prevalence. These findings are crucial for informing global strategies to mitigate the spread of antibiotic resistance and improve public health outcomes.},
}

@article {pmid39606646,
year = {2024},
author = {Wang, Z and Sun, M and Guo, S and Wang, Y and Meng, L and Shi, J and Geng, C and Han, D and Fu, X and Xue, J and Ma, H and Liu, K},
title = {Detection of drug resistance in Escherichia coli from calves with diarrhea in the Tongliao region: an analysis of multidrug-resistant strains.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1466690},
pmid = {39606646},
issn = {2297-1769},
abstract = {INTRODUCTION: Escherichia coli is a major pathogen responsible for calf diarrhea, which has been exacerbated by the irrational and unscientific use of antimicrobial drugs, leading to significant drug resistance.

METHODS: This study focused on the isolation and identification of E. coli from calf diarrhea samples in the Tongliao area of China. Isolation was conducted using selective media, Gram staining, and 16S rRNA sequencing. The minimum inhibitory concentration (MIC) of E. coli was determined through the microbroth dilution method. Additionally, the presence of antibiotic-resistant genes was detected, and multidrug-resistant strains were selected for whole-genome sequencing (WGS).

RESULTS: The results revealed that all 40 isolated strains of E. coli exhibited resistance to sulfadiazine sodium, enrofloxacin, and ciprofloxacin, with 90% of the strains being susceptible to polymyxin B. Notably, strains 11, 23, and 24 demonstrated severe resistance. The detection rates of the antibiotic resistance genes TEM-1, TEM-206, strA, strB, qacH, and blaCTX were 100%, indicating a high prevalence of these genes. Moreover, the majority of strains carried antibiotic resistance genes consistent with their resistance phenotypes. WGS of strains 11, 23, and 24 revealed genome sizes of 4,897,185 bp, 4,920,234 bp, and 4,912,320 bp, respectively. These strains carried two, one, and two plasmids, respectively. The prediction of antibiotic resistance genes showed a substantial number of these genes within the genomes, with strain 24 harboring the highest number, totaling 77 subspecies containing 88 antibiotic resistance genes.

DISCUSSION: In conclusion, all 40 isolated strains of E. coli from calf diarrhea in this study were multidrug-resistant, exhibiting a broad distribution of antibiotic resistance genes and mobile components. This poses a significant risk of horizontal gene transfer, highlighting the critical situation of antibiotic resistance in this region.},
}

@article {pmid39423563,
year = {2024},
author = {Gomberg, AF and Grossman, AD},
title = {It's complicated: relationships between integrative and conjugative elements and their bacterial hosts.},
journal = {Current opinion in microbiology},
volume = {82},
number = {},
pages = {102556},
doi = {10.1016/j.mib.2024.102556},
pmid = {39423563},
issn = {1879-0364},
support = {R35 GM148343/GM/NIGMS NIH HHS/United States ; },
mesh = {*Conjugation, Genetic ; *Bacteria/genetics/metabolism ; *DNA Transposable Elements/genetics ; Chromosomes, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {Integrative and conjugative elements (ICEs) are typically found integrated in a bacterial host chromosome. They can excise, replicate, and transfer from cell to cell. Many contain genes that confer phenotypes to host cells, including antibiotic resistances, specialized metabolisms, phage defense, and symbiosis or pathogenesis determinants. Recent studies revealed that at least three ICEs (ICEclc, Tn916, and TnSmu1) cause growth arrest or death of host cells upon element activation. This review highlights the complex interactions between ICEs and their hosts, including the recent examples of the significant costs to host cells. We contrast two examples of killing, ICEclc and Tn916, in which killing, respectively, benefits or impairs conjugation and emphasize the importance of understanding the impacts of ICE-host relationships on conjugation. ICEs are typically only active in a small fraction of cells in a population, and we discuss how phenotypes normally occurring in a small subset of host cells can be uncovered.},
}

*Conjugation, Genetic
*Bacteria/genetics/metabolism
*DNA Transposable Elements/genetics
Chromosomes, Bacterial/genetics
Gene Transfer, Horizontal

@article {pmid39515144,
year = {2024},
author = {Luo, Y and Xu, T and Li, B and Liu, F and Wu, B and Dobson, PS and Yin, H and Chen, Z and Qiu, Y and Huang, X},
title = {The effects of small plastic particles on antibiotic resistance gene transfer revealed by single cell and community level analysis.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136271},
doi = {10.1016/j.jhazmat.2024.136271},
pmid = {39515144},
issn = {1873-3336},
mesh = {*Escherichia coli/drug effects/genetics ; *Polystyrenes/toxicity/chemistry ; *Particle Size ; Microplastics/toxicity ; Gene Transfer, Horizontal ; Sewage/microbiology ; Single-Cell Analysis ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics/drug effects ; Plastics/toxicity ; Anti-Bacterial Agents/pharmacology/toxicity ; },
abstract = {Small plastic particles with sizes comparable to bacterial cells, widely exist in environment. However, their effects on antibiotic resistance gene (ARG) dissemination remain unclear. Using polystyrene (PS) particles (0.2 µm, 2 µm, 5 µm, 10 µm, 15 µm, 20 µm) as models, conjugative transfer of ARGs between the donor E. coli and different recipients (E. coli or sludge bacterial community) was investigated. Compared to the pure strain, the sludge bacterial community exposed to PS particles showed higher transfer frequencies (1.67 to 14.31 times the blank control). The transfer frequencies first decreased and then increased with particle size, and plastics similar in size to bacteria (e.g., 2 µm) appear to be a transitional zone with minimal impact on ARG transmission. Furthermore, using microfluidics, in-situ observation at single cell level found that 2 µm plastics can act as barriers between donor and recipient bacteria inhibiting growth, but conjugation events mostly occurred around them. Conversely, nanoplastics (e.g., 0.2 µm) and larger microplastics (e.g., 20 µm) significantly promote conjugation, mainly due to increased reactive oxygen species production and cell membrane permeability, or facilitating bacterial adhesion and biofilm formation, respectively. This study aids in assessing environmental risks of small plastic particles on ARG dissemination.},
}

*Escherichia coli/drug effects/genetics
*Polystyrenes/toxicity/chemistry
*Particle Size
Microplastics/toxicity
Gene Transfer, Horizontal
Sewage/microbiology
Single-Cell Analysis
Drug Resistance, Microbial/genetics
Drug Resistance, Bacterial/genetics/drug effects
Plastics/toxicity
Anti-Bacterial Agents/pharmacology/toxicity

@article {pmid39454331,
year = {2024},
author = {Wang, Y and Ren, Z and Wu, Y and Li, Y and Han, S},
title = {Antibiotic resistance genes transfer risk: Contributions from soil erosion and sedimentation activities, agricultural cycles, and soil chemical contamination.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136227},
doi = {10.1016/j.jhazmat.2024.136227},
pmid = {39454331},
issn = {1873-3336},
mesh = {*Agriculture ; *Soil Pollutants/toxicity/analysis ; *Drug Resistance, Microbial/genetics ; *Soil/chemistry ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/toxicity ; Soil Microbiology ; Geologic Sediments/chemistry ; },
abstract = {The transfer of antibiotic resistance genes (ARGs) pose environmental risks that are influenced by soil activity and pollution. Soil erosion and sedimentation accelerate degradation and migration, thereby affecting soil distribution and contamination. This study quantified the vertical and horizontal transfer capabilities of ARGs and simulated soil environments under various scenarios, such as erosion, agricultural cycles, and chemical pollution. The results showed that slope, runoff, and sediment volume significantly affected soil erosion and ARG transfer risks. The response of environmental factors to the transfer risk of ARGs is as follows: the promotion effect of soil deposition (average: 21.41 %) is significantly greater than the inhibitory effect of soil erosion (average: -11.31 %); the planting period (average: -64.654) is greater than the harvest period (average: -56.225); the response to soil chemical pollution is: the impact of phosphate fertilizer residues, antibiotics, and pesticide pollution is more significant. This study constructed a vertical and horizontal transfer system of ARGs in soil erosion and sedimentation environments and proposed a response analysis method for the impact of factors, such as soil erosion and sedimentation activities, agricultural cycles, and soil chemical pollution, on ARGs transfer capabilities.},
}

*Agriculture
*Soil Pollutants/toxicity/analysis
*Drug Resistance, Microbial/genetics
*Soil/chemistry
Gene Transfer, Horizontal
Anti-Bacterial Agents/toxicity
Soil Microbiology
Geologic Sediments/chemistry

@article {pmid39423639,
year = {2024},
author = {Xu, Y and Li, H and Ding, Y and Zhang, D and Liu, W},
title = {How nanoscale plastics facilitate the evolution of antibiotic resistance?.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136157},
doi = {10.1016/j.jhazmat.2024.136157},
pmid = {39423639},
issn = {1873-3336},
mesh = {*Serratia marcescens/drug effects/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Plastics/chemistry ; Gene Transfer, Horizontal ; Nanoparticles/chemistry ; Drug Resistance, Microbial/genetics ; },
abstract = {The plastic can enhance the proliferation of antibiotic resistance genes (ARGs), however, the effect of nanoplastics (NPLs) on bacterial antibiotic resistance has not been clearly explained. Herein, we explored the effects and mechanisms of NPLs of different sizes (200 and 600 nm) on the evolution of antibiotic resistance in Serratia marcescens. The results indicated that the evolution of bacterial antibiotic resistance could be promoted under NPLs exposure, which the median of relative abundance of ARGs was 1.11-1.46 times compared to the treatment without NPLs. Transcriptomic analysis showed that the larger size of NPLs mainly increased the permeability of bacterial cell membranes to efflux antibiotics, thus potentiating antibiotic resistance. While, the smaller NPLs is more than that, its enhanced the expression of antibiotic resistance by modulating bacterial metabolic processes. The genome SNP analysis found that the NPLs could cause the genetic mutation occurrence to alter the membrane transport and metabolism processes, and it increased at a size of 200 nm more than at 600 nm NPLs. Importantly, we demonstrated that the horizontal transfer of ARGs was augmented due to the NPLs could dock to bacterial surface proteins and pull their movement to contact with other bacteria (binding energy of membrane proteins: -8.54 kcal/mol), especially the smaller size. It suggests that NPLs will also contribute to the proliferation of ARGs in the environment. This study provides data for understanding the risk of bacterial resistance.},
}

*Serratia marcescens/drug effects/genetics/metabolism
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Plastics/chemistry
Gene Transfer, Horizontal
Nanoparticles/chemistry
Drug Resistance, Microbial/genetics

@article {pmid39305593,
year = {2024},
author = {Shen, Y and Zhang, B and Yao, Y and Wang, H and Chen, Z and Hao, A and Guo, P},
title = {Insights into the interactions of plant-associated bacteria and their role in the transfer of antibiotic resistance genes from soil to plant.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {135881},
doi = {10.1016/j.jhazmat.2024.135881},
pmid = {39305593},
issn = {1873-3336},
mesh = {*Soil Microbiology ; *Rhizosphere ; *Bacteria/genetics/metabolism/classification ; *Plant Roots/microbiology ; Plants/microbiology ; Microbiota ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Plant Shoots/microbiology/growth & development ; Gene Transfer, Horizontal ; },
abstract = {This study discussed the role of plant-associated microbiome in regulating ARG transfer in soil-plant systems. Results showed that target ARGs in plants were mainly derived from rhizosphere soil. Cooperative interactions among bacteria in rhizosphere soil, plant-roots, plant-shoots, and soil-roots-shoots systems occurred during ARG transfer. The number of modules and keystone taxa identified as positively correlated with ARG transfer in rhizosphere soil, roots, and shoots was 3 and 49, 3 and 41, 2 and 5, respectively. Among these modules, module 3 in roots was significantly positively correlated with module 3 in rhizosphere soils and module 2 in shoots, indicating that module 3 in roots played central hub roles in ARG transfer from rhizosphere soil to roost and shoots. This may be because module 3 in roots increased cell motility and xenobiotics biodegradation and metabolism. These keystone taxa mainly belonged to Proteobacteria that can carry ARGs to transfer in soil-plant systems, especially Clostridium-sensu_stricito and Pseudomonas in rhizosphere soil carried ARGs into the shoot. Additionally, they promoted ARG transfer by increasing plant biomass, net photosynthetic rate and water use efficiency. The findings helped reveal the mechanism of plant-associated bacterial interactions and provided understanding for potential risks of ARG transfer from soil to plants.},
}

*Soil Microbiology
*Rhizosphere
*Bacteria/genetics/metabolism/classification
*Plant Roots/microbiology
Plants/microbiology
Microbiota
Genes, Bacterial
Drug Resistance, Microbial/genetics
Plant Shoots/microbiology/growth & development
Gene Transfer, Horizontal

@article {pmid39605964,
year = {2024},
author = {Jia, J and Liu, Q and Zhao, E and Li, X and Xiong, X and Wu, C},
title = {Biofilm formation on microplastics and interactions with antibiotics, antibiotic resistance genes and pathogens in aquatic environment.},
journal = {Eco-Environment & Health},
volume = {3},
number = {4},
pages = {516-528},
pmid = {39605964},
issn = {2772-9850},
abstract = {Microplastics (MPs) in aquatic environments easily support biofilm development, which can interact with other environmental pollutants and act as harbors for microorganisms. Recently, numerous studies have investigated the fate and behavior of MP biofilms in aquatic environments, highlighting their roles in the spread of pathogens and antibiotic resistance genes (ARGs) to aquatic organisms and new habitats. The prevalence and effects of MP biofilms in aquatic environments have been extensively investigated in recent decades, and their behaviors in aquatic environments need to be synthesized systematically with updated information. This review aims to reveal the development of MP biofilm and its interactions with antibiotics, ARGs, and pathogens in aquatic environments. Recent research has shown that the adsorption capabilities of MPs to antibiotics are enhanced after the biofilm formation, and the adsorption of biofilms to antibiotics is biased towards chemisorption. ARGs and microorganisms, especially pathogens, are selectively enriched in biofilms and significantly different from those in surrounding waters. MP biofilm promotes the propagation of ARGs through horizontal gene transfer (HGT) and vertical gene transfer (VGT) and induces the emergence of antibiotic-resistant pathogens, resulting in increased threats to aquatic ecosystems and human health. Some future research needs and strategies in this review are also proposed to better understand the antibiotic resistance induced by MP biofilms in aquatic environments.},
}

@article {pmid39605872,
year = {2024},
author = {Kettlewell, R and Jones, C and Felton, TW and Lagator, M and Gifford, DR},
title = {Insights into durability against resistance from the antibiotic nitrofurantoin.},
journal = {npj antimicrobials and resistance},
volume = {2},
number = {1},
pages = {41},
pmid = {39605872},
issn = {2731-8745},
abstract = {Nitrofurantoin has shown exceptional durability against resistance over 70 years of use. This longevity stems from factors such as rapid achievement of therapeutic concentrations, multiple physiological targets against bacteria, low risk of horizontal gene transfer, and the need to acquire multiple mutations to achieve resistance. These combined features limit resistance emergence and spread of nitrofurantoin resistance. We propose nitrofurantoin as an exemplar for developing other durable treatments.},
}

@article {pmid39602248,
year = {2024},
author = {Dai, L and Wu, Z and Sahin, O and Zhao, S and Yu, EW and Zhang, Q},
title = {Mutation-based mechanism and evolution of the potent multidrug efflux pump RE-CmeABC in Campylobacter.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {51},
pages = {e2415823121},
doi = {10.1073/pnas.2415823121},
pmid = {39602248},
issn = {1091-6490},
support = {R01AI140669//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Campylobacter jejuni/genetics/metabolism ; *Evolution, Molecular ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacterial Proteins/genetics/metabolism ; *Mutation ; *Membrane Transport Proteins/genetics/metabolism ; Campylobacter/genetics/metabolism ; Humans ; Campylobacter Infections/microbiology ; Promoter Regions, Genetic ; Amino Acid Substitution ; },
abstract = {The resistance-nodulation-cell division (RND) superfamily of multidrug efflux systems are important players in mediating antibiotic resistance in gram-negative pathogens. Campylobacter jejuni, a major enteric pathogen, utilizes an RND-type transporter system, CmeABC, as the primary mechanism for extrusion of various antibiotics. Recently, a functionally potent variant of CmeABC (named RE-CmeABC) emerged in clinical Campylobacter isolates, conferring enhanced resistance to multiple antibiotic classes. Despite the clinical importance of RE-CmeABC, the molecular mechanisms for its functional gain and its evolutionary trajectory remain unknown. Here, we demonstrated that amino acid substitutions in RE-CmeB (inner membrane transporter), but not in RE-CmeA (periplasmic protein) and RE-CmeC (outer membrane protein), in conjunction with a nucleotide mutation in the promoter region of the efflux operon, are responsible for the functional gain of the multidrug efflux system. We also showed that RE-cmeABC is emerging globally and distributed in genetically diverse C. jejuni strains, suggesting its possible spread by horizontal gene transfer. Notably, many of RE-cmeABC harboring isolates were associated with the human host including strains from large disease outbreaks, indicating the clinical relevance and significance of RE-CmeABC. Evolutionary analysis indicated that RE-cmeB likely originated from Campylobacter coli, but its expansion mainly occurred in C. jejuni, possibly driven by antibiotic selection pressure. Additionally, RE-cmeB, but not RE-cmeA and RE-cmeC, experienced a selective sweep and was progressing to be fixed during evolution. Together, these results identify a mutation-based mechanism for functional gain in RE-CmeABC and reveal the key role of RE-CmeB in facilitating Campylobacter adaptation to antibiotic selection.},
}

*Campylobacter jejuni/genetics/metabolism
*Evolution, Molecular
*Drug Resistance, Multiple, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
*Bacterial Proteins/genetics/metabolism
*Mutation
*Membrane Transport Proteins/genetics/metabolism
Campylobacter/genetics/metabolism
Humans
Campylobacter Infections/microbiology
Promoter Regions, Genetic
Amino Acid Substitution

@article {pmid39599864,
year = {2024},
author = {Richards, VA and Ferrell, BD and Polson, SW and Wommack, KE and Fuhrmann, JJ},
title = {Soybean Bradyrhizobium spp. Spontaneously Produce Abundant and Diverse Temperate Phages in Culture.},
journal = {Viruses},
volume = {16},
number = {11},
pages = {},
pmid = {39599864},
issn = {1999-4915},
support = {1736030//National Science Foundation/ ; },
mesh = {*Bradyrhizobium/virology ; *Glycine max/virology/microbiology ; *Bacteriophages/isolation & purification/genetics/classification/physiology/ultrastructure ; Lysogeny ; Genome, Viral ; Symbiosis ; Microscopy, Electron, Transmission ; },
abstract = {Soybean bradyrhizobia (Bradyrhizobium spp.) are symbiotic root-nodulating bacteria that fix atmospheric nitrogen for the host plant. The University of Delaware Bradyrhizobium Culture Collection (UDBCC; 353 accessions) was created to study the diversity and ecology of soybean bradyrhizobia. Some UDBCC accessions produce temperate (lysogenic) bacteriophages spontaneously under routine culture conditions without chemical or other apparent inducing agents. Spontaneous phage production may promote horizontal gene transfer and shape bacterial genomes and associated phenotypes. A diverse subset (n = 98) of the UDBCC was examined for spontaneously produced virus-like particles (VLPs) using epifluorescent microscopy, with a majority (69%) producing detectable VLPs (>1 × 10[7] mL[-1]) in laboratory culture. Phages from the higher-producing accessions (>2.0 × 10[8] VLP mL[-1]; n = 44) were examined using transmission electron microscopy. Diverse morphologies were observed, including various tail types and lengths, capsid sizes and shapes, and the presence of collars or baseplates. In many instances, putative extracellular vesicles of a size similar to virions were also observed. Three of the four species examined (B. japonicum, B. elkanii, and B. diazoefficiens) produced apparently tailless phages. All species except B. ottawaense also produced siphovirus-like phages, while all but B. diazoefficiens additionally produced podovirus-like phages. Myovirus-like phages were restricted to B. japonicum and B. elkanii. At least three strains were polylysogens, producing up to three distinct morphotypes. These observations suggest spontaneously produced phages may play a significant role in the ecology and evolution of soybean bradyrhizobia.},
}

*Bradyrhizobium/virology
*Glycine max/virology/microbiology
*Bacteriophages/isolation & purification/genetics/classification/physiology/ultrastructure
Lysogeny
Genome, Viral
Symbiosis
Microscopy, Electron, Transmission

@article {pmid39599778,
year = {2024},
author = {Yoxsimer, AM and Offenberg, EG and Katzer, AW and Bell, MA and Massengill, RL and Kingsley, DM},
title = {Genomic Sequence of the Threespine Stickleback Iridovirus (TSIV) from Wild Gasterosteus aculeatus in Stormy Lake, Alaska.},
journal = {Viruses},
volume = {16},
number = {11},
pages = {},
pmid = {39599778},
issn = {1999-4915},
support = {Investigator/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; *Phylogeny ; Alaska ; *Smegmamorpha/virology ; *Genome, Viral ; *Fish Diseases/virology ; *Open Reading Frames ; *Iridovirus/genetics/classification/isolation & purification ; *Lakes/virology ; DNA Virus Infections/veterinary/virology ; Genomics/methods ; DNA, Viral/genetics ; },
abstract = {The threespine stickleback iridovirus (TSIV), a double-stranded DNA virus, was the first megalocytivirus detected in wild North American fishes. We report a second occurrence of TSIV in threespine stickleback (Gasterosteus aculeatus) from Stormy Lake, Alaska, and assemble a nearly complete genome of TSIV. The 115-kilobase TSIV genome contains 94 open reading frames (ORFs), with 91 that share homology with other known iridoviruses. We identify three ORFs that likely originate from recent lateral gene transfers from a eukaryotic host and one ORF with homology to B22 poxvirus proteins that likely originated from a lateral gene transfer between viruses. Phylogenetic analysis of 24 iridovirus core genes and pairwise sequence identity analysis support TSIV as a divergent sister taxon to other megalocytiviruses and a candidate for a novel species designation. Screening of stickleback collected from Stormy Lake before and after a 2012 rotenone treatment to eliminate invasive fish shows 100% positivity for TSIV in the two years before treatment (95% confidence interval: 89-100% prevalence) and 0% positivity for TSIV in 2024 after treatment (95% confidence interval: 0 to 3.7% prevalence), suggesting that the rotenone treatment and subsequent crash and reestablishment of the stickleback population is associated with loss of TSIV.},
}

Animals
*Phylogeny
Alaska
*Smegmamorpha/virology
*Genome, Viral
*Fish Diseases/virology
*Open Reading Frames
*Iridovirus/genetics/classification/isolation & purification
*Lakes/virology
DNA Virus Infections/veterinary/virology
Genomics/methods
DNA, Viral/genetics

@article {pmid39597557,
year = {2024},
author = {Shah, Y and Kafaie, S},
title = {Evaluating Sequence Alignment Tools for Antimicrobial Resistance Gene Detection in Assembly Graphs.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
pmid = {39597557},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) is an escalating global health threat, often driven by the horizontal gene transfer (HGT) of resistance genes. Detecting AMR genes and understanding their genomic context within bacterial populations is crucial for mitigating the spread of resistance. In this study, we evaluate the performance of three sequence alignment tools-Bandage, SPAligner, and GraphAligner-in identifying AMR gene sequences from assembly and de Bruijn graphs, which are commonly used in microbial genome assembly. Efficiently identifying these genes allows for the detection of neighboring genetic elements and possible HGT events, contributing to a deeper understanding of AMR dissemination. We compare the performance of the tools both qualitatively and quantitatively, analyzing the precision, computational efficiency, and accuracy in detecting AMR-related sequences. Our analysis reveals that Bandage offers the most precise and efficient identification of AMR gene sequences, followed by GraphAligner and SPAligner. The comparison includes evaluating the similarity of paths returned by each tool and measuring output accuracy using a modified edit distance metric. These results highlight Bandage's potential for contributing to the accurate identification and study of AMR genes in bacterial populations, offering important insights into resistance mechanisms and potential targets for mitigating AMR spread.},
}

@article {pmid39597512,
year = {2024},
author = {Banerji, A and Brinkman, NE and Davis, B and Franklin, A and Jahne, M and Keely, SP},
title = {Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
pmid = {39597512},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.},
}

@article {pmid39516559,
year = {2024},
author = {Ares-Arroyo, M and Nucci, A and Rocha, EPC},
title = {Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids.},
journal = {Nature microbiology},
volume = {9},
number = {12},
pages = {3240-3253},
pmid = {39516559},
issn = {2058-5276},
mesh = {*Plasmids/genetics ; *Escherichia coli/genetics ; *Conjugation, Genetic ; *Klebsiella pneumoniae/genetics ; *Acinetobacter baumannii/genetics/classification ; Computational Biology/methods ; Gene Transfer, Horizontal ; Replication Origin/genetics ; DNA, Bacterial/genetics/chemistry ; },
abstract = {Conjugative plasmids are important drivers of bacterial evolution. Most plasmids lack genes for conjugation and characterized origins of transfer (oriT), which has hampered our understanding of plasmid mobility. Here we used bioinformatic analyses to characterize occurrences of known oriT families across 38,057 plasmids, confirming that most conjugative and mobilizable plasmids lack identifiable oriTs. Recognizable oriT sequences tend to be intergenic, upstream of relaxase genes and specifically associated with relaxase types. We used these criteria to develop a computational method to search for and identify 21 additional families of oriT-containing sequences in plasmids from the pathogens Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. Sequence analyses found 3,072 occurrences of these oriT-containing sequences across 2,976 plasmids, many of which encoded antimicrobial resistance genes. Six candidate oriT-containing sequences were validated experimentally and were shown to facilitate conjugation in E. coli. These findings expand our understanding of plasmid mobility.},
}

*Plasmids/genetics
*Escherichia coli/genetics
*Conjugation, Genetic
*Klebsiella pneumoniae/genetics
*Acinetobacter baumannii/genetics/classification
Computational Biology/methods
Gene Transfer, Horizontal
Replication Origin/genetics
DNA, Bacterial/genetics/chemistry

@article {pmid39596782,
year = {2024},
author = {Mendoza-Guido, B and Barrantes, K and Rodríguez, C and Rojas-Jimenez, K and Arias-Andres, M},
title = {The Impact of Urban Pollution on Plasmid-Mediated Resistance Acquisition in Enterobacteria from a Tropical River.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/antibiotics13111089},
pmid = {39596782},
issn = {2079-6382},
support = {C1455, C2650, C3509//Vicerrectoría de Investigación of the Universidad de Costa Rica/ ; SIA 0483-21//Universidad Nacional, Costa Rica/ ; Proyecto Plasmidoma//Consejo Nacional de Rectores (CONARE), Costa Rica/ ; },
abstract = {Background: The exposure of environmental bacteria to contaminants in aquatic ecosystems accelerates the dissemination of antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Methods: In this study, we sampled three locations along a contamination gradient of a polluted river, focusing on isolating Enterobacteria from the surface waters to investigate the relationship between urban pollution and antibiotic resistance. The genomes of 15 isolates (5 per site) were sequenced to identify plasmid-borne ARGs and their association with resistance phenotypes. Results: Isolates from the site with the highest contamination (Site 3) showeda larger number of ARGs, plasmids, and resistance phenotypes. Notably, one of the isolates analyzed, E. coli A231-12, exhibited phenotypic resistance to seven antibiotics, presumably conferred by a single plasmid carrying 12 ARGs. Comparative analysis of this plasmid revealed its close evolutionary relationship with another IncH plasmid hosted by Salmonella enterica, underscoring its high ARG burden in the aquatic environment. Other plasmids identified in our isolates carried sul and dfrA genes, conferring resistance to trimethoprim/sulfamethoxazole, a commonly prescribed antibiotic combination in clinical settings. Conclusions: These results highlight the critical need to expand research on the link between pollution and plasmid-mediated antimicrobial resistance in aquatic ecosystems, which can act as reservoirs of ARGs.},
}

@article {pmid39596781,
year = {2024},
author = {Ifedinezi, OV and Nnaji, ND and Anumudu, CK and Ekwueme, CT and Uhegwu, CC and Ihenetu, FC and Obioha, P and Simon, BO and Ezechukwu, PS and Onyeaka, H},
title = {Environmental Antimicrobial Resistance: Implications for Food Safety and Public Health.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/antibiotics13111087},
pmid = {39596781},
issn = {2079-6382},
abstract = {Antimicrobial resistance (AMR) is a serious global health issue, aggravated by antibiotic overuse and misuse in human medicine, animal care, and agriculture. This study looks at the different mechanisms that drive AMR, such as environmental contamination, horizontal gene transfer, and selective pressure, as well as the severe implications of AMR for human and animal health. This study demonstrates the need for concerted efforts across the scientific, healthcare, agricultural, and policy sectors to control the emergence of AMR. Some crucial strategies discussed include developing antimicrobial stewardship (AMS) programs, encouraging targeted narrow-spectrum antibiotic use, and emphasizing the significance of strict regulatory frameworks and surveillance systems, like the Global Antimicrobial Resistance and Use Surveillance System (GLASS) and the Access, Watch, and Reserve (AWaRe) classification. This study also emphasizes the need for national and international action plans in combating AMR and promotes the One Health strategy, which unifies environmental, animal, and human health. This study concludes that preventing the spread of AMR and maintaining the effectiveness of antibiotics for future generations requires a comprehensive, multidisciplinary, and internationally coordinated strategy.},
}

@article {pmid39596258,
year = {2024},
author = {Dec, M and Nowak, T and Webster, J and Wódz, K},
title = {Serotypes, Antimicrobial Susceptibility, and Potential Mechanisms of Resistance Gene Transfer in Erysipelothrix rhusiopathiae Strains from Waterfowl in Poland.},
journal = {International journal of molecular sciences},
volume = {25},
number = {22},
pages = {},
doi = {10.3390/ijms252212192},
pmid = {39596258},
issn = {1422-0067},
mesh = {Animals ; Poland ; *Erysipelothrix/genetics ; *Serogroup ; *Anti-Bacterial Agents/pharmacology ; *Geese/microbiology ; Ducks/microbiology ; Microbial Sensitivity Tests ; Erysipelothrix Infections/microbiology/genetics ; Multilocus Sequence Typing ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Erysipelas is a significant problem in the waterfowl farming in Poland, and information on the characteristics of the Erysipelothrix rhusiopathiae strains causing this disease is limited. In this study, we determined the serotypes, antimicrobial susceptibility, and potential mechanisms of resistance gene transfer in E. rhusiopathiae isolates (n = 60) from domestic geese and ducks. We also developed a multiplex PCR for the detection of resistance genes. The antimicrobial susceptibility of the isolates was assessed using the broth microdilution method. Resistance genes, integrative conjugative element (ICE)-specific genes, phage-specific genes, and serotype determinants were detected by PCR. Multilocus sequence typing (MLST) was performed for selected resistant strains. The comparative analyses included 260 E. rhusiopathiae strains whose whole genome sequences (WGSs) are publicly available. E. rhusiopathiae isolates represented 7 serotypes, among which serotypes 5 (38.3%) and 1b (28.3%) were the most common. All strains were susceptible to β-lactams, and the vast majority of them were resistant to tetracycline (85%) and enrofloxacin (80%). The percentages of isolates resistant to other antimicrobials used ranged from 3.3% to 16.7%. Ten isolates (16.7%) were found to be multidrug resistant (MDR). The genotypic resistance profiles of the E. rhusiopathiae strains corresponded to their phenotypic resistance, and the amplification patterns obtained using the 10-plex PCR developed in this study were fully consistent with the results of single PCRs. The most prevalent resistance gene was tetM. In enrofloxacin-resistant strains, nonsynonymous mutations in the gyrA and parC genes were identified. The presence of ICE-specific genes was confirmed in resistant strains, and in MDR isolates of serotype 8 that represented sequence type (ST) 113, prophage DNA (Javan630-like) linked to the lsaE gene was additionally detected. The results indicate that β-lactam antibiotics should be the first choice for the treatment of waterfowl erysipelas in Poland. ICEs, including a transposon from the Tn916/Tn1545 family, and bacteriophages are most likely responsible for the transfer of resistance genes in E. rhusiopathiae.},
}

Animals
Poland
*Erysipelothrix/genetics
*Serogroup
*Anti-Bacterial Agents/pharmacology
*Geese/microbiology
Ducks/microbiology
Microbial Sensitivity Tests
Erysipelothrix Infections/microbiology/genetics
Multilocus Sequence Typing
Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid39592962,
year = {2024},
author = {Mane, A and Sanderson, H and White, AP and Zaheer, R and Beiko, R and Chauve, C},
title = {Plaseval: a framework for comparing and evaluating plasmid detection tools.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {365},
pmid = {39592962},
issn = {1471-2105},
mesh = {*Plasmids/genetics/metabolism ; Software ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them.

RESULTS: We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools-PlasBin-flow, HyAsP, gplas, and MOB-recon-on a data set of 53 E. coli bacterial genomes.

CONCLUSION: Analysis of the results of plasmid binning methods using PlasEval shows that their behaviour varies significantly. PlasEval can be used to decide which specific plasmid binning method should be used for a specific dataset. The disagreement between different methods also suggests that the problem of plasmid binning on short-read contigs requires further research. We believe that PlasEval can prove to be an effective tool in this regard. PlasEval is publicly available at https://github.com/acme92/PlasEval.},
}

*Plasmids/genetics/metabolism
Software
Genome, Bacterial
Sequence Analysis, DNA/methods

@article {pmid39592922,
year = {2024},
author = {Das, VA and Gautam, B and Yadav, PK and Varadwaj, PK and Wadhwa, G and Singh, S},
title = {Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1127},
pmid = {39592922},
issn = {1471-2229},
mesh = {*Bacillus/genetics/physiology ; *Malus/microbiology/genetics ; *Genome, Bacterial ; Genetic Fitness ; Genomics/methods ; Genomic Islands ; Computational Biology/methods ; },
abstract = {A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.},
}

*Bacillus/genetics/physiology
*Malus/microbiology/genetics
*Genome, Bacterial
Genetic Fitness
Genomics/methods
Genomic Islands
Computational Biology/methods

@article {pmid39591316,
year = {2024},
author = {Jafari Jozani, R and Khallawi, MFHA and Trott, D and Petrovski, K and Low, WY and Hemmatzadeh, F},
title = {Unravelling Antimicrobial Resistance in Mycoplasma hyopneumoniae: Genetic Mechanisms and Future Directions.},
journal = {Veterinary sciences},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/vetsci11110542},
pmid = {39591316},
issn = {2306-7381},
support = {2021/0025//Australian Pork (APL)/ ; },
abstract = {Antimicrobial resistance (AMR) in Mycoplasma hyopneumoniae, the causative agent of Enzootic Pneumonia in swine, poses a significant challenge to the swine industry. This review focuses on the genetic foundations of AMR in M. hyopneumoniae, highlighting the complexity of resistance mechanisms, including mutations, horizontal gene transfer, and adaptive evolutionary processes. Techniques such as Whole Genome Sequencing (WGS) and multiple-locus variable number tandem repeats analysis (MLVA) have provided insights into the genetic diversity and resistance mechanisms of M. hyopneumoniae. The study underscores the role of selective pressures from antimicrobial use in driving genomic variations that enhance resistance. Additionally, bioinformatic tools utilizing machine learning algorithms, such as CARD and PATRIC, can predict resistance traits, with PATRIC predicting 7 to 12 AMR genes and CARD predicting 0 to 3 AMR genes in 24 whole genome sequences available on NCBI. The review advocates for a multidisciplinary approach integrating genomic, phenotypic, and bioinformatics data to combat AMR effectively. It also elaborates on the need for refining genotyping methods, enhancing resistance prediction accuracy, and developing standardized antimicrobial susceptibility testing procedures specific to M. hyopneumoniae as a fastidious microorganism. By leveraging contemporary genomic technologies and bioinformatics resources, the scientific community can better manage AMR in M. hyopneumoniae, ultimately safeguarding animal health and agricultural productivity. This comprehensive understanding of AMR mechanisms will be beneficial in the adaptation of more effective treatment and management strategies for Enzootic Pneumonia in swine.},
}

@article {pmid39590772,
year = {2024},
author = {Cui, H and Lu, J and Ding, W and Zhang, W},
title = {Genomic Features and Antimicrobial Activity of Phaeobacter inhibens Strains from Marine Biofilms.},
journal = {Marine drugs},
volume = {22},
number = {11},
pages = {},
pmid = {39590772},
issn = {1660-3397},
mesh = {*Biofilms/drug effects ; *Rhodobacteraceae/genetics ; *Phylogeny ; *Genome, Bacterial ; *Anti-Bacterial Agents/pharmacology ; *Tropolone/pharmacology/analogs & derivatives ; Multigene Family ; Aquatic Organisms ; Vibrio/genetics/drug effects ; Genomics/methods ; Animals ; },
abstract = {Members of the genus Phaeobacter are widely distributed in the marine environment and are known for their ability to produce tropodithietic acid (TDA). Studies investigating the genomic and metabolic features of Phaeobacter strains from marine biofilms are sparse. Here, we analyze the complete genomes of 18 Phaeobacter strains isolated from biofilms on subtidal stones, with the aim of determining their potential to synthesize secondary metabolites. Based on whole-genome comparison and average nucleotide identity calculation, the isolated bacteria are classified as novel strains of Phaeobacter inhibens. Further analysis reveals a total of 153 biosynthetic gene clusters, which are assigned to 32 gene cluster families with low similarity to previously published ones. Complete TDA clusters are identified in 14 of the 18 strains, while in the other 4 strains the TDA clusters are rather incomplete and scattered across different chromosome and plasmid locations. Phylogenetic analysis suggests that their presence or absence may be potentially attributed to horizontal gene transfer. High-performance liquid chromatography-mass spectrometry analysis demonstrates the production of TDA in all the examined strains. Furthermore, the Phaeobacter strains have strong antibacterial activity against the pathogenic strain Vibrio owensii ems001, which is associated with acute hepatopancreatic necrosis in South American white shrimp. Altogether, this study ameliorates our knowledge of marine biofilm-associated Phaeobacter and offers new avenues for exploiting marine antimicrobial agents.},
}

*Biofilms/drug effects
*Rhodobacteraceae/genetics
*Phylogeny
*Genome, Bacterial
*Anti-Bacterial Agents/pharmacology
*Tropolone/pharmacology/analogs & derivatives
Multigene Family
Aquatic Organisms
Vibrio/genetics/drug effects
Genomics/methods
Animals

@article {pmid39589125,
year = {2024},
author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J},
title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0081624},
doi = {10.1128/msphere.00816-24},
pmid = {39589125},
issn = {2379-5042},
abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.

IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.},
}

@article {pmid39587099,
year = {2024},
author = {Sheikh, S and Fu, CJ and Brown, MW and Baldauf, SL},
title = {The Acrasis kona genome and developmental transcriptomes reveal deep origins of eukaryotic multicellular pathways.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10197},
pmid = {39587099},
issn = {2041-1723},
support = {VR 2017-04351//Vetenskapsrådet (Swedish Research Council)/ ; 2100888//National Science Foundation (NSF)/ ; },
mesh = {*Transcriptome ; *Dictyostelium/genetics/growth & development ; Genome, Protozoan ; Amoeba/genetics ; Phylogeny ; Gene Transfer, Horizontal ; Protozoan Proteins/genetics/metabolism ; Proteome/metabolism/genetics ; Genome ; },
abstract = {Acrasids are amoebae with the capacity to form multicellular fruiting bodies in a process known as aggregative multicellularity (AGM). This makes acrasids the only known example of multicellularity among the earliest branches of eukaryotes (the former Excavata). Here, we report the Acrasis kona genome sequence plus transcriptomes from pre-, mid- and post-developmental stages. The genome is rich in novelty and genes with strong signatures of horizontal transfer, and multigene families encode nearly half of the amoeba's predicted proteome. Development in A. kona appears molecularly simple relative to the AGM model, Dictyostelium discoideum. However, the acrasid also differs from the dictyostelid in that it does not appear to be starving during development. Instead, developing A. kona appears to be very metabolically active, does not induce autophagy and does not up-regulate its proteasomal genes. Together, these observations strongly suggest that starvation is not essential for AGM development. Nonetheless, development in the two amoebae appears to employ remarkably similar pathways for signaling, motility and, potentially, construction of an extracellular matrix surrounding the developing cell mass. Much of this similarity is also shared with animal development, suggesting that much of the basic tool kit for multicellular development arose early in eukaryote evolution.},
}

*Transcriptome
*Dictyostelium/genetics/growth & development
Genome, Protozoan
Amoeba/genetics
Phylogeny
Gene Transfer, Horizontal
Protozoan Proteins/genetics/metabolism
Proteome/metabolism/genetics
Genome

@article {pmid39581358,
year = {2024},
author = {Fischer, K and Valentin Jordbræk, S and Olsen, S and Bockwoldt, M and Schwacke, R and Usadel, B and Krause, K},
title = {Taken to extremes: Loss of plastid rpl32 in Streptophyta and Cuscuta's unconventional solution for its replacement.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108243},
doi = {10.1016/j.ympev.2024.108243},
pmid = {39581358},
issn = {1095-9513},
abstract = {The evolution of plant genomes is riddled with exchanges of genetic material within one plant (endosymbiotic gene transfer/EGT) and between unrelated plants (horizontal gene transfer/HGT). These exchanges have left their marks on plant genomes. Parasitic plants with their special evolutionary niche provide ample examples for these processes because they are under a reduced evolutionary pressure to maintain autotrophy and thus to conserve their plastid genomes. On the other hand, the close physical connections with different hosts enabled them to acquire genetic material from other plants. Based on an analysis of an extensive dataset including the parasite Cuscuta campestris and other parasitic plant species, we identified a unique evolutionary history of rpl32 genes coding for an essential plastid ribosomal subunit in Cuscuta. Our analysis suggests that the gene was most likely sequestered by HGT from a member of the Oxalidales order serving as host to an ancestor of the Cuscuta subgenus Grammica. Oxalidales had suffered an ancestral EGT of rpl32 predating the evolution of the genus Cuscuta. The HGT subsequently relieved the plastid rpl32 from its evolutionary constraint and led to its loss from the plastid genome. The HGT-based acquisition in Cuscuta is supported by a high sequence similarity of the mature L32 protein between species of the subgenus Grammica and representatives of the Oxalidales, and by a surprisingly conserved transit peptide, whose functionality in Cuscuta was experimentally verified. The findings are discussed in view of an overall pattern of EGT events for plastid ribosomal subunits in Streptophyta.},
}

@article {pmid39581254,
year = {2024},
author = {Xu, F and Xiang, Q and Xu, ML and Carter, LJ and Du, WC and Zhu, CW and Ai, FX and Yin, Y and Ji, R and Guo, HY},
title = {Elevated CO2 alters antibiotic resistome in soil amended with sulfamethazine via chemical-organic fertilization.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120416},
doi = {10.1016/j.envres.2024.120416},
pmid = {39581254},
issn = {1096-0953},
abstract = {Rising antimicrobial resistance (AMR) is an enormous challenge for global healthcare systems. The effects of elevated CO2 (eCO2) on AMR are poorly characterized. Using a free-air CO2 enrichment system and high-throughput qPCR arrays, we investigated the response of soil antibiotic resistome and bacterial communities to eCO2 (ambient + 200 ppm) in soils amended with sulfamethazine (SMZ) at 0.1 and 1 mg kg[-1] via chemical-organic fertilizer (COL, COH). Results showed that under ambient condition, COH significantly enhanced the diversity of high-risk antibiotic resistance genes (ARGs), relative abundance of low risk ARGs, unassessed ARGs and total ARGs compared to COL. Nevertheless, eCO2 mitigated the effects of COH, with no significant difference found between COL and COH on the above high risk, low risk, unassessed and total ARGs. Meanwhile, eCO2 decreased the relative abundance of spcN, ermA, olec, oprD, sulA-olP, tetB, tetT and vanXD in COL, and alleviated the enrichment of pikR2, ampC, lunC, oprD and pncA caused by the application of SMZ at 1 mg kg[-1]. Correlation and network analysis illustrated that changes of certain bacteria biomarkers and horizontal gene transfer of integrase gene were associated with the altered response of ARGs abundance to eCO2. This study adds knowledge of the potential risk of antibiotic resistance in agricultural exposure scenarios under increasing CO2 concentration.},
}

@article {pmid39581077,
year = {2024},
author = {Guernier-Cambert, V and Trachsel, J and Atkinson, B and Oladeinde, A and Anderson, CL and Bearson, SMD and Monson, MS and Looft, T},
title = {Tetracycline resistance gene transfer from Escherichia coli donors to Salmonella Heidelberg in chickens is impacted by the genetic context of donors.},
journal = {Veterinary microbiology},
volume = {299},
number = {},
pages = {110294},
doi = {10.1016/j.vetmic.2024.110294},
pmid = {39581077},
issn = {1873-2542},
abstract = {Chicken ceca are a rich source of bacteria, including zoonotic pathogens such as Salmonella enterica. The microbiota includes strains/species carrying antimicrobial resistance genes and horizontal transfer of resistance determinants between species may increase the risk to public health and farming systems. Possible sources of these antimicrobial resistance donors - the eggshell carrying bacteria from the hen vertically transmitted to the offspring, or the barn environment where chicks are hatched and raised - has been little explored. In this study, we used Salmonella enterica serovar Heidelberg to evaluate if layer chicks raised in different environments (using combinations of sterilized or non-sterile eggs placed in sterilized isolation chambers or non-sterile rooms) acquired transferable tetracycline resistance genes from surrounding bacteria, especially Escherichia coli. Two-day old chicks were challenged with an antibiotic-susceptible S. Heidelberg strain SH2813nal[R] and Salmonella recovered from the cecum of birds at different timepoints to test the in vivo acquisition of tetracycline resistance. Tetracycline-resistant E. coli isolates recovered from birds from the in vivo experiment were used to test the in vitro transfer of tetracycline resistance genes from E. coli to Salmonella. Even though Salmonella SH2813nal[R] colonized the 2-day old chicks after oral challenge, tetracycline-resistant Salmonella transconjugants were not recovered, as previously observed. In vitro experiments provided similar results. We discuss several hypotheses that might explain the absence of transconjugants in vitro and in vivo, despite the presence of diverse plasmids in the recovered E. coli. The factors that can inhibit/promote antimicrobial resistance transfers to Salmonella for different plasmid types need further exploration.},
}

@article {pmid39577948,
year = {2024},
author = {Sheng, H and Zhao, L and Suo, J and Yang, Q and Cao, C and Chen, J and Cui, G and Fan, Y and Ma, Y and Huo, S and Wu, X and Yang, T and Cui, X and Chen, S and Cui, S and Yang, B},
title = {Niche-specific evolution and gene exchange of Salmonella in retail pork and chicken.},
journal = {Food research international (Ottawa, Ont.)},
volume = {197},
number = {Pt 2},
pages = {115299},
doi = {10.1016/j.foodres.2024.115299},
pmid = {39577948},
issn = {1873-7145},
mesh = {Animals ; *Chickens/microbiology ; *Salmonella/genetics ; Swine ; *Food Microbiology ; China ; *Pork Meat/microbiology ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Meat/microbiology ; Drug Resistance, Bacterial/genetics ; Genetic Variation ; Red Meat/microbiology ; },
abstract = {Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain.},
}

Animals
*Chickens/microbiology
*Salmonella/genetics
Swine
*Food Microbiology
China
*Pork Meat/microbiology
Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal
Meat/microbiology
Drug Resistance, Bacterial/genetics
Genetic Variation
Red Meat/microbiology

@article {pmid39577842,
year = {2024},
author = {Whangsuk, W and Dulyayangkul, P and Loprasert, S and Dubbs, JM and Vattanaviboon, P and Mongkolsuk, S},
title = {Re-sensitization of imipenem-resistant Pseudomonas aeruginosa and restoration of cephalosporins susceptibility in Enterobacteriaceae by recombinant Esterase B.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovae118},
pmid = {39577842},
issn = {1472-765X},
abstract = {Sphingobium sp. SM42 Esterase B (EstB) is an enzyme with a dual function in degrading dibutyl phthalate (DBP) and catalyzing the cleavage of the C-S bond in C3-sidechains of the dihydrothiazine ring of cephalosporins, generating more active β-lactam derivatives. Global prokaryotic genome analysis revealed the existence of a gene identical to estB in Pseudomonas aeruginosa strain PS1 suggesting a horizontal gene transfer event involving estB. To investigate the effect of ectopic expression of EstB in the periplasm of Pseudomonas aeruginosa and several Enterobacteriaceae on antibiotic susceptibility levels, plasmid, pEstB, carrying a recombinant EstB fused with the signal peptide from Escherichia coli outer membrane protein A (OmpA) for periplasmic localization was constructed. The expression of EstB in the periplasm of P. aeruginosa and the Enterobacteriaceae: E. coli, Klebsiella pneumoniae, and Salmonella enterica serovar Typhi, increased susceptibility to carbapenems and cephalosporins. EstB reversed the imipenem resistance of P. aeruginosa ΔmexS and restored the changes in susceptibility to cephalosporins conferred by the downregulation of the outer membrane proteins, OmpK35 and OmpK36, in K. pneumoniae ΔramR-ompK36 to wild-type level. The introduction of EstB to the periplasmic space of Gram-negative bacteria can increase carbapenem and cephalosporin susceptibility.},
}

@article {pmid39577583,
year = {2024},
author = {Yu, K and He, B and Xiong, J and Kan, P and Sheng, H and Zhi, S and Zhu, DZ and Yao, Z},
title = {Deciphering basic and key traits of bio-pollutants in a long-term reclaimed water headwater urban stream.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177696},
doi = {10.1016/j.scitotenv.2024.177696},
pmid = {39577583},
issn = {1879-1026},
abstract = {Reclaimed water has been recognized as a stable water resource for ecological replenishment in riverine environment. However, information about the bio-pollutants spatial and temporal distributions and the associated risk in this environment remains insufficient. Herein, the bio-pollutant profile in a long-term reclaimed water headwater urban stream, including antibiotic resistance genes (ARGs), mobile genetic elements and pathogens, were revealed by metagenomics. Notably, the temporal variation in bio-pollutant levels exceeded spatial fluctuations, possibly due to the varied rainfall intensity. Specially, multidrug resistance genes and Acinetobacter baumannii (A. baumannii) were the dominant ARGs and pathogens, respectively, exhibiting higher abundance in the dry season, especially in the downstream of the receiving point, where the bio-risk also peaked. A. baumannii and Ralstonia solanacearum were found to be the main plasmids contributors inducing the horizontal gene transfer process in this stream. Overall, A. baumannii contributed over 50 % bio-risk values in most samples, indicating that it was the "overlord" in this headwater urban stream. This study revealed characteristics of bio-pollutants in a typical long-term reclaimed water headwater urban stream, highlighting the superiority of A. baumannii in bio-pollutants, which should be a key consideration in the bio-pollutants surveillance for reclaimed waters.},
}

@article {pmid39575186,
year = {2024},
author = {Verma, T and Hendiani, S and Carbajo, C and Andersen, SB and Hammarlund, EU and Burmølle, M and Sand, KK},
title = {Recurrence and propagation of past functions through mineral facilitated horizontal gene transfer.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1449094},
pmid = {39575186},
issn = {1664-302X},
abstract = {Horizontal gene transfer is one of the most important drivers of bacterial evolution. Transformation by uptake of extracellular DNA is traditionally not considered to be an effective mode of gene acquisition, simply because extracellular DNA is degraded in a matter of days when it is suspended in e.g. seawater. Recently the age span of stored DNA was increased to at least 2 Ma. Here, we show that Acinetobacter baylyi can incorporate 60 bp DNA fragments adsorbed to common sedimentary minerals and that the transformation frequencies scale with mineral surface properties. Our work highlights that ancient environmental DNA can fuel the evolution of contemporary bacteria. In contrast to heritable stochastic mutations, the processes by which bacteria acquire new genomic material during times of increased stress and needs, indicate a non-random mechanism that may propel evolution in a non-stochastic manner.},
}

@article {pmid39572773,
year = {2024},
author = {Hoffmann, L},
title = {Finding the sweet spot in the deep ocean.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1544},
pmid = {39572773},
issn = {2399-3642},
abstract = {‘Candidatus Endonucleobacter’ infects the nuclei of deep-sea mussels but it was unknown how they can prevent apoptosis of the host. A new study by Porras and colleagues, published in Nature Microbiology, suggests that the bacterium upregulates host-derived apoptosis inhibitors and genes for digesting sugars, lipids and amino acids acquired through horizontal gene transfer from the mussels.},
}

@article {pmid39571737,
year = {2024},
author = {Jing, T and Yang, J and Pan, J and Liu, X and Yang, X and Farhan, M and Su, H and Ma, X and Zhang, S},
title = {A near-complete genome reveals the population evolution of the cotton-melon aphid Aphis gossypii.},
journal = {Insect biochemistry and molecular biology},
volume = {},
number = {},
pages = {104215},
doi = {10.1016/j.ibmb.2024.104215},
pmid = {39571737},
issn = {1879-0240},
abstract = {The cotton-melon aphid Aphis gossypii Glover is a severe pest worldwide. Interhaplotype genomic variation can be used as a starting point to analyze the adaptability of Ap. gossypii. In this study, we utilized long-read PacBio HiFi sequencing and HiC scaffolding techniques to assemble a near telomere-to-telomere gap-free genome assembly of Hap4. The assembly had two gaps totaling 321.24 Mb. We characterized five telomeric repetitive regions (GGTTA)n, including the four found at the 3' end of the chromosomes, and obtained new structural information about the telomeres. Due to the improved sequencing technology, we also identified more than 55.03 Mb of repetitive DNA in the genome assembly of Hap4, which contributed significantly to the increase in genome size compared to that of Hap1 and Hap3. Most of the additional repetitive DNA content was located on the X chromosome, and the tandem repeat sequence occupied 16.8% of the X chromosome length. The Hap4 assembly showed that the X chromosome exhibited a greater abundance of AT-rich satDNA arrays (11 satDNA arrays longer than 100 kb) than that observed in the autosomes (A1 and A2 harboured 3 and 1 satDNA arrays). We detected presence-absence variations, insertions, and deletions events between Hap1, Hap3, and Hap4 Ap. gossypii, which had significant effects on gene expression. Additionally, we identified a male-specific glyceraldehyde-3-phosphate dehydrogenase of fungal origin in all strains of Ap. gossypii. This comprehensive genome assembly provides valuable insights into the structural characteristics of highly repetitive regions and allows comparative genomic analyses that facilitate our understanding of Ap. gossypii's adaptation and diversification.},
}

@article {pmid39571576,
year = {2024},
author = {Denoeud, F and Godfroy, O and Cruaud, C and Heesch, S and Nehr, Z and Tadrent, N and Couloux, A and Brillet-Guéguen, L and Delage, L and Mckeown, D and Motomura, T and Sussfeld, D and Fan, X and Mazéas, L and Terrapon, N and Barrera-Redondo, J and Petroll, R and Reynes, L and Choi, SW and Jo, J and Uthanumallian, K and Bogaert, K and Duc, C and Ratchinski, P and Lipinska, A and Noel, B and Murphy, EA and Lohr, M and Khatei, A and Hamon-Giraud, P and Vieira, C and Avia, K and Akerfors, SS and Akita, S and Badis, Y and Barbeyron, T and Belcour, A and Berrabah, W and Blanquart, S and Bouguerba-Collin, A and Bringloe, T and Cattolico, RA and Cormier, A and Cruz de Carvalho, H and Dallet, R and De Clerck, O and Debit, A and Denis, E and Destombe, C and Dinatale, E and Dittami, S and Drula, E and Faugeron, S and Got, J and Graf, L and Groisillier, A and Guillemin, ML and Harms, L and Hatchett, WJ and Henrissat, B and Hoarau, G and Jollivet, C and Jueterbock, A and Kayal, E and Knoll, AH and Kogame, K and Le Bars, A and Leblanc, C and Le Gall, L and Ley, R and Liu, X and LoDuca, ST and Lopez, PJ and Lopez, P and Manirakiza, E and Massau, K and Mauger, S and Mest, L and Michel, G and Monteiro, C and Nagasato, C and Nègre, D and Pelletier, E and Phillips, N and Potin, P and Rensing, SA and Rousselot, E and Rousvoal, S and Schroeder, D and Scornet, D and Siegel, A and Tirichine, L and Tonon, T and Valentin, K and Verbruggen, H and Weinberger, F and Wheeler, G and Kawai, H and Peters, AF and Yoon, HS and Hervé, C and Ye, N and Bapteste, E and Valero, M and Markov, GV and Corre, E and Coelho, SM and Wincker, P and Aury, JM and Cock, JM},
title = {Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.10.049},
pmid = {39571576},
issn = {1097-4172},
abstract = {Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate change. In this study, analysis of multiple genomes has provided insights across the entire evolutionary history of this lineage, from initial emergence, through later diversification of the brown algal orders, down to microevolutionary events at the genus level. Emergence of the brown algal lineage was associated with a marked gain of new orthologous gene families, enhanced protein domain rearrangement, increased horizontal gene transfer events, and the acquisition of novel signaling molecules and key metabolic pathways, the latter notably related to biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. We show that brown algal genome diversification is tightly linked to phenotypic divergence, including changes in life cycle strategy and zoid flagellar structure. The study also showed that integration of large viral genomes has had a significant impact on brown algal genome content throughout the emergence of the lineage.},
}

@article {pmid39568508,
year = {2024},
author = {Mukherjee, K and Moroz, LL},
title = {Evolution of g-type lysozymes in metazoa: insights into immunity and digestive adaptations.},
journal = {Frontiers in cell and developmental biology},
volume = {12},
number = {},
pages = {1487920},
pmid = {39568508},
issn = {2296-634X},
abstract = {Exploring the evolutionary dynamics of lysozymes is critical for advancing our knowledge of adaptations in immune and digestive systems. Here, we characterize the distribution of a unique class of lysozymes known as g-type, which hydrolyze key components of bacterial cell walls. Notably, ctenophores, and choanoflagellates (the sister group of Metazoa), lack g-type lysozymes. We reveal a mosaic distribution of these genes, particularly within lophotrochozoans/spiralians, suggesting the horizontal gene transfer events from predatory myxobacteria played a role in their acquisition, enabling specialized dietary and defensive adaptations. We further identify two major groups of g-type lysozymes based on their widespread distribution in gastropods. Despite their sequence diversity, these lysozymes maintain conserved structural integrity that is crucial for enzymatic activity, underscoring independent evolutionary pathways where g-type lysozymes have developed functionalities typically associated with different lysozyme types in other species. Specifically, using Aplysia californica as a reference species, we identified three distinct g-type lysozyme genes: two are expressed in organs linked to both feeding and defense, and the third exhibits broader distribution, likely associated with immune functions. These findings advance our understanding of the evolutionary dynamics shaping the recruitment and mosaic functional diversification of these enzymes across metazoans, offering new insights into ecological physiology and physiological evolution as emerging fields.},
}

@article {pmid39565221,
year = {2024},
author = {Molano, LG and Hirsch, P and Hannig, M and Müller, R and Keller, A},
title = {The PLSDB 2025 update: enhanced annotations and improved functionality for comprehensive plasmid research.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae1095},
pmid = {39565221},
issn = {1362-4962},
support = {//European Commission/ ; 466168626//DFG/ ; },
abstract = {Plasmids are extrachromosomal DNA molecules in bacteria and archaea, playing critical roles in horizontal gene transfer, antibiotic resistance, and pathogenicity. Since its first release in 2018, our database on plasmids, PLSDB, has significantly grown and enhanced its content and scope. From 34 513 records contained in the 2021 version, PLSDB now hosts 72 360 entries. Designed to provide life scientists with convenient access to extensive plasmid data and to support computer scientists by offering curated datasets for artificial intelligence (AI) development, this latest update brings more comprehensive and accurate information for plasmid research, with interactive visualization options. We enriched PLSDB by refining the identification and classification of plasmid host ecosystems and host diseases. Additionally, we incorporated annotations for new functional structures, including protein-coding genes and biosynthetic gene clusters. Further, we enhanced existing annotations, such as antimicrobial resistance genes and mobility typing. To accommodate these improvements and to host the increase plasmid sets, the webserver architecture and underlying data structures of PLSDB have been re-reconstructed, resulting in decreased response times and enhanced visualization of features while ensuring that users have access to a more efficient and user-friendly interface. The latest release of PLSDB is freely accessible at https://www.ccb.uni-saarland.de/plsdb2025.},
}

@article {pmid39565095,
year = {2024},
author = {Bulka, O and Mahadevan, R and Edwards, EA},
title = {Pangenomic insights into Dehalobacter evolution and acquisition of functional genes for bioremediation.},
journal = {Microbial genomics},
volume = {10},
number = {11},
pages = {},
pmid = {39565095},
issn = {2057-5858},
mesh = {*Biodegradation, Environmental ; *Phylogeny ; *Genome, Bacterial ; Evolution, Molecular ; Bacterial Proteins/genetics/metabolism ; Genomics ; Gene Transfer, Horizontal ; Metagenome ; },
abstract = {Dehalobacter is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a Dehalobacter population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the mec cassette, just downstream of its active RDase. A closed genome of this DCM-mineralizing lineage has previously evaded assembly. Here, we present the genomes of two novel Dehalobacter strains, each of which was assembled from the metagenome of a distinct subculture from SC05. A pangenomic analysis of the Dehalobacter genus, including RDase synteny and phylogenomics, reveals at least five species of Dehalobacter based on average nucleotide identity, RDase and core gene synteny, as well as differential functional genes. An integration hotspot is also pinpointed in the Dehalobacter genome, in which many recombinase islands have accumulated. This nested recombinase island encodes the active RDase and mec cassette in both SC05 Dehalobacter genomes, indicating the transfer of key functional genes between species of Dehalobacter. Horizontal gene transfer between these two novel Dehalobacter strains has implications for the evolutionary history within the SC05 subcultures and of the Dehalobacter genus as a whole, especially regarding adaptation to anthropogenic chemicals.},
}

*Biodegradation, Environmental
*Phylogeny
*Genome, Bacterial
Evolution, Molecular
Bacterial Proteins/genetics/metabolism
Genomics
Gene Transfer, Horizontal
Metagenome

@article {pmid39564482,
year = {2024},
author = {Huang, CJ and Wu, TL and Wu, YL and Wang, RS and Lin, YC},
title = {Comparative genomic analysis uncovered phylogenetic diversity, evolution of virulence factors, and horizontal gene transfer events in tomato bacterial spot Xanthomonas euvesicatoria.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1487917},
pmid = {39564482},
issn = {1664-302X},
abstract = {INTRODUCTION: Bacterial spot, caused by diverse xanthomonads classified into four lineages within three species, poses a significant threat to global pepper and tomato production. In Taiwan, tomato bacterial spot xanthomonads phylogenetically related to an atypical Xanthomonas euvesicatoria pv. perforans (Xep) strain NI1 from Nigeria were found.

METHODS: To investigate the genetic structure of Taiwanese Xep strains and determine the phylogenetic position of the atypical strains, we completed high-quality, gap-free, circularized genomes of seven Taiwanese Xep strains and performed comparative genomic analyses with genomes of X. euvesicatoria pathovars. Average nucleotide identity, core genome analysis, and phylogenomic analysis were conducted.

RESULTS: Three sequenced strains were identified as typical Xep, while four clustered with the atypical strain NI1, forming a distinct genomovar within X. euvesicatoria, proposed as X. euvesicatoria genomovar taiwanensis (Xet). This new lineage likely originated in Taiwan and spread to Nigeria through global seed trade. At the genomovar level, chromosomes remained conserved among Taiwanese strains, while plasmids likely contributed to bacterial virulence, avirulence, and field fitness. Gap-free genomes revealed associations between the evolution of type III effectors, horizontal gene transfer events, plasmid diversity, and recombination.

DISCUSSION: This study highlights the critical roles of horizontal gene transfer and plasmids in shaping the genetic makeup, evolution, and environmental adaptation of plant pathogenic xanthomonads. The identification of a new genomovar, X. euvesicatoria genomovar taiwanensis, provides insights into the diversity and global spread of bacterial spot pathogens through seed trade.},
}

@article {pmid39562586,
year = {2024},
author = {Goh, YX and Anupoju, SMB and Nguyen, A and Zhang, H and Ponder, M and Krometis, LA and Pruden, A and Liao, J},
title = {Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10034},
pmid = {39562586},
issn = {2041-1723},
mesh = {*Gene Transfer, Horizontal ; *Soil Microbiology ; *Listeria/genetics/drug effects ; *Phylogeny ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Genome, Bacterial/genetics ; Evolution, Molecular ; Selection, Genetic ; },
abstract = {Soil is an important reservoir of antibiotic resistance genes (ARGs) and understanding how corresponding environmental changes influence their emergence, evolution, and spread is crucial. The soil-dwelling bacterial genus Listeria, including L. monocytogenes, the causative agent of listeriosis, serves as a key model for establishing this understanding. Here, we characterize ARGs in 594 genomes representing 19 Listeria species that we previously isolated from soils in natural environments across the United States. Among the five putatively functional ARGs identified, lin, which confers resistance to lincomycin, is the most prevalent, followed by mprF, sul, fosX, and norB. ARGs are predominantly found in Listeria sensu stricto species, with those more closely related to L. monocytogenes tending to harbor more ARGs. Notably, phylogenetic and recombination analyses provide evidence of recent horizontal gene transfer (HGT) in all five ARGs within and/or across species, likely mediated by transformation rather than conjugation and transduction. In addition, the richness and genetic divergence of ARGs are associated with environmental conditions, particularly soil properties (e.g., aluminum and magnesium) and surrounding land use patterns (e.g., forest coverage). Collectively, our data suggest that recent HGT and environmental selection play a vital role in the acquisition and diversification of bacterial ARGs in natural environments.},
}

*Gene Transfer, Horizontal
*Soil Microbiology
*Listeria/genetics/drug effects
*Phylogeny
*Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Genes, Bacterial
Genome, Bacterial/genetics
Evolution, Molecular
Selection, Genetic

@article {pmid39555914,
year = {2024},
author = {Ulrich, NJ and Miller, SR},
title = {Integration of horizontally acquired light-harvesting genes into an ancestral regulatory network in the cyanobacterium Acaryochloris marina MBIC11017.},
journal = {mBio},
volume = {},
number = {},
pages = {e0242324},
doi = {10.1128/mbio.02423-24},
pmid = {39555914},
issn = {2150-7511},
abstract = {The acquisition of new capabilities by horizontal gene transfer (HGT) shapes the distribution of traits during microbial diversification. In the Chlorophyll (Chl) d-producing cyanobacterium Acaryochloris marina, the genes involved in the production and disassembly of the light-harvesting phycobiliprotein phycocyanin (PC) were lost in the A. marina common ancestor but then subsequently regained via HGT in A. marina strain MBIC11017. However, it remains unknown how the HGT-acquired PC genes in MBIC11017 have been reintegrated into its existing regulatory network after tens of millions of years since their loss. Here, we investigated potential mechanisms of regulatory assimilation of PC genes by comparing the transcriptomes of A. marina strain MBIC11017 and a PC-lacking close relative under both low irradiance far-red light and high irradiance white light. We found that PC assembly and degradation processes have been re-assimilated into a conserved ancestral response to high light. Further, we identified putative regulatory elements that were likely co-transferred with PC genes and could be recognized by A. marina's pre-existing light response machinery. This study offers insights into how HGT-acquired genes can be reintegrated into an existing transcriptional regulatory network that has evolved in their absence.IMPORTANCEHorizontal gene transfer, the asymmetric movement of genetic information between donor and recipient organisms, is an important mechanism for acquiring new traits. In order for newly acquired gene content to be retained, it must be integrated into the genetic repertoire and regulatory networks of the recipient cell. In a strain of the Chlorophyll d-producing cyanobacterium Acaryochloris marina, the recent reacquisition of the genes required to produce the light-harvesting pigment phycocyanin offers a rare opportunity to understand the mechanisms underlying the regulatory assimilation of an acquired complex trait in bacteria. The significance in our research is in characterizing how an ancestrally lost, complex trait can be reintegrated into a conserved regulatory network, even after millions of years.},
}

@article {pmid39552541,
year = {2024},
author = {Singh, CK and Sodhi, KK},
title = {Targeting bioinformatics tools to study the dissemination and spread of antibiotic resistant genes in the environment and clinical settings.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/1040841X.2024.2429603},
pmid = {39552541},
issn = {1549-7828},
abstract = {Antibiotic resistance has expanded as a result of the careless use of antibiotics in the medical field, the food industry, agriculture, and other industries. By means of genetic recombination between commensal and pathogenic bacteria, the microbes obtain antibiotic resistance genes (ARGs). In bacteria, horizontal gene transfer (HGT) is the main mechanism for acquiring ARGs. With the development of high-throughput sequencing, ARG sequence analysis is now feasible and widely available. Preventing the spread of AMR in the environment requires the implementation of ARGs mapping. The metagenomic technique, in particular, has helped in identifying antibiotic resistance within microbial communities. Due to the exponential growth of experimental and clinical data, significant investments in computer capacity, and advancements in algorithmic techniques, the application of machine learning (ML) algorithms to the problem of AMR has attracted increasing attention over the past five years. The review article sheds a light on the application of bioinformatics for the antibiotic resistance monitoring. The most advanced tool currently being employed to catalog the resistome of various habitats are metagenomics and metatranscriptomics. The future lies in the hands of artificial intelligence (AI) and machine learning (ML) methods, to predict and optimize the interaction of antibiotic-resistant compounds with target proteins.},
}

@article {pmid39551215,
year = {2024},
author = {Bierge, P and Sánchez-Osuna, M and Duarte, B and Gómez-Sánchez, I and Espasa, M and Freitas, AR and Peixe, L and Gasch, O and Pich, OQ and Novais, C},
title = {Diverse genomic and epidemiological landscapes of redundant pbp5 genes in Enterococcus spp.: Insights into plasmid mobilization, ampicillin susceptibility, and environmental interactions.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177562},
doi = {10.1016/j.scitotenv.2024.177562},
pmid = {39551215},
issn = {1879-1026},
abstract = {Genetic redundancy in bacteria plays a crucial role in enhancing adaptability and accelerating evolution in response to selective pressures, particularly those associated with rapid environmental changes. Aminopenicillins like ampicillin are important therapeutic options for Enterococcus infections in both humans and animals, with resistance mostly associated with pbp5 gene mutations or overexpression. While the occurrence of redundant pbp5 genes has been occasionally reported, the advantages for the host bacteria have not been explored in detail. During a whole-genome sequencing project of Enterococcus faecium from bacteremic patients, we identified an ST592 strain (Efm57) with redundant pbp5 genes. This presented an opportunity to investigate the prevalence and implications of multiple pbp5 acquisitions in diverse Enterococcus species across various sources, geographical regions, and timeframes. The analysis of 618 complete Enterococcus genomes from public databases revealed that 3.2 % harbored redundant pbp5 genes, located on chromosomes or plasmids across different species from diverse epidemiological backgrounds. The proteins encoded by these genes showed homologies ranging from 51.1 % to 97.5 % compared to native copies. Phylogenetic analysis grouped redundant PBP5 amino acid sequences into three distinct clades, with insertion sequences (mostly IS6-like) facilitating their recent spread to diverse plasmids with varying genetic backbones. The presence of multiple antibiotic resistance genes on pbp5-plasmids, including those conferring resistance to linezolid, underscores their involvement in co-selection and recombination events with other clinically-relevant antibiotics. Conjugation experiments confirmed the transferability of a specific 24 kb pbp5-plasmid from the Efm57 strain. This plasmid was associated with higher minimum inhibitory concentrations of ampicillin and conferred bacteria growth advantages at 22 °C. In conclusion, the widespread distribution of redundant pbp5 genes among Enterococcus spp. highlights the complex interplay between genetic mobility, environmental factors, and multidrug resistance in overlapping ecosystems emphasizing the importance of understanding these dynamics to mitigate antibiotic resistance spread within the One Health framework.},
}

@article {pmid39550371,
year = {2024},
author = {Yang, JX and Peng, Y and Yu, QY and Yang, JJ and Zhang, YH and Zhang, HY and Adams, CA and Willing, CE and Wang, C and Li, QS and Han, XG and Gao, C},
title = {Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {128},
pmid = {39550371},
issn = {2055-5008},
mesh = {*Gene Transfer, Horizontal ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Nitrogen/metabolism ; *Phylogeny ; *Biodiversity ; Metagenome ; DNA, Bacterial/genetics ; Soil Microbiology ; },
abstract = {Horizontal gene transfer (HGT) mediated diversification is a critical force driving evolutionary and ecological processes. However, how HGT might relate to anthropogenic activity such as nitrogen addition, and its subsequent effect on functional diversity and cooccurrence networks remain unknown. Here we approach this knowledge gap by blending bacterial 16S rRNA gene amplicon and shotgun metagenomes from a platform of cessation of nitrogen additions and continuous nitrogen additions. We found that bacterial HGT events, functional genes, and virus diversities increased whereas bacterial taxonomic diversity decreased by nitrogen additions, resulting in a counterintuitive strong negative association between bacterial taxonomic and functional diversities. Nitrogen additions, especially the ceased one, complexified the cooccurrence network by increasing the contribution of vitamin B12 auxotrophic Acidobacteria, indicating cross-feeding. These findings advance our perceptions of the causes and consequences of the diversification process in community ecology.},
}

*Gene Transfer, Horizontal
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Nitrogen/metabolism
*Phylogeny
*Biodiversity
Metagenome
DNA, Bacterial/genetics
Soil Microbiology

@article {pmid39549700,
year = {2024},
author = {Siozios, S and Nadal-Jimenez, P and Azagi, T and Sprong, H and Frost, CL and Parratt, SR and Taylor, G and Brettell, L and Liew, KC and Croft, L and King, KC and Brockhurst, MA and Hypša, V and Novakova, E and Darby, AC and Hurst, GDD},
title = {Genome dynamics across the evolutionary transition to endosymbiosis.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.10.044},
pmid = {39549700},
issn = {1879-0445},
abstract = {Endosymbiosis-where a microbe lives and replicates within a host-is an important contributor to organismal function that has accelerated evolutionary innovations and catalyzed the evolution of complex life. The evolutionary processes associated with transitions to endosymbiosis, however, are poorly understood. Here, we leverage the wide diversity of host-associated lifestyles of the genus Arsenophonus to reveal the complex evolutionary processes that occur during the transition to a vertically transmitted endosymbiotic lifestyle from strains maintained solely by horizontal (infectious) transmission. We compared the genomes of 38 strains spanning diverse lifestyles from horizontally transmitted pathogens to obligate interdependent endosymbionts. Among culturable strains, we observed those with vertical transmission had larger genome sizes than closely related horizontally transmitting counterparts, consistent with evolutionary innovation and the rapid gain of new functions. Increased genome size was a consequence of prophage and plasmid acquisition, including a cargo of type III effectors, alongside the concomitant loss of CRISPR-Cas genome defense systems, enabling mobile genetic element expansion. Persistent endosymbiosis was also associated with loss of type VI secretion, which we hypothesize to be a consequence of reduced microbe-microbe competition. Thereafter, the transition to endosymbiosis with strict vertical inheritance was associated with the expected relaxation of purifying selection, gene pseudogenization, metabolic degradation, and genome reduction. We argue that reduced phage predation in endosymbiotic niches drives the loss of genome defense systems driving rapid genome expansion upon the adoption of endosymbiosis and vertical transmission. This remodeling enables rapid horizontal gene transfer-mediated evolutionary innovation and precedes the reductive evolution traditionally associated with adaptation to endosymbiosis.},
}

@article {pmid39366703,
year = {2024},
author = {Gomez-Simmonds, A and Annavajhala, MK and Seeram, D and Hokunson, TW and Park, H and Uhlemann, AC},
title = {Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla KPC.},
journal = {Genome research},
volume = {34},
number = {11},
pages = {1895-1907},
doi = {10.1101/gr.279355.124},
pmid = {39366703},
issn = {1549-5469},
support = {K23 AI137316/AI/NIAID NIH HHS/United States ; R01 AI175414/AI/NIAID NIH HHS/United States ; },
mesh = {*Plasmids/genetics ; *beta-Lactamases/genetics ; Humans ; *Gene Transfer, Horizontal ; *Bacterial Proteins/genetics ; *Carbapenems/pharmacology ; New York City/epidemiology ; Carbapenem-Resistant Enterobacteriaceae/genetics ; Enterobacteriaceae Infections/microbiology/epidemiology/transmission ; Klebsiella pneumoniae/genetics/drug effects ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Molecular Epidemiology ; Multilocus Sequence Typing ; },
abstract = {Transmission of carbapenem-resistant Enterobacterales (CRE) in hospitals has been shown to occur through complex, multifarious networks driven by both clonal spread and horizontal transfer mediated by plasmids and other mobile genetic elements. We performed nanopore long-read sequencing on CRE isolates from a large urban hospital system to determine the overall contribution of plasmids to CRE transmission and identify specific plasmids implicated in the spread of bla KPC (the Klebsiella pneumoniae carbapenemase [KPC] gene). Six hundred and five CRE isolates collected between 2009 and 2018 first underwent Illumina sequencing for genome-wide genotyping; 435 bla KPC-positive isolates were then successfully nanopore sequenced to generate hybrid assemblies including circularized bla KPC-harboring plasmids. Phylogenetic analysis and Mash clustering were used to define putative clonal and plasmid transmission clusters, respectively. Overall, CRE isolates belonged to 96 multilocus sequence types (STs) encoding bla KPC on 447 plasmids which formed 54 plasmid clusters. We found evidence for clonal transmission in 66% of CRE isolates, over half of which belonged to four clades comprising K. pneumoniae ST258. Plasmid-mediated acquisition of bla KPC occurred in 23%-27% of isolates. While most plasmid clusters were small, several plasmids were identified in multiple different species and STs, including a highly promiscuous IncN plasmid and an IncF plasmid putatively spreading bla KPC from ST258 to other clones. Overall, this points to both the continued dominance of K. pneumoniae ST258 and the dissemination of bla KPC across clones and species by diverse plasmid backbones. These findings support integrating long-read sequencing into genomic surveillance approaches to detect the hitherto silent spread of carbapenem resistance driven by mobile plasmids.},
}

*Plasmids/genetics
*beta-Lactamases/genetics
Humans
*Gene Transfer, Horizontal
*Bacterial Proteins/genetics
*Carbapenems/pharmacology
New York City/epidemiology
Carbapenem-Resistant Enterobacteriaceae/genetics
Enterobacteriaceae Infections/microbiology/epidemiology/transmission
Klebsiella pneumoniae/genetics/drug effects
Phylogeny
Anti-Bacterial Agents/pharmacology
Molecular Epidemiology
Multilocus Sequence Typing

@article {pmid39141706,
year = {2024},
author = {Souque, C and González Ojeda, I and Baym, M},
title = {From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance.},
journal = {Annual review of microbiology},
volume = {78},
number = {1},
pages = {361-382},
doi = {10.1146/annurev-micro-041522-102707},
pmid = {39141706},
issn = {1545-3251},
support = {T32 GM008313/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Evolution, Molecular ; *Drug Resistance, Bacterial/genetics ; Bacterial Infections/microbiology/drug therapy ; },
abstract = {Tackling the challenge created by antibiotic resistance requires understanding the mechanisms behind its evolution. Like any evolutionary process, the evolution of antimicrobial resistance (AMR) is driven by the underlying variation in a bacterial population and the selective pressures acting upon it. Importantly, both selection and variation will depend on the scale at which resistance evolution is considered (from evolution within a single patient to the host population level). While laboratory experiments have generated fundamental insights into the mechanisms underlying antibiotic resistance evolution, the technological advances in whole genome sequencing now allow us to probe antibiotic resistance evolution beyond the lab and directly record it in individual patients and host populations. Here we review the evolutionary forces driving antibiotic resistance at each of these scales, highlight gaps in our current understanding of AMR evolution, and discuss future steps toward evolution-guided interventions.},
}

Humans
*Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
*Evolution, Molecular
*Drug Resistance, Bacterial/genetics
Bacterial Infections/microbiology/drug therapy

@article {pmid39545400,
year = {2024},
author = {Stern, DB and Raborn, RT and Lovett, SP and Boise, NR and Carasquilla, L and Enke, S and Radune, D and Woodruff, DL and Wahl, K and Rosovitz, MJ},
title = {Novel toxin biosynthetic gene cluster in harmful algal bloom-causing Heteroscytonema crispum: Insights into the origins of paralytic shellfish toxins.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae248},
pmid = {39545400},
issn = {1759-6653},
abstract = {Caused by both eukaryotic dinoflagellates and prokaryotic cyanobacteria, harmful algal blooms (HABs) are events of severe ecological, economic, and public health consequence, and their incidence has become more common of late. Despite coordinated research efforts to identify and characterize the genomes of HAB-causing organisms, the genomic basis and evolutionary origins of paralytic shellfish toxins (PSTs) produced by HABs remain at best incomplete. The PST saxitoxin has an especially complex genomic architecture and enigmatic phylogenetic distribution, spanning dinoflagellates and multiple cyanobacterial genera. Using filtration and extraction techniques to target the desired cyanobacteria from non-axenic culture, coupled with a combination of short and long read sequencing, we generated a reference-quality hybrid genome assembly for Heteroscytonema crispum UTEX LB 1556, a freshwater, PST-producing cyanobacterium thought to have the largest known genome in its phylum. We report a complete, novel biosynthetic gene cluster for the PST saxitoxin. Leveraging this biosynthetic gene cluster, we find support for the hypothesis that PST production has appeared in divergent Cyanobacteria lineages through widespread and repeated horizontal gene transfer. This work demonstrates the utility of long-read sequencing and metagenomic assembly toward advancing our understanding of PST biosynthetic gene cluster diversity and suggests a mechanism for the origin of PST biosynthetic genes.},
}

@article {pmid39542384,
year = {2024},
author = {Wang, J and Wu, Y and Zhu, L and Guo, K and Gao, S and Dong, Y},
title = {Genomic evolution and patterns of horizontal gene transfer in Papilio.},
journal = {Genomics},
volume = {116},
number = {6},
pages = {110956},
doi = {10.1016/j.ygeno.2024.110956},
pmid = {39542384},
issn = {1089-8646},
abstract = {The Papilio genus, known for its ecological and phenotypic diversity, is a valuable model for evolutionary studies. This study conducted a comparative genomic analysis of 11 Papilio species, revealing species-specific gene family expansions, including the UDP-glucosyltransferase 2 gene associated with insect detoxification, particularly expanding in Papilio polyxenes. Our analysis also revealed 199 horizontal gene transfer (HGT) acquired genes from 76 microbial species, with Pseudomonadota and Bacillota as common HGT donors across these genomes. Furthermore, we examined the evolutionary patterns of nine ABC transporter subfamilies, uncovering potential links between gene family evolution and environmental adaptation. This study provides new insights into evolutionary relationships and genomic adaptations within the Papilio genus, contributing to broader butterfly evolutionary research.},
}

@article {pmid39542270,
year = {2024},
author = {Yuan, S and Jin, G and Cui, R and Wang, X and Wang, M and Chen, Z},
title = {Transmission and control strategies of antimicrobial resistance from the environment to the clinic: A holistic review.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177461},
doi = {10.1016/j.scitotenv.2024.177461},
pmid = {39542270},
issn = {1879-1026},
abstract = {The environment serves as a significant reservoir of antimicrobial resistance (AMR) microbes and genes and is increasingly recognized as key source of clinical AMR. Modern human activities impose an additional burden on environmental AMR, promoting its transmission to clinical setting and posing a serious threat to human health and welfare. Therefore, a comprehensive review of AMR transmission from the environment to the clinic, along with proposed effective control strategies, is crucial. This review systematically summarized current research on the transmission of environmental AMR to clinical settings. Furthermore, the transmission pathways, horizontal gene transfer (HGT) mechanisms, as well as the influential drivers including triple planetary crisis that may facilitate AMR transfer from environmental species to clinical pathogens are highlighted. In response to the growing trend of AMR transmission, we propose insightful mitigation strategies under the One Health framework, integrating advanced surveillance and tracking technologies, interdisciplinary knowledge, multisectoral interventions, alongside multiple antimicrobial use and stewardship approaches to tacking development and spread of AMR.},
}

@article {pmid39541852,
year = {2024},
author = {Wang, Q and Wang, M and Yang, Q and Feng, L and Zhang, H and Wang, R and Wang, R},
title = {The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122776},
doi = {10.1016/j.watres.2024.122776},
pmid = {39541852},
issn = {1879-2448},
abstract = {Bacteriophages play integral roles in the ecosystem; however, their precise involvement in horizontal gene transfer and the spread of antibiotic resistance genes (ARGs) are not fully understood. In this study, a coculture system involving consortia of bacteriophages and multidrug-resistant bacteria from an aerobic tank in a municipal wastewater treatment plant (WWTP) was established to investigate the functions of bacteriophages in ARG transfer and spread. The results of the cocultivation of the MRB and bacteriophage consortia indicated that the bacterial community remained stable throughout the whole process, but the addition of bacteriophages significantly increased ARG abundance, especially in bacteriophage DNA. Nine out of the 11 identified ARGs significantly increased, indicating that more bacteriophage particles carried ARGs in the system after cocultivation. In addition, 686 plasmids were detected during cocultivation, of which only 3.36 % were identified as conjugative plasmids, which is significantly lower than the proportion found among previously published plasmids (25.2 %, totaling 14,029 plasmids). Our findings revealed that bacteriophages may play important roles in the horizontal transfer of ARGs through both bacteriophage-mediated conduction and an increase in extracellular ARGs; however, conjugative transfer may not be the main mechanism by which multidrug-resistant bacteria acquire and spread ARGs. Unlike in most previous reports, a coculture system of diverse bacteria and bacteriophages was established in this study to assess bacteriophage functions in ARG transfer and dissemination in the environment, overcoming the limitations associated with the isolation of bacteria and bacteriophages, as well as the specificity of bacteriophage hosts.},
}

@article {pmid39541851,
year = {2024},
author = {Wang, F and Huang, W and Chen, J and Luo, Y and Cao, J and Fang, F and Liu, X and Wu, Y and Luo, J},
title = {Non-antibiotic disinfectant synchronously interferes methane production and antibiotic resistance genes propagation during sludge anaerobic digestion: Activation of microbial adaptation and reconfiguration of bacteria-archaea synergies.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122773},
doi = {10.1016/j.watres.2024.122773},
pmid = {39541851},
issn = {1879-2448},
abstract = {Waste activated sludge (WAS) presents both resource recovery potential and pollution risks, making its efficient treatment challenging. Anaerobic digestion is broadly recognized as a green and sustainable approach to WAS treatment, whose efficiency is easily impacted by the exogeneous pollutants in WAS. However, the impact of polyhexamethylene guanidine (PHMG), as a widely-used non-antibiotic disinfectant, on WAS digestion under semi-continuous flow conditions remains unclear. In this study, CH4 production decreased from 16.1 mL/g volatile suspended solids (VSS) in the control to 13.2 mL/g VSS and 0.3 mL/g VSS under low and high PHMG exposure, respectively, while PHMG increased the number of antibiotic resistance gene (ARG) copies per bacterium by 4.6-12.7 %. Molecular docking analysis revealed that PHMG could spontaneously bind to and disintegrate WAS (binding energy:2.35 and -9.62 kcal/mol), increasing the likelihood of microbial exposure to PHMG. This led to an increase in bacterial abundance and a reduction in archaeal populations, resulting in bacterial dominance in ecological niches. The network topology index in PHMG-treated reactors was consistently lower than in the control, with a higher proportion of negatively correlated links, indicating a more antagonistic relationship between bacteria and archaea. Consequently, PHMG significantly interfered with key genes involved in CH4 biosynthesis (e.g., mch and mtd). Interestingly, methanogenic activity and archaeal chemotaxis (e.g., rfk and cheA) partially recovered under low PHMG exposure due to archaeal adaptation through quorum sensing and two-component systems. However, this adaptation process also contributed to the propagation of ARGs through horizontal gene transfer, facilitated by the enhancement of mobile genetic elements and ARGs hosts. These findings confirm the ecological risks of PHMG and highlight the need for effective WAS disposal strategies.},
}

@article {pmid39306135,
year = {2024},
author = {Wang, B and Farhan, MHR and Yuan, L and Sui, Y and Chu, J and Yang, X and Li, Y and Huang, L and Cheng, G},
title = {Transfer dynamics of antimicrobial resistance among gram-negative bacteria.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176347},
doi = {10.1016/j.scitotenv.2024.176347},
pmid = {39306135},
issn = {1879-1026},
mesh = {*Gram-Negative Bacteria/drug effects ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Bacteriophages/physiology ; Plasmids/genetics ; },
abstract = {Antimicrobial resistance (AMR) in gram-negative bacteria (GNBs) is a significant global health concern, exacerbated by mobile genetic elements (MGEs). This review examines the transfer of antibiotic resistance genes (ARGs) within and between different species of GNB facilitated by MGEs, focusing on the roles of plasmids and phages. The impact of non-antibiotic chemicals, environmental factors affecting ARG transfer frequency, and underlying molecular mechanisms of bacterial resistance evolution are also discussed. Additionally, the study critically assesses the impact of fitness costs and compensatory evolution driven by MGEs in host organisms, shedding light on the transfer frequency of ARGs and host evolution within ecosystems. Overall, this comprehensive review highlights the factors and mechanisms influencing ARG movement among diverse GNB species and underscores the importance of implementing holistic One-Health strategies to effectively address the escalating public health challenges associated with AMR.},
}

*Gram-Negative Bacteria/drug effects
*Drug Resistance, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal
Interspersed Repetitive Sequences
Bacteriophages/physiology
Plasmids/genetics

@article {pmid39540883,
year = {2024},
author = {Garcia, LE and Sanchez-Puerta, MV},
title = {Mitochondrial Splicing Efficiency Is Lower in Holoparasites Than in Free-Living Plants.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcae120},
pmid = {39540883},
issn = {1471-9053},
abstract = {Mitochondria play a crucial role in eukaryotic organisms, housing their own genome with genes vital for oxidative phosphorylation. Coordination between nuclear and mitochondrial genomes is pivotal for organelle gene expression. Splicing, editing and processing of mitochondrial transcripts are regulated by nuclear-encoded factors. Splicing efficiency (SEf) of the many group II introns present in plant mitochondrial genes is critical for mitochondrial function since a splicing defect or splicing deficiency can severely impact plant growth and development. This study investigates SEf in free-living and holoparasitic plants, focusing on 25 group II introns from 15 angiosperm species. Our comparative analyses reveal distinctive splicing patterns with holoparasites exhibiting significantly lower SEf, potentially linked to their unique evolutionary trajectory. Given the preponderance of horizontal gene transfer (HGT) in parasitic plants, we investigated the effect of HGT on SEf, such as the presence of foreign introns or foreign nuclear-encoded splicing factors. Contrary to expectations, the SEf reductions do not correlate with HGT events, suggesting that other factors are at play, such as the loss of photosynthesis or the transition to a holoparasitic lifestyle. The findings of this study broaden our understanding of the molecular evolution in parasitic plants and shed light on the multifaceted factors influencing organelle gene expression.},
}

@article {pmid39535289,
year = {2024},
author = {Vanhout, Z and Abdellati, S and Gestels, Z and De Baetselier, I and de Block, T and Vanbaelen, T and Manoharan-Basil, SS and Kenyon, C},
title = {Macrolide resistance is pervasive in oral streptococci in the Belgian general population: a cross-sectional survey.},
journal = {Journal of medical microbiology},
volume = {73},
number = {11},
pages = {},
doi = {10.1099/jmm.0.001932},
pmid = {39535289},
issn = {1473-5644},
mesh = {Humans ; Belgium/epidemiology ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; Child ; Cross-Sectional Studies ; *Macrolides/pharmacology ; *Drug Resistance, Bacterial ; Female ; Adult ; Male ; *Streptococcal Infections/microbiology/epidemiology ; Child, Preschool ; *Streptococcus/drug effects/genetics/isolation & purification ; Mouth/microbiology ; Azithromycin/pharmacology ; Middle Aged ; Adolescent ; Young Adult ; Parents ; Prevalence ; Infant ; },
abstract = {Background. Commensal streptococci are common inhabitants of the oral microbiome and regulate its structure and function in beneficial ways for human health. They can, however, also be opportunistic pathogens and act as a reservoir of resistance genes that can be passed on to other bacteria, including pathogens. Little is known about the prevalence of these commensals in parents and their children and their antimicrobial susceptibilities in the Belgian general population.Gap Statement. The macrolide susceptibility of commensal oral Streptococci in Belgium is unknown.Methods. We assessed the prevalence and azithromycin susceptibility of commensal streptococcal species in the parents (n=38) and children (n=50) of 35 families in Belgium.Results. The most frequently detected taxonomic grouping was Streptococcus mitis/oralis, which was detected in 78/181 (43.1%) of the children's isolates and 66/128 (51.6%) of the parents' isolates. Of the 311 isolates collected in this study, 282 isolates (90.7%) had an azithromycin MIC value greater than the breakpoint of 0.25 mg l[-1] and 146 isolates (46.9%) had azithromycin MICs greater than 2 mg l[-1]. There was no difference in the azithromycin MIC distribution of all streptococcal isolates between children and parents. All individuals were colonized by streptococci with azithromycin MICs greater than 0.25 mg l[-1], and 87.5% of individuals had streptococci with MICs greater than 2 mg l[-1].Interpretation. The most prevalent species identified in both age groups was S. mitis/oralis. All individuals harboured streptococci with macrolide resistance. This highlights the need for additional antimicrobial stewardship initiatives to reduce the consumption of macrolides in the general population.},
}

Humans
Belgium/epidemiology
*Anti-Bacterial Agents/pharmacology
*Microbial Sensitivity Tests
Child
Cross-Sectional Studies
*Macrolides/pharmacology
*Drug Resistance, Bacterial
Female
Adult
Male
*Streptococcal Infections/microbiology/epidemiology
Child, Preschool
*Streptococcus/drug effects/genetics/isolation & purification
Mouth/microbiology
Azithromycin/pharmacology
Middle Aged
Adolescent
Young Adult
Parents
Prevalence
Infant

@article {pmid39527185,
year = {2024},
author = {Kim, K and Islam, MM and Bang, S and Kim, J and Lee, CY and Lee, JC and Shin, M},
title = {H-NS is a Transcriptional Repressor of the CRISPR-Cas System in Acinetobacter baumannii ATCC 19606.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {39527185},
issn = {1976-3794},
support = {2022R1A2C2010683//Ministry of Science and ICT, South Korea/ ; },
abstract = {Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen primarily associated with hospital-acquired infections. The bacterium can gain multidrug resistance through several mechanisms, including horizontal gene transfer. A CRISPR-Cas system including several Cas genes could restrict the horizontal gene transfer. However, the molecular mechanism of CRISPR- Cas transcriptional regulation remains unclear. We identified a type I-F CRISPR-Cas system in A. baumannii ATCC 19606[T] standard strain based on sequence analysis. We focused on the transcriptional regulation of Cas3, a key protein of the CRISPR-Cas system. We performed a DNA affinity chromatography-pulldown assay to identify transcriptional regulators of the Cas3 promoter. We identified several putative transcriptional factors, such as H-NS, integration host factor, and HU, that can bind to the promoter region of Cas3. We characterized AbH-NS using size exclusion chromatography and cross-linking experiments and demonstrated that the Cas3 promoter can be regulated by AbH-NS in a concentration-dependent manner via an in vitro transcription assay. CRISPR-Cas expression levels in wild-type and hns mutant strains in the early stationary phase were examined by qPCR and β-galactosidase assay. We found that H-NS can act as a repressor of Cas3. Our transformation efficiency results indicated that the hns mutation decreased the transformation efficiency, while the Cas3 mutation increased it. We report the existence and characterization of the CRISPR-Cas system in A. baumannii 19606[T] and demonstrate that AbH-NS is a transcriptional repressor of CRISPR-Cas-related genes in A. baumannii.},
}

@article {pmid39526401,
year = {2024},
author = {Jiang, Y and Wang, Y and Che, L and Yang, S and Zhang, X and Lin, Y and Shi, Y and Zou, N and Wang, S and Zhang, Y and Zhao, Z and Li, SC},
title = {GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae1007},
pmid = {39526401},
issn = {1362-4962},
support = {20220814183301001//Shenzhen Science and Technology Program/ ; },
abstract = {Metagenomic studies have revealed the critical roles of complex microbial interactions, including horizontal gene transfer (HGT) and functional redundancy (FR), in shaping the gut microbiome's functional capacity and resilience. However, the lack of comprehensive data integration and systematic analysis approaches has limited the in-depth exploration of HGT and FR dynamics across large-scale gut microbiome datasets. To address this gap, we present GutMetaNet (https://gutmetanet.deepomics.org/), a first-of-its-kind database integrating extensive human gut microbiome data with comprehensive HGT and FR analyses. GutMetaNet contains 21 567 human gut metagenome samples with whole-genome shotgun sequencing data related to various health conditions. Through systematic analysis, we have characterized the taxonomic profiles and FR profiles, and identified 14 636 HGT events using a shared reference genome database across the collected samples. These HGT events have been curated into 8049 clusters, which are annotated with categorized mobile genetic elements, including transposons, prophages, integrative mobilizable elements, genomic islands, integrative conjugative elements and group II introns. Additionally, GutMetaNet incorporates automated analyses and visualizations for the HGT events and FR, serving as an efficient platform for in-depth exploration of the interactions among gut microbiome taxa and their implications for human health.},
}

@article {pmid39521804,
year = {2024},
author = {Jerlström-Hultqvist, J and Gallot-Lavallée, L and Salas-Leiva, DE and Curtis, BA and Záhonová, K and Čepička, I and Stairs, CW and Pipaliya, S and Dacks, JB and Archibald, JM and Roger, AJ},
title = {A unique symbiosome in an anaerobic single-celled eukaryote.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9726},
pmid = {39521804},
issn = {2041-1723},
support = {12188//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 5782//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 12188//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 12188//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; RES0043758//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; RES0046091//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; FRN-142349//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; },
mesh = {*Symbiosis ; Anaerobiosis ; In Situ Hybridization, Fluorescence ; Eukaryota/genetics/metabolism ; Phylogeny ; Gene Transfer, Horizontal ; Microscopy, Electron, Scanning ; },
abstract = {Symbiotic relationships between eukaryotes and prokaryotes played pivotal roles in the evolution of life and drove the emergence of specialized symbiotic structures in animals, plants and fungi. The host-evolved symbiotic structures of microbial eukaryotes - the vast majority of such hosts in nature - remain largely unstudied. Here we describe highly structured symbiosomes within three free-living anaerobic protists (Anaeramoeba spp.). We dissect this symbiosis using complete genome sequencing and transcriptomics of host and symbiont cells coupled with fluorescence in situ hybridization, and 3D reconstruction using focused-ion-beam scanning electron microscopy. The emergence of the symbiosome is underpinned by expansion of gene families encoding regulators of membrane trafficking and phagosomal maturation and extensive bacteria-to-eukaryote lateral transfer. The symbionts reside deep within a symbiosomal membrane network that enables metabolic syntrophy by precisely positioning sulfate-reducing bacteria alongside host hydrogenosomes. Importantly, the symbionts maintain connections to the Anaeramoeba plasma membrane, blurring traditional boundaries between ecto- and endosymbiosis.},
}

*Symbiosis
Anaerobiosis
In Situ Hybridization, Fluorescence
Eukaryota/genetics/metabolism
Phylogeny
Gene Transfer, Horizontal
Microscopy, Electron, Scanning

@article {pmid39518977,
year = {2024},
author = {Traglia, GM and Pasteran, F and Moheb, S and Akhtar, U and Gonzalez, S and Maldonado, C and Furtado, N and Mohamed, A and Escalante, J and Tuttobene, MR and Quillen, A and Fontan, C and Albornoz, E and Corso, A and Bonomo, RA and Rao, GG and Tolmasky, ME and Ramirez, MS},
title = {Insights into Acinetobacter baumannii AMA205's Unprecedented Antibiotic Resistance.},
journal = {International journal of molecular sciences},
volume = {25},
number = {21},
pages = {},
pmid = {39518977},
issn = {1422-0067},
support = {SC3GM125556 to MSR, R01AI100560, R01AI063517, R01AI072219 to RAB, and 2R15 AI047115 to MET/GF/NIH HHS/United States ; },
mesh = {*Acinetobacter baumannii/genetics/drug effects ; Humans ; *beta-Lactamases/genetics/metabolism ; *Acinetobacter Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology ; COVID-19/virology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; SARS-CoV-2/drug effects/genetics ; Genome, Bacterial ; Argentina ; Virulence Factors/genetics ; },
abstract = {The rise of antibiotic-resistant bacteria in clinical settings has become a significant global concern. Among these bacteria, Acinetobacter baumannii stands out due to its remarkable ability to acquire resistance genes and persist in hospital environments, leading to some of the most challenging infections. Horizontal gene transfer (HGT) plays a crucial role in the evolution of this pathogen. The A. baumannii AMA205 strain, belonging to sequence type ST79, was isolated from a COVID-19 patient in Argentina in 2021. This strain's antimicrobial resistance profile is notable as it harbors multiple resistance genes, some of which had not been previously described in this species. The AmpC family β-lactamase blaCMY-6, commonly found in Enterobacterales, had never been detected in A. baumannii before. Furthermore, this is the first ST79 strain known to carry the carbapenemase blaNDM-1 gene. Other acquired resistance genes include the carbapenemase blaOXA-23, further complicating treatment. Susceptibility testing revealed high resistance to most antibiotic families, including cefiderocol, with significant contributions from blaCMY-6 and blaNDM-1 genes to the cephalosporin and carbapenem resistance profiles. The A. baumannii AMA205 genome also contains genetic traits coding for 111 potential virulence factors, such as the iron-uptake system and biofilm-associated proteins. This study underscores A. baumannii's ability to acquire multiple resistance genes and highlights the need for alternative therapies and effective antimicrobial stewardship to control the spread of these highly resistant strains.},
}

*Acinetobacter baumannii/genetics/drug effects
Humans
*beta-Lactamases/genetics/metabolism
*Acinetobacter Infections/microbiology/drug therapy
*Anti-Bacterial Agents/pharmacology
COVID-19/virology
Bacterial Proteins/genetics/metabolism
Drug Resistance, Multiple, Bacterial/genetics
Microbial Sensitivity Tests
Gene Transfer, Horizontal
SARS-CoV-2/drug effects/genetics
Genome, Bacterial
Argentina
Virulence Factors/genetics

@article {pmid39511299,
year = {2024},
author = {Hu, Y and Duan, G and Yan, H and Guo, Y and Chang, J and Zhou, M and Yan, S and Li, W and Ruan, C and Gao, S},
title = {Discovery of the first Tn630 member and the closest homolog of IS630 from viruses.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {27081},
pmid = {39511299},
issn = {2045-2322},
support = {2024-KF-03//the Open Project of Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources/ ; },
mesh = {*DNA Transposable Elements/genetics ; Phylogeny ; Viruses/genetics ; Bacteria/genetics/virology ; Animals ; Host Specificity/genetics ; },
abstract = {IS630/Tc1/mariner (ITm) represents the most widely distributed superfamily of DNA transposons in nature. Currently, bioinformatics research on ITm members primarily involves collecting data of existing and emerging members and organizing them into new groups or families. In the present study, our survey revealed that Tc1 and IS630 members have a broad host range, spanning across all six biological kingdoms (bacteria, fungi, plantae, animalia, archaea and protista) and viruses. The primary discoveries include the first Tn630 member-Tn630-NC1 and the closest homolog of IS630 from viruses-Tc1-C#1. By incorporating our discoveries into existing knowledge, we proposed a model to elucidate the formation of composite transposons. Organization of Tc1 and IS630 members into groups across biological kingdoms facilitates data collection for future research, particularly on their horizontal transfer between different kingdoms. The formation of composite transposons may result from asymmetric of terminal inverted repeats. IS630 should be merged with Tc1 into a single family IS630/Tc1. Furthermore, IS630 and its homologs constitute a valuable resource for studying horizontal gene transfer between gut bacteria and phages, opening up new avenues for research in this field.},
}

*DNA Transposable Elements/genetics
Phylogeny
Viruses/genetics
Bacteria/genetics/virology
Animals
Host Specificity/genetics