Horizontal Gene Transfer, Fitness Costs and Mobility Shape the Spread of Antibiotic Resistance Genes into Experimental Populations ofAcinetobacter Baylyi

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(3)

Published: Feb. 15, 2023

Abstract Horizontal gene transfer (HGT) is important for microbial evolution, but how evolutionary forces shape the frequencies of horizontally transferred genetic variants in absence strong selection remains an open question. In this study, we evolve laboratory populations Acinetobacter baylyi (ADP1) with HGT from two clinically relevant strains multidrug-resistant baumannii (AB5075 and A9844). We find that DNA can cross species barrier, even without selection, despite substantial sequence divergence between species. Our results confirm previous findings drive spread antibiotic resistance genes (ARGs) antibiotic, not all present donor genome. quantify costs benefits use whole population sequencing to track ARGs donors into antibiotic-sensitive recipients. though most are taken up by A. baylyi, long-term fate individual depends both on its fitness cost type element carries gene. Interestingly, also found integron, host plasmid, able deleterious effect. Altogether, our show provides advantage evolving facilitating non-selected variation including costly ARGs.

Language: Английский

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Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility

Microbial Genomics, Journal Year: 2021, Volume and Issue: 7(9)

Published: Sept. 9, 2021

The pangenome contains all genes encoded by a species, with the core genome present in strains and accessory only subset. Coincident gene relationships are expected within genome, where presence or absence of one is influenced another. Here, we analysed an

Language: Английский

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The E phylogroup of Escherichia coli is highly diverse and mimics the whole E. coli species population structure

Environmental Microbiology, Journal Year: 2021, Volume and Issue: 23(11), P. 7139 - 7151

Published: Aug. 25, 2021

Summary To get a global picture of the population structure Escherichia coli phylogroup E, encompassing O157:H7 EHEC lineage, we analysed whole genome 144 strains isolated from various continents, hosts and lifestyles representative diversity. The possess 4331 to 5440 genes with core 2771 pangenome 33 722 genes. distribution these among shows an asymmetric U‐shaped distribution. E phylogenetic have largest genomes species, partly explained by presence mobile genetic elements. Sixty‐eight lineages were delineated, some them exhibiting extra‐intestinal virulence being virulent in mouse sepsis model. Except for reference EPEC, EIEC ETEC strains, very few intestinal Most devoid acquired resistance genes, but eight possessed extended‐spectrum beta‐lactamase Human belong specific lineages, antibiotic‐resistant [sequence type complexes (STcs) 350 2064]. mimics all features species as whole, phenomenon already observed at STc level, arguing fractal E. .

Language: Английский

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Genic Selection Within Prokaryotic Pangenomes

Genome Biology and Evolution, Journal Year: 2021, Volume and Issue: 13(11)

Published: Oct. 15, 2021

Abstract Understanding the evolutionary forces shaping prokaryotic pangenome structure is a major goal of microbial evolution research. Recent work has highlighted that substantial proportion accessory genes appear to confer niche-specific adaptations. This primarily focused on selection acting at level individual cells. Herein, we discuss lower also contributes variation: genic selection. refers cases where genetic elements, rather than cells, are entities under The clearest examples this form selfish mobile which those have either neutral or deleterious effect host fitness. We review classes these and other elements characteristic features such could be how beneficial hosts can selection, scenario may more prevalent but not widely appreciated, because disentangling effects different levels (i.e., organisms vs. genes) challenging. Nonetheless, an appreciation for potential action implications important better understand pangenomes.

Language: Английский

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mOTUpan: a robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation

NAR Genomics and Bioinformatics, Journal Year: 2022, Volume and Issue: 4(3)

Published: July 9, 2022

Abstract Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome-assembled or single-cell genomes. While this diversity can provide novel insights into microbial population structure, most tools available core-genome estimation are sensitive to genome completeness. Consequently, a major portion huge phylogenetic uncovered environmental genomic approaches remains excluded from such analyses. We present mOTUpan, iterative Bayesian method computing core sets highly diverse completeness range. The likelihood each gene cluster belong accessory is estimated probability its presence/absence pattern target set. prediction computationally efficient be scaled up thousands It has shown comparable estimates state-of-the-art Roary PPanGGOLiN high-quality capable using at lower thresholds. mOTUpan wraps bootstrapping procedure estimate quality specific prediction, as accuracy run will depend on distribution number dataset under scrutiny. implemented mOTUlizer software package, github.com/moritzbuck/mOTUlizer, GPL 3.0 license.

Language: Английский

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A metric and its derived protein network for evaluation of ortholog database inconsistency

BMC Bioinformatics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 7, 2025

Abstract Background Ortholog prediction, essential for various genomic research areas, faces growing inconsistencies amidst the expanding array of ortholog databases. The common strategy computing consensus orthologs introduces additional arbitrariness, emphasizing need to examine causes such and identify proteins susceptible prediction errors. Results We introduce Signal Jaccard Index (SJI), a novel metric rooted in unsupervised genome context clustering, designed assess protein similarity. Leveraging SJI, we construct network reveal that peripheral within are primary contributors orthology predictions. Furthermore, show protein's degree centrality serves as strong predictor its reliability sets. Conclusions present an objective, SJI-based encompassing all proteins, which topological features elucidate inconsistencies. (DC) effectively identifies error-prone assignments without relying on arbitrary parameters. Notably, DC is stable, unaffected by species selection, well-suited benchmarking. This approach transcends limitations universal thresholds, offering robust quantitative framework explore evolution functional relationships.

Language: Английский

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Navigating Host Immunity and Concurrent Ozone Stress: Strain‐Resolved Metagenomics Reveals Maintenance of Intraspecific Diversity and Genetic Variation in Xanthomonas on Pepper

Evolutionary Applications, Journal Year: 2025, Volume and Issue: 18(1)

Published: Jan. 1, 2025

The evolving threat of new pathogen variants in the face global environmental changes poses a risk to sustainable crop production. Predicting and responding how climate change affects plant-pathosystems is challenging, as environment host-pathogen interactions from molecular community level, with eco-evolutionary feedbacks at play. To address this knowledge gap, we studied short-term within-host pathogen, Xanthomonas perforans, on resistant susceptible pepper open-top chambers (OTCs) under elevated Ozone (O3) conditions single growing season. We observed increased disease severity greater variance cultivar O3, yet no apparent cultivar. Despite dominance genotype cultivar, supported heterogeneous population. Altered O3 levels led strain turnover, relatively gene flux Both standing genetic variation de novo parallel mutations contributed toward evolutionary modifications during adaptation onto presence however, higher polymorphism, random transient mutations. Population heterogeneity along variation, promotion interdependency are mechanisms by which responds stressors. While may provide clues predicting long-term evolution adaptive potential. And, high proportion suggest less predictable climatic alterations. This relevant study emergence constraints underlying shifts.

Language: Английский

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Population genetic analysis of clinical Mycobacterium abscessus complex strains in China

Frontiers in Cellular and Infection Microbiology, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 20, 2025

Background To explore the genetic characteristics of Mycobacterium abscessus complex (MABC) population in China, given its rising clinical importance among nontuberculous mycobacteria. Methods We conducted analyses on 360 MABC genomes from focusing core genome multilocus sequence typing (cgMLST), pan-genome characterization, genetics, and antimicrobial resistance gene profiling. Results Our analysis identified 273 M. subsp. (Mab A ) 87 massiliense M isolates, uncovering 68 types (STs), with ST5 being most common. cgMLST classified 33.3% isolates into six dominant circulating clones (DCCs) 49.4% 59 genomic clusters at a threshold 25 different alleles, including 18 international linking Chinese seven other countries. The is open, Mab exhibiting greater accessory diversity higher turnover compared to . Mobile elements (MGEs), such as prophages islands, were prevalent across all genomes. 139 151 virulence factors (VFs) per genome, distinct VFs affecting immune modulation metabolism. Resistance profiling revealed ubiquitous mtrA , RbpA bla MAB -specific erm(41) conferring macrolides β-lactams. Common rrs rrl mutations indicated widespread aminoglycosides macrolides, while gyrA suggested emerging fluoroquinolone resistance. An acquired erm(46) gene, likely obtained via phage-mediated horizontal transfer, was detected one strain. Conclusion This study provides key insights dynamics China. distribution DCCs, high clustering rates, open pan-genome, patterns between along MGEs, highlight need for targeted surveillance tailored therapies address challenges infections.

Language: Английский

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Pangenomes suggest ecological-evolutionary responses to experimental soil warming

mSphere, Journal Year: 2025, Volume and Issue: unknown

Published: March 19, 2025

ABSTRACT Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive stress may alter microbial feedback mechanisms. To better define evolutionary responses long-term warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest are continuously heated at 5°C above ambient. We hypothesize across generations of chronic genomic signatures within diverse bacterial lineages reflect adaptations related growth and utilization. From our culture collection isolated experimental control plots, sequenced genomes representing dominant taxa sensitive including Actinobacteria, Alphaproteobacteria, Betaproteobacteria. investigated attributes functional gene content identify adaptation. Comparative pangenomics revealed accessory clusters central metabolism, competition, substrate degradation, with few annotations explicitly associated warming. Trends patterns suggest plots were relatively enriched carbohydrate nitrogen metabolism pathways, while amino acid fatty pathways. observed had less codon bias, suggesting potential or efficiency. Codon usage bias varied organisms similar 16S rrn operon copy number, these experience different selective pressures on Our work suggests the emergence lineage-specific trends as well common ecological-evolutionary change. IMPORTANCE Anthropogenic threatens ecosystem health part by altering below-ground cycling carried out microbes. Microbial often overshadowed community-level ecological responses, changes function. predict microbes adapting stressors like test this, analyzed bacteria where have been experimentally ambient 30 years. While unchanged indicators These new parameters how ecosystems system.

Language: Английский

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Heterogeneity in recombination rates and accessory gene co-occurrence distinguish Pseudomonas aeruginosa phylogroups

mSystems, Journal Year: 2025, Volume and Issue: unknown

Published: April 30, 2025

ABSTRACT Pseudomonas aeruginosa (class Gammaproteobacteria) is a ubiquitous, ecologically widespread, and metabolically versatile species. It also an opportunistic pathogen that causes variety of chronic acute infections in humans. Its ability to thrive diverse environments exhibit wide range phenotypes lies part on its large gene pool, but the processes govern inter-strain genomic variation remain unclear. Here, we aim characterize recombination features accessory genome structure P. using 840 globally distributed sequences. The species can be subdivided into five phylogenetic sequence clusters (corresponding known phylogroups), two which are most prominent. Notable epidemic clones found phylogroups: ST17, ST111, ST146, ST274, ST395 phylogroup 1, ST235 ST253 2. phylogroups differ frequency characteristics homologous their core genomes, including specific genes frequently recombine impact diversity. Each phylogroup’s characterized by unique co-occurrence networks shared genes, anti-phage defense systems. Different pools antimicrobial resistance virulence exist display dissimilar patterns co-occurrence. Altogether, our results indicate each displays distinct histories acquiring exogenous DNA, may contribute predominance global population. Our study has important implications for understanding dynamics, within-species heterogeneity, clinically relevant traits . IMPORTANCE consummate opportunist inhabits many nosocomial non-clinical environments, posing major health burden worldwide. reveals phylogroup-specific differences within This partly explains remarkable ecological phenotypic traits, thus circumventing clinical public intervention strategies contain it. help inform efforts control prevent diseases, managing transmission, therapeutic efforts, circulation environmental reservoirs.

Language: Английский

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