Multidrug resistance plasmids commonly reprogram the expression of metabolic genes in Escherichia coli

mSystems, Journal Year: 2024, Volume and Issue: 9(3)

Published: Feb. 20, 2024

ABSTRACT Multidrug-resistant Escherichia coli is a leading cause of global mortality. Transfer plasmids carrying genes encoding beta-lactamases, carbapenamases, and colistin resistance between lineages driving the rising rates hard-to-treat nosocomial community infections. Multidrug (MDR) plasmid acquisition commonly causes transcriptional disruption, while number studies have shown strain-specific fitness effects an MDR across diverse bacterial lineages, fewer compared impacts different in common host. As such, our ability to predict which are most likely be maintained spread populations limited. Here, we introduced eight resistances against range clinically important antibiotics into E. K-12 MG1655 measured their costs impacts. The scale responses varied substantially plasmids, ranging from >650 <20 chromosomal being differentially expressed. However, regulatory disruption did not correlate significantly with magnitude cost, also plasmids. identities expressed differed transconjugants, although expression certain metabolic functions were convergently affected by multiple including downregulation involved L-methionine transport metabolism. Our data show complexity interaction host genetic background determining impact on . IMPORTANCE increase infections that resistant classes antibiotics, those isolates carry genes, concern. Many these conjugative Understanding more about how isolate responds incoming encodes antibiotic will provide information could used emergence lineages. identification networks as particularly sensitive suggests possible targets for reducing transfer.

Language: Английский

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Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types

Microbial Genomics, Journal Year: 2022, Volume and Issue: 8(11)

Published: Nov. 23, 2022

The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene types. Here, we analyse 21 E. type pangenomes using comparative pangenomics identify variance both pangenome structure content. We present functional breakdowns core genomes enriched metabolism, transcription cell membrane biogenesis genes. also uncover metabolism genes have variable classification, depending on which allele is present. Our approach allows detailed exploration the context species. show ongoing gain loss type-specific, may consequence distinct type-specific evolutionary drivers.

Language: Английский

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Escherichia coli O157:H7, a Common Contaminant of Raw Milk from Ecuador: Isolation and Molecular Identification

Foods, Journal Year: 2025, Volume and Issue: 14(3), P. 410 - 410

Published: Jan. 27, 2025

Escherichia coli (E. coli), especially the Shiga toxin-producing O157:H7 strain, poses severe health risks. In rural Ecuador, raw milk consumption heightens contamination This study analyzed 633 samples from Pichincha and Manabí to assess E. prevalence. The were enriched using BHI broth, then specific culture media used isolate O157:H7. pathogen in was identified, isolates specifically confirmed through application of a newly designed qPCR assay. novel assay demonstrated remarkable sensitivity, capable detecting up one copy genetic material, specificity (no amplification other bacteria). An extremely high prevalence 0.63 (n = 401) detected, where province with highest number positive 72.8% 225/309) 54.3% 179/324) for Pichincha. both provinces, presence exhibited favorable correlation small-scale farms elevated temperatures. research provides valuable data on microbiological present milk, addition an improved method that has been be faster, more sensitive, than conventional previously published methods, highlighting associated risk food-borne infections pointing out potential shortcomings regulation agricultural practices need periodic monitoring bacterial levels updated methods.

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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AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance

BMC Bioinformatics, Journal Year: 2024, Volume and Issue: 25(1)

Published: May 16, 2024

We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive of collection samples directly from raw sequencing data single command line. results in report showing genome structure, annotations, antibiotic resistance virulence profile each sample. pan-genome all analyzed identify core- accessory-genes. Phylogenies whole as well gene clusters are also generated. provides web-based visualization dashboard interactively examine various aspects results. Availability: AMRViz implemented Python NodeJS, publicly available under open source MIT license at https://github.com/amromics/amrviz .

Language: Английский

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Persistent, Private and Mobile genes: a model for gene dynamics in evolving pangenomes

Molecular Biology and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

The pangenome of a species is the set all genes carried by at least one member species. In bacteria, pangenomes can be much larger than single organism. Many questions remain unanswered regarding evolutionary forces shaping patterns presence/absence in given We introduce new model for bacterial evolution along phylogeny that explicitly describes timing appearance each gene and accounts three generic types dynamics: persistent are present ancestral genome, private specific to clade, mobile imported once into pool then undergo frequent horizontal transfers. call this Persistent-Private-Mobile (PPM) model. develop an algorithm fitting PPM apply it dataset 902 Salmonella enterica genomes. show best able reproduce global pattern some multivariate statistics like frequency spectrum parsimony vs. plot. Moreover, classification induced allows us study position accessory on chromosome depending their category, as well functions most category. This work paves way mechanistic understanding evolution, developed here could used dynamics-aware classification.

Language: Английский

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Lineage-specific variation in frequency and hotspots of recombination in invasive Escherichia coli

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

Published: Feb. 24, 2025

The opportunistic bacterium Escherichia coli can invade normally sterile sites in the human body, potentially leading to life-threatening organ dysfunction and even death. However, our understanding of evolutionary processes that shape its genetic diversity this environment remains limited. Here, we aim quantify frequency characteristics homologous recombination E. from bloodstream infections. Analysis 557 short-read genome sequences revealed propensity exchange DNA by varies within a distinct population (bloodstream) at narrow geographic (Dartmouth Hitchcock Medical Center, New Hampshire, USA) temporal (years 2016 – 2022) scope. We identified four largest monophyletic sequence clusters core phylogeny are represented prominent types (ST): BAPS1 (mainly ST95), BAPS4 ST73), BAPS10 ST131), BAPS14 ST58). show dominant vary different recombination: number single nucleotide polymorphisms due recombination, blocks, cumulative bases ratio probabilities given site was altered through mutation (r/m), rates which occurred (ρ/θ). Each cluster contains unique set antimicrobial resistance (AMR) virulence genes have experienced recombination. Common among were recombined with functions associated Curli secretion channel (csgG) ferric enterobactin transport (entEF, fepEG). did not identify any one AMR gene present all clusters. mdtABC, baeSR, emrKY tolC had BAPS4, BAPS10, BAPS14. These differences lie part on contributions vertically inherited ancestral contemporary branch-specific some genomes having relatively higher proportions DNA. Our results highlight variation via ranges. Understanding sources invasive will help inform implementation effective strategies reduce burden disease AMR.

Language: Английский

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Tackling the Pangenome Dilemma Requires the Concerted Analysis of Multiple Population Genetic Processes

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(5)

Published: April 24, 2023

Abstract The pangenome is the set of all genes present in a prokaryotic population. Most pangenomes contain many accessory low and intermediate frequencies. Different population genetics processes contribute to shape these pangenomes, namely selection fitness-independent such as gene transfer, loss, migration. However, their relative importance unknown highly debated. Here, we argue that debate around arose due imprecise application models. importantly, two different horizontal transfer act on populations, which are frequently confused, despite fundamentally behavior. Genes acquired from distantly related organisms (termed here acquiring transfer) most comparable mutation nucleotide sequences. In contrast, gain within spreading has an effect frequencies identical positive single genes. We thus show genetic affecting indistinguishable at level dynamics. Nevertheless, when considering joint distribution across individuals propose that, understand degree shaped diversity, development comprehensive models simulation tools mandatory. Furthermore, need identify summary statistics measurable features can distinguish between processes, where will be particularly relevant.

Language: Английский

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Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models

eLife, Journal Year: 2023, Volume and Issue: 12

Published: May 30, 2023

Metabolic capacity can vary substantially within a bacterial species, leading to ecological niche separation, as well differences in virulence and antimicrobial susceptibility. Genome-scale metabolic models are useful tools for studying the potential of individuals, with rapid expansion genomic sequencing there is wealth data that be leveraged comparative analysis. However, exist few construct strain-specific at scale. Here, we describe Bactabolize, reference-based tool which rapidly produces growth phenotype predictions. We pan reference model priority antimicrobial-resistant pathogen, Klebsiella pneumoniae, quality control framework using draft genome assemblies input Bactabolize. The Bactabolize-derived K. pneumoniae strain KPPR1 performed comparatively or better than currently available automated approaches CarveMe gapseq across 507 substrate 2317 knockout mutant Novel genomes passing our systematically defined criteria resulted high degree completeness (≥99% genes reactions captured compared derived from matched complete genomes) accuracy (mean 0.97, n=10). anticipate described herein will facilitate large-scale modelling analyses broaden understanding diversity species inform novel strategies pathogens.

Language: Английский

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Changing dynamics of antibiotic resistant Escherichia in Caspian gulls shows the importance of longitudinal environmental studies

Environment International, Journal Year: 2024, Volume and Issue: 186, P. 108606 - 108606

Published: March 26, 2024

This study is focused on Escherichia spp. isolates resistant to critically important antibiotics (cefotaxime, ciprofloxacin and colistin) among Caspian gull's (Larus cachinnans) chicks nesting in the Nove Mlyny Water Reservoir, Czech Republic. The prevalence of antimicrobial resistance (AMR) bacteria within wild birds commonly evaluated using a single sampling event, capturing only brief momentary snapshot at particular location. Therefore, gulls our were sampled May 2018 (n = 72) 2019 45), water sample was taken from reservoir (2019). We obtained 197 identified as E. coli by MALDI-TOF MS. A total 158 representative whole-genome sequenced, 17 then reclassified albertii. observed higher (86 %; 62/72) occurrence ESBL/AmpC-producing compared 38 % (17/45) (p < 0.00001). decrease linked clonal lineage ST11893 predominating which carried bla

Language: Английский

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