Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 – tracking phylogenetic trajectories with Bayesian inference

Ny, Sofia; Sandegren, Linus; Salemi, Marco; Giske, Christian G.

doi:10.1038/s41598-019-46580-3

Cited by 18 publications

(14 citation statements)

References 38 publications

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“…This was readily detected thanks to the ODM technique and can be attributed to deletions or insertions between the RUTI episodes. The stability of the plasmids is well in line with the discussed stability of IncF-plasmids by Bahl et al [10] and studies describing high bla CTX-M plasmid stability in isolates of the ST131 lineage [34,35]. It is also in accordance with our previous findings investigating longstanding outbreaks with ESBL E. coli using ODM [12,18].…”

Section: Discussionsupporting

confidence: 91%

“…We also found similarities for the bla CTX-M-14 plasmids detected; again, one of these isolates belonged to ST131 and another common ST (ST69). A close clonal relationship within ST131 and specific plasmids has been reported previously [34,35], suggesting a strong coevolution of strains and plasmids within this conserved lineage, but little is known for other lineages.…”

Section: Discussionsupporting

confidence: 57%

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Identity of blaCTX-M Carrying Plasmids in Sequential ESBL-E. coli Isolates from Patients with Recurrent Urinary Tract Infections

Karami

Yazdanshenas

et al. 2021

Microorganisms

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Plasmid-mediated multidrug resistance in E. coli is becoming increasingly prevalent. Considering this global threat to human health, it is important to understand how plasmid-mediated resistance spreads. From a cohort of 123 patients with recurrent urinary tract infections (RUTI) due to extended spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL E. coli), only five events with a change of ESBL E. coli strain between RUTI episodes were identified. Their blaCTX-M encoding plasmids were compared within each pair of isolates using optical DNA mapping (ODM) and PCR-based replicon typing. Despite similar blaCTX-M genes and replicon types, ODM detected only one case with identical plasmids in the sequential ESBL E. coli strains, indicating that plasmid transfer could have occurred. For comparison, plasmids from seven patients with the same ESBL E. coli strain reoccurring in both episodes were analyzed. These plasmids (encoding blaCTX-M-3, blaCTX-M-14, and blaCTX-M-15) were unaltered for up to six months between recurrent infections. Thus, transmission of blaCTX-M plasmids appears to be a rare event during the course of RUTI. Despite the limited number (n = 23) of plasmids investigated, similar blaCTX-M-15 plasmids in unrelated isolates from different patients were detected, suggesting that some successful plasmids could be associated with specific strains, or are more easily transmitted.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionsupporting

confidence: 57%

Identity of blaCTX-M Carrying Plasmids in Sequential ESBL-E. coli Isolates from Patients with Recurrent Urinary Tract Infections

Karami

Yazdanshenas

et al. 2021

Microorganisms

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“…Fluctuating antibiotic exposure, host type, anatomical niche and immunity mean that resistomes vary [51]. Conjugation, recombination and MGEs help shape ST131 resistome dynamics [2,11,[52][53][54][55]. ST131's plasmids typically are from incompatibility (Inc) groups F, I1, N and A/C [56][57][58].…”

Section: Introductionmentioning

confidence: 99%

Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

Decano

Tran

Al-Foori

et al. 2021

Access Microbiology

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The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes and exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host cell adhesion like type 1 fimbriae. The extent to which commensal E. coli and uropathogenic ExPEC ST131 share AMR genes remains understudied at a genomic level, and we examined this here using a preterm infant resistome. We found that individual ST131 had small differences in AMR gene content relative to a larger shared resistome. Comparisons with a range of plasmids common in ST131 showed that AMR gene composition was driven by conjugation, recombination and mobile genetic elements. Plasmid pEK499 had extended regions in most ST131 Clade C isolates, and it had evidence of a co-evolutionary signal based on protein-level interactions with chromosomal gene products, as did pEK204 that had a type IV fimbrial pil operon. ST131 possessed extensive diversity of selective type 1, type IV, P and F17-like fimbriae genes that was highest in subclade C2. The structure and composition of AMR genes, plasmids and fimbriae vary widely in ST131 Clade C and this may mediate pathogenicity and infection outcomes.

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“…Deducing evolutionary relationships based on the core genome permits the discovery of novel accessory genome events 24 . ST131 evolution has been punctuated by plasmid conjugation, plasmid recombination and mobile genetic element (MGE) rearrangements, particularly of the cefotaximase (CTX-M) class of ESBL genes, bla CTX-M-14/15/27 25–27 that allow third-generation cephalosporin-resistance 28 . These bla CTX-M gene changes correlate strongly with ST131 subclade differentiation, such that the most common one (C2) is typically bla CTX-M-15 -positive 29 .…”

Section: Introductionmentioning

confidence: 99%

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates

Decano

Downing

2019

Sci Rep

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Escherichia coli ST131 is a major cause of infection with extensive antimicrobial resistance (AMR) facilitated by widespread beta-lactam antibiotic use. This drug pressure has driven extended-spectrum beta-lactamase (ESBL) gene acquisition and evolution in pathogens, so a clearer resolution of ST131’s origin, adaptation and spread is essential. E. coli ST131’s ESBL genes are typically embedded in mobile genetic elements (MGEs) that aid transfer to new plasmid or chromosomal locations, which are mobilised further by plasmid conjugation and recombination, resulting in a flexible ESBL, MGE and plasmid composition with a conserved core genome. We used population genomics to trace the evolution of AMR in ST131 more precisely by extracting all available high-quality Illumina HiSeq read libraries to investigate 4,071 globally-sourced genomes, the largest ST131 collection examined so far. We applied rigorous quality-control, genome de novo assembly and ESBL gene screening to resolve ST131’s population structure across three genetically distinct Clades (A, B, C) and abundant subclades from the dominant Clade C. We reconstructed their evolutionary relationships across the core and accessory genomes using published reference genomes, long read assemblies and k-mer-based methods to contextualise pangenome diversity. The three main C subclades have co-circulated globally at relatively stable frequencies over time, suggesting attaining an equilibrium after their origin and initial rapid spread. This contrasted with their ESBL genes, which had stronger patterns across time, geography and subclade, and were located at distinct locations across the chromosomes and plasmids between isolates. Within the three C subclades, the core and accessory genome diversity levels were not correlated due to plasmid and MGE activity, unlike patterns between the three main clades, A, B and C. This population genomic study highlights the dynamic nature of the accessory genomes in ST131, suggesting that surveillance should anticipate genetically variable outbreaks with broader antibiotic resistance levels. Our findings emphasise the potential of evolutionary pangenomics to improve our understanding of AMR gene transfer, adaptation and transmission to discover accessory genome changes linked to novel subtypes.

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Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 – tracking phylogenetic trajectories with Bayesian inference

Cited by 18 publications

References 38 publications

Identity of blaCTX-M Carrying Plasmids in Sequential ESBL-E. coli Isolates from Patients with Recurrent Urinary Tract Infections

Identity of blaCTX-M Carrying Plasmids in Sequential ESBL-E. coli Isolates from Patients with Recurrent Urinary Tract Infections

Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates

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