The Population Genomics of Increased Virulence and Antibiotic Resistance in Human Commensal Escherichia coli over 30 Years in France

Marin, Julie; Clermont, Olivier; Royer, Guilhem; Mercier-Darty, Mélanie; Decousser, Jean‐Winoc; Tenaillon, Olivier; Denamur, Erick; Blanquart, François

doi:10.1128/aem.00664-22

Cited by 32 publications

(40 citation statements)

References 110 publications

(139 reference statements)

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“…However, there are differences in the colonization potential of E. coli lineages and the risk of invasive infection by ESBL-Ec which seems to be clone dependent. 38,41 The higher odds for infection that we detected for ST131 is similar to that of the Swedish study (AOR 3.4, 1.8-6.4) indicating a higher pathogenicity potential of ST131 compared to commensal E. coli lineages of phylogroup A, such as ST10. 13 Moreover, we found that ST131 subclade A, previously reported with less resistance, and the multidrug resistant subclade C2 had higher odds for infection, and this may contribute to the sustained establishment of these subclades among bloodstream infections in Norway.…”

Section: Discussionsupporting

confidence: 82%

Community carriage of ESBL-producingEscherichia coliandKlebsiella pneumoniae: A cross-sectional study of risk factors and comparative genomics of carriage and clinical isolates

Raffelsberger

Buczek

Svendsen

et al. 2022

Preprint

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The global prevalence of infections caused by ESBL-producing Enterobacterales (ESBL-E) is increasing and for Escherichia coli observations indicate that this is partly driven by community-onset cases. The ESBL-E population structure in the community is scarcely described and data on risk factors for carriage are conflicting. Here, we report the prevalence and population structure of fecal ESBL-producing E. coli and Klebsiella pneumoniae (ESBL-Ec/Kp) in a general adult population, examine risk factors, and compare carriage isolates with contemporary clinical isolates. Fecal samples obtained from 4999 participants (54% women) ≥40 years in the seventh survey of the population-based Tromsø Study, Norway (2015-2016) were screened for ESBL-Ec/Kp. In addition, we included 118 ESBL-Ec clinical isolates from the Norwegian surveillance program in 2014. All ESBL-producing isolates were whole-genome sequenced. Risk factors associated with carriage were analyzed using multivariable logistic regression. ESBL-Ec gastrointestinal carriage prevalence was 3.3% (95%CI 2.8-3.9%, no sex difference) and 0.08% (0.02-0.20%) for ESBL-Kp. For ESBL-Ec, travel to Asia was the only independent risk factor (AOR 3.47, 95%CI 2.18-5.51). E. coli ST131 was most prevalent in both collections. However, the ST131 proportion was significantly lower in carriage (24%) vs. clinical isolates (58%, p<0.001). Carriage isolates were genetically more diverse with a higher proportion of phylogroup A (26% vs. 5%, p<0.001), indicating that ESBL gene acquisition occurs in a variety of E. coli lineages colonizing the gut. STs commonly related to extra-intestinal infections were more frequent in the clinical isolates also carrying a higher prevalence of antimicrobial resistance, which could indicate clone associated pathogenicity.

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Section: Discussionsupporting

confidence: 82%

Community carriage of ESBL-producingEscherichia coliandKlebsiella pneumoniae: A cross-sectional study of risk factors and comparative genomics of carriage and clinical isolates

Raffelsberger

Buczek

Svendsen

et al. 2022

Preprint

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“…Multiple-drug resistance in E. coli that cause extraintestinal disease can lead to increased morbidity (extended hospital stays) and mortality and has a dominant influence on the epidemiology and management of infectious disease. E. coli ST1193 has spread globally at a high rate, given that the earliest entry of ST1193 in EnteroBase is 2007 and it was absent, for example, in 403 WGS of human commensal E. coli isolates collected between 1980 and 2010 ( 23 ). Understanding virulence, however, is complex because of the redundancy in the myriad of mobile elements that carry virulence gene cargo, especially in ExPEC.…”

Section: Discussionmentioning

confidence: 99%

“…Notably, a third of the invasive ST1193 isolates studied had acquired bla CTX-M-15 , which encodes an extended spectrum of resistance to β-lactams ( 10 ). ST1193 can also persistently colonize the gastrointestinal tract of healthy women ( 3 ) but was not identified in the feces of healthy women in France prior to 2010 ( 23 ).…”

Section: Introductionmentioning

confidence: 99%

Global Phylogeny and F Virulence Plasmid Carriage in Pandemic Escherichia coli ST1193

et al. 2022

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We have generated an updated ST1193 phylogeny using publicly available sequences, reinforcing previous assertions that Escherichia coli ST1193 is a human-associated lineage, with many examples sourced from human extraintestinal infections. ST1193 from urban-adapted birds, wastewater, and companion animals are frequent, but isolates from animal agriculture are notably absent.

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“…Except for ST154 and ST2858, the remaining STs described here (ST10, ST131, ST206, ST1488 and ST3576) have been previously reported. Whole-genome sequencing of a collection of 403 E. coli isolates from fecal human samples over 30 years (1980 to 2010) revealed that ST10 was one of the five major lineages among healthy humans in France [ 22 ]. ST10 was also found as the predominant clone among E. coli recovered from students in Lisbon [ 23 ] and was found among healthy and sick cats from the same geographical area as well [ 24 ].…”

Section: Discussionmentioning

confidence: 99%

Urban Pigeons (Columba livia) as a Source of Broad-Spectrum β-Lactamase-Producing Escherichia coli in Lisbon, Portugal

et al. 2022

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Wild birds may be healthy carriers, and therefore, may be involved in the dissemination of clinically relevant antimicrobial-resistant bacteria, such as extended-spectrum β-lactamases (ESBL) and carbapenemase-producing Enterobacteriaceae. This study evaluated whether urban pigeons living in five spots in Lisbon, Portugal, may be colonized and, therefore, constitute potential spreaders of multidrug-resistant bacteria. A total of 100 pigeon fecal samples were collected in different urban areas for the detection of ESBL- or carbapenemase-producing Enterobacteriaceae. All b-lactamase-producing isolates were tested for antimicrobial susceptibility and their genetic backgrounds were characterized by multilocus sequence typing. Of the 100 fecal samples collected, nine ESBL-producing Escherichia coli (9%) were identified. Three isolates carried the blaCTX-M-15 gene, three isolates harbored the blaCTX-M-27 and three isolates carried the blaSHV-12 gene. Genotyping of the nine ESBL-producing E. coli strains revealed seven different sequence types (STs) including ST10, ST131, ST154, ST206, ST1488 (SLV ST10), ST2858 and ST3576, most of which have been already described in humans, animals or in the environment. Urban pigeons constitute a potential source of ESBL genes and may be a transmission vehicle of multidrug-resistant bacteria in the environment.

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The Population Genomics of Increased Virulence and Antibiotic Resistance in Human Commensal Escherichia coli over 30 Years in France

Cited by 32 publications

References 110 publications

Community carriage of ESBL-producingEscherichia coliandKlebsiella pneumoniae: A cross-sectional study of risk factors and comparative genomics of carriage and clinical isolates

Community carriage of ESBL-producingEscherichia coliandKlebsiella pneumoniae: A cross-sectional study of risk factors and comparative genomics of carriage and clinical isolates

Global Phylogeny and F Virulence Plasmid Carriage in Pandemic Escherichia coli ST1193

Urban Pigeons (Columba livia) as a Source of Broad-Spectrum β-Lactamase-Producing Escherichia coli in Lisbon, Portugal

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