One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock

Ludden, Catherine; Raven, Kathy E.; Jamrozy, Dorota; Gouliouris, Theodore; Blane, Beth; Coll, Francesc Español i; Goffau, Marcus C. de; Naydenova, Plamena; Horner, Carolyne; Hernandez-Garcia, Juan; Wood, Paul M.; Hadjirin, Nazreen F.; Radakovic, Milorad; Brown, Nicholas M.; Holmes, Mark A.; Parkhill, Julian; Peacock, Sharon J.

doi:10.1128/mbio.02693-18

Cited by 143 publications

(143 citation statements)

References 53 publications

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“…), the strains that encode stx genes may not be capable of causing intestinal disease as they lack many of the genes that typically cooccur with stx . STc117 and STc454 are typically multidrug resistant, with a high proportion of strains producing CTX‐M, especially CTX‐M‐1, in accordance with a recent report (Ludden et al ., ). It has to be noted that strains of these STcs have a high prevalence of genes conferring resistance to antibiotics prescribed in veterinary medicine such as sulphonamides, tetracyclines and chloramphenicol and that three strains in our collection possess the mcr‐1 gene conferring resistance to colistin, a resistance having emerged in pig and poultry isolates in China (Liu et al ., ).…”

Section: Discussionmentioning

confidence: 97%

“…However, STc117 is the most prevalent phylogroup G lineage and is commonly isolated from poultry and poultry meat products in Northern Europe (Ronco et al, 2017) and Canada (Bergeron et al, 2012). Recently, it has been shown in the East of England that ST117 represents 8% and 20% of livestock (poultry and pigs) and poultry meat E. coli isolates respectively (Ludden et al, 2019). In humans, phylogroup G strains represent around 1% of the E. coli isolates and are found both in commensal and extra-intestinal pathogenic conditions, including septicaemia (Table 2) (Kallonen et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

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Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential

Clermont

Dixit

Vangchhia

et al. 2019

Environmental Microbiology

171

144

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Summary The phylogeny of the Escherichia coli species, with the identification of seven phylogroups (A, B1, B2, C, D, E and F), is linked to the lifestyle of the strains. With the accumulation of whole genome sequence data, it became clear that some strains belong to a group intermediate between the F and B2 phylogroups, designated as phylogroup G. Here, we studied the complete sequences of 112 strains representative of the G phylogroup diversity and showed that it is composed of one main sequence type complex (STc)117 and four other STcs (STc657, STc454, STc738 and STc174). STc117, which phylogeny is characterized by very short internal branches, exhibits extensive O diversity, but little H‐type and fimH allele diversity, whereas the other STcs are characterized by a main O, H and fimH type. STc117 strains possess many traits associated with extra‐intestinal virulence, are virulent in a mouse sepsis model and exhibit multi‐drug resistance such as CTX‐M production. Epidemiologic data on 4,524 Australian and French strains suggest that STc117 is a poultry‐associated lineage that can also establish in humans and cause extra‐intestinal diseases. We propose an easy identification method that will help to trace this potentially virulent and resistant phylogroup in epidemiologic studies.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential

Clermont

Dixit

Vangchhia

et al. 2019

Environmental Microbiology

171

144

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“…coli causing human infection via the food chain focus on the comparison of isolates from cross-sectional surveys of livestock and/or food with E. coli causing extra-intestinal infections in humans [27]. In this study, we adopt an alternative approach involving monitoring multidrug resistance in isolates of STEC, an established zoonotic, foodborne pathogen, from human cases of gastrointestinal disease.…”

Section: Discussionmentioning

confidence: 99%

Antimicrobial resistance in Shiga toxin-producing Escherichia coli other than serotype O157 : H7 in England, 2014–2016

Gentle

Day

Hopkins

et al. 2020

Journal of Medical Microbiology

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Introduction. Despite many ongoing surveillance projects and the recent focus on the veterinary and clinical ‘One Health’ aspects of antimicrobial resistance (AMR), evidence of the extent of any public health risk posed by animal reservoirs with respect to the transmission of resistant strains of Escherichia coli to humans remains varied and contentious. In the UK, the main zoonotic reservoir for the foodborne pathogen Shiga toxin-producing E. coli (STEC) is cattle and sheep. In this study, we adopt an alternative approach to the risk assessment of transmission of AMR E. coli from animals to humans, involving monitoring AMR in isolates of STEC, an established zoonotic, foodborne pathogen, from human cases of gastrointestinal disease. Aim. The aim of this study was to determine the genome-derived AMR profiles for STEC from human cases to assess the risk of transmission of multidrug-resistant STEC from ruminants to humans. Methodology. STEC belonging to 10 different clonal complexes (CCs) (n=457) isolated from human faecal specimens were sequenced and genome-derived AMR profiles were determined. Phenotypic susceptibility testing was undertaken on all isolates (n=100) predicted to be resistant to at least one class of antimicrobial. Results. Of the 457 isolates, 332 (72.7 %) lacked identifiable resistance genes and were predicted to be fully susceptible to 11 classes of antimicrobials; 125/332 (27.3 %) carried 1 or more resistance genes, of which 83/125 (66.4 %) were resistant to 3 or more classes of antibiotic. The percentage of isolates harbouring AMR determinants varied between CCs, from 4% in CC25 to 100% in CC504. Forty-six different AMR genes were detected, which conferred resistance to eight different antibiotic classes. Resistance to ampicillin, streptomycin, tetracyclines and sulphonamides was most commonly detected. Four isolates were identified as extended-spectrum β-lactamase producers. An overall concordance of 97.7 % (n=1075/1100) was demonstrated between the phenotypic and genotypic methods. Conclusion. This analysis provided an indirect assessment of the risk of transmission of AMR gastrointestinal pathogens from animals to humans, and revealed a subset of human isolates of the zoonotic pathogen STEC were resistant to the antimicrobials used in animal husbandry. However, this proportion has not increased over the last three decades, and thismay provide evidence that guidancepromoting responsible practice has been effective.

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“…None of the ESBLs found included CTX-M-15, which is the predominant human clinical isolate in the UK [54]. Another study in the UK used genomic surveillance to investigate the role of livestock as a reservoir for drug-resistant E. coli that infect humans [55]. A total of 431 E. coli isolates (including 155 ESBL-producing isolates) from livestock farms (cattle, pig and poultry) and meat in the East of England were compared to isolates from 1517 patients with BSIs in the UK.…”

Section: Studies With Limited Evidence Of An Association Between Amrmentioning

confidence: 99%

Overview of Evidence of Antimicrobial Use and Antimicrobial Resistance in the Food Chain

et al. 2020

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Antimicrobial resistance (AMR) is a global health problem. Bacteria carrying resistance genes can be transmitted between humans, animals and the environment. There are concerns that the widespread use of antimicrobials in the food chain constitutes an important source of AMR in humans, but the extent of this transmission is not well understood. The aim of this review is to examine published evidence on the links between antimicrobial use (AMU) in the food chain and AMR in people and animals. The evidence showed a link between AMU in animals and the occurrence of resistance in these animals. However, evidence of the benefits of a reduction in AMU in animals on the prevalence of resistant bacteria in humans is scarce. The presence of resistant bacteria is documented in the human food supply chain, which presents a potential exposure route and risk to public health. Microbial genome sequencing has enabled the establishment of some links between the presence of resistant bacteria in humans and animals but, for some antimicrobials, no link could be established. Research and monitoring of AMU and AMR in an integrated manner is essential for a better understanding of the biology and the dynamics of antimicrobial resistance.

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One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock

Cited by 143 publications

References 53 publications

Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential

Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential

Antimicrobial resistance in Shiga toxin-producing Escherichia coli other than serotype O157 : H7 in England, 2014–2016

Overview of Evidence of Antimicrobial Use and Antimicrobial Resistance in the Food Chain

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