Whole Genome Sequencing of an Unusual Serotype of Shiga Toxin–producing<i>Escherichia coli</i>

Dallman, Tim; Cross, Lisa Jane; Bishop, Chloe; Perry, Neil T.; Olesen, Bente; Grant, Kathie; Jenkins, Claire

doi:10.3201/eid1908.130016

Cited by 19 publications

(17 citation statements)

References 12 publications

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“…Previous studies on AMR in gastrointestinal pathogens in the UK have shown a significant association between specific AMR determinants and international travel [5, 13]. Travel data were not available to add to the analysis in this study, but CC504 (STEC O117 : H7) has previously been isolated from cases reporting recent travel to regions where the risk of acquiring gastrointestinal pathogens is high, such as Southeast Asia, Africa and Latin America [17], and CC165 (STEC O80 : H2) has previously been described as an emerging STEC serotype in France [18]. STEC isolates belonging to both CCs exhibit reduced susceptibility to ciprofloxacin (MIC>0.064 <0.5 mg l −1 ), a resistance profile rarely detected in STEC known to be domestically acquired in the UK [13].…”

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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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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“…All available sequencing data from STEC O117 : H7 isolates were included in this study. Specifically, this included data from: isolates sequenced as part of our work published in 2013 [ 10 ] ( n =5) and other investigations ( n =5); isolates sequenced as part of the outbreak investigation ( n =6); and all O117 : H7 isolated since the implementation of routine WGSA surveillance at PHE ( n =20). Basic patient epidemiological data from sample submission forms (sex, age, history of recent travel if noted) were also retrieved.…”

Section: Methodsmentioning

confidence: 99%

“…In the UK, STEC O117 : H7 is a rare serotype, often misidentified as Shigella sonnei at local laboratories owing to their biochemical similarities and is typically isolated from patients reporting recent travel abroad [ 10, 11 ]. Hence, a domestically transmitting epidemic of this uncommon serotype was unexpected.…”

Section: Introductionmentioning

confidence: 99%

An outbreak of a rare Shiga-toxin-producing Escherichia coli serotype (O117:H7) among men who have sex with men

et al. 2018

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Sexually transmissible enteric infections (STEIs) are commonly associated with transmission among men who have sex with men (MSM). In the past decade, the UK has experienced multiple parallel STEI emergences in MSM caused by a range of bacterial species of the genus Shigella, and an outbreak of an uncommon serotype (O117 : H7) of Shiga-toxin-producing Escherichia coli (STEC). Here, we used microbial genomics on 6 outbreak and 30 sporadic STEC O117 : H7 isolates to explore the origins and pathogenic drivers of the STEC O117 : H7 emergence in MSM. Using genomic epidemiology, we found that the STEC O117 : H7 outbreak lineage was potentially imported from Latin America and likely continues to circulate both in the UK MSM population and in Latin America. We found genomic relationships consistent with existing symptomatic evidence for chronic infection with this STEC serotype. Comparative genomic analysis indicated the existence of a novel Shiga toxin 1-encoding prophage in the outbreak isolates, and evidence of horizontal gene exchange among the STEC O117 : H7 outbreak lineage and other enteric pathogens. There was no evidence of increased virulence in the outbreak strains relative to contextual isolates, but the outbreak lineage was associated with azithromycin resistance. Comparing these findings with similar genomic investigations of emerging MSM-associated Shigella in the UK highlighted many parallels, the most striking of which was the importance of the azithromycin phenotype for STEI emergence in this patient group.

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“…In contrast, the German STEC O104:H4 strain colonizes humans through aggregative adherence fimbrial pili encoded by the enteroaggregative E. coli plasmid . The Danish O117:K1:H7 strain was not EAEC, but the intimin‐like sivH genes might be a factor responsible for its persistent colonization ability , please see below, however, further studies in this area are needed.…”

Section: Chapter 4 Verotoxin/shiga Toxin‐producing (Vtec/stec) O117:mentioning

confidence: 99%

“…The STEC O117:K1:H7 E. coli clonal group has also been seen in England . During 2004–2013, 19 isolates of STEC O117:K1:H7 were submitted to the Gastrointestinal Bacteria Reference Unit at the Health Protection Agency in London, UK, from laboratories in England and Wales for confirmation of identification and typing.…”

Section: Chapter 4 Verotoxin/shiga Toxin‐producing (Vtec/stec) O117:mentioning

confidence: 99%

Characterization of four Escherichia coli clonal groups

Olesen

2017

APMIS

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(1991)(1992) that involved an unusual multi-resistant E. coli O78:H10 strain. Surprisingly, the isolates qualified as enteroaggregative E. coli (EAEC), a diarrheagenic pathotype, making this the first reported involvement of EAEC in an extraintestinal disease outbreak. Paper IV reports an analysis of 51 archived E. coli O78:H10 isolates (1956 2000) that showed E. coli O78:H10 to be clonally heterogeneous, comprising one dominant clonal group (61% of isolates, including all 19 Copenhagen outbreak isolates) from ST10 (phylogenetic group A), plus several minor clonal groups (phylogenetic groups A and D). The outbreak clone exhibited both extraintestinal pathogenic E. coli (ExPEC) and EAEC characteristics. Paper V reports evidence that the outbreak strain adhered more extensively to human bladder epithelial cells than did prototype uropathogenic (ExPEC) strains thanks to its aggregative adherence fimbriae, the principal adhesins of EAEC, and was capable of extensive biofilm formation on urethral catheters. These findings suggest that certain EAEC-specific virulence factors increase uropathogenicity.Paper VI reports a search for ST131, a globally disseminated, recently emerged multiresistant ExPEC clonal group, among 115 extended-spectrum beta-lactamase (ESBL)-producing E. coli clinical isolates from Danish patients (2008 -2009), to assess ST131's prevalence in Copenhagen among ESBL-producing isolates. ST131 was the most prevalent clonal group (38% of isolates) and compared with other ESBL isolates was more often community-associated and exhibited distinctive and extensive virulence profiles.Paper VII reports temporal trends in antimicrobial resistance and virulence genes among historical E. coli ST131 isolates (1968 -2011). Antimicrobial resistance increased over time due to emergence of the (resistance-associated) H30 and H30-Rx ST131 subclones. Distinctive characteristics of the ST131 H30-Rx subclone including specific virulence factors (iutA, afa/dra, kpsM II), K100 capsule, multidrug resistance, and ESBL production possibly contributed to this lineage's epidemiologic success. These findings confirm that ST131 represents a group of distinctive subclones, not a unitary entity.In conclusion, all four clonal groups were multiresistant and demonstrated the potential to spread locally or globally. A combination of antimicrobial resistance and specific virulence genes likely contributed to their epidemiologic success. Future implementation of rapid methods to screen for such multiresistant high-risk clones and their cardinal virulence genes conceivably could assist in clinical management and prevention efforts.

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Whole Genome Sequencing of an Unusual Serotype of Shiga Toxin–producingEscherichia coli

Cited by 19 publications

References 12 publications

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

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

An outbreak of a rare Shiga-toxin-producing Escherichia coli serotype (O117:H7) among men who have sex with men

Characterization of four Escherichia coli clonal groups

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