Emerging Multidrug-Resistant Hybrid Pathotype Shiga Toxin–Producing <i>Escherichia coli</i> O80 and Related Strains of Clonal Complex 165, Europe

Cointe, Aurélie; Birgy, André; Mariani‐Kurkdjian, Patricia; Liguori, Sandrine; Courroux, Céline; Blanco, Jorge; Delannoy, Sabine; Fach, Patrick; Loukiadis, Estelle; Bidet, Philippe; Bonacorsi, Stéphane

doi:10.3201/eid2412.180272

Cited by 52 publications

(99 citation statements)

References 30 publications

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“…As previously reported by Cointe et al (2018), O80:H2 strains were clustered into three well-supported clusters (Ia, Ib, and II) distinguished by the presence of one cryptic plasmid (plasmid pRDEx444_B) and differentiated virulence gene profiles (Figure 5). Notably, CRISPR typing showed the high accordance with wgSNP typing.…”

Section: Association Among Clustered Regularly Interspaced Short Palisupporting

confidence: 74%

Utilization of Clustered Regularly Interspaced Short Palindromic Repeats to Genotype Escherichia coli Serogroup O80

Long

et al. 2020

Front. Microbiol.

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The hypervariable nature of clustered regularly interspaced short palindromic repeats (CRISPRs) makes them valuable biomarkers for subtyping and epidemiological investigation of Escherichia coli. Shiga toxin-producing E. coli (STEC) serogroup O80 is one hybrid pathotype that is emerging recently in Europe and is involved in hemolytic uremic syndrome with bacteremia. However, whether STEC O80 strains can be genotyped using CRISPR has not been evaluated. In this study, we aimed to characterize the genetic diversity of 81 E. coli serogroup O80 isolates deposited in the National Center for Biotechnology Information databases using CRISPR typing and to explore the association between virulence potential and CRISPR types (CTs). A total of 21 CTs were identified in 80 O80 strains. CRISRP typing provided discrimination with variants of a single serotype, which suggested a stronger discriminatory power. Based on CRISPR spacer profiles, 70 O80:H2 isolates were further divided into four lineages (lineage LI, LII, LIII, and LIV), which correlated well with whole-genome single nucleotide polymorphisms typing and virulence gene profiles. Moreover, the association between CRISPR lineages and virulence gene profiles hinted that STEC O80:H2 strains may originate from O80:H19 or O80:H26 and that lineage LI may have been evolved from lineage LII. CT2 and CT13 were shared by human and cattle isolates, suggesting that there might be the potential transmission between cattle and human. Collectively, CRISPR typing is one technology that can be used to monitor the transmission of STEC O80 strains and provide new insights into microevolution of serogroup O80.

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Section: Association Among Clustered Regularly Interspaced Short Palisupporting

confidence: 74%

Utilization of Clustered Regularly Interspaced Short Palindromic Repeats to Genotype Escherichia coli Serogroup O80

Long

et al. 2020

Front. Microbiol.

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“…This emerging hybrid is associated with invasive infections, and combines intestinal VFs (stx2d, eae-xi and ehxA genes) and extraintestinal genes characteristic of the plasmid pS88 [41,42]. In this O80 clone, it is to highlight the location of MDR and pS88 genes in the same plasmid, as well as the presence of two additional plasmids (a carrier of ehxA gene and a cryptic one) within the isolates [41,42]. The clonal group described here poses also the threat of being MDR and characteristically associated with ESBL-type CTX-M-32.…”

Section: Discussionmentioning

confidence: 99%

Genomic Characterization of Escherichia coli Isolates Belonging to a New Hybrid aEPEC/ExPEC Pathotype O153:H10-A-ST10 eae-beta1 Occurred in Meat, Poultry, Wildlife and Human Diarrheagenic Samples

et al. 2020

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Different surveillance studies (2005–2015) in northwest Spain revealed the presence of eae-positive isolates of Escherichia coli O153:H10 in meat for human consumption, poultry farm, wildlife and human diarrheagenic samples. The aim of this study was to explore the genetic and genomic relatedness between human and animal/meat isolates, as well as the mechanism of its persistence. We also wanted to know whether it was a geographically restricted lineage, or whether it was also reported elsewhere. Conventional typing showed that 32 isolates were O153:H10-A-ST10 fimH54, fimAvMT78, traT and eae-beta1. Amongst these, 21 were CTX-M-32 or SHV-12 producers. The PFGE XbaI-macrorestriction comparison showed high similarity (>85%). The plasmidome analysis revealed a stable combination of IncF (F2:A-:B-), IncI1 (STunknown) and IncX1 plasmid types, together with non-conjugative Col-like plasmids. The core genome investigation based on the cgMLST scheme from EnteroBase proved close relatedness between isolates of human and animal origin. Our results demonstrate that a hybrid MDR aEPEC/ExPEC of the clonal group O153:H10-A-ST10 (CH11-54) is circulating in our region within different hosts, including wildlife. It seems implicated in human diarrhea via meat transmission, and in the spreading of ESBL genes (mainly of CTX-M-32 type). We found genomic evidence of a related hybrid aEPEC/ExPEC in at least one other country.

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“…Whole-genome sequencing. The library preparation and sequencing were carried out as previously described (32). Briefly, DNA was extracted using the MoBio kit (Qiagen).…”

Section: Methodsmentioning

confidence: 99%

Independent Host Factors and Bacterial Genetic Determinants of the Emergence and Dominance of Escherichia coli Sequence Type 131 CTX-M-27 in a Community Pediatric Cohort Study

Birgy

Lévy

Nicolas–Chanoine

et al. 2019

Antimicrob Agents Chemother

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The recent emergence and diffusion in the community of Escherichia coli isolates belonging to the multidrug-resistant and CTX-M-27-producing sequence type 131 (ST131) C1-M27 cluster makes this cluster potentially as epidemic as the worldwide E. coli ST131 subclade C2 composed of multidrug-resistant isolates producing CTX-M-15. Thirty-five extended-spectrum beta-lactamase (ESBL)-producing ST131 isolates were identified in a cohort of 1,885 French children over a 5-year period. They were sequenced to characterize the ST131 E. coli isolates producing CTX-M-27 recently emerging in France. ST131 isolates producing CTX-M-27 (n = 17), and particularly those belonging to the C1-M27 cluster (n = 14), carried many resistance-encoding genes and predominantly an F1:A2:B20 plasmid type. In multivariate analysis, having been hospitalized since birth (odds ratio [OR], 10.9; 95% confidence interval [CI], 2.4 to 48.8; P = 0.002) and being cared for in a day care center (OR, 9.4; 95% CI, 1.5 to 59.0; P = 0.017) were independent risk factors for ST131 CTX-M-27 fecal carriage compared with ESBL-producing non-ST131 isolates. No independent risk factor was found when comparing CTX-M-15 (n = 11)- and CTX-M-1/14 (n = 7)-producing ST131 isolates with ESBL-producing non-ST131 isolates or with non-ESBL-producing isolates. Several factors may contribute to the increase in fecal carriage of CTX-M-27-producing E. coli isolates, namely, resistance to multiple antibiotics, capacity of the CTX-M-27 enzyme to hydrolyze both cefotaxime and ceftazidime, carriage of a peculiar F-type plasmid, and/or capacity to colonize children who have been hospitalized since birth or who attend day care centers.

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Emerging Multidrug-Resistant Hybrid Pathotype Shiga Toxin–Producing Escherichia coli O80 and Related Strains of Clonal Complex 165, Europe

Cited by 52 publications

References 30 publications

Utilization of Clustered Regularly Interspaced Short Palindromic Repeats to Genotype Escherichia coli Serogroup O80

Utilization of Clustered Regularly Interspaced Short Palindromic Repeats to Genotype Escherichia coli Serogroup O80

Genomic Characterization of Escherichia coli Isolates Belonging to a New Hybrid aEPEC/ExPEC Pathotype O153:H10-A-ST10 eae-beta1 Occurred in Meat, Poultry, Wildlife and Human Diarrheagenic Samples

Independent Host Factors and Bacterial Genetic Determinants of the Emergence and Dominance of Escherichia coli Sequence Type 131 CTX-M-27 in a Community Pediatric Cohort Study

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