Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection

Gordon, David M.; Geyik, Sarah; Clermont, Olivier; O’Brien, Claire; Huang, Shiwei; Abayasekara, C. L.; Rajesh, A.; Kennedy, Karina; Collignon, Peter; Pavli, Paul; Rodriguez, Christophe; Johnston, Brian; Johnson, James R.; Decousser, J.-W.; Denamur, Erick

doi:10.1128/msphere.00168-17

Cited by 34 publications

(50 citation statements)

References 55 publications

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“…In silico multilocus sequence typing (MLST) identified MS8345 as ST95. MS8345 was serotyped as O2:K1:H4 and possesses the fimH 27 allele, placing it in the recently defined ST95 subgroup E ( 40 ). Pairwise genome comparisons revealed MS8345 to be highly similar to the human neonatal meningitis E. coli (NMEC) isolate S88 (GenBank accession number CU928161 ) and the avian pathogen APEC-O1 (GenBank accession number CP000468 ) ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Discovery of mcr-1 -Mediated Colistin Resistance in a Highly Virulent Escherichia coli Lineage

Forde

Zowawi

Harris

et al. 2018

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Escherichia coli ST95 is a globally disseminated clone frequently associated with bloodstream infections and neonatal meningitis. However, the ST95 lineage is defined by low levels of drug resistance amongst clinical isolates, which normally provides for uncomplicated treatment options. Here, we provide the first detailed genomic analysis of an E. coli ST95 isolate that has both high virulence potential and resistance to multiple antibiotics. Using the genome, we predicted its virulence and antibiotic resistance mechanisms, which include resistance to last-line antibiotics mediated by the plasmid-borne mcr-1 gene. Finding an ST95 isolate resistant to nearly all antibiotics that also has a high virulence potential is of major clinical importance and underscores the need to monitor new and emerging trends in antibiotic resistance development in this important global lineage.

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Section: Resultsmentioning

confidence: 99%

Discovery of mcr-1 -Mediated Colistin Resistance in a Highly Virulent Escherichia coli Lineage

Forde

Zowawi

Harris

et al. 2018

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“…Using the fimH allele type, we identified six fimH alleles among our 23 ST73 isolates (fimH 10, 12, 13, 27, 30, 32 and 103), that defined six clones, among which B2-CH24-10-ST73 and B2-CH24-103-ST73 clones predominated. Gordon et al [33] studied the phylogeny of 200 STC95 isolates from humans living in France, Australia and the USA. The SNPs analysis revealed five main clusters associated to different fimH alleles and serotypes.…”

Section: Discussionmentioning

confidence: 99%

Clonal Structure, Virulence Factor-encoding Genes and Antibiotic Resistance of Escherichia coli, Causing Urinary Tract Infections and Other Extraintestinal Infections in Humans in Spain and France during 2016

et al. 2020

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Escherichia coli is the main pathogen responsible for extraintestinal infections. A total of 196 clinical E. coli consecutively isolated during 2016 in Spain (100 from Lucus Augusti hospital in Lugo) and France (96 from Beaujon hospital in Clichy) were characterized. Phylogroups, clonotypes, sequence types (STs), O:H serotypes, virulence factor (VF)-encoding genes and antibiotic resistance were determined. Approximately 10% of the infections were caused by ST131 isolates in both hospitals and approximately 60% of these infections were caused by isolates belonging to only 10 STs (ST10, ST12, ST58, ST69, ST73, ST88, ST95, ST127, ST131, ST141). ST88 isolates were frequent, especially in Spain, while ST141 isolates significantly predominated in France. The 23 ST131 isolates displayed four clonotypes: CH40-30, CH40-41, CH40-22 and CH40-298. Only 13 (6.6%) isolates were carriers of extended-spectrum beta-lactamase (ESBL) enzymes. However, 37.2% of the isolates were multidrug-resistant (MDR). Approximately 40% of the MDR isolates belonged to only four of the dominant clones (B2-CH40-30-ST131, B2-CH40-41-ST131, C-CH4-39-ST88 and D-CH35-27-ST69). Among the remaining MDR isolates, two isolates belonged to B2-CH14-64-ST1193, i.e., the new global emergent MDR clone. Moreover, a hybrid extraintestinal pathogenic E.coli (ExPEC)/enteroaggregative isolate belonging to the A-CH11-54-ST10 clone was identified.

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“…This is similar to previous observations for community and hospital derived UPEC isolates from the United Kingdom and from Germany (Croxall et al, 2011 ; Toval et al, 2014 ). By contrast, this clone is more prevalent among UTI in the U.S.A. and Australia (Banerjee et al, 2013a ; Gordon et al, 2017 ). Therefore, although CC95 strains occur globally, their distribution is unequal across continents and countries.…”

Section: Discussionmentioning

confidence: 99%

Clonal Diversity, Virulence Potential and Antimicrobial Resistance of Escherichia coli Causing Community Acquired Urinary Tract Infection in Switzerland

et al. 2017

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Objectives: The aim of this study was to assess the clonal structure, virulence potential and antibiotic susceptibility of uropathogenic Escherichia coli (UPEC) isolates causing community acquired urinary tract infection (CAUTI) in unselected primary care patients in Switzerland.Methods: We performed multilocus sequence typing, virulence factor determination, and phenotypic and genotypic antimicrobial resistance testing on 44 non-duplicate UPEC isolates.Results: Twenty-seven different sequence types (STs) were identified. Major UPEC clones were represented by 19 (43.2%) of the isolates, including E. coli ST131, ST69 (both 13.6%), ST73 (6.8%), ST10 (4.5%), ST127, ST140, (both 2.3%). Five (11.4%) isolates belonged to ST141.Aggregate virulence factor (VF) scores were highest among isolates belonging to ST127 and ST141. Overall, 50% of the isolates were susceptible to all 12 antimicrobials tested, and all isolates remained susceptible to fosfomycin and nitrofurantoin. Resistance to sulfamethoxazole and ciprofloxacin were found in 31.8, and 15.9% of the isolates, respectively. Plasmid-mediated resistance genes were detected in ST69 and ST131 and included aac(6′)-Ib-cr (2.3% of all isolates) blaCTX−M−14 and blaCTX−M−15 (9%), and mph(A) (13.6%). None of the isolates tested positive for mcr-1 or mcr-2.Conclusions: Our results show that CAUTI in Switzerland is caused by a wide variety of UPEC STs for which fosfomycin remains a good treatment option. We suggest that ST141 is an emerging clone associated with UTI in the community, and warrants closer attention. Moreover, the high rate of E. coli harboring mph(A) from patients without a history of antimicrobial therapy or hospitalization indicates that UPEC is an important reservoir for mph(A).

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Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection

Cited by 34 publications

References 55 publications

Discovery of mcr-1 -Mediated Colistin Resistance in a Highly Virulent Escherichia coli Lineage

Discovery of mcr-1 -Mediated Colistin Resistance in a Highly Virulent Escherichia coli Lineage

Clonal Structure, Virulence Factor-encoding Genes and Antibiotic Resistance of Escherichia coli, Causing Urinary Tract Infections and Other Extraintestinal Infections in Humans in Spain and France during 2016

Clonal Diversity, Virulence Potential and Antimicrobial Resistance of Escherichia coli Causing Community Acquired Urinary Tract Infection in Switzerland

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