The <scp>C</scp>lermont <i><scp>E</scp>scherichia coli</i> phylo‐typing method revisited: improvement of specificity and detection of new phylo‐groups

Clermont, Olivier; Christenson, Julia K.; Denamur, Erick; Gordon, David M.

doi:10.1111/1758-2229.12019

Cited by 1,435 publications

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“…PCR assays were used to assign the E. coli isolates to phylogroups A, B1, B2, C, D, E and F (Clermont et al, 2013). Phylogroup B2 isolates were investigated for ST131 status by PCR assays targeting single nucleotide polymorphisms (SNPs) in mdh and gyrB (Johnson et al, 2009) and the O25b variant and SNPs in pabB (Clermont et al, 2009).…”

Section: Methodsmentioning

confidence: 99%

High prevalence of Escherichia coli sequence type 131 among antimicrobial-resistant E. coli isolates from geriatric patients

Chu

et al. 2015

Journal of Medical Microbiology

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Previous work on the subclones within Escherichia coli ST131 predominantly involved isolates from Western countries. This study assessed the prevalence and antimicrobial resistance attributed to this clonal group. A total of 340 consecutive, non-duplicated urinary E. coli isolates originating from four clinical laboratories in Hong Kong in 2013 were tested. ST131 prevalence among the total isolates was 18.5 % (63/340) and was higher among inpatient isolates (23.0 %) than outpatient isolates (11.8 %, P,0.001), and higher among isolates from patients aged ¢65 years than from patients aged 18-50 years and 51-64 years (25.4 vs 3.4 and 4.0 %, respectively, P,0.001). Of the 63 ST131 isolates, 43 (68.3 %) isolates belonged to the H30 subclone, whereas the remaining isolates belonged to H41 (n517), H54 (n52) and H22 (n51). All H30 isolates were ciprofloxacin-resistant, of which 18.6 % (8/43) belonged to the H30-Rx subclone. Twenty-six (41.3 %) ST131 isolates were ESBL-producers, of which 19 had bla CTX-M-14 (12 non-H30-Rx, two H30-Rx and five H41), six had bla CTX-M-15 (five non-H30-Rx and one H30-Rx) and one was bla CTX-M -negative (H30). In conclusion, ST131 accounts for a large share of the antimicrobial-resistant E. coli isolates from geriatric patients. Unlike previous reports, ESBLproducing ST131 strains mainly belonged to non-H30-Rx rather than the H30-Rx subclone, with bla CTX-M-14 as the dominant enzyme type. INTRODUCTIONThe incidence of infections due to antimicrobial-resistant Escherichia coli is increasing worldwide (Barber et al., 2013). Resistance rates for cotrimoxazole, fluoroquinolones and third generation cephalosporins, which are often used for empirical therapy, are now above the 15-20 % threshold recommended for choosing first-line antimicrobial agents for empirical treatment in Hong Kong (Ho et al., 2007b;. Discordant therapy may cause treatment failure, persistence and recurrence of infection, leading to more patient morbidity and mortality (Barber et al., 2013;Shin et al., 2012). Emerging resistance in E. coli involves acquisition of resistance determinants by susceptible strains and the expansion of pre-existing resistant clones (Naseer & Sundsfjord, 2011). ST131 is a highly successful E. coli clone which has received considerable attention due to its wide geographical distribution, ability to cause a wide range of extra-intestinal infections and association with CTX-M b-lactamases and multidrug resistance (NicolasChanoine et al., 2014). ST131 can be divided into different subclones by other typing methods, of which sequencing the type 1 fimbrial adhesin gene fimH is one widely used approach (Weissman et al., 2012). H30, designated according to the fimH30 variant, is currently the most prevalent subclone of ST131 (Nicolas-Chanoine et al., 2014). Two studies involving whole genome sequencing of ST131 isolates collected from multiple countries came to the same conclusion that fluoroquinolone resistance within ST131 was confined almost entirely to the H30 subclone and that CTX-M-15 producers cluste...

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Section: Methodsmentioning

confidence: 99%

High prevalence of Escherichia coli sequence type 131 among antimicrobial-resistant E. coli isolates from geriatric patients

Chu

et al. 2015

Journal of Medical Microbiology

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“…Eight E. coli phylogroups are currently recognised (A, B1, B2, D, E, F, G, and Clade 1) and a new PCR approach enables isolates to be assigned to one of these phylogroups (21).…”

Section: Expec Lineage Determination; a Brief Historymentioning

confidence: 99%

Extra-intestinal pathogenic Escherichia coli (ExPEC): Disease, carriage and clones

Dale

Woodford

2015

Journal of Infection

158

132

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Extra-intestinal pathogenic E. coli (ExPEC) have a complex phylogeny, broad virulence factor (VF) armament and significant genomic plasticity, and are associated with a spectrum of host infective syndromes ranging from simple urinary tract infection to life-threatening bacteraemia. Their importance as pathogens has come to the fore in recent years, particularly in the context of the global emergence of hyper-virulent and antibiotic resistant strains.Despite this, the mechanisms underlying ExPEC transmission dynamics and clonal selection remain poorly understood. Large-scale epidemiological and clinical studies are urgently required to ascertain the mechanisms underlying these processes to enable the development of novel evidence-based preventative and therapeutic strategies. In the current review, we provide a concise summary of the methods utilised for ExPEC phylogenetic genetic delineation before exploring in detail the associations between ExPEC VFs and site-specific disease. We then consider the role of ExPEC as an intestinal colonist before outlining known associations between ExPEC clonal variation, specific disease syndromes and antibiotic resistance.

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“…Nevertheless, the increase in genome research and multi-locus sequence data put forward eight new phylo-groups of E. coli, assigned as A, B1, B2, C, D, E and F which belong to E. coli sensu stricto and one correspond to the Escherichia cryptic clade I (Jaureguy et al 2008;Moissenet et al 2010;Tenaillon et al 2010;Clermont et al 2011;Luo et al 2011). Group E is recognized as a new group that was formerly comprised unassigned strains; group F designated as sister group of B2; group C includes strains closely related but distinct from group B1 and an Escherichia clade I which is considered to be a new phylo-group that is phenotypically indistinguishable but genotypically different from E. coli (Clermont et al 2013). Recently, Clermont et al (2013) improved their method and described a new quadruplex PCR method for the determination of new phylo-groups using gene targets of chuA, yjaA, TspE4.C2 and arpA.…”

Section: Introductionmentioning

confidence: 99%

Phylo-typing of clinicalEscherichia coliisolates originating from bovine mastitis and canine pyometra and urinary tract infection by means of quadruplex PCR

Müştak

Günaydin²,

Kaya

et al. 2015

Veterinary Quarterly

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(2015) Phylo-typing of clinical Escherichiacoli isolates originating from bovine mastitis and canine pyometra and urinary tract infection by means of quadruplex PCR, Veterinary Quarterly, 35:4, 194-199, DOI: 10.1080/01652176.2015 Background: Escherichia coli is one of the major causative agents of bovine mastitis worldwide, and is typically associated with acute, clinical mastitis. Besides this, E. coli strains which belong to the extra-intestinal pathogenic group are also the major cause of urinary tract infections and pyometra in dogs. Objectives: In this study, it was aimed to investigate phylo-groups/subgroups in 155 E. coli isolates obtained from acute bovine mastitis, 43 from urinary tract infections of dogs and 20 from canine pyometra by a formerly described triplex PCR and recently described new quadruplex polymerase chain reaction (PCR) method. Results: Group A 1 (n D 118; 76%) and B1 (n D 71; 46%) were found to be the most prevalent groups by triplex and quadruplex PCR assays in mastitis isolates, respectively. Phylo-typing of 43 urinary tract isolates also revealed that most of the isolates belonged to A 1 (n D 23; 54%) by triplex and B2 (n D 36; 84%) by quadruplex PCR assays. The isolates assigned as group A 1 (n D 17; 85%) by triplex PCR could not be classified by quadruplex PCR in pyometra isolates. Conclusions:The results support the hypothesis that E. coli strains isolated from bovine mastitis cases are environmental. Also, groups C, E and F were identified as new phylo-groups for the first time in acute bovine mastitis cases. The comparison of triplex PCR with quadruplex PCR results revealed that most of the groups assigned in triplex PCR were altered by quadruplex PCR assay.

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The Clermont Escherichia coli phylo‐typing method revisited: improvement of specificity and detection of new phylo‐groups

Cited by 1,435 publications

References 28 publications

High prevalence of Escherichia coli sequence type 131 among antimicrobial-resistant E. coli isolates from geriatric patients

High prevalence of Escherichia coli sequence type 131 among antimicrobial-resistant E. coli isolates from geriatric patients

Extra-intestinal pathogenic Escherichia coli (ExPEC): Disease, carriage and clones

Phylo-typing of clinicalEscherichia coliisolates originating from bovine mastitis and canine pyometra and urinary tract infection by means of quadruplex PCR

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