Sequence Types, Clonotypes, Serotypes, and Virotypes of Extended-Spectrum β-Lactamase-Producing Escherichia coli Causing Bacteraemia in a Spanish Hospital Over a 12-Year Period (2000 to 2011)

Abstract

The aim of the present study was to examine the prevalence and determine the molecular characteristics of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) causing bacteraemia in a Spanish Hospital over a 12-year period (2000 to 2011). As far as we know, this is the first study which has investigated and compared the serotypes, phylogroups, clonotypes, virotypes, and PFGE profiles of ST131 and non-ST131 clones of bacteraemia ESBL-EC isolates. Of the 2,427 E. coli bloodstream isolates, 96 (4.0%) were positive for ESBL production: 40 for CTX-M-15, 36 for CTX-M-14, eight for CTX-M-1, four for CTX-M-9, CTX-M-32, and SHV-12. The number of ESBL-EC increased from 1.0% during 2000 to 2005 to 5.5% during 2006–2011 ( P < 0.001). The 96 ESBL-EC isolates belonged to 36 different STs. The commonest was ST131 (41 isolates), followed by ST58, ST354, ST393 and ST405 (four isolates each). Most CTX-M-15 isolates (87.5%, 35/40) were ST131, whereas the 36 CTX-M-14 isolates belonged to 23 different STs and only 3 (8.3%) of them were ST131. The 35 ST131 CTX-M-15-producing isolates belonged to the H 30Rx subclone and 29 of them showed the virotype A. A drastic change in ST131 virotypes happened in 2011 due to the emergence of the virotypes E ( sat , papGII , cnf1 , hlyA , and kpsMII-K5 ) and F ( sat , papGII , and kpsMII-K5 ) which displaced virotype A ( afa/draBC , afa operon FM955459, sat , and kpsMII-K2 ). Although the 96 ESBL-EC isolates showed 21 O serogroups and 17 H flagellar antigens, 39 belonged to serotype O25b:H4 (ST131 isolates). The second most prevalent serotype (O15:H1) was found to be associated with another important high-risk clone (ST393). In conclusion, the ST131 was the most frequent sequence type, being the H 30Rx subclone responsible for the significant increase of ESBL-EC isolates since 2006. Here, we report two new virotypes (E and F) of the H 30Rx subclone emerged in 2011. Future molecular studies are needed to understand the dynamics of expansion of this successful high-risk subclone in order to prevent its spread and establish the importance of the two new virotypes.

Whole Genome Sequencing and Characteristics of mcr-1–Harboring Plasmids of Porcine Escherichia coli Isolates Belonging to the High-Risk Clone O25b:H4-ST131 Clade B

“…The most common lineages in this clinical collection were the C2-H30Rx (61.6%), B (17%), and C1-nM27 (16%). Recently, Mamani et al (2019) also described the subclade C2-H30Rx as the most prevalent (85%) among 41 ST131 ESBL-producing E. coli causing bacteremia in a Spanish hospital over a 12-year period (2000)(2001)(2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009)(2010)(2011). In contrast, almost all Spanish ST131 isolates obtained from animal origin belonged to clade B.…”

“…Serotyping, Phylogenetic Grouping, Multilocus Sequence Typing, CH Typing, and Virulence Genotyping ST131 isolates were characterized with regard to O:H serotypes, phylogenetic groups, clonotypes (fumC and fimH genes), sequence type by multilocus sequence typing (MLST) (according to the Achtman scheme and by the Pasteur Institute scheme), and 34 extraintestinal virulence-associated genes encoding adhesins (fimH,fimAv MT78 ,papAH,papC,papEF,papGII,papGIII,sfa/focDE,afa/draBC,yfcV),toxins (sat,cnf1,hlyA,hlyF,cdtB,tsh,vat), siderophores-iron uptake (iucD, iutA, iroN, fyuA, chuA), capsule (kpsM II, kpsM II-K2, kpsM II-K5, neuC-K1, kpsM III), and miscellaneous [cvaC, iss, traT, ibeA, malX (PAI), usp, ompT] as described previously (Clermont et al, 2013;Dahbi et al, 2014;Mamani et al, 2019). Based on the definitions given by Johnson et al (2008Johnson et al ( , 2015 and Spurbeck et al (2012), the isolates that genetically satisfied the following criteria (I) positive for ≥2 of 5 markers, including papAH and/or papC, sfa/focDE, afa/draBC, kpsM II, and iutA; (II) positive for three or more of four markers, including chuA, fyuA, vat, and yfcV;…”

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

“…Furthermore, it was described in three human isolates O25b:H4-ST131 ibeA-positive of our region, as early as in 2008 [11]. Of the 2,427 E. coli bloodstream isolates recovered in the hospital of our city (HULA) in the period 2000-2011, 96 were positive for ESBL production, from which 4.2% were CTX-M-32 and 4.2% SHV-12 [36]. The same prevalence was observed in this hospital in 2015 (unpublished data).…”

High Prevalence of ST131 Subclades C2-H30Rx and C1-M27 Among Extended-Spectrum β-Lactamase-Producing Escherichia coli Causing Human Extraintestinal Infections in Patients From Two Hospitals of Spain and France During 2015

“…The following characters were determined as previously described: serotypes using all available O (O1 to O181) and H (H1 to H56) antisera (Guinée et al, 1981), ESBL types (TEM, SHV, and CTX-M enzymes) (Leflon-Guibout et al, 2004), phylogenetic groups (A, B1, B2, C, D, E, F) (Clermont et al, 2013), STs of Achtman scheme (Wirth et al, 2006), clonotypes (fumC and fimH genes) (Weissman et al, 2012), and VF-encoding genes (Mamani et al, 2019). Isolates were classified as extraintestinal pathogenic E. coli (ExPEC) (Johnson et al, 2015) if positive for ≥2 of 5 markers, including papAH and/or papC, sfa/focDE, afa/draBC, kpsM II, and iutA, as uropathogenic E. coli (UPEC) (Spurbeck et al, 2012) if positive for ≥3 of 4 markers, including chuA, fyuA, vat, and yfcV, and as avian pathogenic E. coli (APEC) (Johnson et al, 2008) if positive for ≥4 of 5 markers (hlyF, iutA, iroN, iss, and ompT).…”