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).

Rosalia Mamani,Isidro García-Meniño,Miguel Blanco,Azucena Mora,Vanesa García,Saskia Camille Flament-Simon,Cecilia López,María Pilar Alonso,Jesús E Blanco,Jorge Blanco,Dafne Díaz-Jiménez

doi:10.3389/fmicb.2019.01530

Rosalia Mamani, Isidro García-Meniño + Show 9 more

Open Access

https://doi.org/10.3389/fmicb.2019.01530

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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 H30Rx 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 H30Rx subclone responsible for the significant increase of ESBL-EC isolates since 2006. Here, we report two new virotypes (E and F) of the H30Rx 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.

Highlights

Escherichia coli is the main cause of bloodstream infections (BSIs) and in recent years there has been a very significant increase in the number of infections caused by multidrug-resistant isolates, and especially by extended-spectrum β-lactamase-producing E. coli (ESBL-EC) (Tumbarello et al, 2010; de Kraker et al, 2013; Vihta et al, 2018)
The present study included 2,427 non-duplicate, clinically relevant E. coli isolates recovered from blood of patients at Hospital Universitario Lucus Augusti (HULA) between January 2000 and December 2011
The number of ESBL-Producing E. coli (ESBL-EC) isolates increased from 1.0% (8/827) during 2000–2005 to 5.5% (88/1,600) during 2006–2011 (P < 0.001) (Figure 1, Table 1, and Supplementary Table S2)

Summary

Introduction

Escherichia coli is the main cause of bloodstream infections (BSIs) and in recent years there has been a very significant increase in the number of infections caused by multidrug-resistant isolates, and especially by extended-spectrum β-lactamase-producing E. coli (ESBL-EC) (Tumbarello et al, 2010; de Kraker et al, 2013; Vihta et al, 2018). ESBL production in E. coli has increased due mainly to the spread of CTX-M enzymes. The highrisk clones have played a very important role in the current pandemic spread, especially the ST131 clone associated with the CTX-M-15 enzyme (Nicolas-Chanoine et al, 2008; Chung et al, 2012; Peirano et al, 2012; Adams-Sapper et al, 2013; Banerjee et al, 2013; Colpan et al, 2013; Matsumura et al, 2013; Johnson et al, 2017; Kallonen et al, 2017; Roer et al, 2017; Mendis et al, 2018). Clades A and B show fluoroquinolone (FQ) susceptibility and rarely carry ESBL plasmids, while most isolates of clade C are FQ-resistant. Considering the content of virulence genes, ST131 isolates can be classified into 12 virotypes (A to F) (Blanco et al, 2013; Dahbi et al, 2014; Mora et al, 2014)

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