Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins.

Catherine Branger,Valérie Barbe,Olivier Clermont,Stéphanie Fouteau,Erick Denamur,Olivier Tenaillon,Dominique Decré,Miguel Castellanos,Laurence Drieux-Rouze,Axel Cloeckaert,David Roche,Alice Ledda,Jérémy Glodt,Benoît Doublet,Claudine Médigue,Typhaine Billard-Pomares,Stéphane Cruveiller,Guillaume Arlet

doi:10.1099/mgen.0.000203

Abstract

To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBL-encoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs. The network analysis showed that the plasmids clustered according to their genome backbone type, but not by origin or period of isolation or by antibiotic-resistance type, including type of ESBL-encoding gene. There was no association between the type of plasmid and the phylogenetic history of the parental strains. Finer scale analysis of the more abundant clusters IncF and IncI1 showed that ESBL-encoding plasmids and plasmids isolated before the use of 3GCs had the same diversity and phylogenetic history, and that acquisition of ESBL-encoding genes had occurred during multiple independent events. Moreover, the blaCTX-M-15 gene, unlike other CTX-M genes, was inserted at a hot spot in a blaTEM-1-Tn2 transposon. These findings showed that ESBL-encoding genes have arrived on wide range of pre-existing plasmids and that the successful spread of blaCTX-M-15 seems to be favoured by the presence of well-adapted IncF plasmids that carry a Tn2-blaTEM-1 transposon.

Highlights

The emergence and spread of resistance to third-generation cephalosporins (3GCs), mediated mainly by extendedspectrum b-lactamases (ESBLs) [1], is an increasing health problem
In addition to the selective pressure exerted by the use of 3GCs, other factors may contribute to the emergence and success of E. coli producing ESBLs and in particular those producing CTX-M-15 ESBLs: the mobile elements involved in the capture/mobilization of the ESBL-encoding gene, the genetic background of ESBLcarrying plasmids [7] and the host strain carrying the plasmid
To have a full picture of the spread of ESBL-encoding genes in E. coli, we undertook a comprehensive comparative analysis of the sequences of a large number of diverse plasmids from human and animal strains isolated over a large period of time spanning before and after the use of 3GCs

Summary

Introduction

The emergence and spread of resistance to third-generation cephalosporins (3GCs), mediated mainly by extendedspectrum b-lactamases (ESBLs) [1], is an increasing health problem. ESBLproducing E. coli are commonly isolated from community or hospital infections and from human faecal carriage, and are increasingly detected in food-producing, companion and wildlife animals, as well as in the environment. As a consequence, these resistant E. coli can impact on both animal and human health [1, 5]. E. coli clones of phylogenetic group B2 and sequence type (ST) 131; of phylogenetic group D, and ST315, ST393 and ST405; and of phylogroup F and ST648 have largely contributed to the dissemination of ESBL worldwide [8,9,10,11]

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