Epidemiology of ESBL-producing Escherichia coli from repeated prevalence studies over 11\xa0years in a long-term-care facility

Romain Martischang,Nadia Gaïa,Monica Perez,Stephan Harbarth,Gesuele Renzi,Americo Agostinho,Christophe E Graf,Patrice François,Abdessalam Cherkaoui

doi:10.1186/s13756-021-01013-7

Abstract

BackgroundEscherichia coli sequence type (ST) 131 H30 is an emerging multidrug resistant subclone, known to spread and cause outbreaks in long-term care facilities (LTCFs).Objectives and methodsFrom 2010 through 2020, we performed 11 yearly surveillance studies for determining the prevalence of digestive carriage of ESBL-producing E. coli (ESBL-EC) among residents in a university-affiliated LCTF. Sequencing and genotyping of selected isolates were performed to characterize temporal trends in the prevalence and epidemic potential of ESBL-EC subclones, and for evaluating a potential rebound effect following discontinuation of contact precautions for ESBL-EC carriers in January 2019.ResultsThis study included 2′403 LTCF residents, with 252 (10.5%) positive for ESBL-EC. Among the 236 ESBL-EC isolates available for typing, 58.0% belonged to the ST131 lineage, including 94/137 (68.6%) ST131 H30 isolates. An increasing yearly prevalence was observed for ESBL-EC (from 4.6 to 9.4%; p = 0.11), but not for the ST131 H30 subclone, which peaked in 2015 and declined thereafter. Multiple previously unnoticed ESBL-EC outbreaks occurred in the LTCF. Since 2018, we noted the clonal expansion of a rare ST131 H89 subclone (O16:H5) harboring CTX-M-14 and CTX-M-24. No rebound effect was observed in ESBL-EC prevalence nor in the different subclones following discontinuation of contact precautions for ESBL-EC carriers since 2019.ConclusionClonal fluctuation was observed for ST131 H30 ESBL-EC with a current decline in prevalence. Surveillance should include the evolution of ST131 non-H30 subclones, which may spread in LTCFs. Our findings suggest that discontinuation of contact precautions for ESBL-EC carriers in LTCFs may be safely implemented, in support of European recommendations to limit ESBL-producing Enterobacteriaceae control measures in endemic settings to non-E. coli.

Highlights

The global spread of extended-spectrum beta-lactamase producing Escherichia coli (ESBL-EC) is driven by the emergence of successful clones such as E. coli ST131, transmissible in long-term care facilities (LTCFs) [1, 2]
The increasing prevalence of E. coli ST131 among LTCFs is mostly explained by the clonal expansion of emerging multi-resistant clades of ESBL-EC [6], responsible for silent clusters among residents in LTCFs [7], including the fluoroquinolone-resistant clades C1 (C1/ H30-R) and C2 (C2/H30-Rx) [8]
Secondary outcomes included the overall prevalence of any ESBL-producing Enterobacterales (ESBL-PE), the number of clusters, the prevalence of subclones in the wards concerned by these clusters, and the proportion of clonally related strains among these clusters

Summary

Introduction

The global spread of extended-spectrum beta-lactamase producing Escherichia coli (ESBL-EC) is driven by the emergence of successful clones such as E. coli ST131, transmissible in long-term care facilities (LTCFs) [1, 2]. The increasing prevalence of E. coli ST131 among LTCFs is mostly explained by the clonal expansion of emerging multi-resistant clades of ESBL-EC [6], responsible for silent clusters among residents in LTCFs [7], including the fluoroquinolone-resistant clades C1 (C1/ H30-R) and C2 (C2/H30-Rx) [8] The reasons behind this apparent success remain controversial, but recent genomic and proteomic studies suggest that an improved anaerobic metabolism, as well as other human colonization and virulence factors helped this clone to outcompete the gut commensal niche [9,10,11], with consecutive prolonged colonization [12]. Escherichia coli sequence type (ST) 131 H30 is an emerging multidrug resistant subclone, known to spread and cause outbreaks in long-term care facilities (LTCFs)

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