Abstract
The emergence of carbapenem resistant Escherichia coli represents a serious public health concern. This study investigated the resistome, virulence, plasmids content and clonality of 27 carbapenem resistant E. coli isolated from 27 hospitalized patients at the American University of Beirut Medical Center (AUBMC) in Lebanon between 2012 and 2016. Whole-genome sequencing (WGS) data were used to identify resistance determinants. Multilocus sequence typing (MLST), pulsed field gel electrophoresis (PFGE), phylogenetic grouping and PCR-based replicon typing (PBRT) were also performed. The 27 isolates were distributed into 15 STs, of which ST405 (14.8%; n = 4) was the most prevalent. All of the 27 isolates were carbapenem resistant and 20 (74%) were extended-spectrum β-lactamase (ESBL) gene carriers. The predominant detected carbapenemases were blaOXA-48 (48.1%; n = 13) and blaOXA-181 (7.4%; n = 2), for the ESBLs it was blaCTX-M-15 (55.6%; n = 15) and blaCTX-M-24 (18.5%; n = 5), and for the AmpC-type β–lactamases, blaCMY-42 (40.7%; n = 11) and blaCMY-2 (3.7%; n = 1). Thirteen replicons were identified among the 27 E. coli isolates including: IncL/M, IncFIA, IncFIB, IncFII, IncI1, and IncX3. PFGE revealed a high genetic diversity with the 27 isolates being grouped in 21 different pulsotypes. SNPs analysis and PFGE showed a possible clonal dissemination of ST405, ST1284, ST354 and ST410 and the dominance of certain STs, monitoring of which could help in elucidating routes of transmission. This study represents the first WGS-based in depth analysis of the resistomes and mobilomes of carbapenem resistant E. coli in Lebanon.
Highlights
Escherichia coli are one of the most common members of the family Enterobacteriaceae and often exist as commensal in the gastrointestinal tract of humans and animals
The genomic characteristics of carbapenem resistant clinical E. coli isolates collected from a tertiary hospital in Lebanon were investigated by determining and correlating their resistance gene content, STs, serotypes, plasmid content and replicon types, and virulence factors (VFs)
In 2003, 2.0% of E. coli recovered from Lebanon were reported as being ESBL producers [13]
Summary
Escherichia coli are one of the most common members of the family Enterobacteriaceae and often exist as commensal in the gastrointestinal tract of humans and animals They can colonize, infect and cause both hospital- and community-acquired infections leading to serious clinical disorders at both intra- and extraintestinal sites such as urinary tract. The frequency of infections caused by ESBL-producing Enterobacteriaceae increased from 2000 to 2011 in Lebanon [7]. This drastically surged during the period of 2012 to 2016, when Lebanon witnessed an unprecedented influx of refugees subsequently leading to the dissemination of novel multidrug resistance mechanisms of public health importance such as ESBLs and carbapenemases. We used whole-genome sequencing (WGS) to study the characteristics and determine the genomic profiles and diversity among 27 carbapenem resistant E. coli collected from the American University of Beirut Medical Center (AUBMC) during 2012 to 2016
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