Molecular characterization of Carbapenem resistant Escherichia coli recovered from a tertiary hospital in Lebanon

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 bla(OXA-48) (48.1%; n = 13) and bla(OXA-181) (7.4%; n = 2), for the ESBLs it was bla(CTX-M-15) (55.6%; n = 15) and bla(CTX-M-24) (18.5%; n = 5), and for the AmpC-type β–lactamases, bla(CMY-42) (40.7%; n = 11) and bla(CMY-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.