Whole-Genome Sequence Analysis of Carbapenem-Resistant Enterobacteriaceae Recovered from Hospitalized Patients in Lebanon

Abstract

Antimicrobial resistance is one of the greatest threats to public health. Carbapenems are among the few useful antibiotics against multidrug resistant Enterobacteriaceae. This study aimed at characterizing the plasmid content and resistome of clinical carbapenem-resistant Enterobacteriaceae recovered in the period between 2016-2019 from hospitalized patients in Lebanon. The studied population included: 27 Escherichia coli, 24 Klebsiella pneumoniae, one K. quasipneumoniae, three Morganella morganii, three Citrobacter freundii, five Enterobacter hormaechei, and two Serratia marcescens. Antimicrobial susceptibility testing using the disk diffusion assay, carbapenemase confirmatory testing, and in silico whole-genome based analysis revealed that the majority of the isolates (87.7%; n=57) were carbapenem resistant harboring a broad range of carbapenemases. blaOXA-48 (33.8%; n=22) and blaOXA-48-like genes were among the detected resistance determinants, with two isolates additionally co-harboring the blaNDM-5. All OXA-48 producing isolates were ESBL and/or AmpC producers and were additionally resistant to non-β-lactam antibiotics. Carbapenem resistance determinants related to blaNDM were also detected including blaNDM-1 (16.9%; n=11), blaNDM-5 (9.2%; n=6), blaNDM-7 (9.2%; n=6), and blaNDM-19 (4.6%; n=3). A wide variety of ESBLs (OXA, SHV, TEM, CTX-M) and AmpC β-lactamases (CMY, DHA, ACT) were among the detected resistance determinants and of which blaCTX-M-15 (58.5%; n=38) and blaOXA-1 (53.8%; n=35) were the most common. Our study revealed a wide variety of incompatibility groups to be associated with carbapenem resistance with the IncFIB(K) (43.1%; n=28) being the most prevalent, followed by IncFIA (40.0%), IncL (35.4%), IncX3 (32.3%), IncI1 (32.3%), IncFIIK (29.2%). It was also the largest genome-based study in the region, revealing the tremendous heterogeneity, plasmid content, and various resistance determinants circulating in the country. High-risk carbapenem-resistant Enterobacteriaceae clones pose a significant threat to patients and healthcare systems in Lebanon. The observed plethora of plasmid-encoded resistance genes shed light on implementing corrective measures to mitigate the spread of carbapenem resistance.