Whole-genome sequence analysis of carbapenem-resistant Enterobacteriaceae recovered from hospitalized patients

Objectives: Carbapenems are among the few effective antibiotics against multidrug-resistant Enterobacteriaceae. This study aimed at characterizing the plasmid content and resistome of clinical carbapenemresistant Enterobacteriaceae (CRE) recovered from 2016 to 2019 from hospitalized patients in Lebanon.Methods: Plasmid typing and whole-genome sequencing were used to study the genomic characteristics of 65 clinical CREs including 27 Escherichia coli , 24 Klebsiella pneumoniae , one Klebsiella quasipneumoniae , three Morganella morganii , three Citrobacter freundii , five Enterobacter hormaechei , and two Serratia marcescens .Results: bla OXA -48 (33.8%; n = 22) and bla OXA-48 -like genes were among the detected resistance determinants, with two isolates co-harbouring bla NDM-5 . Various bla NDM variants, bla NDM-1 (16.9%; n = 11), bla NDM-5 (9.2%; n = 6), bla NDM-7 (9.2%; n = 6), and bla NDM-19 (4.6%; n = 3), different ESBLs, and AmpC ,B-lactamases were detected. Carbapenem resistance determinants were linked to a variety of incompatibility groups with IncFIB(K) (43.1%; n = 28) being the most prevalent, followed by IncFIA (40.0%), IncL (35.4%), IncX3 (32.3%), IncI1 (32.3%), and IncFIIK (29.2%).Conclusions: We analysed the clonality and resistance determinants of 65 multidrug-resistant (MDR) Enterobacteriaceae recovered in the period from 2016 to 2019 from a large tertiary hospital in Lebanon. NDM variants, OXA-48, and OXA-181 were the most prevalent detected carbapenemases and were mostly linked to the dissemination of IncL, IncX3, and IncF. This study reinforces the need to track the spread and dominance of clinically relevant carbapenemase-encoding plasmids in healthcare settings.& COPY; 2023 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )

Automated summary

The objective of this study was to characterize the plasmid content and resistome of clinical carbapenem-resistant Enterobacteriaceae (CRE) recovered from hospitalized patients in Lebanon from 2016 to 2019. The results showed that bla OXA-48 and bla OXA-48-like genes were among the detected resistance determinants. Carbapenem resistance determinants were linked to various incompatibility groups, with IncFIB(K) being the most prevalent. This study highlights the importance of tracking the spread and dominance of clinically relevant carbapenemase-encoding plasmids in healthcare settings.