Comparative resistome and virulome analysis of clinical NDM-1-producing carbapenem-resistant Enterobacter cloacae complex

Abstract

Objectives: The Enterobacter cloacae complex (ECC) are causatives of hospital-acquired infections. The antimicrobial resistance (AMR) and virulence profiling of ECC promotes our knowledge for their elimination in clinical settings.Methods: We assembled the whole genome of four clinical carbapenem-resistant ECCs and characterized their AMR and virulence profiles using whole genome sequencing.Results: The chromosomes length scaled from minimum 3 949 952 bp (for P2) to maximum 4 976 575 bp (for P3). Strains P1 and P2 belonged to sequence type (ST)182. P3 and P4 belonged to ST477 and ST134, respectively. The bla CTX-M-15 gene was detected in P1 plasmid. P1 and P4 harboured the bla TEM-1 and bla OXA-1 genes. bla NDM-1 was found in P1, P3, and P4. No bla OXA-48 , bla KPC , bla VIM , or bla IMP were identified. The plasmids were nontransferable and had IncFIB, IncFII, Col, and IncC incompatibility (Inc) groups . Class 1 integron was detected in all strains. Virulence genes related to biofilms, adhesins, siderophores (aerobactin, enterobactin, and salmochelin), intrinsic antimicrobial efflux pumps, secretory systems type I to VI, environmental and antibiotic stress response , outer membrane proteins, and heavy metal (copper, tellurite, arsenic, and zinc) resistance were found. The number of positive virulence factors was higher for P1 compared with other strains.Conclusion: The accumulation of AMR genes in Enterobacter spp. and their high endurance in hostile environments is a serious health problem. More genomic investigations are required to determine their AMR and virulence genetic reservoirs at the global level. (c) 2022 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/ )