Molecular characterization of NDM-1-producing Klebsiella pneumoniae ST29, ST347, ST1224, and ST2558 causing sepsis in neonates in a tertiary care hospital of North-East India

Geographical differences can manifest in different spectra of microorganisms and patterns of antibiotic resistance. Considering this, Enterobacteriacae isolated from septicemic neonates from a tertiary care centre in Agartala, India were studied with focus on carbapenem resistance. Two hundred non-duplicate Enterobacteriaceae, of which 12 NDM-1-producing Klebsiella pneumoniae were recovered. Antibiotic susceptibility tests and detection of ESBLs and carbapenemases were performed for all Enterobacteriaceae. For NDM-1-producing isolates, plasmid-mediated quinolone resistance genes, addiction systems, genetic environment of blaNDM-1 and virulence genes was investigated by PCR. Bacterial clonal relatedness was established using REP-PCR, PFGE, and multi-locus sequence typing (MLST). Transferability of blaNDM-1 was tested by conjugation and transconjugants were characterized. K. pneumoniae was the primary organism causing sepsis in neonates. Resistance to different antimicrobials was high except for aminoglycosides and carbapenems. blaCTX-M was present in all isolates. All carbapenem-resistant isolates harboured blaNDM-1 as the only carbapenemase. blaCTX-M-15 and qnrS1 were detected in all NDM-1-producing isolates. Plasmid analysis of transconjugants revealed that blaNDM-1 along with blaCTX-M-15, qnrS1, qnrB1, aac(6′)-Ib, aac(6′)-Ib-cr and ccdAB or vagCD addiction systems were carried on large IncFIIK conjugative plasmids of varied sizes. blaNDM-1 was associated with ISAba125 or ISEc33 element at its 5′-end. In addition, isolates also harboured wabG, uge, fimH, mrkD, and entB virulence genes. The NDM-1-producing K. pneumoniae belonged to four distinct clones and were distributed in 4 STs (ST347, ST29, ST2558, and ST1224), of which ST347 was predominant. The association of blaNDM-1 with diverse STs in K. pneumoniae from neonates indicates the promiscuity of the gene and its widespread dissemination. •A snapshot of NDM-1-producing K. pneumoniae from septicemic neonates•NDM-1 was the only carbapenemase isolated.•NDM-1-producing K. pneumoniae were of diverse STs (29,347,1224, and 2558).•All isolates harboured blaNDM-1 on IncFIIK plasmids along with blaCTX-M-15 and different PMQRs.•ISAba125 or ISEc33 was present at the 5’end of blaNDM-1.