Genetic Characterisation of Colistin Resistant Klebsiella pneumoniae Clinical Isolates From North India

Abstract

BackgroundIncreasing use of colistin has led to the world-wide emergence of mobile colistin resistant gene (mcr). The present study aimed to identify and characterise mcr and other drug-resistant genes in colistin resistant Klebsiella pneumoniae clinical isolates.MethodsTwenty-two colistin resistant K. pneumoniae were analysed for mcr and other drug-resistant genes, efflux pumps, and virulence genes, and for their biofilm forming ability. Pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) were performed for all mcr-1 positive isolates. S1-PFGE and Southern hybridisation were performed for localisation of mcr-1 and blaNDM.ResultsNineteen colistin resistant K. pneumoniae harboured mcr-1 and 3 had mgrB disruption. All isolates harboured blaOXA-48-type and ESBL genes; eight strains (five with mcr-1 and three with mgrB disruption) co-harboured blaNDM. Efflux pumps genes AcrAB and mdtK were detected in all 22 and tol-C in 21 isolates. Virulence-related genes entB and irp-1 were detected in all 22, mrkD in 20, and fimH-1 in 18 isolates; 11 isolates were strong biofilm producers. PFGE clustered mcr-1 positive isolates into eight groups based on ≥90% similarity; MLST revealed diverse sequence types, predominant being ST-15 (n = 4) and ST-16 (n = 4). Both mcr-1 and blaNDM were localised on plasmid and chromosome; mcr-1 was present on IncFII type and blaNDM on IncFIB and IncA/C type plasmids.ConclusionsColistin resistance in K. pneumoniae was predominantly mediated by mcr-1. Co-existence of colistin, carbapenem, and other drug-resistant genes along with efflux pumps indicates towards enormous genomic plasticity in K. pneumoniae with ability to emerge as super-spreader of drug-resistance.

Screening of mcr-1 among Gram-Negative Bacteria from Different Clinical Samples from ICU Patients in Alexandria, Egypt: One-Year Study

“…bla VIM and bla KPC were not found among these five isolates. Singh et al (2021) reported that all the isolates harboring mcr-1 in their study co-harbored bla OXA-48 . Han et al (2020) reported the identification of the XDR E. coli clinical isolate co-harboring mcr-1 and bla NDM-1 .…”

Outbreak of colistin resistant, carbapenemase (blaNDM, blaOXA-232) producing Klebsiella pneumoniae causing blood stream infection among neonates at a tertiary care hospital in India

“…The isolates were resistant to colistin but we could not detect mcr gene in any of the isolates possibly because the isolates harboured the chromosomal mutations leading to colistin resistance which we did not analyze. In a recent study from our centre we have reported K. pneumoniae ST16 harboring mutations in chromosomal gene mgrB ( Singh et al., 2021 ). Multi-locus sequence typing results revealed that the 5 K. pneumoniae isolates belonged to 3 different sequence types, ST101, ST16 and ST11.…”

“…The resistance mechanisms in the 5 K. pneumoniae isolates were analyzed using polymerase chain reaction to detect the genes encoding carbapenemases ( bla NDM , bla KPC , bla OXA-48 , bla IMP , bla VIM ), ESBLs ( bla CTX-M ), other class A β-lactamases ( bla SHV , bla TEM ) and colistin resistance genes mcr-1 , mcr-2 and mcr-3 using previously described methods and primers ( Singh et al., 2018 ; Singh et al., 2021 ). Following isolates from our previous studies were used as positive controls: K. pneumoniae CR kp 21 and CR kp 22 for bla NDM , bla OXA-48 , bla IMP , bla VIM , bla CTX-M , bla SHV , bla TEM ( Singh et al., 2021 ) while K. pneumoniae CRL3 for mcr gene ( Singh et al., 2018 ). Positive control for bla KPC gene was not available.…”

In Vitro Susceptibility of Colistin Against Multidrug Resistant Klebsiella Pneumoniae Clinical Isolates

“…Unfortunately reports revealing resistance to this drug are also coming up in the literature as we saw in our study and the same has also been reported from our neighbouring countries like Iran, China, and India. [22][23][24] Literature review has shown that some genetic modifications in chromosomal coding regions of some regulator genes have caused this phenotypic resistance to colistin. Regular genomic monitoring is required for all resistant isolates to see the colistin resistance.…”