Detection of blaVIM, blaIMP, blaNDM, blaKPC and blaOXA-48-like carbapenemase genes in carbapenem-resistant Enterobacterales clinical isolates with phenotypic and genotypic antimicrobial susceptibility to colistin

Carbapenem-resistant Enterobacterales (CRE) are WHO critical-priority pathogens, and detection of carbapenemase production and mcr-1-mediated colistin resistance is important for guiding therapy and preventing antimicrobial resistance spread. In this prospective cross-sectional study, a total of 144 non-duplicate CRE clinical isolates were subjected to the Modified Carbapenem Inactivation Method (mCIM) ± EDTA-modified Carbapenem Inactivation Method (eCIM) test, followed by in-house (laboratory-developed) conventional multiplex polymerase chain reaction (PCR) for simultaneous detection of five common carbapenemase genes, viz. bla VIM, bla IMP, bla NDM, bla KPC and bla OXA-48-like genes. Colistin susceptibility was performed by the broth microdilution method, followed by in-house (laboratory-developed) conventional PCR to detect mcr-1 gene. 73.6% (106/144) of CRE isolates were positive for mCIM test, i.e., CP-CRE, while 96% (102/106) of them were positive for eCIM test. Among eCIM positive CRE (i.e., Metallo-β-lactamase producers), 56% (57/102) were positive for bla NDM gene, 9.8% (10/102) were positive for bla VIM gene, and 2.9% (3/102) were positive for bla IMP gene. Among eCIM negative mCIM positive CRE (i.e., Serine ± Metallo-β-lactamase producers), all four were positive for bla OXA-48-like gene. Colistin had intermediate susceptibility of 90.3% (130/144). mcr -1 gene was detected in five isolates i.e., three with colistin resistant isolates (21.4%; 3/14) and two in colistin intermediate cases with MIC 1 and 2 µg/mL each. Majority of CRE in Indian settings were CP-CRE, with predominance of Metallo-β-lactamase producers (MBL-CRE). bla NDM gene was the most common carbapenemase gene. Colistin resistance (9.7%) was spreading fast, with the mcr-1 gene (21.4%) being a significant contributor.