Emergence of concurrently transmissible
mcr-9
and carbapenemase genes in bloodborne colistin-resistant
Enterobacter cloacae
complex isolated from ICU patients in Kolkata, India
Authors: Halder Gourab , Chaudhury Bhaskar Narayan , Denny Priyanka , Chakraborty Mandira , Mandal Subhranshu , Dutta Shanta 
Published: February 2025

ABSTRACT

Colistin resistance in carbapenem-resistant
Enterobacter cloacae
complex (CR-ECC) infections has grown expeditiously but detecting the underlying mechanism of resistance is often challenging in clinical settings. This study, first of its kind from India, determined the resistance mechanisms and characterized colistin-resistant hospital isolates. Twenty-nine bloodborne CR-ECC isolated from ICU patients of eight tertiary care hospitals in Kolkata, India between 2022 and 2023 were screened for colistin resistance. The plasmid-encoded
mcr
-9 gene,
acrAB-tolC
efflux pump (EP) &
phoP/Q,
and
pmr A/B
two-component system (TCS) involved in colistin resistance were examined. In addition, AMR gene profiling and molecular subtypes of
mcr
-9-producing CR-ECC isolates were also investigated. All study isolates showed resistance to ≥5 antimicrobial classes and six (21%) of them were colistin-resistant. The
mcr
-9 gene transferable by IncHI2-HI2A plasmid was detected in both colistin-resistant (67%) and colistin-sensitive (4%) CR-ECC isolates. The
bla
NDM-5 gene was significantly (
P
< 0.05) associated with isolates co-harboring
mcr
-9 genes. A ≥8-fold increase in minimum inhibitory concentration (MIC)
colistin
was observed in the
mcr
-9-producing colistin-sensitive strain after induction. Overexpression of
acrA, ramA, soxS
,
phoP/Q,
and
pmrA/B
genes was found in non-
mcr
-9-producing colistin-resistant isolates. The resistance to colistin in the wild-type appeared to be mediated in part by the
mcr
-9 gene, an active EP, and regulatory TCS. The
mcr
-9-producing isolates were typed into ST932, ST270, and ST1997 by MLST. Heterogeneity (29 pulsotypes; 48.40% similarity coefficient) among the circulating CR-ECC isolates was revealed by PFGE. Robust monitoring of
mcr
genes in both colistin-resistant and -sensitive strains is warranted to curb the menace of AMR in nosocomial pathogens.

IMPORTANCE

Carbapenem-resistant
Enterobacter cloacae
complex (CR-ECC) has become a global nosocomial pathogen in last few years. Colistin, the “last resort antibiotic,” is being widely used in the treatment of CR-ECC and, consequently, there has been a brisk rise in colistin-resistant CR-ECC isolates. This study was necessitated by the dearth of a comprehensive molecular investigation of colistin-resistant CR-ECC from India. The notorious IncHI2-HI2A plasmid-borne mcr-9 gene along with active acrAB-tolC efflux pump and phoP/Q-pmr A/B two-component system was found to mediate colistin resistance in the study isolates. Interestingly, the mcr-9 gene was also discovered in colistin-sensitive strains and MIC of colistin was found to increase under colistin pressure. Diverse phylogenetic clones along with novel sequence types were detected. This study highlights the necessity for intense monitoring of mcr-9 in conjunction with the existing epidemic clones of CR-ECC strains harboring diverse arrays of transmissible AMR genes.