Genomic characterization of non-fermenting gram-negative bacilli with metallo beta lactamase production and mcr based colistin resistance causing soft tissue infections: a seven-year hospital based prospective cross-sectional study.

BACKGROUND: Non-fermenting Gram-negative bacilli (NFGNB) like Pseudomonas aeruginosa and Acinetobacter baumannii have emerged as major nosocomial pathogens, particularly causing tissue infections. Rising resistance to carbapenems and colistin, largely mediated by Metallo-β-lactamase (MBL) and mobile colistin resistance (mcr) genes respectively, has severely limited therapeutic options. This study aimed to determine the proportion of MBL and mcr genes in NFGNB strains causing soft tissue infections and analyze their genetic diversity using ERIC-PCR. METHODS AND RESULTS: A seven-year prospective cross-sectional study (2019-2025) was conducted in a tertiary care hospital in Northeast India with samples collected from superficial and deep tissue infections. Phenotypic detection of MBL was performed using the combined disk test, followed by PCR-based detection of MBL (blaNDM, blaIMP and blaVIM) and mcr (mcr-1 to mcr-9) genes. ERIC-PCR was used for genomic typing using GelJ software and phylogenetic tree was created using Mega XI software. A total of 3,133 samples from soft tissue infections were screened, yielding 351 NFGNB isolates (88.3% Pseudomonas aeruginosa, 11.7% Acinetobacter calcoaceticus- baumannii complex). MBL production was detected in 25 Pseudomonas aeruginosa and 13 Acinetobacter calcoaceticus- baumannii complex isolates. The blaNDM gene was predominant among the isolates. Colistin resistance was observed in 19.5% of Acinetobacter calcoaceticus- baumannii complex isolates, with two strains harboring both blaNDM and mcr-3 genes. ERIC-PCR revealed clonal dissemination, particularly in surgery and burn wards, mostly with cluster-specific resistance patterns, particularly in Pseudomonas aeruginosa strains. CONCLUSION: The co-occurrence of MBL and mcr genes in NFGNB strains highlights the threat of multidrug resistance. Continuous molecular surveillance, hospital infection control, and stringent antibiotic stewardship policy are necessary to limit the spread of resistant clones.