PHENOTYPIC SUSCEPTIBILITY METHODS COMPARED WITH WHOLE GENOME SEQUENCING FOR DETECTION OF ANTIMICROBIAL RESISTANCE IN CLINICAL ISOLATES FROM A TERTIARY CARE CENTRE IN WESTERN INDIA

Abstract

Antimicrobial resistance, particularly carbapenem-resistant Gram-negative organisms and methicillin-resistant Staphylococcus aureus, threatens contemporary clinical practice in India and demands integrated phenotypic-genomic surveillance. The present study evaluated three phenotypic antimicrobial susceptibility methods alongside whole genome sequencing of clinically significant isolates at a tertiary care centre in Silvassa, Western India. A total of 120 clinical samples were processed for culture and identification over a twelve-month period. Susceptibility was determined by disc diffusion, broth microdilution, and Epsilometer test. Whole genome sequencing was performed on seven Klebsiella pneumoniae and eleven S. aureus isolates using the Illumina platform; resistance genes were identified using the Comprehensive Antibiotic Resistance Database, and multilocus sequence typing, plasmid replicons, and SCCmec types were characterised using standard pipelines. Eighty-five isolates were recovered. Carbapenem resistance was identified in 57.9 percent of K. pneumoniae and 87.5 percent of Acinetobacter baumannii. Colistin minimum inhibitory concentration values reached 4 milligrams per litre in K. pneumoniae and A. baumannii with 42.9 percent resistance each. Sequencing identified blaCTX-M-15 in all K. pneumoniae isolates, blaNDM-1 in five of seven, and the plasmid-mediated colistin resistance gene mcr-1 in two isolates of high-risk sequence types. All four methicillin-resistant S. aureus isolates carried mecA on SCCmec types II or III; the Panton-Valentine leukocidin gene was detected in five of eleven isolates. Disc diffusion proved unsuitable for colistin testing. Integration of phenotypic and genomic approaches revealed strong concordance and identified emergent local pandrug-resistance, warranting urgent stewardship and surveillance measures.