Whole genome analysis reveals chromosomal and plasmid-mediated convergence of drug resistance in Klebsiella pneumoniae isolates.

The emergence of antimicrobial resistance (AMR) in Klebsiella pneumoniae poses a significant threat to public health. This study aims to elucidate the mechanisms of colistin and fluoroquinolone resistance using whole-genome sequencing in two K. pneumoniae isolates. Two clinical isolates of K. pneumoniae that phenotypically showed resistance to colistin and ciprofloxacin but did not yield any corresponding drug resistance genes were selected from a tertiary care facility in Chennai, India. Genome sequences of the isolates were generated using the NovaSeq sequencing platform (Illumina, USA). The unprocessed files were transmitted to Galaxy Europe for examination. Additionally, the tools Kleborate 0.3.0, MLST 2.23.0, Ortho Venn tool, Comprehensive AMR Database 3.2.8, and the Centre for Genomic Epidemiology were used for the detailed analysis. The genetic analysis revealed a large number of antibiotic resistance genes. In both isolates, mutations in the gyrA and parC genes were identified, with gyrA harbouring an S83I change and parC harbouring an S80I change, conferring resistance to fluoroquinolones. Both isolates harboured mutations in the ArnT gene, which may be responsible for phenotypic resistance to colistin. The isolates also harboured critical plasmids encoding numerous drug resistance genes. It has been shown that, following exposure, clinical strains of K. pneumoniae rapidly acquire resistance to colistin through distinct evolutionary routes, not involving mcr genes. A mutation in ArnT results in the addition of phosphoethanolamine to lipid A, thereby reducing the binding affinity of colistin. These findings significantly enhance our understanding of colistin resistance and provide crucial insights for identifying novel therapeutic targets.