Comparative molecular profiling of multidrug-resistant identifies novel mutations in regional clinical isolates from South India.

Objectives: We sought to analyse the antibiotic susceptibility profiles and molecular epidemiology of MDR clinical isolates from South India using non-MDR isolates as a reference.

Methods: We established a comprehensive clinical strain library consisting of 58 isolates collected from patients across the South Indian state of Kerala from March 2017 to July 2019. The strains were subject to antibiotic susceptibility testing, modified carbapenem inactivation method assay for carbapenemase production, PCR sequencing, comparative sequence analysis and quantitative PCR of MDR determinants associated with antibiotic efflux pump systems, fluoroquinolone resistance and carbapenem resistance. We performed modelling of MDR-specific SNPs.

Results: Of our collection of South Indian clinical isolates, 74.1% were MDR and 55.8% were resistant to the entire panel of antibiotics tested. All MDR isolates were resistant to levofloxacin and 93% were resistant to meropenem. We identified seven distinct, MDR-specific mutations in , three of which are novel. was significantly overexpressed in strains that were resistant to the entire test antibiotic panel while and were overexpressed in MDR isolates. Mutations in fluoroquinolone determinants were significantly associated with MDR phenotype and a novel GyrA Y100C substitution was observed. Carbapenem resistance in MDR isolates was associated with loss-of-function mutations in and high prevalence of NDM () within our sample.

Conclusions: This study provides insight into MDR mechanisms adopted by clinical isolates, which may guide the potential development of therapeutic regimens to improve clinical outcomes.