High-Risk Clones of Carbapenem-Resistant Pseudomonas aeruginosa in India: Genome and Traits

Abstract

Pseudomonas aeruginosa is a notorious opportunistic pathogen constituting a major cause of health care-associated infections worldwide. Intrinsic resistance to multiple antibiotics, with acquired resistance mechanisms and hypervirulence make it a critical target for genomic investigations. In this study, we investigated AMR determinants and virulence factors using WGS among five extensively drug-resistant (XDR) clinical P. aeruginosa isolates. XDR P. aeruginosa isolates isolated from bile, broncho-alveolar lavage and wound swabs were included in the study. Initially, the isolates were tested for the carbapenemase phenotype and genotype using modified Hodge test and PCR, respectively, followed by WGS. All isolates exhibited resistance to >50% of the antibiotics tested. Conventional PCR analysis identified bla NDM-1 , bla OXA-48 , and bla VIM invariably in the test isolates. Tested isolates were assigned sequence types as ST357 ( n = 2), ST773, ST1047, and ST3043. WGS identified multiple resistant genes including bla OXA-488 and bla VIM-11 (P2356), bla OXA-10 , bla VIM–2 , bla OXA-395 and bla OXA50 (PM381) , bla VEB-9 , bla OXA-50 and bla NDM-1 (PR90), bla OXA-485 (PR126), and bla OXA -50 (PR64). Notably, all the isolates were carrying different variants of bla PDC . The genomes were also associated with the virulence determinants, with genes encoding alginate and biofilm synthesis, quorum sensing, secretion systems, secondary metabolites, lipopolysaccharides, exotoxins, pili, and flagellar structure. All clinical P. aeruginosa isolates exhibited extensive resistance and virulence gene repertoires, also enriched with efflux pumps. Sequence types ST3043 and ST1047 are reported for the first time in India, underscoring the need for continuous genomic surveillance to monitor the emergence and dissemination of high-risk clones.