Genomic characterization of plasmids harboringblaNDM-1,-5,-7carbapenemase alleles in clinicalKlebsiella pneumoniaein Pakistan

Abstract

ABSTRACTKlebsiella pneumoniaeis notorious for causing healthcare-associated infections, which become more complicated by the acquisition ofblaNDMgenes via mobile genetic elements. Although Pakistan is a well-established hot spot ofblaNDM-positiveK. pneumoniae, detailed molecular descriptions ofblaNDM-carrying plasmids are scarce. SevenK. pneumoniaeisolates harboringblaNDMwere recovered from clinical sample sources during a six-month period and tested for antimicrobial susceptibility. A long-read approach was used for whole genome sequencing to obtain circularized plasmids and chromosomes for typing, annotation, and comparative analysis. The isolates were susceptible to colistin and tigecycline only among the tested antibiotics. We identified five STs: ST11, ST16, ST716, ST464, and ST2856. Notably, three strains possessed the hypervirulent capsule KL2, while five were classified as O locus type O2a. Evidence of genetic diversity was further highlighted by the presence of four IncC plasmids harboringblaNDM-1, two IncX3 plasmids harboringblaNDM-5, and a single hybrid IncFIB/IncHI1B plasmid harboringblaNDM-7. These plasmids also carried additional ARGs conferring resistance to aminoglycosides, cephalosporins, and fluoroquinolones. We identified the plasmidome of theK. pneumoniaeisolates and characterized the NDM-carrying plasmids. Genetic analysis confirmed the presence ofblaNDM-1andblaNDM-5on broad host range plasmids andblaNDM-7in a previously unreported hybrid plasmid backbone. We emphasized the critical role of plasmids in spreadingblaNDMin the clinical setting in Pakistan. Hence, we stressed the urgent need for enhanced surveillance, not least in LMICs, infection control measures, and adherence to the AWaRe guidelines in antibiotics use.