Genomic Characterization of Pan-Drug Resistant Klebsiella pneumoniae KPNW Isolated From UTI Patient in Bangladesh

Abstract

Klebsiella pneumoniae is a Gram-negative opportunistic bacterial pathogen and a common cause of urinary tract infections (UTIs). In Bangladesh, a rapid increase in antibiotic resistance in K. pneumoniae, with a concerning prevalence of pan-drug resistant (PDR) isolates, is severely limiting treatment options and posing a threat to public health. K. pneumoniae isolate KPNW was found in a clinical urine sample of a UTI patient from Dhaka, Bangladesh. In the disc diffusion test, KPNW showed resistance to 28 antibiotics across multiple classes, including carbapenems and colistin. Whole genome sequencing, assembly, and annotation yielded a 5.48 Mb genome encoding 5554 genes. Four plasmid replicons—lncFIB(K), lncFII(K), lncN2, and lncX3—were identified, all having known associations with antimicrobial resistance (AMR). KPNW belongs to multilocus sequence typing sequence type ST15 and capsular type KL112 and O1v2. We detected 42 AMR genes, including extended-spectrum β-lactamases, carbapenemase bla_NDM-1, and other families of AMR determinants, which altogether confer resistance to all clinically relevant antibiotics. We also identified 58 virulence determinants, including types 1 and 3 fimbrial proteins, enterobactin, and type VI secretion system proteins. However, major hypervirulence determinants were absent. Heavy metal resistance operons for arsenic, copper, and silver resistance were also detected. KPNW harbors multiple mobile genetic elements, some adjacent to AMR and virulence genes, indicating its capacity for horizontal gene acquisition and evolution as PDR, virulent, and heavy metal resistant. The findings of this study will have implications in public health and help better understand future trends of infections, plan effective treatment strategies, and surveillance.