Genomic characterization of CTX-M-15-producing Klebsiella pneumoniae ST709-KL9 from neonatal bacteraemia in eastern India

Abstract

Klebsiella pneumoniae, a WHO-designated critical-priority pathogen, is a predominant cause of neonatal bacteraemia in India, associated with high morbidity and mortality. The global emergence and spread of high-risk clones, combined with convergence of antimicrobial resistance (AMR) and virulence traits, underscores the need for close genomic surveillance. This study presents AMR and virulence traits of K. pneumoniae ST709-KL9 strain isolated from neonatal blood in West Bengal, India. The blood isolate from a 10-day-old neonate (November 2021) underwent identification, antimicrobial susceptibility testing, hypermucoviscosity assessment, and whole genome sequence analysis. The 5.47 Mb genome comprised one chromosome (5.2 Mb) and three MOB-suite-predicted plasmid-associated contigs [IncFIIK (59.4 kb), IncHI1B: IncFIB (219.7 kb), IncR (13.2 kb)]. Core findings included ST709 (single-locus variant of ST15), KL9/O2 capsular-type, and multidrug-resistant (MDR) phenotype (CeftriaxoneR-CiprofloxacinR-ChloramphenicolR-Co-trimoxazoleR) The strain was treatable with meropenem, amikacin, and colistin. Resistome analysis revealed resistance genes (blaTEM−1B-blaCTX−M−15-qnrS1-strA-strB-catA1-sul1-sul2-dfrA1-dfrA5-fosA6-tetA-tetD) and chromosomal point-mutations (gyrA: Ser83Tyr, Asp87Ala; parC: Ser80Ile; ompK37: Ile70Met, Ile128Met). Virulome included Type-1/3 fimbriae, complete T6SS-I cluster, KL9 capsule biosynthesis, enterobactin siderophore—lacking canonical hvKp markers (iucA-ybt-rmpA/A2-iroB-peg344). This single-isolate genomic study is the first report of blaCTX−M−15-caryying MDR K. pneumoniae ST709-KL9 in India. Systematic and strategic large-scale genomic AMR surveillance is essential to understand the trafficking and contain the transmission of emerging pathogens in India.