Klebsiella pneumoniae is designated a WHO critical-priority pathogen and is a predominant cause of neonatal bacteraemia in India, where infections are associated with substantial morbidity and mortality. The global spread of high-risk clones and the convergence of antimicrobial resistance (AMR) and virulence determinants make genomic surveillance essential to detect and contain emerging threats. This report describes the genomic and phenotypic features of a K. pneumoniae strain recovered from neonatal bacteraemia in West Bengal, India.
The isolate originated from the blood of a 10-day-old neonate in November 2021. Laboratory work included species identification, antimicrobial susceptibility testing, assessment of hypermucoviscosity phenotype, and whole genome sequencing. The assembled genome measured 5.47 Mb in total, consisting of a single chromosome of approximately 5.2 Mb and additional plasmid-associated contigs identified by MOB-suite.
Genome assembly resolved one chromosome (~5.2 Mb) and three MOB-suite–predicted plasmid-associated contigs. The plasmid-associated contigs were annotated as IncFIIK (59.4 kb), IncHI1B:IncFIB (219.7 kb), and IncR (13.2 kb). Multilocus sequence typing placed the isolate as ST709, noted as a single-locus variant of ST15. Capsular typing identified the strain as KL9/O2.
Phenotypic testing classified the isolate as multidrug-resistant (MDR). The strain showed resistance to ceftriaxone, ciprofloxacin, chloramphenicol, and co-trimoxazole, while remaining treatable with meropenem, amikacin, and colistin according to the reported results.
Resistome analysis detected multiple acquired resistance genes, including blaTEM-1B and blaCTX-M-15 (extended-spectrum β-lactamase), qnrS1 (plasmid-mediated quinolone resistance), aminoglycoside resistance genes strA and strB, chloramphenicol acetyltransferase catA1, sulfonamide resistance genes sul1 and sul2, trimethoprim resistance determinants dfrA1 and dfrA5, fosA6 (fosfomycin resistance), and tetracycline determinants tetA and tetD. In addition to acquired genes, chromosomal point mutations associated with fluoroquinolone resistance and possible porin alterations were reported: gyrA substitutions Ser83Tyr and Asp87Ala, parC Ser80Ile, and ompK37 substitutions Ile70Met and Ile128Met.
The isolate harbored virulence-associated loci including genes for Type-1 and Type-3 fimbriae and a complete Type VI secretion system I (T6SS-I) cluster. Capsule biosynthesis genes corresponding to KL9 were present. However, canonical genetic markers typically associated with hypervirulent K. pneumoniae (hvKp) were reported as lacking; the study specifically notes absence of established hvKp determinants such as iucA, rmpA/A2, iroB, and peg344. The authors therefore describe the virulome as containing several adherence and secretion system components without classical hypervirulence markers.
This single-isolate genomic study is presented as the first report from India of an MDR K. pneumoniae blaCTX-M-15–carrying ST709-KL9 recovered from neonatal bacteraemia. Identification of an ST709 strain (a single-locus variant of the internationally distributed ST15 group) carrying a broad complement of acquired resistance genes and chromosomal mutations highlights the risk of dissemination of resistant clones in neonatal settings. The presence of plasmid replicons (IncFIIK, IncHI1B:IncFIB, IncR) that frequently mobilize AMR determinants further underscores the potential for horizontal gene transfer.
Authors conclude that systematic, strategic, large-scale genomic AMR surveillance is essential in India to understand trafficking of such lineages and to design interventions to contain transmission of emerging pathogens, particularly in vulnerable populations such as neonates.
The authors report that informed consent was waived because the study was observational and focused on bacterial characterization without patient interventions. The research received approval from the Institutional Human Ethical Committee of Vidyasagar University (Ref. VU/IEC/122/2020). The authors declared no competing interests.
Limitations inherent in the article include that the report describes a single clinical isolate; broader epidemiologic conclusions or transmission dynamics cannot be established from a single genome. The study advocates larger-scale genomic surveillance to address these gaps.
An MDR CTX-M-15–producing K. pneumoniae ST709-KL9 caused neonatal bacteraemia in eastern India and carried multiple plasmid-associated AMR genes plus chromosomal resistance mutations.
Phenotypic susceptibility retained to meropenem, amikacin, and colistin was noted for this isolate, but the resistome and plasmid content indicate potential for further spread of resistance.
The strain lacked canonical hvKp markers despite carrying other virulence-associated loci; genomic surveillance is needed to monitor possible convergence of AMR and virulence.
The authors recommend systematic genomic AMR surveillance to inform infection control and public health measures in neonatal and other healthcare settings.