High-risk extended-spectrum β-lactamase-producing Klebsiella pneumoniae ST307 in a neonatal sepsis outbreak in Zambia: a secondary genomic analysis

Neonatal sepsis caused by multidrug-resistant Klebsiella pneumoniae contributes substantially to neonatal morbidity and mortality, especially where treatment options and genomic surveillance are limited. Phenotypic microbiology defines susceptibility, whereas Illumina short-read whole-genome sequencing (WGS) links phenotypes to lineage, capsule, resistome, virulome and mobilome contexts. However, complete characterization of mobile genetic element (MGE) structure remains inferential. This secondary analysis re-examined 411 public K. pneumoniae genomes from the University Teaching Hospital neonatal outbreak in Zambia. The population was dominated by ST307/KL102/OL2α.2, a comparatively recent but globally expanding high-risk clone, accounting for 284 out of 411 genomes (69.1%). Minority genomes included established resistance or virulence-associated high-risk backgrounds, including carbapenemase-positive KL15/OL4 lineages and yersiniabactin-positive ST147/ST985. Extended-spectrum β-lactamase (ESBL) genotypes were widespread (396 out of 411; 96.4%) and mainly driven by bla CTX-M-15 (406 out of 411; 98.8%), whereas carbapenemase carriage was restricted to bla NDM-5-positive ST5856/ST340 (11 out of 411; 2.7%). Plasmids were the principal acquired resistance layer, as most AMR genes were plasmid-associated, and similarity analysis revealed a cohesive ST307-linked IncFIB/IncFII AA277 ESBL background, in contrast to distinct minority ESBL and IncX3 bla NDM-5 architectures. This pattern supports clonal maintenance of a stable ESBL plasmid background within ST307, while identifying IncX3 bla NDM-5 plasmids in minority lineages as a key convergence risk. Resistance genes were further structured by integron cassettes, insertion-sequence modules and plasmid cargo containing metal-, biocide- or stress-response genes. Virulence was limited and mainly ICEKp/ybt-associated, and widespread predicted prophages did not carry priority determinants. These findings show that WGS can add mechanistic resolution to routine phenotypic surveillance by identifying clone–MGE configurations that warrant targeted monitoring in neonatal K. pneumoniae outbreaks in Zambia.