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

2. Abstract Neonatal sepsis is a leading cause of mortality worldwide, with outbreaks frequently driven by multidrug-resistant (MDR) Klebsiella pneumoniae in neonatal intensive care units (NICUs). Despite advances in infection control, MDR strains continue to threaten vulnerable newborn populations, especially in resource-limited settings. In this study, we utilised publicly available whole-genome sequencing (WGS) data from the Sepsis Prevention in Neonates in Zambia (SPINZ) project to investigate the population structure, resistance, virulence, plasmid types, and prophage burden of K. pneumoniae linked to neonatal sepsis at the University Teaching Hospital (UTH) in Lusaka, Zambia. The majority of isolates (86.5%) belonged to the high-risk ST307 lineage or closely related variants and carried an extended-spectrum beta-lactamase (ESBL) profile, specifically, blaCTX-M-15 in 99.4%, while carbapenemase genes were absent. ST307 isolates had a high median count of resistance genes (11 across 7 drug classes) and fixed quinolone target-site mutations. Virulence scores were low, and yersiniabactin (ybt) was the only hypervirulence locus present (only in 10.7% of assemblies). Most plasmids were IncF type, predicted to be conjugative, with a highly conserved main cluster (AB060). Prophage regions were detected in 94.9% of genomes, with a notably higher burden in ST307 (median 30 per genome). This analysis demonstrates that an ESBL-dominant, high-risk ST307 population with conserved IncF plasmids and a lineage-specific prophage burden was responsible for neonatal sepsis at UTH, underscoring the need for clone-aware infection prevention and plasmid-informed surveillance strategies.