Whole-Genome Sequencing of Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates from Neonatal Intensive Care Units in Southwest Nigeria: Resistance Mechanisms and Phylogenomic Relationships

Klebsiella pneumoniae is a leading cause of neonatal sepsis and a critical antimicrobial resistance priority pathogen globally. Whole-genome sequencing (WGS) provides comprehensive insights into resistance determinants and outbreak transmission dynamics in hospital settings. This study applied WGS to multidrug-resistant (MDR) K. pneumoniae isolates from neonatal intensive care units (NICUs) at three tertiary hospitals in Lagos, Oyo, and Ogun States. A total of 45 MDR K. pneumoniae clinical isolates were sequenced on the Illumina MiSeq platform. Genome assemblies were annotated using Prokka, and resistome profiling was conducted using the ResFinder 4.0 and AMRFinder databases. Multi-locus sequence typing (MLST) was performed using the Pasteur scheme, and phylogenomic trees were constructed using Roary-derived core genome alignments with RAxML. Sequence type ST11 predominated (36%), followed by ST258 (22%), both globally high-risk hypervirulent clones. BlaNDM-1 was detected in 62% of isolates, with blaOXA-48 co-occurrence in 31%. Phylogenomic clustering revealed two probable nosocomial transmission events involving genetically identical isolates from different hospitals, suggesting inter-hospital pathogen movement via staff or transferred patients. These findings provide the first published WGS-based characterization of NICU-associated MDR K. pneumoniae in Southwest Nigeria and define genomic targets for infection prevention and control. Keywords: Klebsiella pneumoniae, whole-genome sequencing, neonatal ICU, blaNDM, Southwest Nigeria.