Genomic and Transcriptomic Architecture of Virulence Regulation in Hypervirulent Klebsiella pneumoniae Strains Isolated from Neonatal Septicemia Cases in Nigeria

Hypervirulent Klebsiella pneumoniae (hvKP) represents an emerging pathotype distinct from classical K. pneumoniae, characterized by hypermucoviscosity, enhanced iron acquisition, and a propensity to cause severe infections in non-immunocompromised hosts including neonates. The genomic and transcriptomic architecture governing virulence in hvKP isolates from Nigerian neonatal settings has not been investigated, representing a critical knowledge gap. This study performed comparative genomics and transcriptomic profiling of hvKP isolates recovered from neonatal septicemia cases at teaching hospitals in Lagos, Kano, and Enugu States. Whole-genome sequencing of 40 hvKP isolates was performed on Illumina and Oxford Nanopore platforms for hybrid assembly. Virulome, resistome, mobilome, and pan-genome analyses were conducted using Kleborate, CARD, and Roary. Comparative transcriptomics under iron-limited and normoxic conditions was performed using RNA-sequencing to identify differentially expressed virulence regulons. Results revealed co-carriage of virulence loci (iuc, iro, rmpA2, peg-344) in 72.5 percent of isolates, confirming convergent hvKP-AMR plasmids in 40 percent. Pan-genome analysis identified 312 core genes and a large accessory genome (4,891 genes) with significant horizontal gene transfer evidence. RNA-seq revealed upregulation of the iron-acquisition aerobactin operon under iron limitation, modulated by the Fur regulon with 18-fold differential expression. These findings provide the first multi-omics characterization of hvKP virulence regulation in Nigerian neonatal settings and generate molecular targets for future therapeutic and diagnostic innovation. Keywords: hypervirulent Klebsiella pneumoniae, genomics, transcriptomics, neonatal septicemia, virulence regulation.