A Whole-Genome Sequencing Study of Antimicrobial Resistance in Neonatal Sepsis Pathogens Across Nigerian Tertiary Hospitals: Implications for Empirical Therapy Guidelines

The genomic basis of antimicrobial resistance (AMR) in neonatal sepsis pathogens across Nigerian hospitals is largely uncharacterised, hampering the development of rational empirical therapy guidelines adapted to local resistance landscapes. This multi-site whole-genome sequencing (WGS) study characterises the resistome, virulome, and clonal structure of key neonatal sepsis pathogens isolated from blood cultures across eight tertiary hospitals spanning Nigeria's six geopolitical zones. Over 24 months from January 2022 to December 2023, 412 non-duplicate bacterial isolates from confirmed neonatal sepsis cases were collected, transported on appropriate media, and sequenced using Illumina short-read and Oxford Nanopore long-read platforms. Bioinformatic analysis employed ResFinder, VirulenceFinder, and MLST pipelines with phylogenetic reconstruction using RAxML. Klebsiella pneumoniae (28.4%), Staphylococcus aureus (22.8%), and Escherichia coli (18.7%) were the dominant pathogens. WGS revealed that 73.4% of Klebsiella isolates carried ESBL genes (predominantly blaCTX-M-15), with 34.2% additionally harbouring carbapenemase genes (predominantly blaOXA-48). A dominant hypervirulent K. pneumoniae clone (ST307) was identified across five of eight hospital sites, suggesting inter-hospital dissemination. MRSA accounted for 48.6% of Staphylococcus aureus isolates and belonged predominantly to ST88. These findings provide the first Nigeria-wide genomic surveillance dataset for neonatal sepsis AMR, revealing critical resistance gene prevalence and clonal spread patterns. The data mandate urgent revision of empirical neonatal sepsis treatment guidelines and investment in AMR genomic surveillance infrastructure. Keywords: whole-genome sequencing, AMR, neonatal sepsis, Nigeria, genomic surveillance.