Whole Genome Sequencing RevealsEnterobacter hormaecheias a Key Bloodstream Pathogen in Six Tertiary Care Hospitals in Southwestern Nigeria

Enterobacterspp. are an important cause of healthcare-associated bloodstream infections uncommonly reported in Africa. This study used whole genome sequencing (WGS) to characteriseEnterobacterspp. from hospitals in Nigeria’s antimicrobial resistance (AMR) surveillance system. Blood-culture isolates ofEnterobacterfrom six such tertiary-care hospitals recovered between 2014 and 2020 were re-identified and antimicrobial susceptibility-tested using VITEK2. Illumina technology provided whole genome sequences for genome nomenclature, antimicrobial resistance gene prediction, Single Nucleotide Polymorphism (SNP) phylogeny, and multi-locus sequence typing via publicly available bioinformatics pipelines. Initial biochemical delineation often misclassifiedEnterobacter, necessitating whole-genome sequencing for accurate classification. Among 98Enterobacterreceived,Enterobacter hormaecheisubspeciesxiangfangensispredominated (43), followed by otherE. hormacheisubspecies (18),E. cloacae(26),E. roggenkampii(4),E. bugandensis(3),E. kobei(2),E. asburiae(1) andE. cancerogenous(1). Cephalosporins, aminoglycoside, chloramphenicol, macrolide, and carbapenem resistance inE. hormaecheiwas attributed to known resistance genes. They belonged to clusters III, IV, and VIII based onhsp60typing and clades A, B, C, and D according to Sutton and Co’s nomenclature. These isolates and otherEnterobacterspecies recently reported from Nigeria reveal extensiveE. hormaecheidiversity, as well as clusters representing potential outbreaks. Enterobacter hormaechei, often misidentified and rarely reported from Nigeria, is this study’s most common blood culture isolatedEnterobacterspp. Uncovering underappreciated species as important bloodstream pathogens and retrospective detection of likely outbreaks emphasise the value of genomic surveillance in resource-limited settings.