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Whole-genome sequencing reveals Enterobacter hormaechei as a key bloodstream pathogen in six tertiary care hospitals in southwestern Nigeria.

Oni FI., Afolayan AO., Oaikhena AO., Odih EE., Ikhimiukor OO., Ogunleye VO., Aboderin AO., Olabisi OF., Amupitan AA., Fadeyi A., Raheem RA., Olanipekun BA., Elikwu CJ., Sadare OA., Oshun PO., Oduyebo OO., Ojo F., Adeyemo AT., Mba IE., Egwuenu A., Okwor TJ., Underwood A., Argimon S., Ihekweazu C., Aanensen DM., Okeke IN.

Enterobacter spp. are an important cause of healthcare-associated bloodstream infections that are uncommonly reported in Africa. This study utilized whole-genome sequencing to characterize Enterobacter spp. from hospitals in Nigeria's antimicrobial resistance surveillance system. Bloodstream Enterobacter spp. isolates from six sentinel tertiary-care hospitals recovered between 2014 and 2020 were re-identified and antimicrobial susceptibility-tested using VITEK 2 system. Illumina technology provided whole-genome sequences for genome nomenclature, antimicrobial resistance gene prediction, SNP phylogeny and multi-locus sequence typing via publicly available bioinformatics pipelines. Initial biochemical delineation often misclassifies Enterobacter, necessitating whole-genome sequencing for accurate classification. Among 98 Enterobacter received, Enterobacter hormaechei subspecies xiangfangensis predominated (43), followed by other E. hormaechei subspecies (18) and Enterobacter spp. such as Enterobacter cloacae (26), Enterobacter roggenkampii (4), Enterobacter bugandensis (3), Enterobacter kobei (2), Enterobacter asburiae (1) and Enterobacter cancerogenus (1). Resistance to extended-spectrum cephalosporins, aminoglycosides, phenicols, macrolides and carbapenems in E. hormaechei was attributed to known resistance genes. E. hormaechei isolates belonged to clusters III, IV and VIII based on hsp60 typing and clades A, B, C and D according to Sutton and Co's nomenclature. This and other recent reports from Nigeria reveal the extensive diversity of E. hormaechei, as well as clusters representing potential outbreaks. E. hormaechei, often misidentified and rarely reported from Nigeria, is the most common Enterobacter spp. isolated from blood culture in this study. Uncovering underappreciated species as important bloodstream pathogens and retrospective detection of likely outbreaks emphasize the value of genomic surveillance in resource-limited settings.

More information Original publication

DOI

10.1099/mgen.0.001508

Type

Journal article

Publication Date

2025-10-01T00:00:00+00:00

Volume

11

Addresses

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Keywords

Humans, Enterobacter, Bacteremia, Enterobacteriaceae Infections, Cross Infection, Anti-Bacterial Agents, Microbial Sensitivity Tests, Phylogeny, Genome, Bacterial, Nigeria, Multilocus Sequence Typing, Tertiary Care Centers, Whole Genome Sequencing