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

Abstract

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.

Keywords: Enterobacter; Enterobacter cloacae; Enterobacter hormaechei; bacteraemia; bacterial identification; genomic surveillance.

Fig. 1.. (a): Proportion of genera received from invasive infections from six sentinels in the Nigerian AMR surveillance system (2014–2020). (b) Maximum likelihood tree showing whole-genome sequence identifications of Enterobacter isolates recovered from patients admitted to six hospitals in southwestern Nigeria, juxtaposed with identifications of Enterobacter species by the diagnostic lab sentinels and reference lab VITEK 2 reidentification, their clades and Hoffman clusters.

Fig. 2.. Initial identification of the two most frequently detected Enterobacter species by reference and sentinel laboratories, whole-genome sequence ID and their STs (a) E. hormaechei (b) E. cloacae

Fig. 3.. Maximum likelihood phylogenetic trees showing the relationship among Enterobacter isolates belonging to the most frequently encountered species from different hospitals, STs, AMR genes and plasmid replicons detected. (a) E. hormaechei (b) E. cloacae.

Fig. 4.. Comparison of genomes from this study and those of isolates from elsewhere in Nigeria. Genome IDs are prefixed by ERR* if submitted by Sands et al. [8] or G* (this study). (a) ANI analysis of genome-sequenced Enterobacter spp.: E. hormaechei (EHO), E. cloacae (ECL), E. bugandensis (EBU), E. asburiae (EAS), E. roggenkampii (ERO) and E. kobei (EKO). (b) Maximum likelihood tree illustrating the phylogeny among all available Nigerian genomes in the ENA.

Fig. 5.. Geographic source of genome-sequenced Enterobacter in Nigeria. Isolates originated from southwestern Nigeria (this study) and north and central Nigeria [8].