Genome-resolved surveillance of African Klebsiella oxytoca species complex genomes reveals resistome-mobilome and biosynthetic gene cluster diversity
TL;DR
These data define an African genome-resolved baseline for KoSC diversity and identify species-structured biosynthetic loci alongside heterogeneous resistance and mobilome profiles and identify specific lineages and genomic features for future population-based sampling, complete-genome reconstruction, and laboratory validation.
Abstract
The Klebsiella oxytoca species complex (KoSC) comprises taxonomically diverse commensals and opportunistic pathogens, but its genomic diversity remains poorly characterized across Africa. We curated publicly available African KoSC data through raw-read and public-assembly routes and analyzed 163 African genomes together with 282 global comparators. Pangenome, phylogenomic, sequence-typing, surface-locus, antimicrobial-resistance, plasmid-replicon, mobile-element, biosynthetic-gene-cluster, and virulence-component analyses were integrated. The African collection comprised K. michiganensis (112/163), K. oxytoca (36/163), K. pasteurii (8/163), and K. grimontii (7/163) from 13 countries. The African pangenome contained 4,286 core, 4,505 shell, and 18,066 cloud gene families. Official PubMLST sequence types were assigned to 129/163 genomes. Four core/intrinsic antimicrobial-resistance-associated loci (ompA, oqxA, oqxB, and blaOXY) occurred in all genomes, whereas acquired resistance determinants were heterogeneous. Intact til biosynthetic gene clusters occurred in 55/163 genomes and intact leup clusters in 103/163. leup was concentrated in K. michiganensis (102/112), whereas intact til was frequent in K. oxytoca (26/36), K. pasteurii (7/8), and K. grimontii (7/7). Klebsiella-focused Virulence Factor Database screening detected at least one curated component in 112/163 genomes, but no complete curated factor; three K. michiganensis genomes carried complete mrkABCDF structural-operon candidates. These data define an African genome-resolved baseline for KoSC diversity and identify species-structured biosynthetic loci alongside heterogeneous resistance and mobilome profiles. IMPORTANCE The Klebsiella oxytoca species complex contains opportunistic pathogens that can carry antimicrobial-resistance genes and biosynthetic pathways linked to host-associated effects, yet African representatives remain poorly characterized. This study provides a curated genomic view of the complex across 13 African countries and places those genomes in a global context. The analysis shows extensive variation in accessory genes, resistance determinants, and mobile genetic elements, while two biologically important biosynthetic loci have strikingly different species distributions. These findings provide a reproducible baseline for genomic surveillance of this understudied Klebsiella group in Africa and identify specific lineages and genomic features for future population-based sampling, complete-genome reconstruction, and laboratory validation.