Whole genome sequencing of a colistin resistant Salmonella Kedougou ST 1543 clinical isolate from Gombe State, Nigeria.

BACKGROUND

The emergence of plasmid-mediated colistin resistance by mcr genes poses a serious threat to the treatment of invasive non-typhoidal salmonellosis. Salmonella enterica serovar Kedougou is an understudied non-typhoidal serovar increasingly associated with human infections in Africa, yet genomic data on colistin-resistant strains from Nigeria are lacking.

METHODS

A colistin-resistant S. Kedougou isolate recovered from stool culture was confirmed using PCR and multilocus sequence typing (MLST). Antimicrobial susceptibility was determined by disc diffusion. Whole-genome sequencing was performed on the Illumina MiSeq platform. Resistance genes, plasmid content, and phylogenetic relationships were analysed using ResFinder, CARD, MobSuite, and CSI Phylogeny.

RESULTS

The isolate was identified as S. Kedougou ST1543. It harboured the plasmid-mediated colistin resistance gene mcr-4.6 on a ColE10 plasmid, along with multiple additional resistance genes (blaTEM-1, aadA2, lnu(F), mph(A), sul2, dfrA14) distributed across IncI-gamma/K1 and other replicons. Phylogenetic analysis placed the Nigerian isolate within the African S. Kedougou clade, forming a distinct sub-lineage.

CONCLUSIONS

This study provides the first whole-genome sequence of an mcr-4.6-positive colistin-resistant S. Kedougou ST1543 clinical isolate from Nigeria. The findings highlight the silent spread of mobile colistin resistance in non-typhoidal Salmonella and underscore the urgent need for enhanced genomic surveillance and antimicrobial stewardship in sub-Saharan Africa.