Genomic characterization of invasive typhoidal and non-typhoidal <i>Salmonella</i> in southwestern Nigeria

ABSTRACT Background Salmonellosis causes significant morbidity and mortality in Africa. Despite being endemic in Nigeria, information on circulating lineages of invasive Salmonella is sparse. Methods Salmonella enterica isolated from blood (n=60) and cerebrospinal fluid (CSF, n=3) between 2016 and 2020 from five tertiary hospitals in southwest Nigeria were antimicrobial susceptibility-tested and Illumina-sequenced. Genomes were analysed using publicly-available bioinformatic tools. Results Isolates and sequence types (STs) from blood were S . Typhi [ST1, n =1 and ST2, n =43] and invasive non-typhoidal Salmonella (iNTS) ( S. Enteritidis [ST11, n=7], S . Durham [ST10, n=2], S . Rissen [ST8756, n=2], S . Chester [ST2063, n=1], S . Dublin [ST10, n=1], S . Infantis [ST603, n=1], S . Telelkebir [ST8757, n=1] and S . Typhimurium [ST313, n=1], S . Typhi ST2 (n=2) and S . Adabraka ST8757 (n=1) were recovered from CSF. Most S . Typhi belonged to genotype 3.1.1 (n=44), carried an IncY plasmid and had several antibiotic resistance genes (ARGs) including bla TEM-1 (n=38), aph(6)-Id (n=32), tet(A) (n=33), sul2 (n=32), dfrA14 (n=30) as well as quinolone resistance-conferring gyrA_S83Y SNPs (n=37). All S . Enteritidis harboured aph(3’’)-Ib, bla TEM-1 , catA1, dfrA7, sul1, sul2, tet(B) genes, and a single ARG, qnrB19 , was detected in S . Telelkebir.. Typhoidal toxins cdtB, pltA and pltB were detected in S . Typhi, Rissen, Chester, and Telelkebir. Conclusion Most invasive salmonelloses in south west Nigeria are vaccine-preventable infections due to multidrug-resistant, West African dominant Typhi lineage 3.1.1.. Invasive NTS serovars, including some harbouring typhoidal toxin or resistance genes represented a third of the isolates emphasizing the need for better diagnosis and surveillance. Author Summary Whole genome sequencing of 63 invasive Salmonella from 5 tertiary hospitals in Nigeria revealed multiple serovars including a dominant antibiotic-resistance-gene harbouring S . Typhi 3.1.1 genotype comprising a gyrA_S83Y and IncY plasmid. We also report invasive non-typhoidal Salmonella harbouring typhoidal toxins.