Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria.

• Main Authors: Odion O Ikhimiukor (Author), Anderson O Oaikhena (Author), Ayorinde O Afolayan (Author), Abayomi Fadeyi (Author), Aderemi Kehinde (Author), Veronica O Ogunleye (Author), Aaron O Aboderin (Author), Oyinlola O Oduyebo (Author), Charles J Elikwu (Author), Erkison Ewomazino Odih (Author), Ifeoluwa Komolafe (Author), Silvia Argimón (Author), Abiodun Egwuenu (Author), Ini Adebiyi (Author), Oluwadamilola A Sadare (Author), Tochi Okwor (Author), Mihir Kekre (Author), Anthony Underwood (Author), Chikwe Ihekweazu (Author), David M Aanensen (Author), Iruka N Okeke (Author)
• Format: Book
• Published: Public Library of Science (PLoS), 2022-08-01T00:00:00Z.
• Subjects: article
• Online Access: Connect to this object online.
• Notes: 1935-2727; 1935-2735; 10.1371/journal.pntd.0010716
• Keywords: Arctic medicine. Tropical medicine; RC955-962; Public aspects of medicine; RA1-1270
• Source: PLoS Neglected Tropical Diseases, Vol 16, Iss 8, p e0010716 (2022)

<h4>Background</h4>Salmonellosis causes significant morbidity and mortality in Africa. Information on lineages of invasive Salmonella circulating in Nigeria is sparse.<h4>Methods</h4>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.<h4>Results</h4>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, had several antibiotic resistance genes (ARGs) including blaTEM-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 single-nucleotide polymorphisms (n = 37). All S. Enteritidis harboured aph(3")-Ib, blaTEM-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.<h4>Conclusion</h4>Most invasive salmonelloses in southwest Nigeria are vaccine-preventable infections due to multidrug-resistant, West African dominant S. 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.