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. 2022 Aug 26;16(8):e0010716.
doi: 10.1371/journal.pntd.0010716. eCollection 2022 Aug.

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

Odion O Ikhimiukor  1 , Anderson O Oaikhena  1 , Ayorinde O Afolayan  1 , Abayomi Fadeyi  2 , Aderemi Kehinde  3 , Veronica O Ogunleye  3 , Aaron O Aboderin  4 , Oyinlola O Oduyebo  5 , Charles J Elikwu  6 , Erkison Ewomazino Odih  1 , Ifeoluwa Komolafe  1 , Silvia Argimón  7 , Abiodun Egwuenu  8 , Ini Adebiyi  3 , Oluwadamilola A Sadare  6 , Tochi Okwor  8 , Mihir Kekre  7 , Anthony Underwood  7 , Chikwe Ihekweazu  8 , David M Aanensen  7 , Iruka N Okeke  1
Affiliations

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

Odion O Ikhimiukor et al. PLoS Negl Trop Dis. .

Abstract

Background: Salmonellosis causes significant morbidity and mortality in Africa. Information on lineages of invasive Salmonella circulating in Nigeria 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, 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.

Conclusion: 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.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Epidemiological information showing.
(A) number of Salmonella isolated received from the different sentinel hospitals at different years, and (B) Number of different Salmonella serotypes received from the different sentinel hospitals.
Fig 2
Fig 2. Grape tree showing core genome MLST of S. Typhi from human sources in Africa, deposited in the EnteroBase database.
Red leaf labels are genomes from this study.
Fig 3
Fig 3. SNP-phylogeny based tree and gene presence/absence showing the genomic profile of Salmonella Typhi genomes retrieved from 5 sentinel laboratories in Nigeria.
ARGs: antibiotic resistance genes, STs: Sequence types.
Fig 4
Fig 4. Grape tree showing core genome MLST of S. Enteritidis from human sources in Africa, deposited in the EnteroBase database.
Red leaf labels are genomes from this study.
Fig 5
Fig 5. SNP-phylogeny based tree and gene presence/absence map showing the genomic profile of Salmonella Enteritidis retrieved from 3 sentinel laboratories in Nigeria.
ARGs: antibiotic resistance genes, STs: Sequence types.
Fig 6
Fig 6. Gene presence/absence map showing the genomic profile of non-typhoidal Salmonella retrieved from 5 sentinel laboratories in Nigeria.
ARGs: antibiotic resistance genes, STs: Sequence types.
Fig 7
Fig 7. Frequency of occurrence of Salmonella pathogenicity island in TS (Typhoidal Salmonella) and NTS (Non-typhoidal Salmonella) in this study.
See this image and copyright information in PMC

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