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. 2023 Jun 13;23(1):164.
doi: 10.1186/s12866-023-02901-1.

Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria

Kabiru Olusegun Akinyemi  1 , Christopher Oladimeji Fakorede  2 , Jörg Linde  3 , Ulrich Methner  3 , Gamal Wareth  3   4   5 , Herbert Tomaso  3 , Heinrich Neubauer  3
Affiliations

Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria

Kabiru Olusegun Akinyemi et al. BMC Microbiol. .

Abstract

Background: Salmonella infections remain an important public health issue worldwide. Some serovars of non-typhoidal Salmonella (NTS) have been associated with bloodstream infections and gastroenteritis, especially in children in Sub-Saharan Africa with circulating S. enterica serovars with drug resistance and virulence genes. This study identified and verified the clonal relationship of Nigerian NTS strains isolated from humans, animals, and the environment.

Methods: In total, 2,522 samples were collected from patients, animals (cattle and poultry), and environmental sources between December 2017 and May 2019. The samples were subjected to a standard microbiological investigation. All the isolates were identified using Microbact 24E, and MALDI-TOF MS. The isolates were serotyped using the Kauffmann-White scheme. Antibiotic susceptibility testing was conducted using the disc diffusion method and the Vitek 2 compact system. Virulence and antimicrobial resistance genes, sequence type, and cluster analysis were investigated using WGS data.

Results: Forty-eight (48) NTS isolates (1.9%) were obtained. The prevalence of NTS from clinical sources was 0.9%, while 4% was recorded for animal sources. The serovars identified were S. Cotham (n = 17), S. Give (n = 16), S. Mokola (n = 6), S. Abony (n = 4), S. Typhimurium (n = 4), and S. Senftenberg (n = 1). All 48 Salmonella isolates carried intrinsic and acquired resistant genes such as aac.6…Iaa, mdf(A), qnrB, qnrB19 genes and golT, golS, pcoA, and silP, mediated by plasmid Col440I_1, incFIB.B and incFII. Between 100 and 118 virulence gene markers distributed across several Salmonella pathogenicity islands (SPIs), clusters, prophages, and plasmid operons were found in each isolate. WGS revealed that strains of each Salmonella serovar could be assigned to a single 7-gene MLST cluster, and strains within the clusters were identical strains and closely related as defined by the 0 and 10 cgSNPs and likely shared a common ancestor. The dominant sequence types were S. Give ST516 and S. Cotham ST617.

Conclusion: We found identical Salmonella sequence types in human, animal, and environmental samples in the same locality, which demonstrates the great potential of the applied tools to trace back outbreak strains. Strategies to control and prevent the spread of NTS in the context of one's health are essential to prevent possible outbreaks.

Keywords: MLST; Nigeria; Resistant gene; Salmonella; Serotyping; Virulence gene; WGS.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Distribution of Salmonella enterica serovars according to sample source from Lagos, Nigeria
Fig. 2
Fig. 2
Antibiogram of Salmonella enterica serovars isolated from different sources in Nigeria in accordance with EUCAST Expert Rules x 3.2
Fig. 3
Fig. 3
The minimum spanning tree (MST) of Salmonella strains (nodes) was used in this study. The node colour corresponds to the source of the strains (see legend). The allelic distances from cgMLST analysis are denoted at branches. Clusters of genetically similar strains were defined using a cut-off of 10 alleles and are visualized in grey
Fig. 4
Fig. 4
Map of Nigeria showing the location of Lagos State and the distribution of Salmonella enterica serovars across different local government areas of Lagos State
See this image and copyright information in PMC

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