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Salmonella enterica is a major pathogen that causes widespread infections, especially in Africa, where it poses significant public health challenges. However, its genetic diversity remains underexplored. This study investigated the phylogenetic relationships of S. enterica strains isolated from human (18%), food (61%), and environmental (21%) sources across Africa. A total of 575 16S rRNA sequences were retrieved from the SRA-NCBI database, representing isolates from 12 African countries: Congo (2), Tanzania (2), Uganda (2), Sudan (6), Niger (11), Kenya (23), Benin (40), Tunisia (35), Morocco (36), Egypt (88), Nigeria (146), and South Africa (184). Additionally, 8 sequences from non-African regions and one Zika virus sequence were included as outgroup. Phylogenetic analysis via MEGA and iTOL revealed distinct clustering, with evidence of cross-border transmission and regional genetic diversity. The long branch lengths in certain clades suggest accelerated evolution, likely driven by antimicrobial pressure. Phylogeographic analysis via MicroReact identified dominant clusters in Egypt and Nigeria, suggesting regional transmission dynamics and potential global exchange routes. These findings underscore the need for targeted surveillance, genomic monitoring, and stricter antimicrobial resistance management to control Salmonella in Africa.

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Phylogenetic Analysis of Salmonella enterica 16S rRNA Sequences in Africa: Insights into Genetic Diversity and Evolution

  • 会议论文

  • 发表日期：

    2026年

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  • Hajar Esserghini,
  • Malika Allali,
  • Dhaud Odei Ansong,
  • Khaoula Errafii,
  • Imane Benmoussa,
  • Sami Darkaoui,
  • Najib Al Idrissi,
  • Adnane Benmoussa,
  • Salsabil Hamdi,
  • Hassan Ghazal,
  • Nadia Ziyate,
  • Fadil Bakkali

摘要

Salmonella enterica is a major pathogen that causes widespread infections, especially in Africa, where it poses significant public health challenges. However, its genetic diversity remains underexplored. This study investigated the phylogenetic relationships of S. enterica strains isolated from human (18%), food (61%), and environmental (21%) sources across Africa. A total of 575 16S rRNA sequences were retrieved from the SRA-NCBI database, representing isolates from 12 African countries: Congo (2), Tanzania (2), Uganda (2), Sudan (6), Niger (11), Kenya (23), Benin (40), Tunisia (35), Morocco (36), Egypt (88), Nigeria (146), and South Africa (184). Additionally, 8 sequences from non-African regions and one Zika virus sequence were included as outgroup. Phylogenetic analysis via MEGA and iTOL revealed distinct clustering, with evidence of cross-border transmission and regional genetic diversity. The long branch lengths in certain clades suggest accelerated evolution, likely driven by antimicrobial pressure. Phylogeographic analysis via MicroReact identified dominant clusters in Egypt and Nigeria, suggesting regional transmission dynamics and potential global exchange routes. These findings underscore the need for targeted surveillance, genomic monitoring, and stricter antimicrobial resistance management to control Salmonella in Africa.