Drug-resistant Salmonella strains sweep through West Africa’s poultry and food chains, review warns

Non-typhoidal Salmonella, the group of Salmonella strains responsible for gastroenteritis and invasive bloodstream infections rather than typhoid fever, has long been recognized as a major zoonotic threat. A new scoping review published in Frontiers in Bacteriology now offers the most detailed picture yet of which serovars circulate in West Africa and how laboratories there actually identify them. Drawing on studies published between 2000 and 2025, researchers from the University of Abomey-Calavi in Benin, working with a collaborator at the University of Copenhagen, compiled and analyzed the regional literature following the PRISMA reporting guidelines, searching PubMed and Scopus with combinations of Medical Subject Headings and free-text keywords paired with country names across the subregion.

The scale of the problem the review addresses is considerable. At least 2,463 Salmonella serotypes have been identified worldwide, and non-typhoidal Salmonella is estimated to cause roughly 94 million cases of gastroenteritis each year, resulting in approximately 155,000 deaths. In sub-Saharan Africa the burden is compounded by invasive disease: certain serovars are associated with bloodstream infections, particularly among children, and the strains circulating there often carry drug resistance and virulence genes. Humans typically acquire infection through foods of animal origin, with poultry products a dominant route of transmission.

After screening titles, abstracts and full texts independently, the team included 74 articles in its qualitative analysis, published between 2009 and 2025, with 2019 and 2021 the most represented years at 11 articles each. Ten West African countries were covered, although Nigeria dominated the literature with 40 publications. Of the 74 articles, 64 identified non-typhoidal Salmonella and 49 went further to identify specific serovars. A deeper quantitative analysis focused on 28 articles from five countries, again led by Nigeria with 18 studies, published between 2016 and 2025.

From those 28 studies the reviewers extracted 1,202 non-typhoidal Salmonella serovar records from animal, environmental, food and human sources. Animal sources, particularly poultry, yielded the most isolates, followed by environmental samples, with food and human samples contributing the remainder. Three serovars towered over the rest: Salmonella Kentucky, Salmonella Enteritidis and Salmonella Typhimurium, followed by Salmonella Derby and Salmonella Poona. The distribution was source-dependent. Kentucky was most frequently recovered from animal and environmental samples, whereas Enteritidis was mainly associated with food and human samples, a pattern consistent with poultry acting as the principal reservoir from which contaminated products carry the pathogen to consumers.

The antimicrobial resistance findings are among the most alarming in the review. Of the 1,202 isolates documented, 923 lacked phenotypic resistance data, but among the 279 with available profiles, 251, or 89.9 percent, were resistant to at least one antibiotic. Resistance to ciprofloxacin, tetracycline, nalidixic acid and ampicillin was most frequently observed, and resistance ranged from a single drug to as many as ten. Several isolates showed multidrug resistance to between 8 and 10 antimicrobial agents. Salmonella Kentucky exhibited the greatest diversity of resistance profiles.

Genotypic screening told a complementary story. Resistance gene data were available for 309 isolates, or 25.7 percent of the total. The most commonly detected genes belonged to the aac class, found in 66.02 percent of those isolates and conferring aminoglycoside resistance, followed by tet genes at 27.83 percent for tetracycline resistance and qnr genes at 23.94 percent, the principal determinants of quinolone resistance. Intriguingly, the review uncovered mismatches in both directions: some strains carried resistance genes such as aac or fos without showing phenotypic resistance, while others, particularly Kentucky isolates, were phenotypically resistant to quinolones without any detectable quinolone resistance gene, hinting at resistance mechanisms that current genotyping panels miss.

The diagnostic landscape the review maps is one of pragmatic compromise. Three primary approaches were used for serovar identification: molecular methods based on PCR assays or sequencing, including whole-genome sequencing and targeted sequencing; serological methods relying on antigen-antibody reactions such as slide agglutination with specific antisera under the Kauffmann-White scheme; and mass spectrometry, specifically MALDI-TOF MS. Molecular methods were the most commonly used overall, and some studies combined approaches. Serotyping remains valuable for differentiating strains within a species, but the sheer diversity of non-typhoidal Salmonella serovars limits its resolution, especially where comprehensive antisera panels are unavailable.

MALDI-TOF MS, although classified as a phenotypic technique, works by proteomic profiling and has become widely adopted in clinical microbiology because it cuts turnaround time from several days to under an hour while remaining fast, cost-effective and accurate. Its weakness is discrimination: closely related Salmonella isolates can be indistinguishable without complementary analysis. At the other end of the spectrum, whole-genome sequencing offers the highest resolution, enabling not only precise serovar identification but also analysis of genetic relationships, evolutionary patterns, and the determinants of pathogenicity and antimicrobial resistance through workflows that include sequence alignment, variant calling and genome annotation. Emerging innovations, such as coupling MALDI-TOF MS with machine learning algorithms and bacteriophage-based detection systems, promise further gains in speed and specificity.

Yet the review makes clear that advanced tools remain largely inaccessible for routine use in the subregion. The barriers are not only the prohibitive cost of reagents and platform maintenance but also energy instability, which compromises the preservation of DNA and enzyme reagents. Consequently, bacterial culture on selective media such as Salmonella-Shigella or Compass Salmonella agar, coupled with Kauffmann-White serotyping, remains the most viable strategy, ensuring continuity of epidemiological surveillance and the detection of serotypes of public health interest even where molecular platforms are absent. PCR-based assays, meanwhile, are particularly useful for detecting low-abundance pathogens in complex samples and for revealing virulence and resistance markers that phenotypic methods alone cannot assess.

Among the serovars of greatest concern, Enteritidis, Kentucky and Typhimurium stand out. Typhimurium, Enteritidis and Dublin are widely recognized as the serovars most commonly associated with invasive infections, including bloodstream disease and severe gastroenteritis in children in sub-Saharan Africa. Typhimurium is transmitted primarily via the fecal-oral route and has been detected in retail poultry products at prevalence rates reaching up to 44 percent in some settings. Enteritidis is a foodborne zoonotic pathogen whose transmission spans animal reservoirs, environmental contamination and water systems, a clear One Health interface. Most striking is the story of Salmonella Kentucky ST198: 29 strains were reported across the reviewed literature, and every one of them was resistant to gentamicin, tetracyclines and quinolones. Once considered an antibiotic-susceptible poultry-associated serovar, Kentucky ST198 acquired the SGI1 resistance island and has since spread at high prevalence across Africa, the Middle East and South and Southeast Asia, reaching Europe and North America through travel-related infections. Because quinolones are considered last-resort antibiotics, this clone represents a significant public health concern for patient management.

Perhaps the review’s most sobering structural finding is what was missing: not a single one of the reviewed studies employed a comprehensive One Health sampling framework. Each focused exclusively on an isolated component, whether human, animal, food or environmental, limiting any comprehensive understanding of transmission across interconnected systems. The authors also acknowledge substantial limitations, above all a geographic surveillance bias, with more than half of the included studies originating from Nigeria, whose surveillance systems, laboratory capacity and research output outpace those of many neighbors. Heterogeneous study designs, sampling strategies and laboratory methodologies further complicate comparisons, and countries with limited publication output may be underrepresented.

Looking forward, the authors argue that future research should operationalize the One Health framework through integrated multisectoral studies combining human, animal, food and environmental samples; the gradual implementation of genomic surveillance tools including whole-genome sequencing to track transmission routes and antimicrobial resistance; the establishment of regional data-sharing platforms and laboratory networks to harmonize methodologies and strengthen outbreak response; and attention to environmental and socioeconomic determinants such as antimicrobial use practices and food distribution systems. Strengthening interdisciplinary collaboration and investing in scalable, context-appropriate technologies, they conclude, will be essential to close current gaps, improve public health preparedness, and slow the spread of antimicrobial-resistant non-typhoidal Salmonella across West Africa and beyond.

Subject of Research: Diversity and identification methods of non-typhoidal Salmonella serovars in West Africa: a scoping review

Article Title: Diversity and identification methods of non-typhoidal Salmonella serovars in West Africa: a scoping review

Article References: Deguenon, E., Hougbenou, B.-G., Hounkanrin, M., Hounmanou, G., & Dougnon, V. (2026). Diversity and identification methods of non-typhoidal Salmonella serovars in West Africa: a scoping review. Frontiers in Bacteriology, 5, Article 1825225. https://doi.org/10.3389/fbrio.2026.1825225

Image Credits: AI Generated

DOI: 10.3389/fbrio.2026.1825225

Keywords: Salmonella, West Africa, antimicrobial resistance, One Health, poultry, food safety, whole-genome sequencing, MALDI-TOF, public health, zoonoses, Diversity, identification