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

Abstract

Background:

Non-typhoidal Salmonella (NTS) represents a predominant group of zoonotic pathogens responsible for a significant global burden of human infections. These infections have garnered increasing attention due to asymptomatic carriage in livestock and subsequent dissemination through the food chain. This review aims to investigate the diversity of NTS serovars isolated in West Africa and to evaluate the diagnostic methods used for their identification.

Methods:

A systematic literature search was conducted using the PubMed and Scopus databases, covering the period from 2000 to 2025. Study selection and reporting followed the PRISMA guidelines. For the included articles, data on serovar distribution, sample origin, and both phenotypic and genotypic antimicrobial resistance (AMR) profiles were extracted and organized in Microsoft Excel. Statistical analysis was performed using the R statistical software, version 4.5.2.

Results:

A total of 1,202 isolates were identified from animal, environmental, food, and human sources. Salmonella Kentucky, Salmonella Enteritidis, and Salmonella Typhimurium were the most frequently reported serovars. Notably, several isolates exhibited multidrug resistance (MDR) to between 8 and 10 antimicrobial agents. Identification and characterization of these NTS serovars were primarily achieved through molecular, serological, and mass spectrometry methods (particularly MALDI-TOF MS).

Conclusion:

Overall, the findings highlight the predominance of poultry-associated NTS, the circulation of key zoonotic serovars, widespread antimicrobial resistance, and the growing adoption of molecular diagnostics. However, the absence of integrated One Health surveillance across studies underscores critical gaps in regional monitoring systems.

1 Introduction

Salmonellosis is a bacterial zoonosis with considerable public health impact and can be caused by typhoidal and non-typhoidal Salmonella (NTS) organisms (Sanni et al., 2022). The public health impact of typhoidal and invasive non-typhoidal Salmonella infections is significant, particularly in Africa and Asia, where they have a major impact on morbidity and mortality (Ikhimiukor et al., 2022). It is mainly transmitted to humans through foods of animal origin, particularly through the consumption of poultry products (Igbinosa et al., 2023). NTS refers to infections caused by all Salmonella serotypes except those belonging to the typhoidal and paratyphoid groups. At least 2,463 Salmonella serotypes have been identified (Sanni et al., 2022). NTS is estimated to cause approximately 94 million cases of gastroenteritis per year worldwide, resulting in approximately 155,000 deaths (Ikhimiukor et al., 2022; Jibril et al., 2023). Some NTS serovars have been associated with bloodstream infections and gastroenteritis, particularly in children in sub-Saharan Africa, where circulating S. enterica serovars often harbor drug resistance and virulence genes (Akinyemi et al., 2023). The symptoms of NTS infection in humans include diarrhea, vomiting, and abdominal cramps (Sanni et al., 2022). Due to the high diversity of these strains, traditional phenotypic methods have shown important limitations. Moreover, although molecular and mass spectrometry methods provide higher-resolution identification, they are still rarely implemented in West Africa. Therefore, it is essential to review studies focusing on NTS, including those addressing serovar identification across different sample types. This review aims to summarize the methods and techniques used for serovar identification. It will provide an overview of both the most frequently isolated serovars in West African samples and the tools employed for their identification. Overall, this review seeks to summarize the current state of research on NTS serovars and the methods used for their characterization.

2 Methods

2.1 Search strategy

This scoping review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines (Page et al., 2021). A comprehensive literature search was performed to identify studies reporting on the diversity and identification methods of non-typhoidal Salmonella (NTS) serovars in West Africa. The search was conducted from 19 September 2025 to 31 December 2025 using two major electronic databases: PubMed and Scopus. These databases were selected for their broad coverage of biomedical and microbiological research. Additional relevant articles were identified through manual screening of the reference lists of selected studies. A combination of Medical Subject Headings (MeSH) and free-text keywords was used to maximize sensitivity. The search terms included variations and combinations of the following keywords: “Non-typhoidal Salmonella”, “NTS”, “Salmonella serovar”, “Salmonella enterica”, “foodborne Salmonella”, “human Salmonella infection”, and “animal Salmonella”, combined with geographical terms such as “West Africa” and specific country names (e.g., Benin, Nigeria, Ghana, Ivory Coast, Senegal, Togo, Burkina Faso, Mali, Niger, Sierra Leone, Liberia, Guinea, Guinea-Bissau, Gambia, and Cape Verde). Boolean operators (AND, OR) were applied to refine the search strategy. Examples of search strings included: (“Non-typhoidal Salmonella” OR “NTS”) AND (“West Africa”); (“Salmonella serovar” OR “Salmonella enterica”) AND (“food” OR “human” OR “animal”) AND (“West Africa”); and (“Salmonella” AND “identification” OR “serotyping” OR “molecular typing”) AND (“West Africa”). Filters were applied to include only studies published between January 2000 and December 2025. Only original research articles were retained, and review articles were excluded to avoid duplication of data. The search results were exported and managed using Microsoft Excel, where duplicates were identified and removed. The selection process involved two stages: (i) screening of titles and abstracts and (ii) full-text assessment for eligibility. This process was conducted independently by at least two reviewers, and discrepancies were resolved through discussion and consensus.

2.2 Inclusion and exclusion criteria

The eligibility criteria were defined to ensure the inclusion of relevant and high-quality studies addressing the objectives of this scoping review. Studies were included if they met the following criteria: peer-reviewed original research articles published between January 2000 and December 2025; studies conducted in West African countries; studies reporting on non-typhoidal Salmonella (NTS) isolates; and studies describing serovar diversity, distribution, or identification methods, including conventional culture techniques, biochemical tests, serotyping, and molecular approaches such as polymerase chain reaction (PCR) and whole-genome sequencing. In addition, studies involving samples from humans, animals, food, or environmental sources were considered eligible. Only articles published in English or French were included. Studies were excluded if they met any of the following conditions: review articles, systematic reviews, meta-analyses, editorials, commentaries, or conference abstracts; studies focusing exclusively on Salmonella Typhi or Salmonella Paratyphi; studies conducted outside West Africa; articles lacking clear information on serovar identification or the methods used; duplicate publications across databases; articles with inaccessible full texts; and studies published in languages other than English or French without an available translation. All identified records were screened independently by two reviewers based on titles and abstracts, followed by full-text assessment for eligibility. Any disagreements between the reviewers were resolved through discussion and consensus, with the involvement of a third reviewer when necessary to ensure consistency and accuracy in study selection.

2.3 Data extraction

Data from the included studies were systematically extracted using a standardized data extraction form developed in Microsoft Excel. The extraction process was carried out independently by multiple reviewers to ensure accuracy, consistency, and reproducibility of the collected information. For each eligible study, the following data were extracted: bibliographic information, including the first author and year of publication; study characteristics such as country, study design, and study period; and sample-related information, including the source of isolates (human, animal, food, or environmental) and sample size. Microbiological data were also collected, particularly the number of Salmonella isolates identified. Detailed information on isolates was recorded, including the diversity and distribution of non-typhoidal Salmonella (NTS) serovars reported in each study. In addition, data on identification methods were extracted, covering conventional approaches (culture techniques, biochemical tests, and serotyping based on the Kauffmann–White scheme) and molecular methods, including polymerase chain reaction (PCR), multilocus sequence typing (MLST), and whole-genome sequencing. Where available, antimicrobial resistance profiles were also documented. Finally, key findings relevant to NTS diversity and epidemiology were summarized. All extracted data were reviewed and cross-checked for completeness and consistency prior to analysis. Descriptive statistical analyses and graphical visualizations were performed using the R statistical software, version 4.5.2. Due to the heterogeneity in study designs, sampling frameworks, and laboratory methodologies across the included studies, a quantitative meta-analysis was not undertaken. Instead, the findings were synthesized qualitatively, with an emphasis on identifying trends and patterns in serovar diversity and the range of identification methods used across West Africa.

3 Results

3.1 Qualitative analysis

A total of 74 articles were included in the qualitative analysis (Figure 1). These articles were published between 2009 and 2025. The years 2019 and 2021 were the most represented, with 11 articles each (Figure 2A). Additionally, 10 West African countries were represented, with Nigeria accounting for the majority, with 40 publications (Figure 2B). Figure 3 shows the distribution of publication years based on whether NTS serovars were detected. From 2009 to 2025, NTS serovars were identified (Figure 3A). Out of a total of 74 articles, 64 identified NTS. Of these, 49 identified NTS serovars (Figure 3B). For serovar identification, molecular methods and serological methods were used (Figure 4A). Some studies used both approaches. Notably, molecular methods were the most commonly used (Figure 4B).

Figure 1

Figure 2

Figure 3

Figure 4

3.2 Quantitative analysis

3.2.1 Metadata description of the included articles

A total of 28 articles from different countries in West Africa were included in this qualitative review (Table 1). The 28 articles were published between 2016 and 2025 (Figure 5A), with the highest number of publications recorded in 2021 (n = 9). Five countries were represented, with Nigeria contributing the majority of articles (n = 18) (Figure 5B). Figure 5C shows the distribution of studies by publication year and country. In some years, studies were reported from all five countries.

Figure 5

3.2.2 NTS serovar distribution

A total of 1,202 NTS serovar records were collected from the 28 included articles. The strains were most frequently isolated from animal sources (Figure 6A), followed by environmental sources, with additional isolates originating from food and human samples. Across all sources, Salmonella Kentucky and Salmonella Enteritidis were the most prevalent serovars, followed by Salmonella Typhimurium, Salmonella Derby, and Salmonella Poona (Figure 6B). By source of origin, Salmonella Kentucky was most frequently isolated from animal (Figure 7A) and environmental samples (Figure 7B), whereas Salmonella Enteritidis was mainly associated with food (Figure 7C) and human samples (Figure 7E). Notably, none of the reviewed studies employed a comprehensive One Health sampling framework; rather, individual studies focused exclusively on isolated components.

Figure 6

Figure 7

3.2.3 Phenotypic and genotypic antimicrobial resistance characterization

Of the 1,202 total NTS isolates documented, 923 lacked corresponding phenotypic antimicrobial resistance data. Among the 279 isolates with available AMR profiles, 251 (89.9%) demonstrated resistance to at least one antibiotic. Ciprofloxacin, tetracycline, nalidixic acid, and ampicillin were the antibiotics for which resistance was most frequently observed (Figure 8A). In addition, the isolates displayed varying levels of antimicrobial resistance, ranging from resistance to one antibiotic to resistance to 10 antibiotics (Figure 8B). Salmonella Kentucky exhibited the greatest diversity of resistance profiles (Figure 8C). Regarding genotypic data, 309 (25.70%) isolates had information on antimicrobial resistance genes. The most frequently detected genes were those of the aac (66.02%; n = 204) class, associated with aminoglycoside resistance, followed by tet genes (27.83%; n = 86), associated with tetracycline resistance, and qnr genes (23.94%; n = 74), the principal determinants of quinolone resistance. It is important to note that some strains did not exhibit phenotypic resistance but harbored one or two antimicrobial resistance genes, most commonly belonging to the aac or fos classes. Conversely, some strains, particularly Salmonella Kentucky, showed phenotypic resistance to quinolone-class antibiotics without detectable quinolone resistance genes.

Figure 8

3.2.4 Diagnostic methods

Three primary methods were utilized in the included articles for NTS serovar identification: molecular methods, serological methods, and mass spectrometry (specifically MALDI-TOF MS).

Molecular methods were based on PCR assays or sequencing approaches, including whole-genome sequencing (WGS) and targeted sequencing. Serological methods relied on antigen–antibody reactions, such as serotyping using antisera and the Kauffmann–White scheme. Mass spectrometry methods were mainly based on MALDI-TOF MS.

4 Discussion

The identification of Salmonella isolates can be broadly categorized into phenotypic and molecular approaches. In the studies included in this review, phenotypic methods comprised primarily serological techniques (Fagbamila et al., 2017; Mshelbwala et al., 2017; Ahmed et al., 2019; Agbaje et al., 2021; Nikiema et al., 2021a; Nikiema et al., 2021b; Raji et al., 2021), including slide agglutination using specific antisera based on the Kauffmann–White scheme and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) (Dekker et al., 2019). In contrast, molecular approaches included polymerase chain reaction (PCR)-based assays (Mshelbwala et al., 2017; Fuche et al., 2018; Jibril et al., 2020; Kagambèga et al., 2021; Akinola et al., 2022) and DNA sequencing methods (Useh et al., 2016; Sanchez Leon et al., 2017; Aldrich et al., 2019; Post et al., 2019; Jibril et al., 2020; Jibril et al., 2021; Kagambèga et al., 2021; Nikiema et al., 2021b; Raufu et al., 2021; Darboe et al., 2022; Ikhimiukor et al., 2022; Zakaria et al., 2022; Sati et al., 2024; Adetunji et al., 2025; Raufu et al., 2025), including whole-genome sequencing (Váradi et al., 2017). Serological testing remains a widely used and valuable tool for microbial identification, enabling the differentiation of strains within the same species through the detection of specific antigen–antibody interactions. This approach relies on the use of well-characterized antisera targeting known Salmonella serovars. However, the extensive diversity of non-typhoidal Salmonella (NTS) serovars limits the efficiency and resolution of conventional serotyping methods, particularly in settings with limited access to comprehensive antisera panels (Lee et al., 2015). To overcome these limitations, MALDI-TOF MS has emerged as a rapid and reliable alternative for bacterial identification, significantly reducing turnaround time from several days to less than one hour. Although classified as a phenotypic method, MALDI-TOF MS is based on proteomic profiling and has become widely adopted in clinical microbiology laboratories due to its speed, cost-effectiveness, and accuracy (Ren et al., 2025). Nevertheless, its ability to discriminate between closely related Salmonella isolates remains limited without complementary analytical approaches. The choice of Salmonella identification methods in West Africa is largely influenced by contextual constraints. Conventional phenotypic approaches, including culture and serotyping, remain predominant due to their affordability, accessibility, and relatively low technical requirements. However, these methods have limited discriminatory power and may not adequately capture the diversity of non-typhoidal Salmonella (NTS) serovars. In contrast, advanced molecular techniques such as PCR and whole-genome sequencing offer higher-resolution identification and improved epidemiological insights but are still not widely implemented in the region. This is mainly due to barriers such as high operational costs, limited laboratory infrastructure, lack of specialized equipment, and insufficient technical expertise. Nevertheless, increasing investments in laboratory capacity and international collaborations are progressively facilitating the adoption of these advanced tools, highlighting a transition toward more robust surveillance systems in West Africa. Molecular serotyping methods provide a high-throughput and more discriminatory alternative to conventional techniques, thereby strengthening public health surveillance and outbreak response capacities (Yoshida et al., 2016). Amplification-based methods such as PCR are particularly useful for detecting low-abundance pathogens in complex samples, where target bacteria may be present alongside large populations of other microorganisms (Ranieri et al., 2013; Tang et al., 2019). Furthermore, these techniques enable the detection of specific genetic markers associated with virulence and antimicrobial resistance, which cannot be reliably assessed using phenotypic methods alone (Anjum et al., 2011; Farahani et al., 2022). Whole-genome sequencing (WGS) provides the highest resolution for characterizing Salmonella, offering comprehensive insights into the entire genome. Beyond accurate serovar identification, WGS enables the analysis of genetic relationships, evolutionary patterns, and the identification of determinants associated with pathogenicity and antimicrobial resistance (Ferrari et al., 2017; Diep et al., 2019; Deng et al., 2025). The standard WGS workflow typically includes sequence alignment, variant calling, genome annotation, and the calculation of related genomic metrics. More recently, innovative approaches have been developed to further enhance the rapid and accurate detection of Salmonella serovars. These include the integration of MALDI-TOF MS with machine learning algorithms to improve discriminatory power and bacteriophage-based detection systems, which offer promising alternatives for sensitive and specific pathogen identification (Phothaworn et al., 2024; Ren et al., 2025). NTS identification in West Africa, while essential for monitoring circulating invasive strains, faces persistent logistical challenges. Although WGS now allows for the differentiation of specific clades with high invasive potential, this technology remains largely inaccessible for routine use in the subregion. Obstacles include not only the prohibitive cost of reagents and platform maintenance but also energy instability, which compromises the preservation of DNA and enzyme reagents. Consequently, the use of traditional methods such as bacterial culture on selective media (e.g., Salmonella–Shigella or Compass Salmonella agar), coupled with Kauffmann–White serotyping, remains the most viable strategy. This methodological choice ensures continuity of epidemiological surveillance and allows for the collection of locally relevant data, compensating for the lack of molecular platforms while ensuring the detection of key serotypes of public health interest. Across the 28 studies included in this review, a total of 1,202 non-typhoidal Salmonella (NTS) serovar records were collected. The majority of these serovars were isolated from animal sources, particularly poultry, followed by food samples. This distribution is consistent with the well-established role of poultry as a major reservoir of Salmonella. Indeed, salmonellosis outbreaks are frequently associated with chicken products, as poultry can asymptomatically harbor Salmonella in their gastrointestinal tract, with the potential for both horizontal and vertical transmission (Ramatla et al., 2024). Historically, the detection of Salmonella spp. in poultry-derived food products increased significantly during the 1980s (Igbinosa et al., 2023), followed by numerous foodborne disease outbreaks in humans linked to the consumption of contaminated poultry products in the 1990s. In recent decades, factors such as commercialization, globalization, and the expansion of food distribution networks have further amplified the risk, enabling contaminated food products to affect populations across multiple countries simultaneously. This highlights the transboundary nature of foodborne pathogens and the need for coordinated surveillance systems. Several NTS serovars identified in this review are of major public health concern. In particular, Salmonella enterica serovars Enteritidis, Kentucky, and Typhimurium were among the most frequently reported. Notably, S. Typhimurium, S. Enteritidis, and S. Dublin are widely recognized as the serovars most commonly associated with invasive infections (Traore et al., 2024), including bloodstream infections and severe gastroenteritis, especially among children in sub-Saharan Africa (Akinyemi et al., 2023). Salmonella enterica serovar Enteritidis is a foodborne zoonotic pathogen with significant implications for both animal production and human health. It contributes to substantial economic losses in the livestock sector while causing a high burden of morbidity and mortality in humans. Its transmission dynamics are complex and involve multiple interconnected pathways, including animal reservoirs, environmental contamination, and water systems, reflecting a clear One Health interface (Liu et al., 2023). Similarly, Salmonella enterica serovar Typhimurium is one of the most prevalent serotypes associated with human infections and is primarily transmitted via the fecal–oral route. It is frequently detected in retail poultry products, with reported prevalence rates reaching up to 44% in some settings. Infection with this serovar commonly results in acute gastroenteritis, although more severe invasive forms may occur in vulnerable populations (Ren et al., 2024; Wigley, 2024). Across the reviewed literature, a total of 29 Salmonella Kentucky ST198 strains were reported. These isolates exhibited concerning resistance to specific antibiotics, particularly quinolones. All (100%) of these strains were resistant to gentamicin, tetracyclines, and quinolones. Given that quinolones are considered last-resort antibiotics, this represents a significant public health concern, particularly in terms of patient management (Ramatla et al., 2024). S. Kentucky was initially associated with poultry and generally considered antibiotic-susceptible, but it has emerged as a human pathogen, particularly the ST198 clone, following the acquisition and integration of SGI1 (Jiang et al., 2023; Jiang et al., 2024). It is commonly linked to the consumption of contaminated poultry products globally. Since then, this clone has been detected with high prevalence in Africa, the Middle East, and South and Southeast Asia, and has also disseminated to Europe and North America through travel-related infections (Hawkey et al., 2019; Chen et al., 2021). It may acquire resistance readily in response to selective pressure exerted by antibiotic use (Hawkey et al., 2019; Coipan et al., 2020; Mashe et al., 2023). Future research should prioritize the operationalization of the One Health framework through: (i) the design of integrated multisectoral studies combining human, animal, food, and environmental samples; (ii) the gradual implementation of genomic surveillance tools, including whole-genome sequencing, to track transmission routes and antimicrobial resistance; (iii) the establishment of regional data-sharing platforms and laboratory networks to harmonize methodologies and strengthen outbreak response; and (iv) the consideration of environmental and socioeconomic determinants, such as antimicrobial use practices and food distribution systems, to better contextualize transmission risks. Strengthening interdisciplinary collaboration and investing in scalable, context-appropriate technologies will be essential to address current gaps. Promoting a functional One Health strategy in West Africa is therefore not only a scientific priority but also a crucial step in improving public health preparedness and mitigating the spread of antimicrobial-resistant non-typhoidal Salmonella (NTS).

4.1 Limitations

This scoping review has several limitations that should be acknowledged when interpreting the findings. The most important limitation is the substantial geographic surveillance bias within the available literature. More than half of the included studies originated from Nigeria, reflecting the greater availability of surveillance systems, laboratory capacity, and research output in Nigeria compared with many other West African nations. Consequently, the observed distribution of non-typhoidal Salmonella (NTS) serovars, antimicrobial resistance (AMR) patterns, and reported transmission dynamics may disproportionately reflect the epidemiological situation in Nigeria rather than the broader West African region. The limited availability of data from several countries, including those with weak surveillance infrastructure and restricted diagnostic capacity, creates important knowledge gaps and may have resulted in the underrepresentation of locally circulating serovars, resistance determinants, and transmission pathways. Therefore, the regional trends identified in this review should be interpreted cautiously and should not be assumed to be uniformly applicable across all West African settings. In addition, the heterogeneity of study designs, sampling strategies, laboratory methodologies, and reporting practices across the included studies may have affected the comparability of the results. Variations in antimicrobial susceptibility testing methods, serotyping approaches, and genomic characterization techniques could have influenced estimates of AMR prevalence and serovar diversity. Finally, because this review relied on published literature, countries and settings with limited publication output may be underrepresented, further reinforcing existing surveillance and reporting biases. These limitations underscore the urgent need for more geographically representative surveillance systems, harmonized laboratory protocols, and expanded genomic monitoring across West Africa to generate a more accurate understanding of NTS epidemiology and antimicrobial resistance in the region.

5 Conclusion

This scoping review highlights the wide diversity of non-typhoidal Salmonella (NTS) serovars circulating in West Africa, with a predominance of Salmonella Kentucky, Salmonella Enteritidis, and Salmonella Typhimurium, along with a concerning level of multidrug resistance. Despite the increasing use of molecular and advanced diagnostic tools, conventional methods remain predominant due to infrastructural and economic constraints. One of the key findings of this analysis is the limited implementation of integrated One Health approaches. Most studies focus on a single sector—human, animal, or environmental—thereby limiting a comprehensive understanding of NTS transmission dynamics across interconnected systems. Limited access to advanced tools such as whole-genome sequencing further restricts the capacity to conduct higher-resolution intersectoral investigations. These challenges are compounded by insufficient interdisciplinary training and expertise and by regulatory and administrative barriers related to multisectoral research approvals and sample management. Overall, this gap represents a major obstacle to the effectiveness of surveillance and control strategies in the region.

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