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Resistance and virulence determinants of faecal Salmonella spp. isolated from slaughter animals in Benin



Salmonella spp. are one of the leading foodborne pathogens worldwide naturally found in the intestines of many animals. People that are in direct contact with the infected animals or their cages may become ill. The aim of this study was to determine the prevalence, antibiogram and virulence genes associated with Salmonella serovars from fecal samples of animals intended for consumption in Southern Benin.


Out of a total of 406 samples, 2.46% were positive. The isolates identified were multidrug-resistant Salmonella spp. to penicillins, first generation cephalosporins and some aminoglycosides. All Salmonella isolates produced invA gene of 284 bp, fimA of 85 bp and stn of 260 bp. The spvC gene (571 bp) was present in 10% of the isolates whereas the spvR gene (310 bp) was found in 20% of the isolates. The control strain possessed all the tested genes. The invA gene implies that strains are able to invade epithelial cells. The fimA and stn genes present in all isolates show that they are capable of causing gastrointestinal illness in humans. The presence of spvC and spvR genes suggests the possibility of these strains to produce toxins.


Salmonella is a genus of rod-shaped Gram-negative bacteria of Enterobacteriaceae family. Salmonella are common causes of human foodborne outbreaks in the world [1]. Every year, thousands of cases of salmonellosis-related illness and death are reported worldwide [2]. Poor hygiene standards favor the spread of Salmonella spp. [3]. Different serovars of Salmonella enterica subspecies enterica are potentially zoonotic pathogens. Different animal species, have been detected as carriers of this pathogenic agent [4]. More than 2610 S. enterica serovars have been recognized worldwide, being major causative agents of diseases in humans and animals [5]. Non-typhoid Salmonella is most often transmitted to humans through contaminated food [6].

Most cases of salmonellosis in humans are sporadic. In principle, livestock can be contaminated and therefore pose a risk to humans. The problem of the contamination of the farms is thus a concern to take into account to stop the spread of the germ. Consumption of raw or undercooked products and out-of-home catering are known risk factors, especially for Salmonella infections [7]. The importance of foodborne illness cannot be really estimated, but is measured in millions of annual cases [8]. Molecular characteristics of Salmonella in the animal population in Benin are poorly known. The present study is therefore a contribution to the knowledge of the real health risks and the exact prevalence of Salmonella strains of animal origin circulating in southern Benin.

Main text


Area of study

The study was conducted in southern Benin, between 6°25′N and 7°30′N and covering an area of 17,109 km2. The average annual temperature is 28 °C, and the humidity varies between 69 and 97% [9]. Phytogeographically, southern Benin is subdivided into four phytogeographic districts: Coastal, Pobè, Ouémé Valley and Plateau [10].

Fecal carriage of Salmonella spp. in farms and markets for slaughter meat

The collection of animal faeces, namely poultry, sheep and pigs for the search for Salmonella was conducted in the cities of Allada, Abomey-Calavi, Cotonou, Porto-Novo, Adjarra and Cocotomey characterized by the strong presence of breeders and large markets. Additional file 1: Figure S1 shows the cities covered by the study.

Period of study

The study was conducted from May to September 2018 on a sample of thirty breeding farms and nine markets. Breeding and markets selection was based on the willingness of farm owners and poultry retailers to cooperate. One visit per farm and per market was conducted. The different collections were made very early in the morning.

Collection of samples

Faecal samples from the available various animals in farms were collected in sterile pots using sterile swabs. The same operation was carried out in the markets. The samples were sent to the Research Unit in Applied Microbiology and Pharmacology of natural substances of the University of Abomey-Calavi for the different bacteriological analysis. The molecular identification was done at the Faculty of Arts and Sciences (University of Balamand, Lebanon) and the Laboratory of Livestock Management (Parakou, Benin).

Bacteriological analysis

The bacteriological analysis was conducted according to the current AFNOR standard (NF U: 47–100). Twenty-five grams of each sample were pre-enriched in 225 ml of buffered peptone water and incubated for 18 h at 37 °C. Pre-enrichment medium (0.1 ml) was then inoculated in 10 ml of selenite cystine broth for 24 h. Petri-dishes containing xylose lysine decarboxylase medium were then inoculated. Culture media were incubated at 37 °C for 24 h. Sub-cultures were done after 24 h in order to have pure colonies. After incubation at 37 °C for 24 h, the characteristic colonies of Salmonella spp. were considered. The urea test was performed and the colonies with this negative character were confirmed from biochemical criteria. Antibiotic susceptibility testing and molecular identification was performed for the strains identified by API20E Gallery.

Salmonella phenotypic susceptibility

An overnight bacterial pre-culture was diluted to obtain a turbidity of 0.5 McFarland (in sterile distilled water). Kirby Bauer techniques were used to perform the susceptibility testing [11]. Antibiotics of different families were chosen for the resistance pattern of the isolates: imipenem, cefotaxim, cefalotin, cefoxitin, ceftriaxone, amikacin, trimetoprim sulfamethoxazole, tobramycin, colistin, ciprofloxacin, gentamicin, nalidixic acid, chloramphenicol, amoxicillin, augmentin and fosfomicin. Salmonella Typhimurium ATCC 14028 was tested for quality assurance. All tests were performed in triplicates.

Molecular detection of virulence-associated genes

Isolates of DNA were extracted using the Qiagen blue extraction kit. The isolates were tested for different virulent genes using PCR with five sets of specific primer pairs. Several quantities of the mix were prepared (Additional file 1: Table S1).

The genes of virulence that were targeted for amplification by PCR were invA, spvR, spvC, fimA and stn (Additional file 1: Table S2).

The amplification of invA gene was carried out using the method described by Kumar et al. [12]. The amplification of spvR gene was performed using a temperature of 57 °C for 30 s [13]. fimA gene fragment was amplified at a temperature of 56 °C with extension for 30 s. spvC gene fragment was amplified at a temperature of 63 °C for 60 s. stn gene amplification was carried out at 55 °C. The amplification products were separated by 2% agarose gel electrophoresis with 5 μg/ml red gel and a 100 bp DNA ladder as a molecular weight marker. The migration was carried out at a scale of 80 V/cm for 25 min. The amplification bands were visualized and photographed under ultraviolet light (UV).

Statistical data processing

The data collected was coded and analyzed using Graph Pad prism 7 software.


Sample collection

A total of 406 samples of slaughter animal faeces were collected. Figure 1 shows the different categories of animals included in the collection.

Fig. 1
figure 1

Identification of Salmonella spp. and resistance profile

Chicken samples were the only ones collected in the markets. A large panel of animals was obtained at the farm level. The colonies obtained after culture gave rise to the suspicion of the presence of Salmonella strains, especially from chickens and sheep faeces.

Chicken faeces were the most contaminated with Salmonella spp. (Fig. 1). Additional file 1: Figure S2 shows the appearance of a faecal sample inoculated on XLD agar.

The colonies characterize Salmonella colonies on this selective medium. The isolates were then purified and identified by API20E Gallery. The prevalence of Salmonella isolated from faeces of slaughter animals was 2.46% during the period from May to September 2018.

Susceptibility test of Salmonella strains

Figure 1 shows the resistance profile of Salmonella spp. identified. Strains were resistant to all penicillins, aminoglycosides and to first and second generation cephalosporins. 10% of the strains were resistant to fluoroquinolones. Additional file 1: Figure S3 shows inhibition zone of antibiotics on isolated Salmonella species. Salmonella has natural resistance to generation one and two of cephalosporins. Aminoglycosides were tested only as reference and not meant for clinical treatment since susceptibility does not reflect in vivo only in vitro activity [14]. Additional file 1: Table S3 shows the antibiotic susceptibility patterns (%) of isolates strains of Salmonella spp.

Molecular identification

All Salmonella isolates were positive for the presence of invA genes (284 bp), fimA (85 bp) and stn (260 bp). The spvC gene was present in 10% and spvR gene (310 bp) in 20% of the isolates. The reference strain was positive for all genes and served as control. Table 1 shows the genes isolated from each isolate of Salmonella spp.

Table 1 Virulence genes identified

Salmonella strain P19 found in faeces of local hens sold on the market was the only with all the virulences genes. Figure 2 shows the agarose gels after PCR.

Fig. 2
figure 2

Agarose gels after PCR. gel. a invA genes (284 bp), b spvR gene (310 bp), c spvC (571 bp), d fimA (85 bp), e stn


The study carried out revealed the prevalence of virulence genes of circulating strains in Southern Benin. It should be noted that Salmonella are mostly used as markers of biological risk [15]. From the results obtained, a prevalence of 2.46% Salmonella spp. was isolated from market poultry faeces and from farm sheep. This prevalence is low compared to 20% of René et al. [16] in Abidjan and 3.6% found by Barilli et al. [17] in Northern Italy. However, in the studies mentioned, only pigs and cattle were considered respectively. The low prevalence found in the present study can be attributed to climate conditions. Indeed, sample collection was made in dry season characterized by humidity absence. The antimicrobial resistance profile showed resistance of all strains to penicillins, to first and second generation cephalosporins, to aminoglycosides and partially to fluoroquinolones. These results are contradictory to those of Dong et al. [18] which revealed a sensitivity of Salmonella strains to penicillins. Other studies have also reported the problem of multiresistance of Salmonella spp. [19]. The importance of Salmonella spp. as potentially dangerous bacteria can be influenced by both multidrug resistance and presence of virulence genes. Salmonella enterica has several pathogenicity islands in its genome, which are genetic elements that harbor genes associated with virulence [20]. The results obtained after PCR confirmed the presence of invA, spvR, spvC, fimA and stn genes. The presence of invA in all isolates proves that they have a potentially invasive power. Chaudhary et al. [21] reported similar results. Oliveira et al. [22] reported that the search for invA, specific for Salmonella spp. significantly reduces the number of false negatives that occur in laboratory diagnostics. The amplification of invA is currently recognized as international standard for the detection of Salmonella [23]. The spvR gene present in 20% of the strains, gives them capacity to cause systemic infections. These results are consistent with those of Chaudhary et al. [21] and Araque [24].

The spvC gene was present in 10% of the isolates. This gene is able to inhibit the activation of macrophages and initiate their apoptosis [25]. The results obtained are similar to those of Bolton et al. [26]. On the other hand, Chaudhary et al. [21] reported the total absence of this gene in all isolates. This gene is therefore not systematically found in the Salmonella genome but is of paramount importance when present. Kryzanowski et al. [27] found a low rate of Salmonella strains possessing spvC gene, suggesting his particularity in the virulence of Salmonella. The rarity of spv genes in the Salmonella genome has also been demonstrated in other studies, which have revealed that they are responsible for the systemic infection and multidrug resistance in humans and animals [28]. They are also involved in intracellular bacterial proliferation [29]. The search for the presence of spv genes can increase the possibility of Salmonella strains to be of significant clinical interest [30]. As for fimA gene, its presence indicates the presence of fimbriae, important factor for Salmonella to adhere to epithelial cells. This result is similar to those of Boriello et al. [31]. Similar to the work of Barilli et al. [14], the stn gene was present in all isolates. Nakano et al. [32] revealed that stn is suspected to contribute to enterotoxigenic potency.


The presence of multidrug resistant Salmonella spp. in the faeces of animals is of major concern and the presence of virulence genes confirms the possible pathogenicity of these strains. The present study is therefore of paramount importance in the surveillance of salmonellosis.


Sequencing of Salmonella genome is not possible in Benin.

Availability of data and materials

All data generated or analysed during this study is included in this published article and Additional file.


  1. Alvarez AM. Integrated approaches for detection of plant pathogenic bacteria and diagnosis of bacterial diseases. Ann Rev Phytopathol. 2004;42:339–66.

    Article  CAS  Google Scholar 

  2. Hung YT, Lay CJ, Wang CL, Koo M. Characteristics of nontyphoidal gastroenteritis in Taiwanese children: a 9-year period retrospective medical record review. J Infect Public Health 2017;10:518–21.

    Article  PubMed  Google Scholar 

  3. Das S, Singh S, McClelland M, Forst S, Gyaneshwar P. Characterization of an acid-inducible sulfatase in Salmonella enteric Serovar Typhimurium. Appl Environ Microbiol. 2013;79:03707–12.

    Article  Google Scholar 

  4. Martelli F, Davies RH. Review host adapted serotypes of Salmonella enterica. Salmonella serovars isolated from table eggs: an overview. Food Res Int. 2012;45:745–54.

    Article  Google Scholar 

  5. Guibourdenche M, Roggentin P, Mikoleit M, Fields PI, Bockemühl J, Grimont PAD, Weill FX. Supplement 2003–2007 (No. 47) to the White-Kauffmann-Le Minor scheme. Res Microbiol. 2010;161:26–9.

    Article  Google Scholar 

  6. De Knegt LV, Pires SM, Hald T. Attributing foodborne salmonellosis in humans to animal reservoirs in the European Union using a multi-country stochastic model. Epidemiol Infect. 2015;143:1175–86.

    Article  Google Scholar 

  7. Hennessy TW, Cheng LH, Kassenborg H, Ahuja SD, Mohle-Boetani J, Marcus R, Shiferaw B, Angulo FJ. Egg consumption is the principal risk factor forsporadic Salmonella serotype heidelberg infections: a case–control study in foodnetsites. Clin Infect Dis. 2004;38(SUPPL. 3):S237–43.

    Article  Google Scholar 

  8. Flint JA, Van Duynhoven YT, Angulo FJ, DeLong SM, Braun P, Kirk M, Scallan E, Fitzgerald M, Adak GK, Sockett P, Ellis A, Hall G, Gargouri N, Walke H, Braam P. Estimating the burden of acute gastroenteritis, foodborne disease, and pathogens commonly transmitted by food: an international review. Clin Infect Dis. 2005;41:698–704.

    Article  Google Scholar 

  9. Dougnon TV, Déguénon E, Fah L, Lègba B, Hounmanou YMG, Agbankpè J, Amadou A, Koudokpon H, Fabiyi K, Aniambossou A, Assogba P, Hounsa E, de Souza M, Avlessi F, Dougnon TJ, Gbaguidi F, Boko M, Bankolé HS, Baba-Moussa L. Traditional treatment of human and animal salmonellosis in Southern Benin: knowledge of farmers and traditherapists. Vet World. 2017;10(6):580–92.

    Article  CAS  Google Scholar 

  10. Yedomonhan H, Adomou AC, Aguessy M, Bossou FG. Evaluation des caractéristiques ethnobotaniques et structurales de Nesogordonia kabingaensis (K. Schum.) Capuron ex R. Germ. (Sterculiaceae) dans la forêt sacrée d’Ewè au Bénin en vue de la définition des stratégies de sa conservation. Int J Biol Chem Sci. 2017;11(5):2481–94.

    Article  Google Scholar 

  11. Déguénon E, Atchade P, Avocèfohoun A, Jerrold A, Mariama N, Dougnon V, Baba-Moussa L, Jacques D. Exploration of antibacterial and chemical potential of Corchorus olitorus Linn: a vegetable used in Beninese traditional pharmacopoeia. Int J Biosci. 2018;13(4):427–36.

    Google Scholar 

  12. Kumar V, Mohanty S, Kumar A. Effect of community-based behavior change management on neonatal mortality in Shivgarh, Uttar Pradesh, India: a cluster-randomised controlled trial. Lancet. 2008;372(9644):1151–62.

    Article  PubMed  Google Scholar 

  13. Pasmans F, Van Immerseel F, Heyndrickx M. Host adaptation of pigeon isolates Salmonella enterica subsp. Enterica Serovar Typhimurium variant Copenhagen phage type 99 is associated with enhanced macrophage cytotoxicity. Infect Immun. 2003;71(10):6068–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Marchese A, Esposito S, Barbieri R, Bassetti M, Debbia E. Does the adoption of EUCAST susceptibility breakpoints affect the selection of antimicrobials to treat acute community-acquired respiratory tract infections? BMC Infect Dis. 2012;12(1):181.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Van Cauteren D, Le Strat Y, Sommen C, Bruyand M, Tourdjman M, Da Silva NJ, Couturier E, Fournet N, de Valk H, Desenclos JC. Estimated annual numbers of foodborne pathogen associated illnesses, hospitalizations, and deaths, France, 2008–2013. Emerg Infect Dis. 2017;23(9):1486–92.

    Article  Google Scholar 

  16. René YK, Julien CK, Souleymane C, Bertin TK, Bernadette GG, Roméo GK, Felix YH, Joseph DA. Prevalence of Salmonella strains in cattle breeding in the district of Abidjan (Côte d’Ivoire). Int J Curr Microbiol Appl Sci. 2017;6(3):1154–62.

    Article  Google Scholar 

  17. Barilli E, Bacci C, Villa ZS, Merialdi G, D’Incau M, Brindani F, Vismarra A. Antimicrobial resistance, biofilm synthesis and virulence genes in Salmonella isolated from pigs bred on intensive farms. Ital J Food Saf. 2018;7:7223.

    PubMed  PubMed Central  Google Scholar 

  18. Gad AK, Abo-Shama UH, Harclerode KH, Fakhr M. Prevalence, serotyping, molecular typing, and antimicrobial resistance of Salmonella isolated from conventional and organic retail ground poultry. Front Microbiol. 2018;9: 2653.

    Article  Google Scholar 

  19. Yang B, Qu D, Zhang X, Shen J, Cui S. Prevalence and characterization of Salmonella serovars in retail meats of marketplace in Shaanxi, China. Int J Food Microbiol. 2010;141:63–72.

    Article  CAS  Google Scholar 

  20. Sabbagh SC, Forest CG, Lepage C, Leclerc JM, Daigle F. So similar, yet so different: uncovering distinctive features in the genomes of Salmonella enterica serovars Typhimurium and Typhi. FEMS Microbiol Lett. 2010;305(1):1–13.

    Article  CAS  Google Scholar 

  21. Chaudhary JH, Nayak JB, Brahmbhatt MN, Makwana PP. Virulence genes detection of Salmonella serovars isolated from pork and slaughterhouse environment in Ahmedabad, Gujarat. Vet World. 2015;8:121–24.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Oliveira SD, Rodenbusch CR, Ce MC, Rocha SLS, Canal CW. Evaluation of selective and non-selective enrichment PCR. Lett Appl Microbiol. 2003;36(4):217–21.

    Article  CAS  Google Scholar 

  23. Yanestria SM, Rahmaniar RP, Wibisono FJ, Effendi MH (2019) Detection of invA gene of Salmonella from milkfish (Chanos chanos) at Sidoarjo wet fish market, Indonesia, using polymerase chain reaction technique. Vet World. 12(1):170–75.

    Article  Google Scholar 

  24. Araque M. Non typhoid Salmonella gastroenteritis in pediatric patients from urban areas in the city of Mérida. J Infect Dev Ctries: Venezuela; 2009.

    Google Scholar 

  25. Guiney DG, Fierer J. The role of the spv genes in Salmonella pathogenesis. Front Microbiol. 2011;2:129.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Bolton DJ, O‘Neill CJ, Fanning S. A preliminary study of Salmonella, verocytotoxigenic Escherichia coli/Escherichia coli O157 and Campylobacter on four mixed farms. Zoonoses Pub Health. 2011.

    Article  Google Scholar 

  27. Kryzanowski F, Zappelini L, Martone-Rocha S, Dropa M, Matté MH, Nacache F, Razzolini MTP. Quantification and characterization of Salmonella spp. isolates in sewage sludge with potential usage in agriculture. BMC Microbiol. 2014;14:263.

    Article  Google Scholar 

  28. Chiu CH, Su LH, Chu CH, Wang MH, Yeh CM, Weill FX, Chu C. Detection of multidrug-resistant Salmonella enterica serovar Typhimurium phage types DT102, DT104 and U302 by multiplex PCR. J Clin Microbiol. 2006;10:2354–8.

    Article  Google Scholar 

  29. Kurita AI, Gotoh H, Eguchi M, Okada N, Matsuura S, Matsui H, Danbara H, Kikuchi Y. Intracellular expression of the Salmonella plasmid virulence protein, SPVB, causes apoptotic cell death ineukaryotic cells. Microb Pathog. 2003;35:43–8.

    Article  CAS  Google Scholar 

  30. Gebreyes WA, Thakur S, Dorr P, Tadesse DA, Post K, Wolf L. Occurrence of spvA virulence gene and clinical significance for multidrug-resistant Salmonella strains. J Clin Microbiol. 2009;10:777–80.

    Article  Google Scholar 

  31. Boriello G, Lucibelli MG, Pesciaroli M, Curallo MR, Graziani C, Ammendola S, Battistoni A, Ercolini D, Pasquali P, Galiero G. Diversity of Salmonella spp. serovars isolated from the intestines of water buffalo calves with gastroenteritis. BMC Vet Res. 2012;8:201.

    Article  Google Scholar 

  32. Nakano M, Yamasaki E, Ichinose A, Shimohata T, Takahashi A, Akada J, Nakamura K, Moss J, Hirayama T, Kurazono H. Salmonella enterotoxin (Stn) regulates membrane composition and integrity. Dis Model Mech. 2012;5:515–21.

    Article  CAS  Google Scholar 

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Authors thank the staff of the Laboratory of Veterinary Diagnosis and Serosurveillance of Parakou (LADISERO/Benin), Ministry of Agriculture, Livestock and Fisheries (Benin) for their support: Rachida ADJIN, Ghislaine AKPO and Rogatien TOHOZIN. They also express special thank to Inqaba Biotec West Africa Ltd through M. Lukman Abiodun AROWORAMIMO.

Permissions required to obtain the samples

Authors received written approval from livestock managers prior to collecting animal faeces samples. It should be noted that before the visit of the farms, the study protocol was approved by the Directorate of Livestock of Benin, Ministry of Agriculture and Livestock.


The authors are very grateful to The World Academy of Sciences (TWAS) and the United Nations Educational, Scientific and Cultural Organization (UNESCO). These two institutions have made this research possible through research funding allocated to the research team under the number 487RG/BIO/AF/AC_G-FR3240293303. They have reviewed the research protocol and validated the design of the study and collection, analysis, and interpretation of data. The authors are also grateful to The TWAS Young Affiliates Network (TYAN) that supported the cooperation with Lebanon through the TYAN Collaborative Grant Award F.R. 3240300824. The TWAS Young Affiliates Network (TYAN) through its Executive Commitee has reviewed the research protocol and improved its implementation.

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ED, VD, EL, NM, JA, FD, LB-M and JD wrote the protocol. VD got the funding. ED, VD, NM, JA and RA-M processed the samples. VD did the statistical analyses. VD, ED and NM wrote the draft of the manuscript. VD, RA-M, JD and LB-M reviewed the manuscript. All authors read and approved the final manuscript.

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Correspondence to Victorien Dougnon.

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Additional file

Additional file 1: Figure S1.

Map of Southern Benin showing cities covered by the study. Figure S2. Appearance of Salmonella strains on XLD medium. Figure S3. Inhibition zones of different antibiotics on isolated strains of Salmonella spp. Table S1. PCR Reaction Medium. Table S2. Resistance genes. Table S3. Resistance profile of Salmonella spp. strains against antibiotics.

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Deguenon, E., Dougnon, V., Lozes, E. et al. Resistance and virulence determinants of faecal Salmonella spp. isolated from slaughter animals in Benin. BMC Res Notes 12, 317 (2019).

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