Asymptomatic Carriage and Antimicrobial Resistance of Salmonella in Humans and Poultry in Rural Burkina Faso: Phenotypic and Genotypic Profiles and Associated Risk Factors

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Résumé

Food-borne diseases affect nearly 10% of the global population annually, with Salmonella
being a major cause, particularly impacting children, the elderly, and populations in
low- and middle-income countries. This study aimed to assess the prevalence, serotype
distribution, antibiotic resistance profiles, and genetic determinants of resistance and
virulence of Salmonella enterica in humans and poultry in the Nanoro health district. A
community-based cross-sectional study involving humans and poultry was conducted in
the Nanoro health district. Fresh stool samples (human and poultry cloacal/cecal) were
collected, transported under sterile conditions, and processed within two hours using
standard bacteriological methods. Phenotypic antibiotic resistance was determined by the
Kirby–Bauer disk diffusion method, and whole-genome sequencing (Illumina) identified
serotypes, resistance genes, and virulence factors. Logistic regression analyzed associa-
tions between Salmonella carriage and host or environmental factors. Salmonella enterica
carriage was detected in 8.7% of humans and 7.2% of poultry. Human isolates showed
24% resistance to cephalosporins, while poultry isolates showed 36.8% resistance. Re-
sistance genes, including fosA7, qnrB19, and a cryptic aminoglycoside resistance gene,
and virulence genes encoding T3SS-1 and T3SS-2, were detected in both hosts. Logis-
tic regression indicated that residence in Sitaon and Zimidin was associated with ~70%
lower odds of carriage (aOR = 0.3), while individuals aged 11–20 and 51–60 years had
2.8-fold higher odds. Carriage was also 60% higher during the rainy season. These
findings suggest possible cross-transmission of Salmonella between humans and poul-
try and the circulation of resistant, potentially virulent strains in the community. Sea-
sonal and age-related variations highlight environmental and behavioral influences on
asymptomatic carriage. Integrated One Health surveillance and targeted hygiene inter-
ventions are essential to reduce Salmonella transmission and antimicrobial resistance in
rural settings.

Mots-clés

Salmonella enterica; asymptomatic carriage; antimicrobial resistance; poultry and human infections; resistance and virulence genes; risk factors; Burkina Faso