Incidence and antimicrobial resistance of non-typhoidal Salmonella enterica in stool samples from children under five in peri-urban Ouagadougou, Burkina Faso

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Résumé

Abstract
Background: Non-typhoidal Salmonella (NTS) causes significant illness worldwide, particularly in sub-Saharan Africa. Poor sanitation, limited healthcare, and rising antimicrobial resistance (AMR) worsen its impact on children under five. This study estimated the incidence and described AMR patterns of NTS among children under five in peri-urban Ouagadougou, Burkina Faso.

Methods: A 12-month longitudinal cohort (ShigaPlexIM baseline study) was conducted in peri-urban Ouagadougou, Burkina Faso. Between December 2020 and March 2021, 750 children under five were enrolled and followed individually for 12 months, with study activities spanning 16 months in total. Stool samples were collected during diarrheal episodes and scheduled visits. Salmonella spp. was identified by stool culture, and antimicrobial susceptibility testing (AST) was performed using the Kirby-Bauer disc diffusion method per CLSI 2020 guidelines. Incidence rates were calculated using survival analysis over child-months of follow-up.

Results: Of 750 children enrolled, 680 (90.7%) completed follow-up, contributing 7,992.9 child-months. Salmonella was isolated from 97 of 2,401 (4.0%) stool samples. After excluding 33 isolates (29 prevalent cases and 4 typhoidal cases), 64 incident NTS cases were identified, resulting in an incidence rate of 8.0 per 1,000 child-months (95% CI: 6.3-10.2). The highest incidence was observed among children aged 12-23 months (10.3, 95% CI: 6.7-15.6) and in males (8.7, 95% CI: 6.3-12.1); however, sex differences were not significant (IRR = 0.75, 95% CI: 0.49-1.15, p = 0.184). Incidence in diarrheal stools was 43.7 per 1,000 child-months (95% CI: 23.5-81.2). All isolates were fully susceptible to imipenem, ciprofloxacin, ceftriaxone, and aztreonam. High susceptibility (≥ 96.7%) was observed for ceftazidime, cefotaxime, chloramphenicol, cefepime, and tobramycin. Moderate resistance was found for trimethoprim-sulfamethoxazole (4.4%), ampicillin (5.6%), nalidixic acid (5.6%), and streptomycin (6.7%). Resistance to tetracycline was highest at 74.4%. Multidrug resistance (MDR) was detected in 4.4% of isolates.

Conclusion: This study demonstrates a substantial burden of NTS infections in children under five in peri-urban Burkina Faso. Although MDR prevalence was low, high tetracycline resistance indicates widespread circulation of resistant strains. Continuous AMR surveillance is essential to guide treatment and preserve antibiotic efficacy.

Keywords: Salmonella enterica; Salmonella infections, Non-Typhoidal; Antimicrobial susceptibility tests; Child, preschool; Diarrhea; Drug resistance, bacterial; Incidence; Infant, suburban health, burkina faso.

Mots-clés

Salmonella enterica; Salmonella infections, Non-Typhoidal; Antimicrobial susceptibility tests; Child, preschool; Diarrhea; Drug resistance, bacterial; Incidence; Infant, suburban health, burkina faso.