Laboratory Epidemiology of Salmonella Infections and Multi-Drug Resistance Profiles in Nigeria: Barriers, Challenges and Proposed Solutions

Abstract Background National surveillance data on Salmonella antimicrobial resistance (AMR) and associated laboratory challenges are limited. There is a critical need to identify and address the barriers and challenges to strengthen the national AMR surveillance and policy guide targeted interventions for Salmonella infections in different geographical areas. We investigated multi-laboratory culture records to quantify AMR profiles for Salmonella infections, diagnostic gaps, and challenges in Nigeria. Methods Using a retrospective study, we analysed a total of 84,548 culture results from 26,630 patients across 25 public laboratories participated in the AMR surveillance report from Nigeria. Salmonella species and stool culture positivity rates were compared throughout the 3 years period. Stool sampling gaps were quantified and Salmonella species AMR for key antibiotic classes were assessed. Chi-square test and Wald risk ratios (RR) were used for statistical analysis, a p-value of <0.05 was considered statistically significant. Results Out of 84,548 culture results, a total of 621 Salmonella species were isolated with Salmonella typhi being the most commonly reported species. Stool samples represented only 3% of all collected specimens, yet Salmonella species culture positivity escalated from 64% to 97% (2016 to 2017; RR 1.51, 95% CI 1.37–1.65, p<0.001 ). AMR remained entrenched: trimethoprim– sulfamethoxazole ≥90%, fluoroquinolones ≥69%, and nalidixic acid 91%; cephalosporin resistance climbed from 60% to 88%. We identified a limited stool collection compared to other samples, which impacted identification of Salmonella infections in an endemic area like Nigeria. The key barriers were limited laboratory data integration and lack of One Health surveillance which amplified Salmonella infections AMR threat. Conclusion Limited stool culture and escalating multi-drug resistance jeopardise the empirical therapy for Salmonella infections. Our study offers immediate, scalable interventions to strengthen One-Health Salmonella infections AMR control in Nigeria. Highlights Exceptionally high Salmonella positivity rate in underutilized stool samples. >75% resistance to core antibiotics, fluoroquinolones and cephalosporins threatens empirical Salmonella infections treatment. Limited species-level reporting on Salmonella cultures and low One Health Salmonella surveillance. Novel framework links microbiological gaps to targeted antimicrobial resistance (AMR) containment strategies for Salmonella infections. Significant contribution This work provides a rare, multi-site analysis of Salmonella diagnostic patterns, resistance profiles, and laboratory performance, revealing critical microbiological gaps and underutilized diagnostics potential. It contributes a novel, evidence-driven recommendations framework that integrates species-level data, AMR surveillance, and stewardship strategies, advancing precision microbiology for Salmonella infection control in resource-limited settings. Graphical abstract