Prevalence and antibiotic resistance characteristics of non-typhoidal Salmonella enterica serotypes isolated from food and water consumed by children under five years in Karamoja sub-region of Uganda

Karamoja, a sub-region in North Eastern Uganda, has consistently experienced a high prevalence of diarrhoea and undernutrition among children under five (CUF) for over a decade. Microbiologically unsafe food is believed to be a key factor for the high prevalence of diarrhoea-associated undernutrition CUF in the sub-region, but specific causative agents have largely remained undelineated. This study investigated the prevalence, serotypes, antibiotic resistance (AMR) characteristics, and association between AMR phenotypes and AMR genes (ARGs) among non-typhoidal Salmonella (NTS) enterica serotypes isolated from water and food in the sub-region. Isolates (45) confirmed by invA PCR amplification were PCR-serotyped targeting various serotype-conserved genes and tested for phenotypic AMR against nine antibiotics and for the presence of ARGs using PCR. Overall prevalence of NTS was at 50%, with S. Typhimurium (53%) being the most dominant, followed by S. Infantis (16%), S. Enteritidis (9%), and S. Dublin (4%). Phenotypic resistance was highest for azithromycin (91.1%) followed by ciprofloxacin (31.1%), cefixime (20%), cefotaxime (20%), ceftazidime (15.6%), ceftriaxone (6.7%), cotrimoxazole (6.7%), chloramphenicol (6.7%) and amoxicillin-clavulanic acid (2.2%). The most prevalent ARGs were mefA (95.3%), gyrA (94.9%), parC (92.3%), blaPSE (81.3%), sul1 (66.6%), and sul2 (66.6%) encoding for macrolides, quinolones, beta-lactams, and sulphonamides, respectively. Phenotypic resistance to beta-lactams, chloramphenicol, cotrimoxazole, and ciprofloxacin was strongly correlated with the presence of blaPSE, floR, sul1, and parC, respectively (p < 0.05). This study has revealed that foods and water in Karamoja sub-region are contaminated with antibiotic-resistant NTS enterica serotypes and therefore need remediation.