Identification of multidrug-resistant monophasic Salmonella Typhimurium ST34 and other NTS from animal-environmental origins in South Africa

Non-typhoidal Salmonella (NTS) causes approximately 155 000 deaths annually and poses significant risks to both human and animal health. Antimicrobial resistance (AMR) in NTS is a growing global public health threat. Using a One Health approach, this study investigated NTS in swine, poultry, and wastewater in Gauteng Province, South Africa. From May 2019 to August 2020, 507 samples were collected, including animal faeces (n = 388), hand swabs (n = 104), abattoir and farm run-off (n = 10), and hospital (n = 1) and municipal wastewater (n = 4). Whole genome sequencing of recovered isolates revealed a 2.37% (12/507) NTS prevalence, identifying four serovars: Salmonella Enteritidis sequence type (ST) 11 (n = 3), S. Infantis ST32 (n = 4), S. Irumu ST2026 (n = 2), and multidrug-resistant S. Typhimurium monophasic variant 1,4,[5],12:i:- ST34 (n = 3). The ST34 strains, detected in swine, exhibited ASSuT (ampicillin, streptomycin, sulfamethoxazole, tetracycline) resistance pattern and marked the first detection of ST34 from an animal source in Africa. The strains harboured a novel sopE-phage (AmTI) and SGI-4. Phylogenetic analysis linked these strains to human cases in South Africa and the UK, which could indicate transmission of MDR S. Typhimurium between animals and humans, underscoring the importance of enhanced AMR surveillance using a One Health approach.