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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.

In southern Africa, clade 2.3.4.4B H5N1 high pathogenicity avian influenza (HPAI) was first detected in South African (SA) poultry in April 2021, followed by outbreaks in poultry or wild birds in Lesotho and Botswana. In this study, the complete or partial genomes of 117 viruses from the SA outbreaks in 2021–2022 were analyzed to decipher the sub-regional spread of the disease. Our analysis showed that seven H5N1 sub-genotypes were associated with the initial outbreaks, but by late 2022 only two sub-genotypes still circulated. Furthermore, SA poultry was not the source of Lesotho’s outbreaks, and the latter was most likely an introduction from wild birds. Similarly, SA and Botswana’s outbreaks in 2021 were unrelated, but viruses of Botswana’s unique sub-genotype were introduced into SA later in 2022 causing an outbreak in ostriches. At least 83% of SA’s commercial poultry cases in 2021–2022 were point introductions from wild birds. Like H5N8 HPAI in 2017–2018, a coastal seabird-restricted sub-lineage of H5N1 viruses emerged in the Western Cape province in 2021 and spread to Namibia, causing mortalities in Cape Cormorants. In SA ~24,000 of this endangered species died, and the loss of >300 endangered African penguins further threatens biodiversity.

Migratory birds carried clade 2.3.4.4B H5Nx highly pathogenic avian influenza (HPAI) viruses to South Africa in 2017, 2018 and 2021, where the Gauteng Province is a high-risk zone for virus introduction. Here, we combined environmental faecal sampling with sensitive rRT-PCR methods and direct Ion Torrent sequencing to survey wild populations between February and May 2022. An overall IAV incidence of 42.92% (100/231) in water bird faecal swab pools or swabs from moribund or dead European White Storks (Ciconia ciconia) was detected. In total, 7% of the IAV-positive pools tested H5-positive, with clade 2.3.4.4B H5N1 HPAI confirmed in the storks; 10% of the IAV-positive samples were identified as H9N2, and five complete H9N2 genomes were phylogenetically closely related to a local 2021 wild duck H9N2 virus, recent Eurasian LPAI viruses or those detected in commercial ostriches in the Western and Eastern Cape Provinces since 2018. H3N1, H4N2, H5N2 and H8Nx subtypes were also identified. Targeted surveillance of wild birds using environmental faecal sampling can thus be effectively applied under sub-Saharan African conditions, but region-specific studies should first be used to identify peak prevalence times which, in southern Africa, is linked to the peak rainfall period, when ducks are reproductively active.