What insights can whole-genome sequencing provide during foodborne disease investigations?
Salmonella enterica serotype Enteritidis (Salmonella Enteritidis) remains a leading cause of foodborne disease outbreaks globally and continues to pose a public health challenge in South Africa. Non-typhoidal Salmonella (NTS) infections account for a substantial proportion of foodborne illnesses worldwide, with the World Health Organization estimating that unsafe food causes approximately 600 million cases annually. The burden is particularly high in the African region, although it is under-reported in the literature.
In South Africa, Salmonella Enteritidis has become the predominant cause of salmonellosis, representing the majority of clinical Salmonella isolates nationally. Infection generally presents with mild gastrointestinal symptoms, but children, older persons, and institutionalised populations are at risk of severe dehydration and life-threatening complications. Identifying outbreak sources is therefore critical to limit transmission and inform prevention strategies.
Whole-genome sequencing (WGS) has increasingly transformed investigations of foodborne disease outbreaks by providing high-resolution characterisation of bacterial pathogens and enabling precise identification of transmission sources. Since 2017, the Centre for Enteric Diseases (CED) at the National Institute for Communicable Diseases (NICD) has used WGS routinely for diarrhoeal disease-associated outbreaks in South Africa, enhancing public health surveillance and response capacity.
In July 2024, a foodborne disease outbreak was reported at a mental healthcare institution in Gauteng Province. Laboratory and epidemiological investigations were conducted to determine the outbreak source and assess the relatedness of isolates. This report presents the full investigation, including laboratory methods, WGS analysis, results, and public health implications.
Materials and Methods
On 30 July 2024, the CED was notified by the provincial surveillance team of a potential foodborne disease outbreak at a mental healthcare institution in Gauteng. Patients presented to a private hospital with gastrointestinal symptoms occurring over a similar timeframe.
Stool specimens or rectal swabs were initially processed at peripheral laboratories using standard microbiological methods. Cultured Salmonella isolates were referred to the CED, where confirmation was performed using standard serotyping techniques according to the White-Kauffmann-Le Minor scheme.
Genomic DNA was extracted using the Invitrogen PureLink Microbiome DNA Purification Kit (Invitrogen, Waltham, Massachusetts, USA). WGS was performed on the Illumina NextSeq 2000, with DNA libraries prepared using the Illumina DNA Prep Kit with a 300–400 bp insert size, followed by 2 × 150 paired-end sequencing runs at approximately 80× coverage.
Results
A line list of 27 symptomatic individuals was provided to the CED, including 21 patients and six staff members. All isolates were confirmed as Salmonella Enteritidis through standard serotyping. Core genome multilocus sequence typing (cgMLST) indicated that all outbreak-associated isolates differed by two alleles or fewer, demonstrating high genetic relatedness.
No antimicrobial resistance genes were detected through WGS, and all isolates were considered susceptible to tested antibiotics.
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