Whole-Genome Sequencing assisted outbreak investigation of Salmonella Enteritidis, at a hospital in South Africa, September 2022

Introduction Health authorities were notified of a suspected outbreak of foodborne disease in a hospital in South Africa. Staff and patients reported acute onset of abdominal cramps, diarrhoea, fever and rigors after eating a chicken pasta meal. Aim To report on the use whole-genome sequencing (WGS) analysis of bacterial isolates to support an epidemiological investigation. Methodology Epidemiological investigation of the outbreak was led by the Infection Control Manager of the hospital and supported by an outbreak response team. Standard microbiological procedures were used to process stool samples and culture/identify diarrhoeal pathogens. Bacterial cultures were investigated using WGS performed using Illumina NextSeq technology. WGS data were analyzed using multiple bioinformatics tools, including those available at the Center for Genomic Epidemiology and EnteroBase. Core-genome multilocus sequence typing (cgMLST) was used to investigate the phylogeny of isolates. Results Forty-nine cases were identified. Stool samples were collected from 21 cases and nontyphoidal Salmonella was isolated from 19/21 (90%) of the samples. All isolates were identified as Salmonella enterica serovar Enteritidis. All isolates differed from each other by allele differences on cgMLST, indicating that isolates are highly genetically related. Delays in testing of food retention samples rendered the negative test results of limited value. A case control study was conducted; eating chicken pasta was strongly associated with developing gastroenteritis (Haldane-Anscombe Adjusted Odds Ratio, 15.398) Conclusion The epidemiological evidence suggests that the chicken pasta was the likely vehicle of transmission in this outbreak. The source of Salmonella enterica serovar Enteritidis remains unknown.