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

Health authorities were notified of a suspected outbreak of foodborne disease in a hospital in South Africa, where staff and patients reported acute onset of abdominal cramps, diarrhoea, fever, and rigors after eating a chicken pasta meal. The aim of this report is to discuss the use of whole-genome sequencing (WGS) analysis of bacterial isolates to support an epidemiological investigation. An epidemiological investigation led by the Infection Control Manager of the hospital and supported by an outbreak response team was conducted. 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, and WGS data were analysed 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. Forty-nine cases were identified, with stool samples collected from 21 cases, and nontyphoidal Salmonella isolated from 19/21 (90%) of the samples. All isolates were identified as Salmonella enterica serovar Enteritidis and differed from each other by ≤2 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 (OR=15.4, Chi-Square test with Yates correction p-value = 0.02). The epidemiological evidence suggests that the chicken pasta was the likely vehicle of transmission in this outbreak, although the source of Salmonella enterica serovar Enteritidis remains unknown.