Whole-genome sequencing to investigate two concurrent outbreaks of Salmonella Enteritidis in South Africa, 2018

Abstract

<i>Salmonella enterica</i> serotype Enteritidis (<i>Salmonella</i> Enteritidis) is a major cause of foodborne disease outbreaks worldwide. In 2018, two concurrent outbreaks of <i>Salmonella</i> Enteritidis gastroenteritis in one district of South Africa were investigated. We describe the use of whole-genome sequencing (WGS) analysis of bacterial isolates to assist with the investigation of these outbreaks. Outbreak A affected children (<i>n</i>=27) attending a day-care centre, while outbreak B affected adults (<i>n</i>=16) who ate breakfast at the same restaurant. <i>Salmonella</i> Enteritidis was isolated from stool samples in both outbreaks (four children in outbreak A; 12 restaurant customers and three restaurant food-handlers in outbreak B). In outbreak B, <i>Salmonella</i> Enteritidis was isolated from three food retention samples (raw chicken egg, hollandaise sauce and rocket-herb). Available isolates from both outbreaks (<i>n</i>=13) were investigated using WGS analysis. Sequencing data for isolates were analysed at the EnteroBase web-based platform and included core-genome multi-locus sequence typing (cgMLST). Isolates with epidemiological links to the restaurant (<i>n</i>=10) and day-care centre (<i>n</i>=3), were shown by cgMLST to be highly genetically related, with no more than five allele differences when comparing one isolate against another. On food history, eggs and hollandaise sauce were the common food items consumed by ill restaurant customers. Unfortunately, <i>Salmonella</i> Enteritidis isolated from the egg and hollandaise sauce were not available for WGS analysis. Our investigation concluded that the two concurrent outbreaks were caused by a highly related strain of <i>Salmonella</i> Enteritidis, suggesting the possibility of a common contaminated food source, of which contaminated eggs are strongly implicated.