Use of whole-genome sequencing for public health intervention: outbreak investigation of a cluster of cases of salmonella foodborne illness in England, 2016

Background Preventing foodborne outbreaks of gastrointestinal disease is a public health priority; however, outbreak investigations into non-typhoidal Salmonella enterica infections are challenging. Only cases with confirmed microbiological diagnoses are investigated, and links are hard to identify. Microbiological tests that offer greater discrimination between isolates are thus, in theory, attractive public health tools to identify, and interrupt, transmission. Whole-genome sequencing (WGS) was introduced in England in 2016 as part of routine surveillance. Here we describe its usefulness to support public health action. Methods We were alerted to a cluster of isolates of Salmonella enterica subsp enterica serovar Enteritidis (S Enteritidis) that were linked by single nucleotide polymorphism (SNP) comparison to a reference genome to determine genetic relatedness of bacterial isolates after whole-genome sequencing. The isolates (from stool samples) were from 18 individuals living in London in 2016 with gastrointestinal disease. We contacted all cases and undertook a standard questionnaire, and then focused questioning on, and food sampling at, the suspected infectious source, to direct public health intervention, in collaboration with environmental health officers. Findings All 18 cases were adults (age 21–70 years), five of whom were admitted to hospital. From whole-genome sequencing data, nine of the 18 isolates had no SNP differences, and nine had fewer than five SNP differences from these, of which six were identical. We identified an epidemiological link, in all cases, to a food establishment in London. S Enteritidis was subsequently isolated from food samples from this establishment and linked to isolates from the cases through whole-genome sequencing. An enforcement action and notice was served by environmental health officers to the establishment because of breaches in food hygiene, and we notified the Food Standards Agency, the Department for Environment, Food and Rural Affairs, and the Animal and Plant Health Agency. The contaminated food source was successfully removed to prevent further linked cases. Interpretation The introduction of whole-genome sequencing to public health surveillance, despite demanding resources, refines the microbiological data provided to public health practitioners, allowing focused epidemiological investigation on likely linked cases. As illustrated here, this can allow identification of an ongoing source, and action to prevent further transmission. Funding None.