Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame

Marie Anne Chattaway,Elsie Acheampong,Martin Cormican,Anaïs Painset,Bharat Patel,Martin Sergeant,Paul Crook,Victoria Shah,Lesley Larkin,Janice Lo,Eva Litrup,Nastassya Chandra,Peter Lamb

doi:10.1099/mgen.0.000248

Abstract

In 2017, an outbreak of gastroenteritis in England attributed to Salmonella Adjame was detected and investigated. With the introduction of whole genome sequencing (WGS) for microbial typing, methods for comparing international outbreak data require evaluation. A case was defined as a person resident in England with a clinical sample from 1 June 2017 to 27 July 2017 from whom S. Adjame was isolated. Cases were interviewed and exposures analysed. Backward tracing of food provenance was undertaken. WGS was performed on isolates from cases and historical isolates and compared using Public Health England’s SnapperDB high-quality SNP pipeline and Enterobase’s Salmonella core genome multi-locus sequence typing (cgMLST) scheme. In total, 14 cases were identified. The majority were vegetarian, probably of South Asian descent, with a median age of 66.5 years with no recent international travel reported. Cases consumed a range of fresh food products including herbs and spices bought from South Asian grocers. Backward tracing did not identify a common source. WGS typing showed sub-clustering and considerable genetic variation across human samples. cgMLST allele-based analysis was comparable to SNP-derived phylogenetic analysis and clusters were defined using each method. Imported herbs or spices were suspected vehicles. The cases were linked in time and place but WGS showed marked heterogeneity, atypical of a point source Salmonella outbreak. The application of incorporating SNP or allelic differences into the case definition may not always be appropriate. With further validation, cgMLST could be used for international outbreak alerts when WGS analysis is being undertaken to facilitate comparison.

Highlights

Non-typhoidal Salmonella (NTS) causes an estimated 93.8 million illnesses globally each year with the majority of infections attributable to Salmonella enterica subsp. enterica [1]
We describe the epidemiological and microbiological findings of the outbreak investigation and compare the microbial typing data derived from the routine Public Health England (PHE) SNP-based pipeline and those derived from core genome multi-locus sequence typing (cgMLST)
All but one of the cases were considered to be of South Asian descent based on a review of names

Summary

Introduction

Non-typhoidal Salmonella (NTS) causes an estimated 93.8 million illnesses globally each year with the majority of infections attributable to Salmonella enterica subsp. enterica [1]. Non-typhoidal Salmonella (NTS) causes an estimated 93.8 million illnesses globally each year with the majority of infections attributable to Salmonella enterica subsp. In England and Wales, S. enterica serovars Enteritidis and Typhimurium are associated with the majority of NTS outbreaks and sporadic cases [51 % (4391/8691) of NTS isolates reported in 2017, Public Health England (PHE) unpublished data]. Rare serovars of Salmonella cause outbreaks and knowledge of previous likely vehicles of infection can help inform epidemiological investigations. Enterica Serovar Adjame was first isolated from a clinical case from the Cote d’Ivoire and described in 1967 [2] but there have been no published reports regarding human infection or associated sources after this date. S. Adjame is a rare serovar in the UK.

Methods

Results

Discussion

Conclusion