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Microb Genom. 2019 Jan;5(1). doi: 10.1099/mgen.0.000248. Epub 2019 Jan 16.

Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame.

Author information

1
1​Gastrointestinal Bacteria Reference Unit, Public Health England, London, UK.
2
2​Field Epidemiology Service, Public Health England, London, UK.
3
3​North West London Health Protection Team, Public Health England, London, UK.
4
4​Public Health Laboratory, Public Health England, London, UK.
5
5​Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK.
6
6​University of Warwick, Warwick, UK.
7
7​School of Medicine, National University of Ireland Galway, Galway, Ireland.
8
8​Bacterial Typing, Statens Serum Institute, Copenhagen, Denmark.

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.

KEYWORDS:

Adjame; England; Salmonella; Wales; surveillance; whole genome sequencing

PMID:
30648934
DOI:
10.1099/mgen.0.000248
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