title: Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis.
abstract: Since April 2015, whole genome sequencing (WGS) has been the routine test for Salmonella identification, surveillance and outbreak investigation at the national reference laboratory in England and Wales. In May 2015, an outbreak of Salmonella Enteritidis cases was detected using WGS data and investigated. UK cases were interviewed to obtain a food history and links between suppliers were mapped to produce a food chain network for chicken eggs. The association between the food chain network and the phylogeny was explored using a network comparison approach. Food and environmental samples were taken from premises linked to cases and tested for Salmonella. Within the outbreak single nucleotide polymorphism defined cluster, 136 cases were identified in the UK and 18 in Spain. One isolate from a food containing chicken eggs was within the outbreak cluster. There was a significant association between the chicken egg food chain of UK cases and phylogeny of outbreak isolates. This is the first published Salmonella outbreak to be prospectively detected using WGS. This outbreak in the UK was linked with contemporaneous cases in Spain by WGS. We conclude that UK and Spanish cases were exposed to a common source of Salmonella-contaminated chicken eggs.
authors: Field Epidemiology Services, Public Health England, UK.|University of Liverpool, UK.|NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, UK.
authors: T
authors: T
authors: Inns
authors: Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, UK.
authors: P M
authors: PM
authors: Ashton
authors: Instituto de Salud Carlos III, Laboratorio de Referencia e Investigación en Enfermedades Bacterianas Transmitidas por Agua y Alimentos. Centro Nacional de Microbiología, Madrid, Spain.
authors: S
authors: S
authors: Herrera-Leon
authors: Food Standards Agency, UK.
authors: J
authors: J
authors: Lighthill
authors: Field Epidemiology Services, Public Health England, UK.
authors: S
authors: S
authors: Foulkes
authors: Department of Infectious Disease Epidemiology, Imperial College London, UK.
authors: T
authors: T
authors: Jombart
authors: Field Epidemiology Services, Public Health England, UK.
authors: Y
authors: Y
authors: Rehman
authors: Food Water and Environmental Microbiology Laboratory, Public Health England, UK.
authors: A
authors: A
authors: Fox
authors: NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, UK.|Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, UK.
authors: T
authors: T
authors: Dallman
authors: Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, UK.
authors: E
authors: E
authors: DE Pinna
authors: Health Protection Scotland, Gastrointestinal Disease and Zoonoses, UK.
authors: L
authors: L
authors: Browning
authors: Scottish Microbiology Reference Laboratories, Glasgow, UK.
authors: J E
authors: JE
authors: Coia
authors: Field Epidemiology Services, Public Health England, UK.
authors: O
authors: O
authors: Edeghere
authors: Field Epidemiology Services, Public Health England, UK.|University of Liverpool, UK.|NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, UK.
authors: R
authors: R
authors: Vivancos
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000818:Animals; D002645:Chickens; D002648:Child; D002675:Child, Preschool; D016000:Cluster Analysis; D004196:Disease Outbreaks; D004531:Eggs / Q000382:microbiology; D005260:Female; D005517:Foodborne Diseases / Q000453:epidemiology* / Q000382:microbiology; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007223:Infant; D008297:Male; D008460:Meat / Q000382:microbiology; D008875:Middle Aged; D017720:Molecular Epidemiology; D020641:Polymorphism, Single Nucleotide; D012480:Salmonella Infections / Q000453:epidemiology* / Q000382:microbiology; D012477:Salmonella enteritidis / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D013030:Spain / Q000453:epidemiology; D011795:Surveys and Questionnaires; D006113:United Kingdom / Q000453:epidemiology; D055815:Young Adult
keywords: Epidemiology; outbreak; salmonellosis; traceback; whole genome sequencing