title: Phylogenetic structure of EuropeanSalmonellaEnteritidis outbreak correlates with national and international egg distribution network.
abstract: Outbreaks ofSalmonellaEnteritidis have long been associated with contaminated poultry and eggs. In the summer of 2014 a large multi-national outbreak ofSalmonellaEnteritidis phage type 14b occurred with over 350 cases reported in the United Kingdom, Germany, Austria, France and Luxembourg. Egg supply network investigation and microbiological sampling identified the source to be a Bavarian egg producer. As part of the international investigation into the outbreak, over 400 isolates were sequenced including isolates from cases, implicated UK premises and eggs from the suspected source producer. We were able to show a clear statistical correlation between the topology of the UK egg distribution network and the phylogenetic network of outbreak isolates. This correlation can most plausibly be explained by different parts of the egg distribution network being supplied by eggs solely from independent premises of the Bavarian egg producer (Company X). Microbiological sampling from the source premises, traceback information and information on the interventions carried out at the egg production premises all supported this conclusion. The level of insight into the outbreak epidemiology provided by whole-genome sequencing (WGS) would not have been possible using traditional microbial typing methods.
authors.affiliation: 1​Public Health England, UK.
authors.forename: Tim
authors.initials: T
authors.lastname: Dallman
authors.affiliation: 1​Public Health England, UK.
authors.forename: Thomas
authors.initials: T
authors.lastname: Inns
authors.affiliation: 2​Department of Infectious Disease Epidemiology, Imperial College, London, UK.
authors.forename: Thibaut
authors.initials: T
authors.lastname: Jombart
authors.affiliation: 1​Public Health England, UK.
authors.forename: Philip
authors.initials: P
authors.lastname: Ashton
authors.affiliation: 3​Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Loman
authors.affiliation: 1​Public Health England, UK.
authors.forename: Carol
authors.initials: C
authors.lastname: Chatt
authors.affiliation: 4​Bavarian Health and Food Safety Authority, Oberschleissheim, Germany.
authors.forename: Ute
authors.initials: U
authors.lastname: Messelhaeusser
authors.affiliation: 5​Robert Koch Institute, Division for Enteropathogenic Bacteria and Legionella, Wernigerode, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Rabsch
authors.affiliation: 5​Robert Koch Institute, Division for Enteropathogenic Bacteria and Legionella, Wernigerode, Germany.
authors.forename: Sandra
authors.initials: S
authors.lastname: Simon
authors.affiliation: 6​Department for Infectious Disease Epidemiology at the Robert Koch Institute, Berlin, Germany.
authors.forename: Sergejs
authors.initials: S
authors.lastname: Nikisins
authors.affiliation: 6​Department for Infectious Disease Epidemiology at the Robert Koch Institute, Berlin, Germany.
authors.forename: Helen
authors.initials: H
authors.lastname: Bernard
authors.affiliation: 7​Institut Pasteur, Centre national de reference des E. coli, Shigella et Salmonella, Paris, France.
authors.forename: Simon
authors.initials: S
authors.lastname: le Hello
authors.affiliation: 8​French Institute for Public Health Surveillance, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Jourdan da-Silva
authors.affiliation: 9​Austrian Agency for Health and Food Safety, National Reference Centre for Salmonella, Graz, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Kornschober
authors.affiliation: 10​Surveillance & epidemiology of infectious diseases, Laboratoire National de Santé, Dudelange, Luxembourg.
authors.forename: Joel
authors.initials: J
authors.lastname: Mossong
authors.affiliation: 3​Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Hawkey
authors.affiliation: 1​Public Health England, UK.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: de Pinna
authors.affiliation: 1​Public Health England, UK.
authors.forename: Kathie
authors.initials: K
authors.lastname: Grant
authors.affiliation: 1​Public Health England, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Cleary
mesh_terms: D000818:Animals; D004196:Disease Outbreaks; D004531:Eggs / Q000382:microbiology*; D005060:Europe / Q000453:epidemiology; D005516:Food Microbiology; D016680:Genome, Bacterial / Q000235:genetics; D006801:Humans; D010802:Phylogeny; D012478:Salmonella Food Poisoning / Q000453:epidemiology / Q000382:microbiology*; D012477:Salmonella enteritidis / Q000145:classification* / Q000235:genetics; D000073336:Whole Genome Sequencing
keywords: Salmonella; foodborne outbreak; traceback investigation; whole-genome sequencing