title: Spread of avian pathogenic Escherichia coli ST117 O78:H4 in Nordic broiler production.
abstract: Escherichia coli infections known as colibacillosis constitute a considerable challenge to poultry farmers worldwide, in terms of decreased animal welfare and production economy. Colibacillosis is caused by avian pathogenic E. coli (APEC). APEC strains are extraintestinal pathogenic E. coli and have in general been characterized as being a genetically diverse population. In the Nordic countries, poultry farmers depend on import of Swedish broiler breeders which are part of a breeding pyramid. During 2014 to 2016, an increased occurrence of colibacillosis on Nordic broiler chicken farms was reported. The aim of this study was to investigate the genetic diversity among E. coli isolates collected on poultry farms with colibacillosis issues, using whole genome sequencing.
  
  
  
  Hundred and fourteen bacterial isolates from both broilers and broiler breeders were whole genome sequenced. The majority of isolates were collected from poultry with colibacillosis on Nordic farms. Subsequently, comparative genomic analyses were carried out. This included in silico typing (sero- and multi-locus sequence typing), identification of virulence and resistance genes and phylogenetic analyses based on single nucleotide polymorphisms.
  
  
  
  In general, the characterized poultry isolates constituted a genetically diverse population. However, the phylogenetic analyses revealed a major clade of 47 closely related ST117 O78:H4 isolates. The isolates in this clade were collected from broiler chickens and breeders with colibacillosis in multiple Nordic countries. They clustered together with a human ST117 isolate and all carried virulence genes that previously have been associated with human uropathogenic E. coli.
  
  
  
  The investigation revealed a lineage of ST117 O78:H4 isolates collected in different Nordic countries from diseased broilers and breeders. The data indicate that the closely related ST117 O78:H4 strains have been transferred vertically through the broiler breeding pyramid into distantly located farms across the Nordic countries.
authors.affiliation: National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark. troro@vet.dtu.dk.
authors.forename: Troels
authors.identifier: 0000-0001-7873-2816
authors.initials: T
authors.lastname: Ronco
authors.affiliation: Statens Serum Institut, Department of Microbiology and Infection Control, Artillerivej 5, 2300, Copenhagen S, Denmark.
authors.forename: Marc
authors.initials: M
authors.lastname: Stegger
authors.affiliation: Department of Veterinary Disease Biology, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark.
authors.forename: Rikke Heidemann
authors.initials: RH
authors.lastname: Olsen
authors.affiliation: Norwegian Veterinary Institute, Ullevaalsveien 68, 0454, Oslo, Norway.
authors.forename: Camilla
authors.initials: C
authors.lastname: Sekse
authors.affiliation: Norwegian Veterinary Institute, Ullevaalsveien 68, 0454, Oslo, Norway.
authors.forename: Anne Bang
authors.initials: AB
authors.lastname: Nordstoga
authors.affiliation: Finnish Food Safety Authority, Veterinary Bacteriology, Neulaniementie 4, FI-70210, Kuopio, Finland.
authors.forename: Tarja
authors.initials: T
authors.lastname: Pohjanvirta
authors.affiliation: Statens Serum Institut, Department of Microbiology and Infection Control, Artillerivej 5, 2300, Copenhagen S, Denmark.
authors.forename: Berit
authors.initials: B
authors.lastname: Lilje
authors.affiliation: National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Lyhs
authors.affiliation: Statens Serum Institut, Department of Microbiology and Infection Control, Artillerivej 5, 2300, Copenhagen S, Denmark.
authors.forename: Paal Skytt
authors.initials: PS
authors.lastname: Andersen
authors.affiliation: National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
authors.forename: Karl
authors.initials: K
authors.lastname: Pedersen
mesh_terms: D000818:Animals; D002645:Chickens; D004926:Escherichia coli / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D004927:Escherichia coli Infections / Q000662:veterinary*; D014644:Genetic Variation; D016680:Genome, Bacterial; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011201:Poultry Diseases / Q000382:microbiology*; D012703:Serotyping; D014774:Virulence / Q000235:genetics
keywords: APEC; Colibacillosis; Comparative genomics; Phylogenetic analysis; Virulence factors