title: Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork.
abstract: Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry. C. jejuni lineages vary in host range and prevalence in human infection, suggesting differences in survival throughout the poultry processing chain. From 7343 MLST-characterised isolates, we sequenced 600 C. jejuni and C. coli isolates from various stages of poultry processing and clinical cases. A genome-wide association study (GWAS) in C. jejuni ST-21 and ST-45 complexes identified genetic elements over-represented in clinical isolates that increased in frequency throughout the poultry processing chain. Disease-associated SNPs were distinct in these complexes, sometimes organised in haplotype blocks. The function of genes containing associated elements was investigated, demonstrating roles for cj1377c in formate metabolism, nuoK in aerobic survival and oxidative respiration, and cj1368-70 in nucleotide salvage. This work demonstrates the utility of GWAS for investigating transmission in natural zoonotic pathogen populations and provides evidence that major C. jejuni lineages have distinct genotypes associated with survival, within the host specific niche, from farm to fork.
authors.affiliation: Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Yahara
authors.affiliation: The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Méric
authors.affiliation: Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.
authors.forename: Aidan J
authors.initials: AJ
authors.lastname: Taylor
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, Madingley, Cambridge, UK.
authors.forename: Stefan P W
authors.initials: SP
authors.lastname: de Vries
authors.affiliation: Swansea University Medical School, Institute of Life Science, Swansea University, Swansea, UK.
authors.forename: Susan
authors.initials: S
authors.lastname: Murray
authors.affiliation: The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.|MRC CLIMB Consortium, Oxford Bath, UK.
authors.forename: Ben
authors.initials: B
authors.lastname: Pascoe
authors.affiliation: Swansea University Medical School, Institute of Life Science, Swansea University, Swansea, UK.
authors.forename: Leonardos
authors.initials: L
authors.lastname: Mageiros
authors.affiliation: Swansea University Medical School, Institute of Life Science, Swansea University, Swansea, UK.
authors.forename: Alicia
authors.initials: A
authors.lastname: Torralbo
authors.affiliation: Animal and Plant Health Agency (APHA), Addlestone, UK.
authors.forename: Ana
authors.initials: A
authors.lastname: Vidal
authors.affiliation: Animal and Plant Health Agency (APHA), Addlestone, UK.
authors.forename: Anne
authors.initials: A
authors.lastname: Ridley
authors.affiliation: Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan.
authors.forename: Sho
authors.initials: S
authors.lastname: Komukai
authors.affiliation: Department of Zoology, Oxford University, Oxford, UK.
authors.forename: Helen
authors.initials: H
authors.lastname: Wimalarathna
authors.affiliation: Department of Zoology, Oxford University, Oxford, UK.
authors.forename: Alison J
authors.initials: AJ
authors.lastname: Cody
authors.affiliation: Department of Zoology, Oxford University, Oxford, UK.
authors.forename: Frances M
authors.initials: FM
authors.lastname: Colles
authors.affiliation: Department of Zoology, Oxford University, Oxford, UK.|NIHR Health Protections Research Unit in Gastrointestinal Infections, University of Oxford, Oxford, UK.
authors.forename: Noel
authors.initials: N
authors.lastname: McCarthy
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: David
authors.initials: D
authors.lastname: Harris
authors.affiliation: Department of Zoology, Oxford University, Oxford, UK.
authors.forename: James E
authors.initials: JE
authors.lastname: Bray
authors.affiliation: Department of Zoology, Oxford University, Oxford, UK.
authors.forename: Keith A
authors.initials: KA
authors.lastname: Jolley
authors.affiliation: Department of Zoology, Oxford University, Oxford, UK.|NIHR Health Protections Research Unit in Gastrointestinal Infections, University of Oxford, Oxford, UK.
authors.forename: Martin C J
authors.initials: MC
authors.lastname: Maiden
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: Department of Genetics, University of Leicester, Leicester, UK.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Bayliss
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, Madingley, Cambridge, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Grant
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, Madingley, Cambridge, UK.
authors.forename: Duncan
authors.initials: D
authors.lastname: Maskell
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College, London, UK.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.affiliation: Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Kelly
authors.affiliation: The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.|MRC CLIMB Consortium, Oxford Bath, UK.|Department of Zoology, Oxford University, Oxford, UK.
authors.forename: Samuel K
authors.initials: SK
authors.lastname: Sheppard
mesh_terms: D000818:Animals; D002169:Campylobacter Infections / Q000382:microbiology* / Q000662:veterinary*; D016123:Campylobacter jejuni / Q000145:classification / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification*; D000072480:Farms; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D058885:Multilocus Sequence Typing; D010641:Phenotype; D011200:Poultry; D011201:Poultry Diseases / Q000382:microbiology*