Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork
Author and article information
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 7,343 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.
Cite this as
2016. Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork. PeerJ Preprints 4:e2300v1 https://doi.org/10.7287/peerj.preprints.2300v1Author comment
This is a preprint submission to PeerJ Preprints.
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Supplemental Information
Figure S1
Null and empirical distributions of the association score in ST-45 clonal complex.
Figure S2
Distribution of squared correlation coefficient (linkage disequilibrium r2) values between SNPs across C. jejuni genomic regions longer than 100 kb. (A) Core and (B) disease-associated SNPs with 25% minor allele frequency are used for calculation.
Figure S3
Clinical strains from ST-21 clonal complex analysed in this study. Clinical strains used for discovery and replication in GWAS are coloured in red and pink, respectively. The tree was constructed from the core genes in ST-21 clonal complex by using FastTree.
Figure S4
Sensitivity of C. jejuni NCTC11168 and nucleotide salvage mutants to toxic nucleotide analogues. (A) C. jejuni NCTC11168 wildtype was assessed for its sensitivity to the toxic nucleotide analogues AZ (8-Azaxanthine monohydrate), DP (2,6-Diaminopurine), FU (5-Fluorouracil), MP (6-Mercaptopurine) and TG (6-Thioguanine) with a DMSO control. Of those tested, sensitivity was only seen towards MP and TG. * p<0.05, *** p<0.001 (B) Disc diffusion assays were used to evaluate the resistance of nucleotide salvage mutants cj1368-70 to 6-Mercaptopurine (MP) and 6-Thioguanine (TP). Each single mutant, and a triple mutant, were completely resistant compared to wildtype.
Figure S5
Prevalence of associated words in Campylobacter genomes from various sources. (A) Prevalence on 354 genomes from cattle (n=43) chicken (n=300) and wild birds (n=11). Genomes have been previously published or are part of this study. (B) Prevalence on the 209 clinical genomes sampled before 2010, in 2010, and in 2011.
Table S1
Description of sequenced isolates used in this study.
Table S2
Primers and vectors used for mutant construction in this study.
Table S3
Summary of the classification of the survival-associated words.
Table S4
Allelic types and predicted protein variants of the nuoK gene in 44 ST-21 clonal complex and 37 ST-45 clonal complex isolates used in the GWAS and phenotypical testing.
Table S5
List and description of disease-associated SNPs identified in this study.
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Koji Yahara conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Guillaume Méric conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Aidan J Taylor conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Stefan PW de Vries conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.
Susan Murray conceived and designed the experiments, performed the experiments.
Ben Pascoe conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools.
Leonardos Mageiros conceived and designed the experiments, performed the experiments.
Alicia Torralbo conceived and designed the experiments, performed the experiments.
Ana Vidal contributed reagents/materials/analysis tools.
Anne M Ridley contributed reagents/materials/analysis tools.
Sho Komukai conceived and designed the experiments, performed the experiments.
Helen Wimalarathna contributed reagents/materials/analysis tools.
Alison J Cody contributed reagents/materials/analysis tools.
Frances M Colles contributed reagents/materials/analysis tools.
Noel D McCarthy contributed reagents/materials/analysis tools, reviewed drafts of the paper.
David Harris contributed reagents/materials/analysis tools.
James E Bray contributed reagents/materials/analysis tools.
Keith A Jolley contributed reagents/materials/analysis tools.
Martin CJ Maiden contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Stephen D Bentley contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Julian Parkhill contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Christopher D Bayliss conceived and designed the experiments, performed the experiments.
Andrew J Grant conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Duncan Maskell conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Xavier Didelot conceived and designed the experiments, reviewed drafts of the paper.
David J Kelly conceived and designed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Samuel K Sheppard conceived and designed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
Assembled genome files are archived in the Dryad repository (doi:10.5061/dryad.8t80s). Raw reads are available on the European Nucleotide Archive (ENA) and the Short Read Archive (SRA) (see Table S1 for accession numbers).
Data Deposition
The following information was supplied regarding data availability:
The research in this article did not generate, collect or analyse any raw data or code.
Funding
This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/I02464X/1, the Medical Research Council (MRC) grants MR/M501608/1 and MR/L015080/1, and the Wellcome Trust grants 088786/C/09/Z and 098051. KY was supported by a JSPS Research Fellowship for Young Scientists. GM was supported by a NISCHR Health Research Fellowship (HF-14-13). AT was supported by a BBSRC DTP PhD studentship. XD was supported by BBSRC grant BB/L023458/1 and NIHR grant HPRU-2012-10080. SdV was supported by BBSRC grant RG66581. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
