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Supplemental Information

Figure S1

Null and empirical distributions of the association score in ST-45 clonal complex.

DOI: 10.7287/peerj.preprints.2300v1/supp-1

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.

DOI: 10.7287/peerj.preprints.2300v1/supp-2

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.

DOI: 10.7287/peerj.preprints.2300v1/supp-3

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.

DOI: 10.7287/peerj.preprints.2300v1/supp-4

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.

DOI: 10.7287/peerj.preprints.2300v1/supp-5

Table S1

Description of sequenced isolates used in this study.

DOI: 10.7287/peerj.preprints.2300v1/supp-6

Table S2

Primers and vectors used for mutant construction in this study.

DOI: 10.7287/peerj.preprints.2300v1/supp-7

Table S3

Summary of the classification of the survival-associated words.

DOI: 10.7287/peerj.preprints.2300v1/supp-8

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.

DOI: 10.7287/peerj.preprints.2300v1/supp-9

Table S5

List and description of disease-associated SNPs identified in this study.

DOI: 10.7287/peerj.preprints.2300v1/supp-10

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.


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