Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork
- Published
- Accepted
- Subject Areas
- Genetics, Genomics, Microbiology
- Keywords
- population genomics, GWAS, zoonosis, survival, poultry processing chain, Campylobacter, industrial food safety
- Copyright
- © 2016 Yahara et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 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.2300v1
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.
Author Comment
This is a preprint submission to PeerJ Preprints.
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.