Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork

Abstract

Summary 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.

Genomic variations leading to alterations in cell morphology of Campylobacter spp

“…We investigated the presence and allelic variances of pgp1 and pgp2 in 859 genomes of C. jejuni and C. coli . The genomes were from a wide range of isolates: 192 from clinical, agricultural and wild bird sources48, 319 from multiple stages of poultry processing, including farms, abattoirs and retail chicken meat50 and 348 from clinical human cases51. Analysis of these genomes revealed that all isolates contained pgp1 and pgp2 , suggesting that these genes are core to C. jejuni and C. coli .…”

Lineage‐specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group

“…As in recent publications on other species (Meric, Hitchings, Pascoe, & Sheppard, ; Monteil et al., ; Morley et al., ; Murray et al., ; Yahara et al., ), a reference pan‐genome approach was used with gene‐by‐gene alignment, consistent with whole‐genome MLST (Jolley & Maiden, ; Maiden et al., ; Meric et al., ; Sheppard, Jolley, & Maiden, ), implemented in BIGSdb open‐source software. Briefly, the reference pan‐genome was constructed by combining the genomes of several reference strains ( Bt strain YBT020 (Zhu et al., ), Bc strain ATCC 14579 (Ivanova et al., ) and Ba strain Ames (Read et al., )) with whole‐genome annotations from all the other genomes of this study to derive a single gene list.…”

Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease

“…Broadly, the spread of AMR can be defined as a clonal transmission or gene pool transmission. In clonal transmission, bacteria that have acquired AMR in one niche are transmitted to another where they retain resistance, such as in the survival of resistant Campylobacter through the food production chain to infect humans (Yahara et al ., ). In gene pool transmission, HGT facilitates the spread of resistance genes between strains and species and the movement of genes (rather than clones) into multiple genetic backgrounds can be seen to spread AMR.…”