Genome-wide association study identifies vitamin B ₅ biosynthesis as a host specificity factor in Campylobacter

Abstract

Genome-wide association studies have the potential to identify causal genetic factors underlying important phenotypes but have rarely been performed in bacteria. We present an association mapping method that takes into account the clonal population structure of bacteria and is applicable to both core and accessory genome variation. Campylobacter is a common cause of human gastroenteritis as a consequence of its proliferation in multiple farm animal species and its transmission via contaminated meat and poultry. We applied our association mapping method to identify the factors responsible for adaptation to cattle and chickens among 192 Campylobacter isolates from these and other host sources. Phylogenetic analysis implied frequent host switching but also showed that some lineages were strongly associated with particular hosts. A seven-gene region with a host association signal was found. Genes in this region were almost universally present in cattle but were frequently absent in isolates from chickens and wild birds. Three of the seven genes encoded vitamin B 5 biosynthesis. We found that isolates from cattle were better able to grow in vitamin B 5 -depleted media and propose that this difference may be an adaptation to host diet.evolution | genomics | host adaptation | transmission ecology C olonization of multiple host species increases the number of transmission opportunities for animal pathogens and symbionts but depends on making rapid adjustments to each new host (1). For organisms such as Campylobacter, relatively small genome size (1.6 Mb) limits the phenotypic flexibility of each bacterium. Single clones can multiply to large numbers within hosts, and genetic variation arising among these bacteria increases the range of available phenotypes. This might allow a bacterial lineage to passage successfully through multiple hosts by repeatedly evolving host adaptive traits.Experimental work has shown that a large proportion of adaptations to new environments incur an equal or greater cost in other environments (2). This cost of adaptation might make a strategy of continuous evolution unstable by causing a progressive loss of fitness in the course of repeated host switching. Three factors that could reduce this cost of readaptation are canalization of genetic change via contingency loci (3, 4); coordinated genetic regulation of host-specific factors (5, 6); and import of DNA by recombination from other, already adapted, lineages in each new host species (7). The relative importance of these mechanisms for host specificity in Campylobacter remains unknown.Campylobacter jejuni and Campylobacter coli are common components of the gut microbiota in numerous wild and domesticated animal species, as well as, together, being one of the most common causes of food poisoning in humans. The characterization of large numbers of C. jejuni and C. coli isolates from diverse sources and locations by multilocus sequence typing (MLST) has shown that there is genetic differentiation among sequence types (STs) associated with diffe...

The Evolution ofCampylobacter jejuniandCampylobacter coli

“…The application of genome-wide association studies (GWAS) to bacteria (Sheppard et al 2013a) has great potential for enhancing understanding of the genetic basis of phenotypic variation in Campylobacter and other organisms. As with similar approaches in human genomics, GWAS deviate from conventional, "bottom-up," approaches that begin with the identification of a gene and then test its function-typically using knockout mutants-in favor of a "topdown" approach that groups isolates by phenotype, and then identifies genetic elements associated with a particular phenotype.…”

“…As with similar approaches in human genomics, GWAS deviate from conventional, "bottom-up," approaches that begin with the identification of a gene and then test its function-typically using knockout mutants-in favor of a "topdown" approach that groups isolates by phenotype, and then identifies genetic elements associated with a particular phenotype. Early applications of this approach have identified host-associated genes and alleles (Sheppard et al 2013a), and there is considerable potential for unraveling other complex phenotypes, such as survival, through the food chain and virulence.…”

“…A seven-gene region associated with vitamin B5 biosynthesis was almost universally present in cattle isolates, but was frequently absent in isolates from chickens and wild birds. Laboratory experiments confirmed that isolates from cattle were better able to grow in a vitamin B5 -depleted media and this is possibly advantageous in the gut of animals with a low vitamin B5 diet, such as ruminants (Sheppard et al 2013a). More generally, the persistence of elements that are necessary for colonization of cattle in some isolates from chickens provides evidence for the mechanism by which these bacteria might achieve a "host generalist" lifestyle.…”

“…Wherever multiple clonal complexes are found in the same agricultural animals, they frequently share numerous alleles, indicating that they occupy the same physical space and can recombine; however, there are differences among lineages. For example, clonally related strains with very similar core genomes and identical MLST clonal complexes can differ at accessory genome loci if they are isolated from cattle or chicken (Sheppard et al 2013a). Understanding hidden niche structure that exists within hosts is an important area of future research.…”

“…In the first application of a formal genome-wide association mapping approach to bacteria, some of the genetic elements associated with adaptation to life in the cattle gut have been identified in C. jejuni genomes (Sheppard et al 2013a). A seven-gene region associated with vitamin B5 biosynthesis was almost universally present in cattle isolates, but was frequently absent in isolates from chickens and wild birds.…”