Genomics and population dynamics of phase variable genes in Campylobacter

Phase variation is a feature of many pathogenic bacteria, including Campylobacter jejuni – a leading cause of food-borne gastroenteritis. C. jejuni has many phase variable (PV) genes which exhibit high frequency, stochastic, reversible switching between ON and OFF expression states. This results from instability in simple sequence repeats (SSRs). This study is the first to conduct a widescale survey of the Campylobacter ‘phasome’ (the set of PV genes present in a genome). A new program, PhasomeIt, was developed to identify and compare all SSR-mediated phase variable genes in 77 complete Campylobacter genomes. Surprisingly, there are a large number of rare PV genes with few, or no, homologues in other genomes. These exist alongside a “core phasome” of PV genes associated with particular species. This suggests a significant role for phasome diversity in Campylobacter population and disease dynamics. SSR tract length influences rates of PV, however it is not known whether differences in PV rate are biologically significant or whether a threshold effect exists. A cyclical assaywas developed which allows alternation of experimental conditions favouring the ON and OFF states of cj1421c. Bacteriophage F336 selects for the OFF state whilst human serum selects for the ON state, and both produce complete selective sweeps. These agents were combined for a complete ON→OFF→ON cycle. Using an in silico model of this assay it was demonstrated that a broad range of conditions favour PV over non-PV genes whilst variation rate is primarily dependent on duration of selection. Extending this modelling approach to the interaction of non-selective bottlenecks and PV loci indicated that smaller bottlenecks have a disruptive effect on population dynamics whilst larger bottlenecks preserve increased diversity. These differences are capable of producing stochastic differences in output populations that may drive host-to-host diversity and result in rare occurrence of disease sequelae.