Novel Metabolic Genes and an Altered Phasome in Campylobacter hepaticus Genomes are Potential Determinants of Spotty Liver Disease

Abstract S6

Presenter: Jonathan Holmes (University of Leicester)

Spotty liver disease is endemic to free range poultry and is characterised by low egg yield and increased mortality rates. In 2015, Crawshaw and colleagues attributed this disease to a novel Campylobacter sub-species Campylobacter hepaticus. C. hepaticus is able to readily colonise the liver of chickens whereas the closely related species, Camplyobacter jejuni, colonises the gastrointestinal tract only occasionally spreading to the liver and spleen of poultry. The mechanism of infection and niche liver occupation of C. hepaticus remains unknown. Using a range of in silico techniques we investigated reported gene loss in C. hepaticus and comment on possible gene function gains of relevance to niche liver occupation. We quantified variation in core and pan genome size and content across a wide selection of C. hepaticus isolates from poultry sources in the United Kingdom and Australia. A key focus was on differences in the core genome make up of C. hepaticus from other Campylobacter species and variations in allelic identity between C. hepaticus and C. jejuni. Finally, we considered phase variation as a key influencer of niche environmental adaption, identifying novel short sequence repeat tracts and comparing the phasome of C. hepaticus to C. jejuni. The majority of genic differences between C. hepaticus and C. jejuni result from gene absence in C. hepaticus but a small subset (38%) resulted from genes identified in C. hepaticus not in C. jejuni. These included the opp gene cluster, and a number of genes involved in glycerol uptake and metabolism. Nucleotide polymorphisms were found to play a large role in gene variation. A background nucleotide substitution rate of 8-11% per gene per isolate was detected across the core genome of C. hepaticus compared to C. jejuni, indels and orthologous genes play a greater role in driving highly divergent genes. Analysis of phase variable genes showed that both species possessed a similar sized sets of poly G/C phase variable genes but with an altered genomic distribution. However, a higher degree of sequence similarity was found within the C. hepaticus gene set compared to C. jejuni where only 25% of the genes showed similarity. Sequence similarity was further reduced between the two sets, with only 14% observable. 75% of these phase-variable genes were functionally annotated as sugar/glycosyltransferases. Analysis of the DNA region shared by the two sets revealed that these phase variable genes were located downstream and upstream of genes involved processes including flagella and capsule biosynthesis. In summary, we have identified a number of putative metabolic pathways and phase variable systems which have driven the divergence of C. hepaticus from C. jejuni and other Campylobacters. These novel core genes and phasome may enable C. hepaticus to adapt to different ecological niches to C. jejuni and specifically facilitate profuse proliferation of C. hepaticus in the livers of chickens.

Presenting in Speaking session 4 - Survival and application