Local genes, for local bacteria: biogeographical variation in Campylobacter accessory genome content

Diarrhoeal disease remains a major cause of child morbidity, growth faltering and mortality in low and middle income countries (LMICs), with Campylobacter among the most common causes. Previous work has identified the major sources in the UK and US (e.g. contaminated poultry), however little is known about the risk factors and transmission routes in LMICs, where incidence is extremely high (up to 85 % of children infected before 1 year) and suggests a different epidemiology. Risk factors such as household crowding, poor sanitation, consumption of contaminated water and cohabitation with animals, all constitute potential transmission risks but their relative importance is unknown. This is a major concern as frequent or chronic enteric (re)infection is linked to significant morbidity and growth faltering in children. Comparative genomics offers a solution for untangling complex transmission networks. Campylobacter jejuni and C. coli primarily inhabit the gut of birds and mammals and signatures of adaptation can be detected in their genomes. Therefore, by sequencing the genome of human clinical isolates and faecally contaminated environments it is possible to discern its origin. Pilot genomics studies of strains from humans, animals and food in LMICs have identified genomic variation in strains that may indicate differences in source, survival, transmission or virulence (compared to the UK). In particular we have identified globally distributed strains and lineages; country-specific strains; rapid dissemination of accessory genes in specific regions; evidence of within-household spread and strains associated with asymptomatic infection or high levels of antimicrobial resistance.