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Campylobacter jejuni and Campylobacter coli are the biggest causes ofbacterial gastroenteritis in the developed world, with human infectionstypically arising from zoonotic transmission associated with infected meat,especially poultry. Because this organism is not thought to survive welloutside of the gut, host associated populations are genetically isolated tovarying degrees. Therefore the likely origin of most Campylobacter strains canbe determined by host-associated variation in the genome. This is instructivefor characterizing the source of human infection at the population level.However, some common strains appear to have broad host ranges, hindering sourceattribution. Whole genome sequencing has the potential to reveal fine-scalegenetic structure associated with host specificity within each of thesestrains.  We found that rates of zoonotic transmission among animal host species inST-21, ST-45 and ST-828 clonal complexes were so high that the signal of hostassociation is all but obliterated. We attributed 89% of clinical cases to achicken source, 10% to cattle and 1% to pig. Our results reveal that commonstrains of C. jejuni and C. coli infectious to humans are adapted to ageneralist lifestyle, permitting rapid transmission between different hosts.Furthermore, they show that the weak signal of host association within thesecomplexes presents a challenge for pinpointing the source of clinicalinfections, underlining the view that whole genome sequencing, powerful thoughit is, cannot substitute for intensive sampling of suspected transmissionreservoirs.

Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections