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

Campylobacter jejuni and Campylobacter coli are the biggest causes of
bacterial gastroenteritis in the developed world, with human infections
typically arising from zoonotic transmission associated with infected
meat. Because Campylobacter is not thought to survive well outside the
gut, host-associated populations are genetically isolated to varying
degrees. Therefore, the likely origin of most strains can be determined by
host-associated variation in the genome. This is instructive for
characterizing the source of human infection. However, some common
strains, notably isolates belonging to the ST-21, ST-45 and ST-828 clonal
complexes, appear to have broad host ranges, hindering source attribution.
Here whole-genome sequencing has the potential to reveal fine-scale
genetic structure associated with host specificity. We found that rates of
zoonotic transmission among animal host species in these clonal complexes
were so high that the signal of host association is all but obliterated,
estimating one zoonotic transmission event every 1.6, 1.8 and 12 years in
the ST-21, ST-45 and ST828 complexes, respectively. We attributed 89% of
clinical cases to a chicken source, 10% to cattle and 1% to pig. Our
results reveal that common strains of C. jejuni and C. coli infectious to
humans are adapted to a generalist lifestyle, permitting rapid
transmission between different hosts. Furthermore, they show that the weak
signal of host association within these complexes presents a challenge for
pinpointing the source of clinical infections, underlining the view that
whole-genome sequencing, powerful though it is, cannot substitute for
intensive sampling of suspected transmission reservoirs.