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.空肠弯曲杆菌（Campylobacter jejuni）和结肠弯曲杆菌（Campylobacter coli）是发达国家细菌性肠胃炎的最主要致病原，人类感染通常源于与受感染肉类相关的人畜共患传播。由于弯曲杆菌在肠道外难以存活，宿主相关种群在不同程度上存在遗传隔离。因此，多数菌株的潜在感染来源可通过基因组内的宿主关联变异进行推断，这对解析人类感染的源头具有重要指导价值。然而，部分常见菌株，尤其是隶属于ST-21、ST-45和ST-828克隆复合体的分离株，展现出宽泛的宿主范围，阻碍了感染源溯源工作。本研究中，全基因组测序（whole-genome sequencing）有望揭示与宿主特异性相关的精细遗传结构。我们发现，上述克隆复合体在不同动物宿主物种间的人畜共患传播速率极高，以至于宿主关联的遗传信号几乎被完全抹除；经估算，ST-21、ST-45和ST-828复合体每1.6年、1.8年和12年就会发生一次人畜共患传播事件。我们将89%的临床感染病例归因于鸡源，10%归因于牛源，1%归因于猪源。本研究结果显示，可感染人类的空肠弯曲杆菌和结肠弯曲杆菌常见菌株均已适应了泛宿主生活方式，能够在不同宿主间实现快速传播。此外，研究结果还表明，这些克隆复合体内部微弱的宿主关联信号为临床感染源的精准溯源带来了挑战，这进一步印证了一个观点：尽管全基因组测序功能强大，但无法替代对疑似传播宿主库的高强度采样工作。