That previous work was based on partial genome sequencing known as MLST. In MLST, less than 1% of the information in the genome is captured. Now that whole genome sequencing is available, the expectation was that we should be able to distinguish easily between between ST-21, 45 and 828 strains contaminating poultry versus beef versus lamb, and so on.
What we found was surprising. Instead of these strains harbouring previously unobserved sub-structure that allowed them to be associated with different animal sources, we found rapidly mixing populations undergoing extremely fast transmission between animal species, with campylobacter strains ricocheting among animal species on a timescale of just a few years. This is faster than they can accumulate enough mutations to differentiate populations colonizing different animal species.
Our results present an unforeseen roadblock to tracing transmission with whole genome sequencing, and suggests these strains are adapted to a generalist lifestyle, shedding new light on the ecology of this pathogen. These findings push back against the tide of opinion that whole genome sequencing is necessarily a panacea for detecting transmission, and demonstrate that going forwards, a detailed understanding of the biology of zoonotic bacteria (those transmitting between multiple species) and intensive sampling of potential sources are essential for effectively tracing the source of human infection.
