Campylobacter spp. within the UK poultry industry: prevalence, risk factors and the chicken microbiome

To date a fail-safe method of excluding Campylobacter from commercial UK and Irish poultry farms remains elusive.<br><br>This body of research is unique in that it was done in conjunction with the commercial poultry industry, subsequently allowing access to a greater depth of metadata associated with Campylobacter prevalence on farm. Questions that were off interest to this work were i) the understanding of prevalence at a UK level and associated risk factors ii) the effect of Campylobacter on chicken health and performance at commercial farm level iii) investigate the chicken gut microbiome over time and how this may influence Campylobacter appearance and performance; and iv) assess the impact of farming production system parameters on the chicken microbiome, its influence on Campylobacter and performance. <br><br>Our results are the first to analyse Campylobacter prevalence on farm during the period 2014 – 2016, during which Campylobacter reduction was a clear focus for the industry.

We identified a year on year reduction in Campylobacter positive flocks from 60% in 2014 to 46% in 2016. Furthermore, we identified key risk factors associated with Campylobacter for UK poultry farmers. Unsurprisingly seasonality was a clear risk but other factors such as those in relation to farm infrastructure were identified and will ultimately inform the industry on best practice for the future.

This research also sets out clearly the impact Campylobacter can have on flock performance, providing a clear incentive for farmers to invest and adhere to best practice biosecurity. <br><br>Nonetheless, it is recognised that biosecurity alone will not prevent Campylobacter colonisation and further understanding of the chicken gut microbiome, how it interacts with Campylobacter and how commercial farm practices influence this, is required.

Our chicken gut microbiome analysis clearly shows rapidly increasing microbial diversity up to day 12 with variation observed both in terms of genera and abundance, before a stabilization of the microbial diversity after day 20. In particular, we identified a shift from competitive to environmental drivers of microbial community from days 12 to 20 creating a window of opportunity whereby Campylobacter can appear. Additionally, we demonstrated for the first time how different production systems influence chicken microbial communities and as such could ultimately lead to improved performance and better intervention strategies against Campylobacter within the food chain.