Rapid Oxford Nanopore Technologies MinION Sequencing Workflow for Campylobacter jejuni Identification in Broilers on Site—A Proof-of-Concept Study

SIMPLE SUMMARY: Current culture methods for Campylobacter enumeration in poultry meat require at least five days. To improve this outcome, we have assembled a portable sequencing kit consisting of the Bento Lab and the MinION and developed a workflow for on-farm use that can detect and report the presence of Campylobacter in less than five hours from sampling to data. In addition, this workflow allows for the determination of microbiota profiles within those five hours. Overall, this workflow and approach can be helpful in the control of zoonotic agents, with a particular focus on poultry meat, where it takes less than 24 h from the time the animals arrive at the slaughterhouse to the time the carcasses are available on the supermarket shelves. ABSTRACT: Campylobacter is recognised as one of the most important foodborne bacteria, with a worldwide health and socioeconomic impact. This bacterium is one of the most important zoonotic players in poultry, where efficient and fast detection methods are required. Current official culture methods for Campylobacter enumeration in poultry usually include >44 h of culture and >72 h for identification, thus requiring at least five working shifts (ISO/TS 10272-2:2017). Here, we have assembled a portable sequencing kit composed of the Bento Lab and the MinION and developed a workflow for on-site farm use that is able to detect and report the presence of Campylobacter from caecal samples in less than five hours from sampling time, as well as the relationship of Campylobacter with other caecal microbes. Beyond that, our workflow may offer a cost-effective and practical method of microbiologically monitoring poultry at the farm. These results would demonstrate the possibility of carrying out rapid on-site screening to monitor the health status of the poultry farm/flock during the production chain.