Deep learning from videography as a tool for measuring E. coli infection in poultry.

Poultry farming is threatened by regular outbreaks of Escherichia coli (E. coli) that lead to significant economic losses and public health risks. However, traditional surveillance methods often lack sensitivity and scalability. Early detection of infected poultry using minimally invasive procedures is thus essential for preventing epidemics. To that end, we leverage recent advancements in computer vision, employing deep learning-based tracking to detect behavioural changes associated with E. coli infection in a case-control trial comprising two groups of 20 broiler chickens: (i) a healthy control group and (ii) a group infected with a pathogenic E. coli field strain from the poultry industry. More specifically, kinematic features derived from deep learning-based tracking data revealed markedly reduced activity in the challenged group compared with the negative control. These findings were validated by lower mean optical flow in the infected flock, suggesting reduced movement and activity, and post-mortem physiological markers of inflammation that confirmed the severity of infection in the challenged group. Overall, this study demonstrates that deep learning-based tracking offers a promising solution for real-time monitoring and early infection detection in poultry farming, with the potential to help reduce economic losses and mitigate public health risks associated with infectious disease outbreaks in poultry.