Early-life shedding and environmental presence of Mycobacterium avium ssp. paratuberculosis in Chilean dairy calves.

Neonatal dairy calves are highly susceptible to Mycobacterium avium ssp. paratuberculosis (MAP) infection, but data remain limited on early infection prevalence and transmission drivers. This study aimed to estimate the true prevalence of MAP infection and identify associated risk factors in Chilean dairy calves younger than 60 d of age. Fecal and environmental samples were collected from 579 calves across 39 dairy herds. The MAP detection used a phage-based method (magnetic phage separation-quantitative PCR) that selectively identifies viable bacteria, and a Bayesian model was used to account for biased diagnostics test results. The overall estimated true prevalence of MAP infection was 4.4% (95% posterior probability intervals [PPI]: 0%-19.4%). Environmental contamination with MAP was frequently detected in calf pens (19.4% of pens; 30.7% of herds). Although multiple transmission routes exist, the presence of viable MAP in the calf's immediate pen environment was identified as the primary risk factor associated with infection in these neonatal calves (odds ratio: 3.7; 95% PPI: 1.2-9.0). These findings suggest that MAP infection could occur very early in life in this population, and that contamination within the calf's immediate environment is a key determinant of early-life MAP infection status. This highlights the critical need for implementing rigorous environmental hygiene control measures, specifically within calving and calf-rearing areas, starting immediately after birth, to effectively mitigate early MAP exposure and transmission in dairy herds.