Longitudinal study of diagnostic sample matrices for respiratory pathogens on Irish farrow-to-finish pig herds

Porcine respiratory disease complex (PRDC) involves multifactorial pathogen interactions that complicate surveillance strategies in commercial pig production. Current individual animal sampling methods present logistical constraints and animal welfare concerns. This longitudinal study evaluated the antibody responses and diagnostic efficacy of matched antemortem sample specimens (serum, nasal and pen-based oral fluids) for detecting Actinobacillus pleuropneumoniae (App), Mycoplasma hyopneumoniae (Mhyo), porcine reproductive and respiratory syndrome virus (PRRSV) and influenza A virus (IAV) across all production stages from weaning to slaughter (5 to 24 weeks of age) in seven Irish farrow-to-finish herds. High-herd seroprevalence was observed at all five time-points, with concurrent antibody detection for the targeted respiratory pathogens occurring in 27.2% [95% confidence interval (CI) = 24.4–30.2%] of individual samples and 64.7% (95% CI = 46.5–80.3%) at herd level. Nucleic acid co-detection from two pathogens occurred in 11.1% of oral fluid and 15.3% of nasal swab samples, indicating widespread co-infection patterns. McNemar’s test demonstrated significant discordance between pathogen-specific immunoassays and PCR methodologies across all matrices (p < 0.05). Cohen’s kappa (κ) analysis revealed pathogen-specific agreement patterns. Slight matrix concordance was observed between nasal swabs and oral fluids for App (κ = 0.177) and Mhyo (κ = 0.135), while substantial agreement was demonstrated for PRRSV-1 (κ = 0.752) and IAV (κ = 0.629). Detection of PRRSV-1 showed moderate agreement between serum and nasal swabs (κ = 0.570) or oral fluids (κ = 0.575). Pathogen-specific detection peaks varied by agent and sample matrix with peaks for App and IAV at 5 weeks of age, Mhyo during finishing stages and extended PRRSV-1 detection window (10–19 weeks of age) in oral fluids. Prevalence detection rates were consistently equivalent or superior in oral fluids compared to nasal swabs, with significantly higher PRRSV-1 detection in oral fluids versus serum. Quantitative analysis validates oral fluid sampling as a diagnostically robust alternative to conventional matrices. The documented pathogen-specific temporal patterns and matrix-specific performance data provide evidence-based parameters for refining surveillance protocols. Statistical validation of oral fluid efficacy, combined with operational and welfare advantages, supports adoption of oral fluid sampling for comprehensive PRDC monitoring to enhance early pathogen detection, improve diagnostic accuracy, boost production efficiency and assist herd health management decisions in intensive pig production systems.