Environmental surveillance: harnessing environmental sample data to protect animal health

Abstract

Infectious diseases in domestic animals—including those with zoonotic potential—impose a substantial global burden on food security, livelihoods, and public health. Environmental surveillance (ES) offers a critical complement to conventional animal-level diagnostics by detecting pathogens or their genetic signatures directly in the matrices through which they persist and spread: water, soil, air, manure, fomites, and arthropod vectors. This review synthesizes evidence across three analytical dimensions—matrix suitability, detection method performance, and wastewater-based epidemiology (WBE)—for 15 viral, bacterial, and parasitological diseases of domestic animals. Key findings reveal that matrix choice profoundly governs detection sensitivity: surface water and wetland sediments support infectious avian influenza virus isolation; pooled environmental feces and slurry outperform individual animal sampling for Mycobacterium avium subsp. paratuberculosis (MAP); and electrostatic dust cloths enable simultaneous detection of peste-des-petits ruminants virus (PPRV) and capripoxviruses at livestock markets. Molecular methods, principally quantitative RT-PCR and droplet digital PCR, consistently outperform conventional culture in sensitivity and turnaround time, though viability-linked assays remain an important unresolved need. WBE is increasingly applied beyond human pathogens: piggery effluent surveillance for Japanese encephalitis virus and wastewater metagenomics for antimicrobial resistance exemplify its veterinary potential. Interpretive limitations persist, including matrix-driven inhibition, absence of harmonized protocols, and the challenge of equating nucleic-acid signals with infectious risk. Realizing the full promise of ES within a One Health framework requires standardized, field-validated sampling workflows, viability-linked molecular assays, and formal integration of environmental signals into routine veterinary surveillance and outbreak-response systems.