One Health Molecular Surveillance for Emerging and Zoonotic Parasitic Diseases

Abstract

Emerging and zoonotic parasitic diseases are sustained by transmission systems that cross human, domestic-animal, wildlife, vector, food and environmental compartments. Molecular methods can reveal parasite identity, genetic diversity and connectivity across those compartments, but technological sensitivity alone does not produce actionable One Health surveillance. This critical narrative review evaluates how targeted amplification, genotyping, deep amplicon sequencing, whole-genome and target-enrichment approaches, metagenomics, cell-free DNA analysis and environmental DNA surveillance can be combined within decision-oriented systems. Literature published from 1 January 2000 to 4 July 2026 was selected from multidisciplinary, biomedical and agricultural scholarly sources, with foundational earlier work retained when necessary. The evidence is strongest where matched sampling across hosts and environments is linked to explicit epidemiological questions, validated assays, interpretable denominators and timely public-health or veterinary action. Molecular surveillance has clarified zoonotic assemblages of enteric protozoa, population structure in Toxoplasma and Echinococcus, hybridisation among schistosomes, reservoir-linked transmission of trypanosomatids, landscape-associated zoonotic malaria and the emergence of human babesiosis. Its recurrent weaknesses are fragmented sectoral sampling, convenience-based host selection, inconsistent marker resolution, uncertain viability of environmental detections, contamination and reference-database error, limited metadata interoperability and under-representation of low-resource endemic settings. Detection of parasite DNA should therefore be separated analytically from inference about viable organisms, transmission direction, reservoir competence and disease risk. A tiered architecture is proposed in which inexpensive targeted assays provide routine coverage, sequencing resolves anomalous or high-consequence signals, and integrated analysis links molecular findings to ecological, clinical and operational data. The principal priority is not universal adoption of the most complex platform, but harmonised surveillance capable of converting comparable molecular evidence into proportionate interventions across sectors.