Applications of Metabolomics in the Diagnosis of Animal Protozoan Diseases and Antiprotozoal Drug Resistance: A Review

Abstract

This review highlights the expanding role of metabolomics in understanding animal protozoan diseases and detecting antiprotozoal drug resistance. Articles published in English were searched and identified through databases, including PubMed, Scopus, Web of Science, and Google Scholar, using combinations of keywords related to metabolomics, metabolomic profiling, protozoan diseases, biomarkers, metabolic pathways, and antiprotozoal drug resistance from 02 November 2025 to 28 December 2025. Protozoan parasites including Trypanosoma, Leishmania, Babesia, Theileria, Eimeria, Cryptosporidium, and Toxoplasma induce significant metabolic disturbances detectable through advanced platforms such as NMR, LC–MS, and GC–MS. Metabolomics enables early diagnosis by identifying distinct biochemical fingerprints in biofluids (blood, saliva, urine, feces, and breath), differentiating infected from healthy animals while providing insight into host–parasite interactions, immune responses, and disease progression. Blood protozoan infections are associated with disruptions in amino acid, lipid, energy, and oxidative stress pathways, including ionone-related markers in trypanosomiasis, altered aldehydes and hydrocarbons in leishmaniasis, and amino acid and bile acid imbalances in babesiosis and theileriosis. Comparable metabolic alterations occur in intestinal and tissue infections, where changes in short-chain fatty acids, glycerophospholipids, long-chain fatty acids, and oxidative stress markers reflect gut dysbiosis, immune activation, and parasite nutrient exploitation. Metabolomics also facilitates detection of drug resistance by revealing metabolic reprogramming in resistant strains, including altered glycolysis, glutathione metabolism, and amino acid pathways, as well as sterol biosynthesis and oxidative stress adaptations. However, most reported biomarkers remain at the discovery or candidate stage and should not be considered clinically validated diagnostic tests or universal markers of drug resistance without independent validation. High analytical costs, pre-analytical and biological variation, incomplete metabolite annotation, small study populations, and limited external validation remain important barriers to routine veterinary application