Molecular Epidemiology and Genetic Diversity of Zoonotic Pathogens in Domestic and Wild Animals in Pakistan

Abstract

Pakistan, positioned at the crossroads of South Asia, Central Asia, and the Middle East, harbors exceptional ecological and epidemiological diversity that facilitates the circulation and emergence of zoonotic pathogens across domestic livestock, wildlife, and human populations. This review synthesizes molecular epidemiological data and genetic diversity studies on key zoonotic agents in Pakistani animals, focusing on high-burden pathogens including Brucella spp., Coxiella burnetii (Q fever), Toxoplasma gondii, Theileria spp. (theileriosis), Babesia spp., Crimean-Congo hemorrhagic fever virus (CCHFV), and tick-borne rickettsiae. Livestock particularly small ruminants (sheep and goats), cattle, and camels serve as primary reservoirs, with prevalence often exceeding 20–50% in endemic regions, driven by communal grazing, transhumance, communal water sources, and close human–animal contact. Molecular tools (PCR, qPCR, MLST, whole-genome sequencing, and phylogenetics) reveal significant genetic heterogeneity: multiple Brucella abortus and B. melitensis biovars, diverse T. gondii genotypes (predominantly types I and III with atypical recombinant strains), and geographically structured CCHFV clades linked to Hyalomma ticks. Wildlife (e.g., rodents, bats, wild ungulates) acts as spillover/amplification hosts for several agents, while interspecies transmission is amplified by pastoral practices and climate-driven vector range expansion. Economic losses from tick-borne diseases alone approach USD 200 million annually, compounded by public health risks from under-diagnosed human cases. The review highlights critical surveillance gaps, the need for One Health-integrated molecular monitoring, and the importance of genotyping for tracing transmission dynamics and informing targeted control strategies in this high-risk zoonotic hotspot.