Population genetic structure of zoonotic Toxoplasma gondii in China revealed using multi-locus sequence typing

Background The zoonotic pathogen Toxoplasma gondii exhibits a diverse global population structure, with a few dominant lineages primarily in the Northern Hemisphere. However, reliance on low-resolution, restriction-based genotyping methods has created a “resolution ceiling,” potentially masking hidden genetic diversity and complex transmission dynamics. Methods In this study, we combined conventional PCR-restriction fragment length polymorphism (RFLP) screening with high-resolution Sanger sequencing targeting 16 genetic markers to unravel the fine-scale epidemiology of 96 T. gondii DNA samples collected from various hosts (including pigs, cats, sheep, birds, bats, and captive wildlife) across 12 provinces and regions in China. Results Our analysis identifies ToxoDB#9 as the dominant lineage (41/96 samples), revealing substantial intra-clonal diversity within this lineage. We report the North American sylvatic ToxoDB#5 (Haplogroup 12) lineage in a captive caracal in China, documenting the presence of this rare lineage outside its previously recognized range, although its public health significance remains uncertain. Population genetic analyses show high haplotype diversity consistent with clonal diversification with limited geographic structuring. Conclusion Our study provides an updated baseline for T. gondii genetic diversity in China and supports the value of systematic molecular monitoring within a One Health framework, with whole-genome sequencing required to confirm introduction scenarios, resolve transmission routes, and assess recombination.