Genetic diversity and zoonotic transmission potential of Blastocystis sp. in Southeast Asia: A scoping review of molecular evidence

<i>Blastocystis</i> sp. is a biological paradox, functioning as both a prevalent gut inhabitant and a potential pathogen. This scoping review synthesizes molecular evidence on the genetic diversity and zoonotic transmission dynamics of this species across Southeast Asia. Following PRISMA-ScR guidelines, we analyzed 61 molecular studies published through November 15, 2025, to map the organism's regional footprint. The results characterize <i>Blastocystis</i> sp. as a genetically diverse species complex deeply embedded in the region's human-animal interface. While ST1 and ST3 are the predominant human subtypes, Southeast Asia exhibits distinct epidemiological patterns driven by zoonotic pressure. Avian subtypes (ST6 and ST7) show unusually high prevalence in the Philippines and Indonesia, suggesting active spillover from poultry. Similarly, ST1 infections in Thailand are genetically linked to porcine reservoirs, highlighting the role of livestock and organic fertilizers in transmission. Water sources also act as critical environmental sinks for diverse subtypes (ST1-ST4), facilitating community-wide exposure. Regarding clinical significance, pathogenicity appears context-dependent rather than intrinsic. Statistical analyses associate ST1 and ST3 with Irritable Bowel Syndrome (IBS) and chronic urticaria. Conversely, other subtypes, such as ST4, are often associated with healthy gut microbiomes. Current evidence supports a passenger hypothesis, suggesting that routine treatment might not be justified based on current molecular data. However, the substantial overlap of subtypes between humans, livestock, and companion animals underscores the need for One Health-oriented control strategies. Future research must prioritize longitudinal studies to clarify when this common colonizer shifts from a commensal passenger to a driver of disease.