Metatranscriptomic surveillance reveals overlooked liver-associated parasite diversity and broad host ranges in small mammals from southern China

Abstract

Parasite communities in the internal organs of small mammals remain poorly characterized because metatranscriptomic pathogen discovery has largely focused on viruses and bacteria. We individually sequenced liver transcriptomes from 351 small mammals collected across 14 cities in Guangdong Province, China, and combined sequence-based detection with phylogenetic, abundance, transcriptional, and morphological analyses. Parasites were detected in 148 animals (42.2%). Four liver-associated taxa were identified, including three putatively novel or highly divergent lineages. Trichinellidae sp1 dominated the community, occurring in 36.2% of animals (127/351), five host species spanning Rodentia and Eulipotyphla, and all surveyed cities. Hydatigera taeniaeformis occurred in 3.7% (13/351), and its identification was supported by hepatic cysts and morphologically recovered strobilocerci. Eucoccidiorida sp1 and Trypanosoma sp1 were detected sporadically. Mapping to available reference genomes revealed transcripts from multiple genes and functional categories, supporting genuine biological signals rather than isolated marker-gene matches. Amsterdam virus covaried with Trichinellidae sp1 (r = 0.59), whereas Wenzhou tapeworm virus 1 covaried with H. taeniaeformis (r = 0.47). These findings reveal an unexpectedly prevalent, phylogenetically diverse, and broadly distributed liver-associated parasite community and establish individual-organ metatranscriptomics as a useful framework for parasite discovery and surveillance. Author summary Rodents and shrews can host parasites of medical or veterinary importance, but their liver-associated parasites have rarely been surveyed systematically. We examined liver RNA from 351 small mammals collected throughout Guangdong Province. More than two-fifths carried at least one parasite. The most striking finding was an uncharacterized trichinellid parasite in over one-third of the animals. It occurred in five host species—including both rodents and shrews—and in every surveyed city, indicating an unusually broad host and geographic distribution. We also detected the tapeworm Hydatigera taeniaeformis, supported by visible liver cysts and recovered larvae, and two rare protozoan lineages. These findings reveal how much parasite diversity can remain hidden when surveillance overlooks particular organs or focuses on other pathogens. Individual-organ RNA sequencing can therefore complement conventional parasitology and help prioritize widespread or unusual lineages for taxonomic, ecological, and public-health investigation.