Broad-spectrum molecular detection of zoonotic agents in wild micromammals: a nationwide surveillance study in the Republic of Korea

Abstract Background Wild micromammals serve as key hosts for diverse zoonotic pathogens, maintaining these agents in natural ecosystems and facilitating potential spillover to humans. Assessing pathogen prevalence in micromammals is essential for evaluating zoonotic risk and informing public health interventions. Methods In this study, we applied the TaqMan Array Card (TAC) platform, a high-throughput molecular diagnostic tool, to micromammal-borne zoonotic pathogen surveillance. From October to November 2022, a total of 160 wild micromammals, including Apodemus agrarius (Striped field mouse) (90.6, n = 145) and Crocidura lasiura (Ussuri white-toothed shrew) (9.4%, n = 15), were collected from 12 regions. Spleen tissues were screened for 45 viral, bacterial, and protozoan pathogens using the TAC platform. Results Viral pathogens were detected at lower frequencies, including Junin virus (2.5%, n = 4) and lymphocytic choriomeningitis virus (0.6%, n = 1). In contrast, bacterial pathogens showed high prevalence, including Bartonella spp. (78.8%, n = 126), Ehrlichia spp. (47.5%, n = 76), Anaplasma spp. (46.9%, n = 75), Borrelia spp. (36.3%, n = 58), Orientia tsutsugamushi (25.6%, n = 41), Rickettsia spp. (4.4%, n = 7), and Leptospira spp. (2.5%, n = 4) as well as protozoan pathogens such as Trypanosoma spp. (87.5%, n = 140), Cryptosporidium (20.0%, n = 32), and Toxoplasma gondii (1.3%, n = 2). However, some detections particularly viral pathogens were based solely on the TAC platform and were not confirmed by conventional PCR and sequencing. Phylogenetic analyses of TAC-positive samples revealed the presence of diverse zoonotic agents, including Anaplasma phagocytophilum , Ehrlichia muris , Candidatus Ehrlichia khabarensis, Candidatus Neoehrlichia mikurensis, Borreliella afzelii , Borrelia miyamotoi , O. tsutsugamushi Saitama and Young-worl strains, Bartonella quintana , B. fuyuanensis , and B. japonica . Conclusions These findings demonstrate the widespread regional distribution of micromammal-borne zoonotic pathogens across the ROK and provide essential baseline data to support integrated One Health surveillance frameworks for emerging and re-emerging micromammal-borne zoonoses.