Detection of Zoonotic Spp. in Small Wild Rodents Using Amplicon-based Next-generation Sequencing

Rodents may serve as reservoirs of zoonotic species of ; however, data from molecular surveys in support of this hypothesis are still scarce. In this study, we screened faeces and rectal content from murid and cricetid rodents ( = 58) caught around three farms in Zealand, Denmark, for spp. by amplicon-based next-generation sequencing (NGS) of ribosomal genes. Selected samples were further examined using nested conventional PCR targeting SSU rRNA, gp60, and actin genes. specific DNA was identified in 40/58 (69%) samples, and in 12 (30%) of the 40 positive animals, mixed cryptosporidial infections were observed. was the species most commonly identified, found in 28 (48%) of the animals. was identified in 4 (7%) of the animals, all of which were co-infected with . The present study is the first to utilize NGS-based screening for species in wild rodents. Moreover, it is the first study to provide molecular data on in rodents sampled in Denmark and to detect DNA of in and The NGS approach was successfully applied to yield new knowledge, and the results showed that zoonotic species of are common in murid and cricetid rodents in Zealand, Denmark.