subtype distribution in domestic and captive wild bird species from Brazil using next generation amplicon sequencing.

is a food and water borne intestinal parasite commonly identified in humans and many other animals worldwide. Of the nine potentially zoonotic subtypes of , seven have been reported in bird species. However molecular studies of subtype diversity in birds are limited. In this study, fecal samples from 109 domestic and captive wild birds from Minas Gerais, Brazil were tested for the presence of subtypes using PCR and next generation amplicon sequencing of a fragment of the small subunit ribosomal RNA (SSU rRNA) gene. Birds from 11 orders and 38 species from both local markets and bird conservation facilities were sampled. was present in 14.7% of samples, and eight subtypes, six previously reported (ST5, ST6, ST7, ST10, ST14, ST24) and two novel subtypes (named ST27 and ST28), were identified. The most commonly identified subtypes were ST7 and ST6 identified in 10 (62.5%) and 6 (37.5%) of 16 positive samples. At least one of the three zoonotic subtypes identified (ST5, ST6, and ST7) was found in 81.3% of positive samples. Infection with multiple subtypes was common and identified in 62.5% of positive samples. This study is the first to use next generation amplicon sequencing to characterize subtype diversity in birds. The findings presented here confirm that birds may serve as reservoirs of zoonotic subtypes of and that the role of birds in transmission of to humans requires further study.