| Summary: | Microsporidia are considered to be highly diverged and specialized parasites, and can infect a wide variety of vertebrate and invertebrate hosts. <i>Enterocytozoon bieneusi</i> is the most prevalent species in humans and various livestock, wildlife, and companion mammals. Dogs being the most popular companion animals of humans become more and more regarded. In this study, 272 fecal specimens were collected from stray dogs from Shanghai, but the dogs were adopted in a shelter in Zhenjiang, Jiangsu Province, China. <i>E. bieneusi</i> was examined by PCR amplification of the internal transcribed spacer (ITS) region and sequence analysis. The total positive rate of <i>E. bieneusi</i> was 8.8% (24/272). Moreover, 8 genotypes were found, including three known (genotypes EbpA, Henan V and Type IV) and 5 novel genotypes (genotypes SHZJD1–5). Two samples were positive for two genotypes, one was positive fortype SHZJD4 and Henan V, the other was positive for Henan V and Type IV. In addition, phylogenetic analysis showed all genotypes obtained in this study were all clustered into the zoonotic group 1. Therefore, the risk of zoonotic transmission of pathogens such as <i>E. bieneusi</i> from stray dogs to humans potentially threaten human health, and it is time to strengthen their health management.
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