Molecular Characterization of <i>Cryptosporidium</i> spp., <i>Giardia duodenalis</i>, <i>Enterocytozoon bieneusi</i> and <i>Escherichia coli</i> in Dairy Goat Kids with Diarrhea in Partial Regions of Shaanxi Province, China

<i>Cryptosporidium</i> spp., <i>Giardia duodenalis</i>, <i>Enterocytozoon bieneusi</i> and <i>Escherichia coli</i> are important diarrheal pathogens threatening the health of humans and various animals. Goats, especially pre-weaned goat kids, that carry these pathogens are important reservoirs related to human infection. In the present study, PCR-based sequencing techniques were applied to characterize <i>Cryptosporidium</i> spp., <i>G. duodenalis</i>, <i>E. bieneusi</i> and <i>E. coli</i> in 202 fecal samples of diarrheal kids for Guanzhong dairy goats from five locations in Shaanxi Province. The positive rates of <i>Cryptosporidium</i> spp., <i>G. duodenalis</i>, <i>E. bieneusi</i> and <i>E. coli</i> were 37.6% (76/202), 16.3% (33/202), 55.4% (112/202) and 78.7% (159/202) in these goat kids, respectively. Co-infection of two to four pathogens was found in 114 of 202 fecal samples. Significant differences (<i>p</i> < 0.001) in the positive rates of <i>Cryptosporidium</i> spp. and <i>G. duodenalis</i> were found among locations and age groups. Furthermore, two <i>Cryptosporidium</i> species (<i>C. parvum</i> and <i>C. xiaoi</i>), two <i>G. duodenalis</i> assemblages (E and A), nine <i>E. bieneusi</i> genotypes (CHG3, CHG1, BEB6, CHG5, CHG2, SX1, CHG28, COS-II and CD6) and two <i>E. coli</i> pathotypes (EPEC and EHEC) were identified. As for <i>Cryptosporidium</i>, two (IIdA19G1 and IIdA19G2) and two (XXIIIa and XXIIIg) subtypes were recognized in samples positive for <i>C. parvum</i> and <i>C. xiaoi</i>, respectively. A phylogenetic analysis based on the ITS locus of <i>E. bieneusi</i> indicated that all nine genotypes of <i>E. bieneusi</i> identified in this study belonged to the group 2. Four virulence factors (<i>ehxA</i>, <i>eae</i>, <i>stx2</i> and <i>stx1</i>) of EPEC and EHEC were found in <i>E. coli</i> strains. Collectively, this study explored the colonization frequency of <i>Cryptosporidium</i> spp., <i>G. duodenalis</i>, <i>E. bieneusi</i> and <i>E. coli</i> in diarrheal kids of Guanzhong dairy goats in Shaanxi Province and expanded our understanding of the genetic composition and zoonotic potential of these pathogens in goats.