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Background   Cryptosporidium  is a key genus of parasitic protists that infect humans and other vertebrates (mammals and birds). Birds are typically infected with  C. avium ,  C. baileyi ,  C. galli  and/or  C. meleagridis , the latter of which is recognised as being zoonotic. Stimulated by the previous finding of  C. meleagridis  subtypes IIIbA21G1R1, IIIbA22G1R1 and IIIbA26G1R1 in diarrhoeic children in Wuhan city and environs in Hubei Province, China, we performed a molecular epidemiological survey to explore whether these or similar subtypes might occur in farmed chickens in this province.    Methods  PCR-coupled sequencing analyses of regions in the small subunit ( SSU ) of the nuclear ribosomal RNA and 60 kDa glycoprotein ( gp60 ) genes were utilised to characterise  Cryptosporidium  in faecal samples from chickens ( n  = 471) from 14 farms from six distinct regions in Hubei Province.    Results   Cryptosporidium baileyi  (33/471; 7.0%) and  C. meleagridis  (15/471; 3.2%) were identified in chickens on eight farms in five of the six distinct geographical regions. No significant age-associated difference in the prevalence of  C. baileyi  was evident, whereas the prevalence of  C. meleagridis  was significantly higher in younger (≤ 4 months) than in older chickens (> 4 months). For  C. meleagridis , two subtype families, IIIb and IIIe, were defined; some of the subtypes (i.e. IIIbA26G1R1b and IIIbA22G1R1c) characterised here matched those identified previously in diarrhoeic children in Wuhan.    Conclusions  This is the first molecular study reporting the genetic identity and prevalence of  C. baileyi  and  C. meleagridis  in chickens in Hubei. The findings suggest that  C. meleagridis  subtypes IIIbA26G1R1b and IIIbA22G1R1c are cross-transmissible between chickens and humans, raising awareness about the significance of birds as potential reservoirs of zoonotic variants of  Cryptosporidium.  Future studies might focus on investigating the prevalence of ‘zoonotic’ subtypes of  Cryptosporidium meleagridis  in various species of wild and domesticated birds, and on comparing them with those found in humans in China and other countries.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-3056-5) contains supplementary material, which is available to authorized users.

Molecular investigation of Cryptosporidium in farmed chickens in Hubei Province, China, identifies ‘zoonotic’ subtypes of C. meleagridis