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Background  Avian coccidiosis is an intracellular intestinal parasitic disease, caused by intracellular intestinal parasites from the genus  Eimeria , among which  Eimeria tenella  is one of the most pathogenic species and causes great economic losses. Frequent applications of anticoccidial drugs have resulted in the development of drug-resistance in  E. tenella . In the present study, we sought to determine the genetic diversity of  E. tenella  isolates prevalent in chicken farms in Hubei Province of China and examine their sensitivity to three anticoccidial drugs. The results provide useful information for the prevention and control of coccidiosis in this region.    Methods    Eimeria tenella  oocysts were isolated from faecal samples collected from different commercial broiler production farms in Hubei Province, China. After oocyst sporulation and animal inoculation for expansion of the field isolates, DNA and RNA were extracted from excysted sporozoites for molecular characterization. Species identification of field isolates were performed by polymerase chain reaction (PCR) amplification of the internal transcribed spacer 1 (ITS1) region of ribosomal DNA. Random amplified polymorphic DNA (RAPD) was used for population genetic analysis. Subsequently, sequences of the major sporozoite surface antigen (SAG), micronemal protein 2 (MIC-2) and cytochrome  b  ( cytb ) genes from genomic DNA, and the  Eimeria tenella  cation-transport ATPase ( Et Cat ATPase) gene from cDNA were obtained for genotyping using multi-sequence alignments. Finally, sensitivity of the field isolates to three commonly used anticoccidial drugs (diclazuril, decoquinate and maduramycin) were tested to assess the prevalence of drug resistance in  E. tenella  in Hubei Province of China.    Results  Analysis of the ITS1 sequences indicated that all the isolates were  E. tenella . RAPD analysis and multi-sequence alignments of the SAG, MIC-2,  Et Cat ATPase and  cytb  showed genetic diversity among these isolates. Finally, drug sensitivity tests demonstrated that all field isolates were sensitive to diclazuril but resistant to decoquinate (except for the isolates from eastern Hubei) and maduramicin.    Conclusions  Population genetic analysis indicated that genetic polymorphisms among field isolates were closely related with their regional distributions. Drug sensitivity testing demonstrated that  E. tenella  isolates in Hubei Province were sensitive to diclazuril, but resistant to maduramycin and decoquinate. The results presented here provide important information for the control and preventions of coccidiosis in the Hubei Province of China.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-017-2067-y) contains supplementary material, which is available to authorized users.

Genetic diversity and drug sensitivity studies on Eimeria tenella field isolates from Hubei Province of China