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Cattle are the main reservoir host of  C. andersoni , which shows a predominance in yearlings and adults of cattle. To understand the subtypes of  C. andersoni  and the population genetic structure in Heilongjiang Province, fecal specimens were collected from 420 dairy cattle and 405 beef cattle at the age of 12–14 months in eight cattle farms in five areas within this province and were screened for the presence of  Cryptosporidium  oocysts by microscopy after Sheather’s sugar flotation technique. The average prevalence of  Cryptosporidium  spp. was 19.15% (158/825) and all the  Cryptosporidium  isolates were identified as  C. andersoni  by the SSU rRNA gene nested PCR-RFLP using  SspI ,  VspI  and  MboII  restriction enzymes. A total of 50  C. andersoni  isolates were randomly selected and sequenced to confirm the RFLP results before they were subtyped by multilocus sequence typing (MLST) at the four microsatellite/minisatellite loci (MS1, MS2, MS3 and MS16). Four, one, two and one haplotypes were obtained at the four loci, respectively. The MLST subtype A4,A4,A4,A1 showed an absolute predominance and a wide distribution among the six MLST subtypes obtained in the investigated areas. Linkage disequilibrium analysis showed the presence of a clonal population genetic structure of  C. andersoni  in cattle, suggesting the absence of recombination among lineages. The finding of a clonal population genetic structure indicated that the prevalence of  C. andersoni  in cattle in Heilongjiang Province is not attributed to the introduction of cattle. Thus, prevention and control strategies should be focused on making stricter measures to avoid the occurrence of cross-transmission and re-infection between cattle individuals. These molecular data will also be helpful to explore the source attribution of infection/contamination of  C. andersoni  and to elucidate its transmission dynamics in Heilongjiang Province, even in China.

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MLST Subtypes and Population Genetic Structure of Cryptosporidium andersoni from Dairy Cattle and Beef Cattle in Northeastern China’s Heilongjiang Province