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Background  The genetic characterization of  Cryptosporidium  and  Giardia  has important implications for investigating their epidemiology and underpins their control. We undertook the first molecular epidemiological survey of domestic bovids in selected regions of Sri Lanka to establish whether they excreted  Cryptosporidium  and/or  Giardia  with zoonotic potential.    Methods  Faecal samples were collected from dairy calves (n = 340;  Bos taurus ; < 3 months of age; weekly sampling for six weeks) and water buffaloes (n = 297;  Bubalus bubalis ; <6 months and ≥6 months of age; one sampling) from seven different farms in Sri Lanka. Genomic DNAs were extracted from individual faecal samples and then tested for the presence of parasite DNA using a PCR-based mutation scanning-targeted sequencing-phylogenetic approach, employing genetic markers within the small subunit of nuclear ribosomal RNA and 60 kDa glycoprotein genes (designated p SSU  and p gp60 , respectively) for  Cryptosporidium , and within the triose phosphate isomerise (p tpi ) gene for  Giardia .    Results  Based on p SSU  sequence data,  C. bovis ,  C. ryanae  and six new genotypes that were genetically similar but not identical to  C. andersoni  (n = 1),  C. bovis  (n = 1),  C. ryanae  (n = 3) and  C. suis  (n = 1) were recorded in cattle. For p SSU , two other, new genotypes were defined in water buffalo, which were genetically most similar to  Cryptosporidium  genotypes recorded previously in this host species in other countries including Australia. Consistent with the findings for p SSU , no species or genotypes of  Cryptosporidium  with zoonotic potential were detected using p gp60.  Based on p tpi  sequence data,  G. duodenalis  assemblages A and E were detected in four and 137 samples from cattle, respectively, and assemblage E in two samples from water buffaloes.    Conclusions  The present study showed that  C. parvum , the most commonly reported zoonotic species of  Cryptosporidium  recognised in bovine calves globally, was not detected in any of the samples from pre-weaned calves tested in the present study. However, eight new genotypes were recorded. Future studies of different host species in various regions are required to investigate the molecular epidemiology of cryptosporidiosis and giardiasis in Sri Lanka and neighbouring countries in South Asia.

parasites and vectors

First molecular characterization of Cryptosporidium and Giardia from bovines (Bos taurus and Bubalus bubalis) in Sri Lanka: unexpected absence of C. parvum from pre-weaned calves