Prevalence and infection characteristics of common pathogens associated with calf diarrhoea in Danish dairy calves.

Diarrhoea in calves is one of the most common disease manifestations, particularly within the first weeks of life. In the present study, 392 diarrhetic faecal samples from calves 0-28 days old were obtained from Danish dairy farms through routine veterinary diagnostics. Bovine pathogens (Clostridium perfringens type A, B and C, Salmonella enterica serovar Dublin, coronavirus, rotavirus, Cryptosporidium parvum, Coccidia (Eimeria) and Escherichia coli F5) were detected and quantified by qPCR (Enterit4calves assay). In addition, samples were cultured to semi-quantify the level of E. coli. Samples were primarily obtained from calves within the first two weeks (∼90 % of the samples), reflecting this critical period for diarrhoea development. Overall, C. perfringens type A, rotavirus and C. parvum were the most prevalent pathogens, detected in 28-39 % of the samples, while coronavirus and E. coli F5 were found in less than five percent of the samples. The remaining pathogens were not detected by qPCR in any of the samples. Culturing demonstrated moderate to massive growth of E. coli in 75 % of the samples, independent of the age of the sampled calves. For all qPCR detected pathogens, except for coronavirus and E. coli F5, dual-infection with the presence of two pathogenic agents in the sample, was the most common infection type. In samples with more than one pathogen, the quantity of each pathogen according to Ct-value was not significantly different from quantity of the same pathogen in samples where it was the only pathogen. The importance of the high prevalence of non-F5 E. coli needs to be further clarified, in particular for the types of E. coli found in moderate to massive growth in fecal samples negative for all qPCR included pathogens.