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Updated: May 5, 2026
Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
Published on: March 19, 2018
Comparing diarrhoeic grades and pathogens present in faecal samples obtained from Danish calves infected with one or
John Elmerdahl Olsen1, Birgitta Svensmark2, Lene Agerskov2
1Section of Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.
Background:
Calf diarrhoea is a common disease manifestation caused by a variety of pathogens, which are often concurrently detectable in faecal samples from affected calves. It is unknown if co-infections lead to more severe diarrhoea than single-pathogen infections.
Methods:
A total of 170 faecal samples were obtained from diarrhoeic calves, and the faecal material was graded in diarrhoeic severity from I to III. The pathogens present in the samples were then identified using a multiplex qPCR assay.
Results:
Clostridium perfringens type A and Cryptosporidium parvum were the most frequently detected pathogens and were present in 47% and 42% of the faecal samples, respectively. C. parvum was the most frequently detected pathogen in samples with diarrhoeic grade III, while Escherichia coli F5-positive samples had the highest relative frequency of samples with diarrhoeic grade III. Approximately one-third of the samples contained at least two different pathogens. For all diarrhoeic grades, the number of samples with one or more pathogens detected was greater than the number of samples with no pathogens detected, but this difference was only significant for diarrhoeic grade III.
Limitations:
Only pathogens detected by one specific multiplex qPCR assay were identified, meaning that other pathogens causing diarrhoea in these calves could have been overlooked.
Conclusions:
Co-infections were not associated with a higher diarrhoeic grade compared to single-pathogen infections in calves. In single-pathogen infections, C. parvum was significantly more prevalent in samples with diarrhoeic grade III, when compared to diarrhoeic grades I and II combined.
