Mycobacterium avium subsp. paratuberculosis isolates from Canadian dairy cows (Raw sequence reads), April 26 2023

Whole genome sequencing (WGS) was performed to genetically characterize bacterial isolates from Johne's disease (JD) cattle infected with Mycobacterium avium ssp paratuberculosis (MAP). The objective of the project was to perform an analysis based on the basic SNPs to assign an individual signature to each isolate in order to identify the presence of a mixed genotype infection and to document the transmission of the disease between the herds, confirmed by animal movement data.Source populations were selected from 22 Canadian herds, including major dairy herds in the provinces of Quebec and Ontario, based on the reported incidence of JD in these herds. During a longitudinal study (3 to 5 years), biological samples (blood and feces) were taken every six months from all cows. Fecal PCR and blood ELISA were used to diagnose MAP-infected cows. The bacterial culture was carried out from fecal samples whose presence of MAP had been confirmed by PCR. Agriculture and Agri-Food Canada was responsible for the logistics of collecting MAP isolates from fecal samples and preparing them for sequencing, including mycobacterial culture, collection of MAP phenotypes, cryopreservation, axenic cultures and DNA extraction. This research was supported by Agriculture and Agri-Food Canada for the collection of biological samples and phenotypes during two overlapping longitudinal studies (research projects J-000075 and J-000079).Drs. Nathalie Bissonnette (Sherbrooke Research and Development Center of Agriculture and Agri-Food Canada) and Kapil Tahlan (Memorial University, Newfoundland and Labrador) are co-investigators of the project. All sequenced MAP isolates were collected from a single colony selected on Herrold's egg yolk agar slants. On-farm monitoring, identification of cows with paratuberculosis, analysis of feces, and cultivation and storage of strains were carried out by Agriculture and Agri-Food Canada. WGS analysis was supported by Dairy Research Cluster 3 Activity 9 (Dairy Farmers of Canada, Canadian Dairy Network and Agriculture and Agri-Food Canada J-002095) under the AgriScience Program of the Canadian Partnership for Food 'agriculture.