The invention concerns the detection of pathogenic mycobacterium comprising Mycobacterium avium subsp. paratuberculosis (Map) and genomic variants in a bulk milk sample, and more particularly a method for herd management that stratifies the risk of bulk tank milk lots derived from diagnostic-tested subgroups potentially containing DNA from pathogenic mycobacterium including Map. The method involves creating defined risk groups (categories) of milk-producing animals, such as dairy cows, for the presence of Map or related genomic variants in their milk. Another aspect of the invention concerns a method to strengthen the ability of milk-producing animals to resist environmental challenges by Map based on identifying those animals that have and maintain a low antibody level to Map using their female progeny as replacement animals.