Fundamentals overview


Pathobiology studies were intended to provide an understanding of the complex interactions between the animal, Mycobacterium avium subspecies paratuberculosis (MAP), the organism responsible for causing Johne’s disease, and the environment. Methods and understanding gained through “pathobiology” studies supported other JDRC research programmes.

The pathobiology programme had three strands of work in the JDRC research programme. 

The most substantive part was the development of strain typing to investigate the nature of MAP infections in New Zealand. Both VNTR (Variable number tandem repeat) and SSR (short sequence repeat) methods were developed and used to examine deer, sheep and cattle samples from across New Zealand and support our understanding of disease and disease transmission. We now understand there are multiple sub-types of MAP within our livestock and that co-grazed animals are likely to be infected with the same strain. With the rapid development of technology in this field VNTR and SSR typing is being superseded by genome sequencing and the later stages of the JDRC programme were focused on providing preliminary data on MAP lineages in cattle, sheep and deer.

In the second strand of work, we investigated the nature of gut immune response in cattle exposed to both experimental and natural MAP infection. Those animals that developed clinical disease failed to recognise MAP as a pathogen and mount the correct immune response to the disease. A number of genes were identified as targets for markers of disease susceptibility from this study. 

The final strand of work established the relationship between age and disease susceptibility in deer; where it was found that younger deer were more likely to become infected and progress to clinical disease on exposure to the bacteria than more mature animals therefore practical steps should be taken on farm to isolate young deer from the disease as they are most susceptible to infection. This project was funded by the Foundation of Research Science and Technology for a number of years prior to the formation of JDRC. 

Strain typing


  • Preliminary Report on Whole Genome Sequencing, 2016 (pending publication).
  • Dairy VNTR/SSR subtyping, 2015. Download here.
  • Deer and Sheep VNTR/SSR subtyping, 2015. Download here.
  • Science review report 2011 – 2012: Molecular Strain Typing.  Desmond M. Collins,2012. Download here.
  • Science review report 2010 – 2011: Molecular Strain Typing.  Des Collins, 2011. Download here.

Papers/ Proceedings

  • DNA Typing of Recent New Zealand Isolated of Mycobacterium Avium Subsp. Paratuberculosis from Cattle, Sheep and Deer by VNTR and SSR.  Collins DM, et al.  Proceedings 11th International Colloquium on Paratuberculosis, Sydney, 2011. Download here.


  • DNA strain typing of Mycobacterium avium subsp. paratuberculosis (MAP).  Des Collins,, April 2011. Download here.

Gut immune responses


  • Veterinary Immunology and Immunopathology 145 (2012) 471– 478. Altered patterns of toll-like receptor gene expression in cull cows infected with Mycobacterium avium subsp. paratuberculosis; Supatsak Read more here.
  • Clinical and Vaccine Immunology, Sept. 2011, p. 1467–1476 Vol. 18, No. 9, Diverse Cytokine Profile from Mesenteric Lymph Node Cells of Cull Cows Severely Affected with Johne’s Disease.  Dairu Shu, et al.  Download here.
  • Veterinary Immunology and Immunopathology 149(3-4):225-36. Immune Responses associated with progression and control of infection in calves experimentally challenged with Mycobacterium avium subsp. paratuberculosis. Read more here.


  • Mucosal immune responses to Johne’s disease in cattle. Supatsak Subharat. Download here.
  • Dis-regulation of immune responses during early M. paratuberculosis infection of calves. Supatsak Subharat. June 2011. Download here.
  • Possible mechanisms how Mycobacterium avium subsp. paratuberculosis may evade host immune responses in naturally-infected cows, Bruce Buddle. Download here.
  • Reduction in the severity of Mycobacterium avium subsp. paratuberculosis infection as calves age. Dairu Shu. Download here.

Deer age susceptibility


  • Age susceptibility of red deer (Cervus elaphus) to paratuberculosis. Colin Mackintosh. 10th International Colloquium of Paratuberculosis, Minnesota, USA. Download here.


  • Veterinary Microbiology 143 (2010) 255–261. Age susceptibility of red deer (Cervus elaphus) to paratuberculosis.  C.G. Mackintosh. Read more here.
  • Veterinary Medicine International, 2012, vol 2012, Article ID 931948, 8 pages.  Longitudinal Pathogenesis Study of Young Red Deer (Cervus elaphus) after Experimental Challenge with Mycobacterium avium subsp. paratuberculosis (MAP).  Colin Mackintosh Read more here or download here.