Protocol for detection of

1. A method of diagnosing inflammatory bowel disease in those patients who have bowel disease caused by Mycobacterium avium subspecies paratuberculosis (MAP) using a sample of peripheral blood tissue comprising the steps of:

selecting a blood sample from at least a single patient of selected patients;

culturing the blood sample for a period of time sufficient to obtain a sufficient growth of MAP to subject to PCR; and

detecting MAP therefrom, said PCR method used to detect MAP comprising using one or more of the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3 and SEQ ID NO:4 as primers for nested PCR, said patients being human patients, and said sample of blood consisting of the buffy coat.

2. The method of claim 1 , wherein the human patient has inflammatory bowel disease selected from at least one of: Crohn's disease, irritable bowel disease (IBD), and ulcerative colitis.

3. The method of claim 1 wherein the inflammatory bowel disease is Crohn's disease.

4. The method of claim 1 , further comprising treating MAP infected patients who have MAP detected in their blood with an anti-MAP effective amount of an anti-MAP compound and a pharmaceutically acceptable excipient therefor.

5. The method of claim 2 , further comprising treating MAP infected patients who have MAP detected in their blood with an anti-MAP effective amount of an anti-MAP compound and a pharmaceutically acceptable excipient therefor.

6. The method of claim 4 wherein said anti-MAP compound comprises an antibiotic.

7. The method of claim 6 , wherein said effective amount is an amount sufficient to eliminate MAP from registering positive in a blood test.

8. The method of claim 1 wherein the time required to culture the blood sample is approximately 8 weeks to approximately 12 weeks.

9. The method of claim 8 , wherein the time required to culture the blood sample is approximately 12 weeks.

10. The method of claim 1 where the blood sample is cultured in media selective for MAP.

11. The method of claim 1 wherein the media selective for MAP is selected from the group consisting of Mycobacterial Growth Indicator Tube (MGIT) or BACTEC.

12. The method of claim 11 , wherein the MGIT or BACTEC is further supplemented with 1% sucrose.

13. The method of claim 1 wherein the primers comprise one or more of the group consisting of Seq ID 1, Seq ID 2, Seq ID 3 and Seq ID 4 and nucleotide polymorphisms thereof.

14. The method of claim 1 wherein one or more of Seq ID 1 or Seq ID 2 are used as primers in the first round of PCR and one or more of Seq ID 3 or Seq ID 4 were used in the second round of PCR.

15. The method, as in claim 13 wherein one or more of Seq ID 1 or Seq ID 2 are used as primers in the first round of PCR and one or more of Seq ID 3 or Seq ID 4 are used in the second round of PCR.

16. A method for monitoring and evaluating the course of inflammatory bowel disease caused by MAP comprising:

selecting a blood sample from at least a single patient of selected patients;

culturing the blood sample for a period of time sufficient to obtain a sufficient growth of MAP to subject to PCR;

detecting MAP therefrom;

obtaining a positive result from MAP; and

continuing to repeat said test at intervals throughout treatment wherein the method PCR method used to detect MAP comprises using one of more of the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3 and SEQ ID NO:4 as primers for nested PCR, said patients being human patients, and said sample of blood consisting of the buffy coat.

17. The method, as in claim 16 wherein the inflammatory bowel disease is Crohn's disease.

18. The method, as in claim 1 wherein the volume of blood extracted from the patient for use in the test is 4 mls or greater.