Method and system for detection of mycobacteria in human samples

A method of treating Crohn's Disease in a subject in need thereof comprising the steps of:

• a) obtaining a human blood or peripheral blood mononuclear cell (PBMC) sample from a subject diagnosed with Crohn's Disease;
• b) lysing cells of the sample to release any viable target mycobacterial cell;
• c) admixing a broad host range mycobacteriophage with the sample under conditions suitable to allow the bacteriophage to infect any viable target mycobacterial cell present in the sample;
• d) removing any bacteriophage not infecting a viable target mycobacterial cell;
• e) admixing at least a portion of the admixture of step c) following the removal of step d) with bacteria capable of supporting replication of the bacteriophage;
• f) plating at least a portion of the admixture of step e) on a substrate to support growth of the bacteria;
• g) quantifying the number of bacteriophage plaques that form;
• h) discriminating between infected and asymptomatic subjects, comprising identifying the subject as infected when the number of bacteriophage plaques is statistically significantly greater than a reference number of bacteriophage plaques, or as asymptomatic when the number of bacteriophage plaques is not statistically significantly greater than a reference number of bacteriophage plaques, wherein the reference number of bacteriophage plaques is a reference number of plaques in asymptomatic human hosts;
• and
• i) administering a pharmaceutical composition for inhibiting or disrupting microorganism growth or treating a microbial infection to a subject identified as infected.