Computer controlled methods, systems and apparatus for detecting an infectious agent in a host cell, an animal cell, or plant cell, a body fluid or tissue sample to provide information useful to diagnose a disease or prognosticate disease susceptibility, extent or outcome are provided. In one illustrative embodiment, the infected animal cell is a Chlamydia infected mononuclear phagocyte in a blood sample. In another illustrative embodiment, the infected body fluid is a blood sample infected with “fee floating”Chlamydia. Detection and preferably, quantification of such an infected mononuclear phagocyte(s) or blood sample provides information useful in diagnosing or prognosticating susceptibility, extent or outcome of patients suspected of suffering from vascular, coronary or central nervous disease(s) or disorder(s).