The invention provides a method for detecting a low-virulence infection in a patient, by distinguishing true infections from false positives. The method comprises testing for the presence or amount of commensal microorganism(s) in a patient sample, and in particular, the commensal microorganism is one that may be causative of a low-virulence infection. Since testing for commensal microorganisms will lead to a large number of false-positives due to frequent sample contamination, the sample is also tested to discriminate true chronic infection from these false positives. In accordance with the invention, false positives are discriminated by evaluating a nucleic acid profile from the sample.
