Abstract: The present invention provides, inter alia, methods for detecting whether a subject has an infection. These methods include (a) incubating a test sample from a subject suspected of having an infection with a labeled molecule, such as a labeled nucleoside analog, that is preferentially incorporated into a pathogenic microorganism for a period of time sufficient for the pathogenic microorganism to incorporate the labeled molecule; (b) removing any unincorporated labeled molecule from the test sample; and (c) detecting the labeled molecule within the pathogenic microorganism, if any, in the test sample, wherein the presence of labeled molecule within the pathogenic microorganism indicates that the subject has an infection.