Methods for the identification of microorganisms or infectious disorders are disclosed, comprising obtaining a suitable sample from sources such as persons, animals, plants, food, water or soil. The methods also comprise providing tailored nucleic acid substrate(s) designed to react with a type 1 topoisomerase from one or more microorganism(s) or infectious agent(s), and incubating said substrate with said sample, or extracts or preparations from the sample, so that the substrate is processed by said topoisomerase if said microorganism(s) or infectious agent(s) is present in the sample. Finally, processed substrates are identified and potentially quantified by one or more of a range of standard molecular biology methods and read-out systems. The identification and potential quantification of microorganisms and infectious agents, including but not limited to Plasmodium falciparum and Mycobacterium tuberculosis, in single or multiplexed formats enable diseases to be diagnosed, treated, or prevented through the identification of potentially harmful organisms. This disclosure includes also follow-up tests or continued monitoring to evaluate responses to treatment or eradication efforts. In a further aspect the technology enables the testing of medical or chemical treatments designed to cure or prevent diseases based upon drugs targeting type 1 topoisomerases. Finally, the reagents and platforms needed for said purposes can be compiled from loose parts or provided as user-friendly kits, potentially enabling home testing for a multitude of microorganisms or infectious agents.