Differentiation of Hard-to-Type Bacterial Strains by RNA Mismatch Cleavage

Many bacteria are difficult to subtype due to high genetic relatedness. In the cases of pathogens of medical or veterinary importance, subtyping is an essential tool of epidemiologists. This report describes a method for molecular subtyping based on the detection of point mutations without DNA sequencing or specialized equipment. The method, known as RNA mismatch cleavage, hybridizes RNA transcripts derived from PCR-amplified DNA, with a control RNA transcript followed by RNase cleavage at point-mutation mismatches. The method was successful in distinguishing all six Brucella species tested and was able to distinguish 11 of the 18 biovars studied. Of the remaining seven biovars (all of which are Brucella abortus strains), three subgroups were identified. The method should be applicable to all hard-to-subtype bacterial strains.