Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays

Species identification within the genus Mycobacterium and subsequent antibi otic susceptibility testing still rely on time-consuming, culture-based met hods. Despite the recent development of DNA probes, which greatly reduce as say time, there is a need for a single platform assay capable of answering the multitude of diagnostic questions associated with this genus. We descri be the use of a DNA probe array based on two sequence databases: one for th e species identification of mycobacteria (82 unique 16S rRNA sequences corr esponding to 54 phenotypical species) and the other for detecting Mycobacte rium tuberculosis rifampin resistance (rpoB alleles). Species identificatio n or rifampin resistance was determined by hybridizing fluorescently labele d, amplified genetic material generated from bacterial colonies to the arra y. Seventy mycobacterial isolates from 27 different species and 15 rifampin -resistant M. tuberculosis strains were tested. A total of 26 of 27 species were correctly identified as well as all of the rpoB mutants. This paralle l testing format opens new perspectives in terms of patient management for bacterial diseases by allowing a number of genetic tests to be simultaneous ly run.