Sequence-based identification of Mycobacterium species using the MicroSeq 500 16S rDNA bacterial identification system

We evaluated the MicroSeq 500 16S rDNA Bacterial Sequencing Ei;it (PF, Appl ied Biosystems), a 500 bp sequence-based identification system, for its abi lity to identify clinical Mycobacterium isolates. The organism identity was determined by comparing the 16S rDNA sequence to the MicroSeq database, wh ich consists primarily of type strain sequences. A total of 113 isolates (1 8 different species), previously recovered and identified by routine method s from two clinical laboratories, were analyzed by the MicroSeq method. Iso lates with discordant results were analyzed by hsp65 gene sequence analysis and in same cases repeat phenotypic identification, AccuProbe rRNA. hybrid ization (Gen-Probe, Inc., San Diego, Calif.), or high-performance liquid ch romatography of mycolic acids. For 93 (82%) isolates, the MicroSeq identity was concordant with the previously reported identity. For 18 (16%) isolate s, the original identification was discordant with the MicroSeq identificat ion. Of the 18 discrepant isolates, 7 (six unique sequences) were originall y misidentified by phenotypic analysis or the AccuProbe assay but were corr ectly identified by the MicroSeq assay. Of the 18 discrepant isolates, 11 ( seven unique sequences) were unusual species that were difficult to identif y by phenotypic methods and, in all but one case, by molecular methods. The remaining two isolates (2%) failed definitive phenotypic identification, b ut the MicroSeq assay was able to definitively identify one of these isolat es. The MicroSeq identification system is an accurate and rapid method for the identification of Mycobacterium spp.