Nonpigmented and late-pigmenting rapidly growing mycobacteria (RGM) are increasingly isolated in clinical microbiology laboratories. Their accurate identification remains problematic because classification is labor intensive work and because new taxa are not often incorporated into classification databases. Also, 16S rRNA gene sequence analysis underestimates RGM diversity and does not distinguish between all taxa. We determined the complete nucleotide sequence of the rpoB gene, which encodes the bacterial ␤ subunit of the RNA polymerase, for 20 RGM type strains. After using in-house software which analyzes and graphically represents variability stretches of 60 bp along the nucleotide sequence, our analysis focused on a 723-bp variable region exhibiting 83.9 to 97% interspecies similarity and 0 to 1.7% intraspecific divergence. Primer pair Myco-F-Myco-R was designed as a tool for both PCR amplification and sequencing of this region for molecular identification of RGM. This tool was used for identification of 63 RGM clinical isolates previously identified at the species level on the basis of phenotypic characteristics and by 16S rRNA gene sequence analysis. Of 63 clinical isolates, 59 (94%) exhibited <2% partial rpoB gene sequence divergence from 1 of 20 species under study and were regarded as correctly identified at the species level. Mycobacterium abscessus and Mycobacterium mucogenicum isolates were clearly distinguished from Mycobacterium chelonae; Mycobacterium mageritense isolates were clearly distinguished from "Mycobacterium houstonense." Four isolates were not identified at the species level because they exhibited >3% partial rpoB gene sequence divergence from the corresponding type strain; they belonged to three taxa related to M. mucogenicum, Mycobacterium smegmatis, and Mycobacterium porcinum. For M. abscessus and M. mucogenicum, this partial sequence yielded a high genetic heterogeneity within the clinical isolates. We conclude that molecular identification by analysis of the 723-bp rpoB sequence is a rapid and accurate tool for identification of RGM.Rapidly growing mycobacteria (RGM) that require less than 7 days to produce easily visible colonies on solid media (42) comprise 56 environmental species. Fifteen species commonly encountered in humans and animals (7, 39) belong primarily to the Mycobacterium chelonae-abscessus, Mycobacterium fortuitum, and Mycobacterium smegmatis groups (7). They are increasingly encountered in clinical microbiology laboratories (54,65,67,70,76). They are responsible for pseudo-outbreaks of health care-associated septicemia and lung disease following bronchoscopy (1, 2, 37, 69). They are also responsible for colonization of airways (8, 15); skin and soft-tissue infections characterized by slowly progressive granulomatous inflammation, lymphadenitis, disseminated infection, and chronic pulmonary disease (4,7,26,28,66,69,75). Also, communityacquired outbreaks of skin infection following liposuction (43), M. fortuitum furunculosis following footbaths (73), hypersensitivit...

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