Mycobacterium arupense sp. nov., a non-chromogenic bacterium isolated from clinical specimens

1 ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA 2 Department of Pathology, University of Utah, Salt Lake City, UT 84108, USA 3 Texas Department of State Health Services, Austin, TX 78756, USA 4 Microbiology Division, Johns Hopkins University School of Medicine, Baltimore, MD 21087, USA Correspondence Joann L. Cloud cloudjl{at}aruplab.com Several Mycobacterium -like organisms related to the Mycobacterium terrae complex have been isolated from clinical samples. In the clinical microbiology laboratory, partial 16S rRNA gene sequencing (approximately the first 500 bp) rather than full 16S rRNA gene sequencing is often used to identify Mycobacterium species. Partial 16S rRNA gene sequence analysis revealed 100 % similarity between 65 clinical isolates and Mycobacterium sp. MCRO 6 (GenBank accession no. X93032 ). Even after sequencing the nearly full-length 16S rRNA gene, closest similarity was only 99.6 % to Mycobacterium nonchromogenicum ATCC 19530 T . Sequencing of the nearly full-length 16S rRNA gene, the 16S–23S internal transcribed spacer region and the hsp65 gene did not reveal genotypic identity with the type strains of M. nonchromogenicum , M. terrae or Mycobacterium triviale . Although sequence analysis suggested that these clinical isolates represented a novel species, mycolic acid analysis by HPLC failed to distinguish them from M. nonchromogenicum . Therefore, phenotypic analysis including growth characterization, antibiotic susceptibility testing and biochemical testing was performed. These strains from clinical samples should be recognized as representing a novel species of the genus Mycobacterium , for which the name Mycobacterium arupense sp. nov. is proposed. The type strain is AR30097 T (=ATCC BAA-1242 T =DSM 44942 T ). Abbreviations: FL-HPLC, fluorescence detection HPLC; ITS1, internal transcribed spacer region 1; NTM, non-tuberculous mycobacteria The GenBank/EMBL/DDBJ accession numbers for the sequences of the 16S rRNA gene ( E. coli bases 8–1494), hsp65 gene and 16S–23S ITS1 region of M. arupense AR30097 T are respectively DQ157760 , DQ168662 and DQ168663 . Details of PCR primers, a comparison of the 16S rRNA gene V3 region among various Mycobacterium species and a sequence chromatogram and sequence alignment showing polymorphisms observed in the ITS1 region of M. arupense strains are available as supplementary material in IJSEM Online. Present address: Department of Pathology and Laboratory Services,