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rpoB gene sequence-based characterization of emerging non-tuberculous mycobacteria with descriptions of Mycobacterium bolletii sp. nov., Mycobacterium phocaicum sp. nov. and Mycobacterium aubagnense sp. nov.

Unité des Rickettsies, CNRS UMR 6020 IFR 48, Faculté de Médecine, 27, Boulevard Jean Moulin, Université de la Méditerranée and Assistance Publique-Hôpitaux de Marseille Timone, Fédération de Microbiologie Clinique, Marseille, France

Correspondence
Michel Drancourt
Michel.Drancourt{at}medecine.univ-mrs.fr

Over the past 10 years, 16S rRNA gene sequencing has contributed to the establishment of more than 45 novel species of non-tuberculous mycobacteria and to the description of emerging mycobacterial infections. Cumulative experience has indicated that this molecular tool underestimates the diversity of this group and does not distinguish between all recognized mycobacterial taxa. In order to improve the recognition of emerging rapidly growing mycobacteria (RGM), rpoB gene sequencing has been developed. Our previous studies have shown that an RGM isolate is a member of a novel species if it exhibits >3 % sequence divergence in the rpoB gene from the type strains of established species. When applied to a collection of 59 clinical RGM isolates, rpoB gene sequencing revealed nine novel isolates (15·3 %) whereas only two isolates (3·4 %) were deemed to be novel by conventional 16S rRNA gene sequence analysis. A polyphasic approach, including biochemical tests, antimicrobial susceptibility analyses, hsp65, sodA and recA gene sequence analysis, DNA G+C content determination and cell-wall fatty acid composition analysis, supported the evidence that these nine isolates represent three novel species. Whereas Mycobacterium phocaicum sp. nov. (type strain N4^T=CIP 108542^T=CCUG 50185^T) and Mycobacterium aubagnense sp. nov. (type strain U8^T=CIP 108543^T=CCUG 50186^T; Mycobacterium mucogenicum group) were susceptible to most antibiotics, Mycobacterium bolletii sp. nov. (type strain BD^T=CIP 108541^T=CCUG 50184^T; Mycobacterium chelonae–abscessus group) was resistant to the quinolones, tetracycline, macrolides and imipenem. Only M. bolletii was resistant to clarithromycin. These data illustrate that rpoB gene sequence-based identification is a powerful tool to characterize emerging RGM and mycobacterial infections and provides valuable help in differentiating RGM at both the intra- and interspecies level, thus contributing to a faster and more efficient diagnosis and epidemiological follow-up.

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, recA, hsp65 and sodA genes of Mycobacterium bolletii BD^T, Mycobacterium phocaicum N4^T and Mycobacterium aubagnense U8^T are AY859681–AY859683, AY859687–AY859689, AY859675–AY859677 and AY862403 and AY859706–AY859707, respectively.

A table detailing whole-cell fatty acid content and a figure showing the hypervariable region of the rpoB gene are available as supplementary material in IJSEM Online.

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