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J Med Microbiol 56 (2007), 1033-1041; DOI: 10.1099/jmm.0.47105-0
© 2007 Society for General Microbiology
ISSN 1473-5644

Identification of Mycobacterium using the EF-Tu encoding (tuf) gene and the tmRNA encoding (ssrA) gene

Sophie Mignard1,2,3 and Jean-Pierre Flandrois1,2,3

1 Universite de Lyon, Universite de Lyon 1, CNRS, UMR5558, Biometrie et Biologie Evolutive, Villeurbanne F-69622, France

2 Hospices Civils de Lyon, Lyon F-69001, France

3 Laboratoire de Bacteriologie, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Chemin du Grand Revoyet, Pierre-Benite 69495, France

Correspondence
Sophie Mignard
sophie.mignard{at}chu-lyon.fr

Received 30 November 2006
Accepted 14 March 2007

The partial nucleotide sequences encoding the elongation factor Tu (tuf gene) (652 bp) and transfer-mRNA (tmRNA or ssrA gene) (340 bp) were determined to assess the suitability of these two genes as phylogenetic markers for the classification of mycobacteria, and thus as alternative target molecules for identifying mycobacteria. A total of 125 reference strains of the genus Mycobacterium and 74 clinical isolates were amplified by PCR and sequenced. Phylogenies of the two genes constructed by the neighbour-joining method were created and compared to a concatenated tree of 16S rDNA, hsp65, sodA and rpoB genes. The phylogenetic trees revealed the overall natural relationships among Mycobacterium species. The tmRNA phylogeny was similar to that of 16S rDNA, with low resolving power. The tuf gene provided better resolution of each mycobacterial species, with a phylogeny close to that of hsp65. However, none of these methods differentiated between the members of the Mycobacterium tuberculosis complex or the subspecies of the Mycobacterium avium complex. The correct identification of clinical isolates confirms the interest of these genes, especially tuf. It is suggested from these findings that tmRNA might be useful as another housekeeping gene in a polyphyletic approach to Mycobacterium species, but not as a first-line marker of species. tuf gene analysis suggests that this gene could be used effectively for phylogenetic analysis and to identify mycobacteria.

Abbreviations: MTBC, Mycobacterium tuberculosis complex; RG, rapidly growing; SG, slowly growing.

A table of the reference strains used is available as supplementary material with the online version of this paper.






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