Sequence analysis of the internal gene transcribed spacers of 16S-23S rRNA in clinical isolates of mycobacteria

To establish a method of sequence analysis to identify the internal gene transcribed spacers (ITS) of 16S rRNA in the clinical isolates of mycobacteria.The ITS fragment of 19 clinical isolates from sputa of patients with mycobacterial infections in a hospital in Chongqing were amplified by PCR, and the amplified fragments were directly sequenced. The sequences of the isolates were compared with those in GenBank with soft wares for DNA analysis. Experimental results showed that the levels of the ITS sequences in different isolates were quite different, and ranged from 27.1% to 99.2%. The ITS sequences of 10 strains were identical to those of Mycobacterium tuberculosis complex (MTB), M.gordanae and M.abscessus, and the ITS sequences in some isolates were not similar to any sequence in GenBank. Four isolates unidentified in the 16S rRNA analysis were proved to be M.gordanae(M4,M5,M12) or M.abscessus (M23) by the 16S 23S rRNA ITS sequence analysis. It is concluded that the sequences of ITSs of mycobacteria are much more mutable than the 16S rRNA sequences, and the sequence analysis with 16S 23S rRNA ITS may be used as a supplement for the 16S rDNA analysis in the identification of mycobacteria.