Evaluation of PCR–RFLP analysis targeting hsp65 and rpoB genes for the typing of mycobacterial isolates in Malaysia

In this study, PCR–RFLP analysis (PRA) targeting <i>hsp65</i> and <i>rpoB</i> gene regions was evaluated for the identification of mycobacterial species isolated from Malaysian patients. Overall, the <i>hsp65</i> PRA identified 92.2 % of 90 isolates compared to 85.6 % by the <i>rpoB</i> PRA. With 47 rapidly growing species, the <i>hsp65</i> PRA identified fewer (89.4 %) species than the <i>rpoB</i> PRA (95.7 %), but with 23 slow-growing species the reverse was true (91.3 % identification by the <i>hsp65</i> PRA but only 52.5 % by the <i>rpoB</i> PRA). There were 16 isolates with discordant PRA results, which were resolved by 16S rRNA and <i>hsp65</i> gene sequence analysis. The findings in this study suggest that the <i>hsp65</i> PRA is more useful than the <i>rpoB</i> PRA for the identification of <i>Mycobacterium</i> species, particularly with the slow-growing members of the genus. In addition, this study reports 5 and 12 novel restriction patterns for inclusion in the <i>hsp65</i> and <i>rpoB</i> PRA algorithms, respectively.