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The Journal of the Japanese Society for Clinical Microbiology |
Biblioraphy Information
| ArticleTitle |
Novel identification of clinical mycobacterium isolates by pyrosequencing of 16S ribosomal RNA gene |
| Language |
J |
| AuthorList |
Shiomi Yoshida1), Motohisa Tomita2) |
| Affiliation |
1) Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Osaka, Japan
2) Clinical Laboratory, National Hospital Organization Kinki-chuo Chest Medical Center, Osaka, Japan |
| Publication |
J.J.C.M.: 25 (1), 26-33, 2014 |
| Received |
May 13, 2014 |
| Accepted |
September 8, 2014 |
| Abstract |
Conventional methods for identification of mycobacterium isolates are often inexact and time consuming. Pyrosequencing of a short hypervariable 16S rRNA gene fragment is accurate, rapid and effective. We have retrospectively evaluated the discriminative power of pyrosequencing for mycobacterium identification, and compared with the results of the routine laboratory tests and conventional 16S rRNA gene sequencing (Sanger sequencing). A series of 100 clinical isolates were investigated, furthermore, growth rate and pigment production were annotated when species could not be resolved by pyrosequencing alone. 93 of the identified isolates by commercial kits and phenotypic characterization were unambiguously identified by both Sanger sequencing and pyrosequencing. An additional 3 isolates were directly identified to same species by Sanger sequencing and routine test, but the discrepancies with pyrosequencing (1 M. avium complex, 2 M. parascrofulaceum). By both sequencing methods, one isolate was identified as M. mageritense, however, identified as M. peregrinum by routine test. The remaining 3 isolates needed both sequencings because the discrepancies between Runyon classification (IV, III and II) and both sequencings were resulted (Tsukamurella sp, M. szulgai or M. angelicum, and M. colombiense or M. bouchedurhonense). We consider the pyrosequencing procedure to be a useful alternative for the identification of several mycobacterium species, and a versatile tool for the characterization of clinical mycobacterium isolates. At times it requires additional tests for definite species diagnosis and correct identification. |
| Keywords |
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