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Journal of Clinical Microbiology, January 2000, p. 246-251, Vol. 38, No. 1
0095-1137/0/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Sequence-Based Identification of Mycobacterium Species Using the MicroSeq 500 16S rDNA Bacterial Identification System

Jean Baldus Patel,1,* Debra G. B. Leonard,1 Xai Pan,2 James M. Musser,2 Richard E. Berman,3 and Irving Nachamkin1

Department of Pathology and Laboratory Medicine, The University of Pennsylvania, Philadelphia,1 and Pennsylvania State Public Health Laboratory, Pennsylvania Department of Health, Lionville,3 Pennsylvania, and Department of Pathology, Baylor College of Medicine, Houston, Texas2

Received 8 June 1999/Returned for modification 22 July 1999/Accepted 8 October 1999

We evaluated the MicroSeq 500 16S rDNA Bacterial Sequencing Kit (PE Applied Biosystems), a 500-bp sequence-based identification system, for its ability to identify clinical Mycobacterium isolates. The organism identity was determined by comparing the 16S rDNA sequence to the MicroSeq database, which consists primarily of type strain sequences. A total of 113 isolates (18 different species), previously recovered and identified by routine methods from two clinical laboratories, were analyzed by the MicroSeq method. Isolates with discordant results were analyzed by hsp65 gene sequence analysis and in some cases repeat phenotypic identification, AccuProbe rRNA hybridization (Gen-Probe, Inc., San Diego, Calif.), or high-performance liquid chromatography of mycolic acids. For 93 (82%) isolates, the MicroSeq identity was concordant with the previously reported identity. For 18 (16%) isolates, the original identification was discordant with the MicroSeq identification. Of the 18 discrepant isolates, 7 (six unique sequences) were originally misidentified by phenotypic analysis or the AccuProbe assay but were correctly identified by the MicroSeq assay. Of the 18 discrepant isolates, 11 (seven unique sequences) were unusual species that were difficult to identify by phenotypic methods and, in all but one case, by molecular methods. The remaining two isolates (2%) failed definitive phenotypic identification, but the MicroSeq assay was able to definitively identify one of these isolates. The MicroSeq identification system is an accurate and rapid method for the identification of Mycobacterium spp.

* Corresponding author. Mailing address: Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, 4th Floor, Gates Bldg., 3400 Spruce St., Philadelphia, PA 19104-4283. Phone: (215) 662-6651. Fax: (215) 662-6655. E-mail: jbpatel{at}mail.med.upenn.edu.

Journal of Clinical Microbiology, January 2000, p. 246-251, Vol. 38, No. 1
0095-1137/0/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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