Simultaneous Genotyping and Species Identification Using Hybridization Pattern Recognition Analysis of Generic Mycobacterium DNA Arrays
- Thomas R. Gingeras1,7,
- Ghassan Ghandour1,
- Eugene Wang1,
- Anthony Berno1,
- Peter M. Small2,
- Francis Drobniewski3,
- David Alland4,
- Edward Desmond5,
- Mark Holodniy6, and
- Jorg Drenkow1
- 1Affymetrix, Santa Clara, California 95051 USA; 2Division of Infectious Disease, Stanford University, Stanford, California 94305 USA; 3Public Health Laboratory and Medical Microbiology, Kings College School of Medicine and Dentistry, East Dulwich Grove, London SE22 8QF, UK; 4Division of Infectious Disease, Montefiore Medical Center, Bronx, New York 10467 USA; 5Microbial Disease Lab, California Department of Health, Berkeley, California 94704 USA; 6Palo Alto VA Medical Center, Palo Alto, California 94304 USA
Abstract
High-density oligonucleotide arrays can be used to rapidly examine large amounts of DNA sequence in a high throughput manner. An array designed to determine the specific nucleotide sequence of 705 bp of therpoB gene of Mycobacterium tuberculosis accurately detected rifampin resistance associated with mutations of 44 clinical isolates of M. tuberculosis. The nucleotide sequence diversity in 121 Mycobacterial isolates (comprised of 10 species) was examined by both conventional dideoxynucleotide sequencing of the rpoB and 16S genes and by analysis of the rpoB oligonucleotide array hybridization patterns. Species identification for each of the isolates was similar irrespective of whether 16S sequence, rpoBsequence, or the pattern of rpoB hybridization was used. However, for several species, the number of alleles in the 16S andrpoB gene sequences provided discordant estimates of the genetic diversity within a species. In addition to confirming the array’s intended utility for sequencing the region of M. tuberculosis that confers rifampin resistance, this work demonstrates that this array can identify the species of nontuberculous Mycobacteria. This demonstrates the general point that DNA microarrays that sequence important genomic regions (such as drug resistance or pathogenicity islands) can simultaneously identify species and provide some insight into the organism’s population structure.
[The sequence data described in this paper have been submitted to GenBank under accession nos. AF09766–AF059853 and AF060279–AF060367.]
Footnotes
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↵7 Corresponding author.
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E-MAIL tom_gingeras{at}affymetrix.com; FAX (408) 481-0422.
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- Received December 10, 1997.
- Accepted February 17, 1998.
- Cold Spring Harbor Laboratory Press
