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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
medicine
Computational approach involving use of the internal transcribed spacer 1 region for identification of Mycobacterium species
Journal of Clinical Microbiology, Volume 43, No. 8, Year 2005
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Description
The rapid and reliable identification of clinically significant Mycobacterium species is a challenge for diagnostic laboratories. This study evaluates a unique sequence-dependent identification algorithm called MycoAlign for the differential identification of Mycobacterium species. The MycoAlign system uses pan-Mycobacterium-specific primer amplification in combination with a customized database and algorithm. The results of testing were compared with conventional phenotypic assays and GenBank sequence comparisons using the 16S rRNA target. Discrepant results were retested and evaluated using a third independent database. The custom database was generated using the hypervariable sequences of the internal transcribed spacer 1 (ITS-1) region of the rRNA gene complex from characterized Mycobacterium species. An automated sequence-validation process was used to control quality and specificity of evaluated sequence. A total of 181 Mycobacterium strains (22 reference strains and 159 phenotypically identified clinical isolates) and seven nonmycobacterial clinical isolates were evaluated in a comparative study to validate the accuracy of the MycoAlign algorithm. MycoAlign correctly identified all referenced strains and matched species in 94% of the phenotypically identified Mycobacterium clinical isolates. The ITS-1 sequence target showed a higher degree of specificity in terms of Mycobacterium identification than the 16S rRNA sequence by use of GenBank BLAST. This study showed the MycoAlign algorithm to be a reliable and rapid approach for the identification of Mycobacterium species and confirmed the superiority of the ITS-1 region sequence over the 16S rRNA gene sequence as a target for sequence-based species identification. Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Authors & Co-Authors
Mohamed, Amr M.
United States, Omaha
University of Nebraska Medical Center
Egypt, Asyut
Faculty of Veterinary Medicine
Kuyper, Dan J.
United States, Omaha
University of Nebraska Omaha
Iwen, Peter Charles
United States, Omaha
University of Nebraska Medical Center
Ali, Hesham H.
United States, Omaha
University of Nebraska Omaha
Bastola, Dhundy R.
United States, Omaha
University of Nebraska Medical Center
Hinrichs, Steven H.
United States, Omaha
University of Nebraska Medical Center
Statistics
Citations: 36
Authors: 6
Affiliations: 3
Identifiers
Doi:
10.1128/JCM.43.8.3811-3817.2005
ISSN:
00951137
Research Areas
Genetics And Genomics