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Title |
A Genomic Signature for Genotyping Mycobacterium tuberculosis
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Authors |
David Tarazona, Luis Jaramillo, Victor Borda, Kelly Levano, Marco Galarza, Heinner Guio*
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Affiliation |
1Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú.
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heinnerguio@gmail.com
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Article Type |
Hypothesis
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Date |
Received July 7, 2017; Revised July 13, 2017; Accepted July 23, 2017; Published July 31, 2017
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Abstract |
Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has a vast diversity of genotypes including Beijing, CAS, EAI, Haarlem, LAM, X, Ural, T, AFRI1 and AFRI2. However, genotyping can be expensive, time consuming and in some cases, results may vary depending on methodology used. Here, we proposed a new set of 10 SNPs using a total of 249 MTB genomes, and selected by first the inclusion/ exclusion (IE) criteria using spoligotyping and phylogenies, followed by the selection of the nonsynonymous SNPs present in the most conserved cluster of orthologous groups (COG) of each genotype of MTB. Genotype assignment of the new set of 10 SNPs was validated using an additional of 34 MTB genomes and results showed 100% correlation with their known genotypes. Our set of 10 SNPs have not been previously reported and cover the MTB genotypes that are prevalent worldwide. This set of SNPs could be used for molecular epidemiology with drug resistant markers.
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Keywords |
Genomic signature, Genotyping, Mycobacterium tuberculosis
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Citation |
David Tarazona et al. Bioinformation 13(7): 224-230 (2017)
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Edited by |
P Kangueane
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ISSN |
0973-2063
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Publisher |
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License |
This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.
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