The Reproducibility of the Multiplex RAPD-PCR Assay in Genotyping of Mycobacterium Tuberculosis Isolates from Sulawesi, Indonesia

Mochammad Hatta; AndiRofian Sultan; Ressy Dwiyanti; Muhammad Sabir; Andini Febrianty; Ahmad Adhyka; Nur Indah Purnamasari; Muhammad Reza Primaguna; Juhri Saning; Yusriani Mangarengi; Munawir Muhammad; Nataniel Tandirogang; Yadi Yasir; Masyhudi Amir

doi:doi:10.11648/j.ajcem.20140202.12

The Reproducibility of the Multiplex RAPD-PCR Assay in Genotyping of Mycobacterium Tuberculosis Isolates from Sulawesi, Indonesia

Mochammad Hatta, AndiRofian Sultan, Ressy Dwiyanti, Muhammad Sabir, Andini Febrianty, Ahmad Adhyka, Nur Indah Purnamasari, Muhammad Reza Primaguna, Juhri Saning, Yusriani Mangarengi, Munawir Muhammad, Nataniel Tandirogang, Yadi Yasir, Masyhudi Amir

Published in American Journal of Clinical and Experimental Medicine (Volume 2, Issue 2)

Received: 20 February 2014 Published: 20 March 2014

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Abstract

Background: Random Amplified Polymorphic DNA (RAPD) assay has recently emerged as a genotyping method which is both robust and highly discriminatory for bacterial strain differentiation. However, RAPD assessment for Mycobacterium tuberculosiscomplex (MTC) isolates is still limited. Despite its simplicity and rapidity, conventional RAPD also has low reproducibility due to its sensitivity to several factors. Therefore we studied the feasibility of an RAPD-PCR assay to define the genetic diversity of MTC isolates and to evaluate its reproducibility.Methods:493clinical MTC isolates from the island of Sulawesi in Eastern Indonesia, collected from 2005-2012were subjected to Multiplex RAPD assay using 11 random decamer primers instead of one primer which is common in conventional RAPD. All 11 primers were found to be differentiated and produced specific RAPD profiles. The polymorphic amplicons served as RAPD markers for MTC. The dendrograms, obtained by different primers, showed the discriminatory ability of the primers.Results:Multiplex RAPD-PCR results show that the majority of the isolates from South Sulawesi, Southeast Sulawesi andCentral Sulawesiin eastern region of Indonesia belong to group MT-C (80.7%, 80.0% and 62.6 % respectively) with result reproducibility as high as 100%. Conclusion:Molecular typing with multiplex RAPD-PCR is a powerful approach to show the genetic heterogeneity of MTC isolates. The discrimination power and reproducibility of this multiple loci-based RAPD was higher than conventional fewer loci-targeted RAPD.

Published in	American Journal of Clinical and Experimental Medicine (Volume 2, Issue 2)
DOI	10.11648/j.ajcem.20140202.12
Page(s)	14-21
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2014. Published by Science Publishing Group

Keywords

RAPD-PCR, Genotyping, Mycobacterium Tuberculosis Complex, Sulawesi Indonesia

References

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[17]	Maidin MA, Lidjaja A, Hatta M: Random Amplified Polymorphic DNA Analysis of Mycobacterium tuberculosis isolates Resistant to Isoniazid in Indonesia. J Tuberculosis Res 2013, 1:10-13.
[18]	Singh JP, Verma R, Chaudhuri P: Random amplified polymorphic DNA (RAPD) analysis of Mycobacterium tuberculosis strains in India. Journal of veterinary science 2006, 7(2):181-187.
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APA Style

Mochammad Hatta, AndiRofian Sultan, Ressy Dwiyanti, Muhammad Sabir, Andini Febrianty, et al. (2014). The Reproducibility of the Multiplex RAPD-PCR Assay in Genotyping of Mycobacterium Tuberculosis Isolates from Sulawesi, Indonesia. American Journal of Clinical and Experimental Medicine, 2(2), 14-21. https://doi.org/10.11648/j.ajcem.20140202.12

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ACS Style

Mochammad Hatta; AndiRofian Sultan; Ressy Dwiyanti; Muhammad Sabir; Andini Febrianty, et al. The Reproducibility of the Multiplex RAPD-PCR Assay in Genotyping of Mycobacterium Tuberculosis Isolates from Sulawesi, Indonesia. Am. J. Clin. Exp. Med. 2014, 2(2), 14-21. doi: 10.11648/j.ajcem.20140202.12

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AMA Style

Mochammad Hatta, AndiRofian Sultan, Ressy Dwiyanti, Muhammad Sabir, Andini Febrianty, et al. The Reproducibility of the Multiplex RAPD-PCR Assay in Genotyping of Mycobacterium Tuberculosis Isolates from Sulawesi, Indonesia. Am J Clin Exp Med. 2014;2(2):14-21. doi: 10.11648/j.ajcem.20140202.12

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@article{10.11648/j.ajcem.20140202.12,
  author = {Mochammad Hatta and AndiRofian Sultan and Ressy Dwiyanti and Muhammad Sabir and Andini Febrianty and Ahmad Adhyka and Nur Indah Purnamasari and Muhammad Reza Primaguna and Juhri Saning and Yusriani Mangarengi and Munawir Muhammad and Nataniel Tandirogang and Yadi Yasir and Masyhudi Amir},
  title = {The Reproducibility of the Multiplex RAPD-PCR Assay in Genotyping of Mycobacterium Tuberculosis Isolates from Sulawesi, Indonesia},
  journal = {American Journal of Clinical and Experimental Medicine},
  volume = {2},
  number = {2},
  pages = {14-21},
  doi = {10.11648/j.ajcem.20140202.12},
  url = {https://doi.org/10.11648/j.ajcem.20140202.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajcem.20140202.12},
  abstract = {Background: Random Amplified Polymorphic DNA (RAPD) assay has recently emerged as a genotyping method which is both robust and highly discriminatory for bacterial strain differentiation. However, RAPD assessment for Mycobacterium tuberculosiscomplex (MTC) isolates is still limited. Despite its simplicity and rapidity, conventional RAPD also has low reproducibility due to its sensitivity to several factors. Therefore we studied the feasibility of an RAPD-PCR assay to define the genetic diversity of MTC isolates and to evaluate its reproducibility.Methods:493clinical MTC isolates from the island of Sulawesi in Eastern Indonesia, collected from 2005-2012were subjected to Multiplex RAPD assay using 11 random decamer primers instead of one primer which is common in conventional RAPD. All 11 primers were found to be differentiated and produced specific RAPD profiles. The polymorphic amplicons served as RAPD markers for MTC. The dendrograms, obtained by different primers, showed the discriminatory ability of the primers.Results:Multiplex RAPD-PCR results show that the majority of the isolates from South Sulawesi, Southeast Sulawesi andCentral Sulawesiin eastern region of Indonesia belong to group MT-C (80.7%, 80.0% and 62.6 % respectively) with result reproducibility as high as 100%. Conclusion:Molecular typing with multiplex RAPD-PCR is a powerful approach to show the genetic heterogeneity of MTC isolates. The discrimination power and reproducibility of this multiple loci-based RAPD was higher than conventional fewer loci-targeted RAPD.},
 year = {2014}
}

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TY  - JOUR
T1  - The Reproducibility of the Multiplex RAPD-PCR Assay in Genotyping of Mycobacterium Tuberculosis Isolates from Sulawesi, Indonesia
AU  - Mochammad Hatta
AU  - AndiRofian Sultan
AU  - Ressy Dwiyanti
AU  - Muhammad Sabir
AU  - Andini Febrianty
AU  - Ahmad Adhyka
AU  - Nur Indah Purnamasari
AU  - Muhammad Reza Primaguna
AU  - Juhri Saning
AU  - Yusriani Mangarengi
AU  - Munawir Muhammad
AU  - Nataniel Tandirogang
AU  - Yadi Yasir
AU  - Masyhudi Amir
Y1  - 2014/03/20
PY  - 2014
N1  - https://doi.org/10.11648/j.ajcem.20140202.12
DO  - 10.11648/j.ajcem.20140202.12
T2  - American Journal of Clinical and Experimental Medicine
JF  - American Journal of Clinical and Experimental Medicine
JO  - American Journal of Clinical and Experimental Medicine
SP  - 14
EP  - 21
PB  - Science Publishing Group
SN  - 2330-8133
UR  - https://doi.org/10.11648/j.ajcem.20140202.12
AB  - Background: Random Amplified Polymorphic DNA (RAPD) assay has recently emerged as a genotyping method which is both robust and highly discriminatory for bacterial strain differentiation. However, RAPD assessment for Mycobacterium tuberculosiscomplex (MTC) isolates is still limited. Despite its simplicity and rapidity, conventional RAPD also has low reproducibility due to its sensitivity to several factors. Therefore we studied the feasibility of an RAPD-PCR assay to define the genetic diversity of MTC isolates and to evaluate its reproducibility.Methods:493clinical MTC isolates from the island of Sulawesi in Eastern Indonesia, collected from 2005-2012were subjected to Multiplex RAPD assay using 11 random decamer primers instead of one primer which is common in conventional RAPD. All 11 primers were found to be differentiated and produced specific RAPD profiles. The polymorphic amplicons served as RAPD markers for MTC. The dendrograms, obtained by different primers, showed the discriminatory ability of the primers.Results:Multiplex RAPD-PCR results show that the majority of the isolates from South Sulawesi, Southeast Sulawesi andCentral Sulawesiin eastern region of Indonesia belong to group MT-C (80.7%, 80.0% and 62.6 % respectively) with result reproducibility as high as 100%. Conclusion:Molecular typing with multiplex RAPD-PCR is a powerful approach to show the genetic heterogeneity of MTC isolates. The discrimination power and reproducibility of this multiple loci-based RAPD was higher than conventional fewer loci-targeted RAPD.
VL  - 2
IS  - 2
ER  -

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Author Information

Mochammad Hatta

Molecular Biology and Immunology Laboratory for Infectious Diseases, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
AndiRofian Sultan

Molecular Biology and Immunology Laboratory for Infectious Diseases, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
Ressy Dwiyanti

Molecular Biology and Immunology Laboratory for Infectious Diseases, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
Muhammad Sabir

Molecular Biology and Immunology Laboratory for Infectious Diseases, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
Andini Febrianty

Molecular Biology and Immunology Laboratory for Infectious Diseases, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
Ahmad Adhyka

Molecular Biology and Immunology Laboratory for Infectious Diseases, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
Nur Indah Purnamasari

Department of Microbiology, Faculty of Medicine, Haluoleo University, Kendari, Indonesia
Muhammad Reza Primaguna

Department of Microbiology, Faculty of Medicine, Haluoleo University, Kendari, Indonesia
Juhri Saning

Department of Microbiology, Faculty of Medicine, Tadulako University, Palu, Indonesia
Yusriani Mangarengi

Department of Microbiology, Faculty of Medicine, Tadulako University, Palu, Indonesia
Munawir Muhammad

Department of Microbiology, Faculty of Medicine, Tadulako University, Palu, Indonesia
Nataniel Tandirogang

Department Microbiology, Faculty of Medicine, Mulawarman University, Samarinda, Indonesia
Yadi Yasir

Department Microbiology, Faculty of Medicine, Mulawarman University, Samarinda, Indonesia
Masyhudi Amir

Department Microbiology, Faculty of Medicine, Mulawarman University, Samarinda, Indonesia

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Mochammad Hatta, AndiRofian Sultan, Ressy Dwiyanti, Muhammad Sabir, Andini Febrianty, et al. (2014). The Reproducibility of the Multiplex RAPD-PCR Assay in Genotyping of Mycobacterium Tuberculosis Isolates from Sulawesi, Indonesia. American Journal of Clinical and Experimental Medicine, 2(2), 14-21. https://doi.org/10.11648/j.ajcem.20140202.12

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ACS Style

Mochammad Hatta; AndiRofian Sultan; Ressy Dwiyanti; Muhammad Sabir; Andini Febrianty, et al. The Reproducibility of the Multiplex RAPD-PCR Assay in Genotyping of Mycobacterium Tuberculosis Isolates from Sulawesi, Indonesia. Am. J. Clin. Exp. Med. 2014, 2(2), 14-21. doi: 10.11648/j.ajcem.20140202.12

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AMA Style

Mochammad Hatta, AndiRofian Sultan, Ressy Dwiyanti, Muhammad Sabir, Andini Febrianty, et al. The Reproducibility of the Multiplex RAPD-PCR Assay in Genotyping of Mycobacterium Tuberculosis Isolates from Sulawesi, Indonesia. Am J Clin Exp Med. 2014;2(2):14-21. doi: 10.11648/j.ajcem.20140202.12

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@article{10.11648/j.ajcem.20140202.12,
  author = {Mochammad Hatta and AndiRofian Sultan and Ressy Dwiyanti and Muhammad Sabir and Andini Febrianty and Ahmad Adhyka and Nur Indah Purnamasari and Muhammad Reza Primaguna and Juhri Saning and Yusriani Mangarengi and Munawir Muhammad and Nataniel Tandirogang and Yadi Yasir and Masyhudi Amir},
  title = {The Reproducibility of the Multiplex RAPD-PCR Assay in Genotyping of Mycobacterium Tuberculosis Isolates from Sulawesi, Indonesia},
  journal = {American Journal of Clinical and Experimental Medicine},
  volume = {2},
  number = {2},
  pages = {14-21},
  doi = {10.11648/j.ajcem.20140202.12},
  url = {https://doi.org/10.11648/j.ajcem.20140202.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajcem.20140202.12},
  abstract = {Background: Random Amplified Polymorphic DNA (RAPD) assay has recently emerged as a genotyping method which is both robust and highly discriminatory for bacterial strain differentiation. However, RAPD assessment for Mycobacterium tuberculosiscomplex (MTC) isolates is still limited. Despite its simplicity and rapidity, conventional RAPD also has low reproducibility due to its sensitivity to several factors. Therefore we studied the feasibility of an RAPD-PCR assay to define the genetic diversity of MTC isolates and to evaluate its reproducibility.Methods:493clinical MTC isolates from the island of Sulawesi in Eastern Indonesia, collected from 2005-2012were subjected to Multiplex RAPD assay using 11 random decamer primers instead of one primer which is common in conventional RAPD. All 11 primers were found to be differentiated and produced specific RAPD profiles. The polymorphic amplicons served as RAPD markers for MTC. The dendrograms, obtained by different primers, showed the discriminatory ability of the primers.Results:Multiplex RAPD-PCR results show that the majority of the isolates from South Sulawesi, Southeast Sulawesi andCentral Sulawesiin eastern region of Indonesia belong to group MT-C (80.7%, 80.0% and 62.6 % respectively) with result reproducibility as high as 100%. Conclusion:Molecular typing with multiplex RAPD-PCR is a powerful approach to show the genetic heterogeneity of MTC isolates. The discrimination power and reproducibility of this multiple loci-based RAPD was higher than conventional fewer loci-targeted RAPD.},
 year = {2014}
}

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TY  - JOUR
T1  - The Reproducibility of the Multiplex RAPD-PCR Assay in Genotyping of Mycobacterium Tuberculosis Isolates from Sulawesi, Indonesia
AU  - Mochammad Hatta
AU  - AndiRofian Sultan
AU  - Ressy Dwiyanti
AU  - Muhammad Sabir
AU  - Andini Febrianty
AU  - Ahmad Adhyka
AU  - Nur Indah Purnamasari
AU  - Muhammad Reza Primaguna
AU  - Juhri Saning
AU  - Yusriani Mangarengi
AU  - Munawir Muhammad
AU  - Nataniel Tandirogang
AU  - Yadi Yasir
AU  - Masyhudi Amir
Y1  - 2014/03/20
PY  - 2014
N1  - https://doi.org/10.11648/j.ajcem.20140202.12
DO  - 10.11648/j.ajcem.20140202.12
T2  - American Journal of Clinical and Experimental Medicine
JF  - American Journal of Clinical and Experimental Medicine
JO  - American Journal of Clinical and Experimental Medicine
SP  - 14
EP  - 21
PB  - Science Publishing Group
SN  - 2330-8133
UR  - https://doi.org/10.11648/j.ajcem.20140202.12
AB  - Background: Random Amplified Polymorphic DNA (RAPD) assay has recently emerged as a genotyping method which is both robust and highly discriminatory for bacterial strain differentiation. However, RAPD assessment for Mycobacterium tuberculosiscomplex (MTC) isolates is still limited. Despite its simplicity and rapidity, conventional RAPD also has low reproducibility due to its sensitivity to several factors. Therefore we studied the feasibility of an RAPD-PCR assay to define the genetic diversity of MTC isolates and to evaluate its reproducibility.Methods:493clinical MTC isolates from the island of Sulawesi in Eastern Indonesia, collected from 2005-2012were subjected to Multiplex RAPD assay using 11 random decamer primers instead of one primer which is common in conventional RAPD. All 11 primers were found to be differentiated and produced specific RAPD profiles. The polymorphic amplicons served as RAPD markers for MTC. The dendrograms, obtained by different primers, showed the discriminatory ability of the primers.Results:Multiplex RAPD-PCR results show that the majority of the isolates from South Sulawesi, Southeast Sulawesi andCentral Sulawesiin eastern region of Indonesia belong to group MT-C (80.7%, 80.0% and 62.6 % respectively) with result reproducibility as high as 100%. Conclusion:Molecular typing with multiplex RAPD-PCR is a powerful approach to show the genetic heterogeneity of MTC isolates. The discrimination power and reproducibility of this multiple loci-based RAPD was higher than conventional fewer loci-targeted RAPD.
VL  - 2
IS  - 2
ER  -

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