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Journal of Clinical Microbiology, October 2008, p. 3338-3345, Vol. 46, No. 10
0095-1137/08/$08.00+0     doi:10.1128/JCM.00770-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Discordance between Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Typing and IS6110 Restriction Fragment Length Polymorphism Genotyping for Analysis of Mycobacterium tuberculosis Beijing Strains in a Setting of High Incidence of Tuberculosis{triangledown} ,{dagger}

M. Hanekom,2,{ddagger} G. D. van der Spuy,1,{ddagger} N. C. Gey van Pittius,1 C. R. E. McEvoy,1 K. G. P. Hoek,1 S. L. Ndabambi,1 A. M. Jordaan,1 T. C. Victor,1 P. D. van Helden,1 and R. M. Warren1*

DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics,1 Division of Anatomy and Histology, Faculty of Health Sciences, Stellenbosch University, South Africa2

Received 23 April 2008/ Returned for modification 8 June 2008/ Accepted 7 August 2008

IS6110 restriction fragment length polymorphism (RFLP) genotyping is the most widely used genotyping method to study the epidemiology of Mycobacterium tuberculosis. However, due to the complexity of the IS6110 RFLP genotyping technique, and the interpretation of RFLP data, mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping has been proposed as the new genotyping standard. This study aimed to determine the discriminatory power of different MIRU-VNTR locus combinations relative to IS6110 RFLP genotyping, using a collection of Beijing genotype M. tuberculosis strains with a well-established phylogenetic history. Clustering, diversity index, clustering concordance, concordance among unique genotypes, and divergent and convergent evolution were calculated for seven combinations of 27 different MIRU-VNTR loci and compared to IS6110 RFLP results. Our results confirmed previous findings that MIRU-VNTR genotyping can be used to estimate the extent of recent or ongoing transmission. However, molecular epidemiological linking of cases varied significantly depending on the genotyping method used. We conclude that IS6110 RFLP and MIRU-VNTR loci evolve independently and at different rates, which leads to discordance between transmission chains predicted by the respective genotyping methods. Concordance between the two genotyping methods could be improved by the inclusion of genetic distance (GD) into the clustering formulae for some of the MIRU-VNTR loci combinations. In summary, our findings differ from previous reports, which may be explained by the fact that in settings of low tuberculosis incidence, the genetic distance between epidemiologically unrelated isolates was sufficient to define a strain using either marker, whereas in settings of high incidence, continuous evolution and persistence of strains revealed the weaknesses inherent to these markers.

* Corresponding author. Mailing address: DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, P.O. Box 19063, Tygerberg, South Africa 7505. Phone: 021-938 9073. Fax: 021-938 9476. E-mail: rw1{at}sun.ac.za

{triangledown} Published ahead of print on 20 August 2008.

{dagger} Supplemental material for this article may be found at http://jcm.asm.org/.

{ddagger} M. Hanekom and G. D. van der Spuy shared joint first authorship for this report.

Journal of Clinical Microbiology, October 2008, p. 3338-3345, Vol. 46, No. 10
0095-1137/08/$08.00+0     doi:10.1128/JCM.00770-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



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