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Journal of Clinical Microbiology, December 2005, p. 5978-5982, Vol. 43, No. 12
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.12.5978-5982.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Analysis of Genomic Downsizing on the Basis of Region-of-Difference Polymorphism Profiling of Mycobacterium tuberculosis Patient Isolates Reveals Geographic Partitioning

K. Rajender Rao,¹ Farhana Kauser,¹ Sriramula Srinivas,¹ Stefania Zanetti,² Leonardo A. Sechi,² Niyaz Ahmed,¹ and Seyed E. Hasnain^1,3*

Pathogen Evolution Group, Laboratory of Molecular and Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad, India,¹ Department of Biomedical Sciences, University of Sassari, Sassari, Italy,² Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, India³

Received 10 April 2005/ Returned for modification 24 June 2005/ Accepted 2 September 2005

Mycobacterium tuberculosis, the etiological agent of tuberculosis, has lost many coding and noncoding regions in its genome during the course of evolution. We performed region-of-difference (RD) analysis using PCR-based genotyping of 131 M. tuberculosis clinical isolates obtained from four different countries, namely, India, Peru, Libya, and Angola. Our studies revealed that RD patterns are often distinct for strains circulating in specific geographical regions and can be used to trace the descent and spread of an isolate from its original reservoir. We describe our findings, which show that no single isolate from the four countries (n = 131) had all the 15 RDs either deleted or retained. Tuberculosis-specific deletion 1 (TbD1) was found to be conserved in 23% of the Indian isolates, indicating their possible ancient origin. RD9 was the most conserved region, RD11 was predominantly deleted, and RD6 was the most variable among the isolates in our collection irrespective of their geographic region. In contrast to earlier reports, our results demonstrate that the deletion of RD1 does not correlate with a decrease in the virulence potential of M. tuberculosis, as Indian isolates (n = 30) examined by us were from diseased individuals and yet had lost the RD1 region. Our results further illustrated that the intactness of the RD5 region may be associated with increased virulence of the organism. This study highlights that the RDs in M. tuberculosis genomes are geographically distributed and specific and may possibly be associated with virulence spectrum.

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* Corresponding author. Mailing address: Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 076, India. Phone: 91 40 2715 5604. Fax: 91 40 2715 5610. E-mail: hasnain{at}cdfd.org.in.

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Journal of Clinical Microbiology, December 2005, p. 5978-5982, Vol. 43, No. 12
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.12.5978-5982.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

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