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Journal of Bacteriology, June 2006, p. 4271-4287, Vol. 188, No. 12
0021-9193/06/$08.00+0     doi:10.1128/JB.01783-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Novel Genetic Polymorphisms That Further Delineate the Phylogeny of the Mycobacterium tuberculosis Complex{dagger}

Richard C. Huard,1,{ddagger} Michel Fabre,2 Petra de Haas,3 Luiz Claudio Oliveira Lazzarini,1 Dick van Soolingen,3 Debby Cousins,4 and John L. Ho1*

Division of International Medicine and Infectious Diseases, Department of Medicine, Joan and Sanford I. Weill Medical College, Cornell University, New York, New York,1 Laboratoire de Mycobactériologie, HIA Percy, 92140 Clamart, France,2 National Institute of Public Health and the Environment, Bilthoven, The Netherlands,3 Australian Reference Laboratory for Bovine Tuberculosis, Department of Agriculture, South Perth 6151, Australia4

Received 22 November 2005/ Accepted 3 April 2006

In a previous report, we described a PCR protocol for the differentiation of the various species of the Mycobacterium tuberculosis complex (MTC) on the basis of genomic deletions (R. C. Huard, L. C. de Oliveira Lazzarini, W. R. Butler, D. van Soolingen, and J. L. Ho, J. Clin. Microbiol. 41:1637-1650, 2003). That report also provided a broad cross-comparison of several previously identified, phylogenetically relevant, long-sequence and single-nucleotide polymorphisms (LSPs and SNPs, respectively). In the present companion report, we expand upon the previous work (i) by continuing the evaluation of known MTC phylogenetic markers in a larger collection of tubercle bacilli (n = 125), (ii) by evaluating additional recently reported MTC species-specific and interspecific polymorphisms, and (iii) by describing the identification and distribution of a number of novel LSPs and SNPs. Notably, new genomic deletions were found in various Mycobacterium tuberculosis strains, new species-specific SNPs were identified for "Mycobacterium canettii," Mycobacterium microti, and Mycobacterium pinnipedii, and, for the first time, intraspecific single-nucleotide DNA differences were discovered for the dassie bacillus, the oryx bacillus, and the two Mycobacterium africanum subtype I variants. Surprisingly, coincident polymorphisms linked one M. africanum subtype I genotype with the dassie bacillus and M. microti with M. pinnipedii, thereby suggesting closer evolutionary ties within each pair of species than had been previously thought. Overall, the presented data add to the genetic definitions of several MTC organisms as well as fine-tune current models for the evolutionary history of the MTC.

* Corresponding author. Mailing address: Division of International Medicine and Infectious Diseases, Department of Medicine, Joan and Sanford I. Weill Medical College, Cornell University, Room A-421, 525 East 68th St., New York, NY 10021. Phone: (212) 746-6316. Fax: (212) 746-8975. E-mail: jlho{at}med.cornell.edu.

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

{ddagger} Present address: Clinical Microbiology Service and the Department of Pathology, Columbia University Medical Center, New York-Presbyterian Hospital, New York, NY 10032.

Journal of Bacteriology, June 2006, p. 4271-4287, Vol. 188, No. 12
0021-9193/06/$08.00+0     doi:10.1128/JB.01783-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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