JB
Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental material
Right arrow An erratum has been published
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Filliol, I.
Right arrow Articles by Alland, D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Filliol, I.
Right arrow Articles by Alland, D.

 Previous Article  |  Next Article 

Journal of Bacteriology, January 2006, p. 759-772, Vol. 188, No. 2
0021-9193/06/$08.00+0     doi:10.1128/JB.188.2.759-772.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Global Phylogeny of Mycobacterium tuberculosis Based on Single Nucleotide Polymorphism (SNP) Analysis: Insights into Tuberculosis Evolution, Phylogenetic Accuracy of Other DNA Fingerprinting Systems, and Recommendations for a Minimal Standard SNP Set{dagger}

Ingrid Filliol,1,{ddagger} Alifiya S. Motiwala,1,{ddagger} Magali Cavatore,1 Weihong Qi,2 Manzour Hernando Hazbón,1 Miriam Bobadilla del Valle,3 Janet Fyfe,4 Lourdes García-García,5 Nalin Rastogi,6 Christophe Sola,6 Thierry Zozio,6 Marta Inírida Guerrero,7,§ Clara Inés León,7,§ Jonathan Crabtree,8 Sam Angiuoli,8 Kathleen D. Eisenach,9 Riza Durmaz,10 Moses L. Joloba,11 Adrian Rendón,12 José Sifuentes-Osornio,3 Alfredo Ponce de León,3 M. Donald Cave,9 Robert Fleischmann,8 Thomas S. Whittam,2 and David Alland1*

Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Re-emerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, New Jersey,1 National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan,2 The Institute for Genomic Research, Rockville, Maryland,8 Central Arkansas Veterans Healthcare System (CAVHS), Departments of Pathology, Microbiology-Immunology, and Neurobiology and Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas,9 Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán,3 Unidad de Tuberculosis Instituto Nacional de Salud Publica, Mexico City,5 Pulmonary Services, University Hospital of Monterrey, Universidad Autónoma de Nuevo León, Nuevo León, Mexico,12 Victorian Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, North Melbourne Victoria 3051, Australia,4 Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Morne Jolivière, F-97183 Abymes-Cedex, Guadeloupe,6 Grupo de Micobacterias, Subdirección de Investigación, Instituto Nacional de Salud, Bogotá, Colombia,7 Department of Clinical Microbiology, Faculty of Medicine, Inonu University, Malatya, Turkey,10 Departments of Medicine and Medical Microbiology, Makerere University, Kampala, Uganda,11

Received 17 August 2005/ Accepted 25 October 2005

We analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and 96% of the SNP locus pairs were in complete linkage disequilibrium. Cluster analyses identified six deeply branching, phylogenetically distinct SNP cluster groups (SCGs) and five subgroups. The SCGs were strongly associated with the geographical origin of the M. tuberculosis samples and the birthplace of the human hosts. The most ancestral cluster (SCG-1) predominated in patients from the Indian subcontinent, while SCG-1 and another ancestral cluster (SCG-2) predominated in patients from East Asia, suggesting that M. tuberculosis first arose in the Indian subcontinent and spread worldwide through East Asia. Restricted SCG diversity and the prevalence of less ancestral SCGs in indigenous populations in Uganda and Mexico suggested a more recent introduction of M. tuberculosis into these regions. The East African Indian and Beijing spoligotypes were concordant with SCG-1 and SCG-2, respectively; X and Central Asian spoligotypes were also associated with one SCG or subgroup combination. Other clades had less consistent associations with SCGs. Mycobacterial interspersed repetitive unit (MIRU) analysis provided less robust phylogenetic information, and only 6 of the 12 MIRU microsatellite loci were highly differentiated between SCGs as measured by GST. Finally, an algorithm was devised to identify two minimal sets of either 45 or 6 SNPs that could be used in future investigations to enable global collaborations for studies on evolution, strain differentiation, and biological differences of M. tuberculosis.

* Corresponding author. Mailing address: Division of Infectious Disease, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave., MSB A920C, Newark, NJ 07103. Phone: (973) 972-2179. Fax: (973) 972-0713. E-mail: allandda{at}umdnj.edu.

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

{ddagger} These authors contributed equally to this work.

§ Present address: Unidad de Genética Facultad de Medicina, Universidad del Rosario, Bogotá, Colombia.

Journal of Bacteriology, January 2006, p. 759-772, Vol. 188, No. 2
0021-9193/06/$08.00+0     doi:10.1128/JB.188.2.759-772.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:



Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Appl. Environ. Microbiol. Infect. Immun. Eukaryot. Cell
Mol. Cell. Biol. J. Virol. Microbiol. Mol. Biol. Rev.
ALL ASM JOURNALS

Copyright © 2006 by the American Society for Microbiology. All rights reserved.