Research article
Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology
-
* Corresponding authors: Nalin Rastogi nrastogi@pasteur-guadeloupe.fr - Christophe Sola csola@pasteur-guadeloupe.fr
1 Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
2 Wadsworth Center, New York State Dept. of Health, Albany, NY, USA
3 Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
4 Dept. Hygiene Microbiology and Social Medicine, Innsbruck Medical University, Innsbruck, Austria
5 Dept of Infectious Diseases, Institut of Infectious Diseases, Milano, Italy
6 Department of Comparative Medicine, King Faisal specialist Hospital and Research Center, Riyadh, Saudi Arabia
7 Laboratoire de la Tuberculose, Institut Pasteur de Bruxelles, Belgique
8 Universidad Centrooccidental Lisandro Alvarado, Barquisimeto, Venezuela and Universidad de Zaragoza, Spain
9 All India Institute of Medical Sciences, New Delhi, India
10 Biomedical Research and Study Center, Riga, Latvia
11 Institut for Hygiene, Microbiologie and Tropical Medicine, Austria
12 Universidade Federal do Rio Grande de Soul, Brazil
13 Instituto de Biotecnologia INTA, Castelar, Argentina
14 Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
15 University of Düsseldorf, Heinrich-Heine-University, Düsseldorf
16 Dept of Internal Medicine II, University of Regensbourg, Germany
17 Public Health Laboratory, Hearltlands Hospital, Birmingham, UK
18 Dept of Clinical Microbiology and Infectious Diseases, Hospital Gregorio Marañon, Madrid, Spain
19 Dept. of Experimental Pathology, Medical Biotechnology, Infection and Epidemiology, Pisa University, Pisa, Italy
20 Laboratory of Molecular Biology applied to Mycobacteria, Dept. Mycobacteriosis, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
21 Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France
22 MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
23 Laboratory Nuclear Medicine Section, Isotope group, Bhabha Atomic Research Centre c/T.M.H. Annexe, Parel, Mumbai-400012, India
24 Public Health Research Institute, Newark, NJ, USA
25 Mycobacteria reference unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
26 Municipal Institute of Hygiene, Prague, Czech Republic
27 Statens Serum Institute, Int. Ref. lab. for Mycobacteriology, Copenhagen Denmark
28 Institute of Hygiene and Epidemiology, Hanoi, Vietnam
29 Universidad de Zaragoza, Zaragoza, Spain
30 Laboratoire de Bactério-virologie-hygiène, CHU Dupuytren, Limoges, France
31 Institut Pasteur de Saint-Petersbourg, Saint Petersbourg, Russia
32 Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
33 Forschungszentrum, National Reference Center for Mycobacteria, Borstel, Germany
34 Dept of Clinical Pathology, Padjadjaran University, Dr. Hasan Sadikin Hospital, Bandung, Indonesia
35 Tuberculosis Laboratory, International Centre for Diarrhoeal Research, Dhaka, Bangladesh
36 Institut Pasteur de Madagascar, Tananarive, Madagascar
37 Dept of Genetics of Microorganisms, University of Lódz, Lodz, Poland
38 Servicio Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain
39 State Research Center for Applied Microbiology, Obolensk, Russian Federation
40 Dept. of Respiratory Medicine School of Medicine Semmelweis University, Budapest, Hungary
41 Veterinary Sciences Division, Department of agriculture for Northern Ireland, Belfast, UK
42 Centro regionale di Riferimento per i Micobatteri, Laboratorio de Microbiologia e Virologia, Ospedale Careggi, Firenze, Italy
BMC Microbiology 2006, 6:23 doi:10.1186/1471-2180-6-23
Published: 6 March 2006Abstract
Background
The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database.
Results
The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network.
Conclusion
Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.