Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology

Karine Brudey¹ , Jeffrey R Driscoll² , Leen Rigouts³ , Wolfgang M Prodinger⁴ , Andrea Gori⁵ , Sahal A Al-Hajoj⁶ , Caroline Allix⁷ , Liselotte Aristimuño⁸ , Jyoti Arora⁹ , Viesturs Baumanis¹⁰ , Lothar Binder¹¹ , Patricia Cafrune¹² , Angel Cataldi¹³ , Soonfatt Cheong¹⁴ , Roland Diel¹⁵ , Christopher Ellermeier¹⁶ , Jason T Evans¹⁷ , Maryse Fauville-Dufaux⁷ , Séverine Ferdinand¹ , Dario Garcia de Viedma¹⁸ , Carlo Garzelli¹⁹ , Lidia Gazzola⁵ , Harrison M Gomes²⁰ , M Cristina Guttierez²¹ , Peter M Hawkey¹⁷ , Paul D van Helden²² , Gurujaj V Kadival²³ , Barry N Kreiswirth²⁴ , Kristin Kremer²⁵ , Milan Kubin²⁶ , Savita P Kulkarni²³ , Benjamin Liens¹ , Troels Lillebaek²⁷ , Ho Minh Ly²⁸ , Carlos Martin²⁹ , Christian Martin³⁰ , Igor Mokrousov³¹ , Olga Narvskaïa³¹ , Yun Fong Ngeow¹⁴ , Ludmilla Naumann³² , Stefan Niemann³³ , Ida Parwati³⁴ , Zeaur Rahim³⁵ , Voahangy Rasolofo-Razanamparany³⁶ , Tiana Rasolonavalona³⁶ , M Lucia Rossetti¹² , Sabine Rüsch-Gerdes³³ , Anna Sajduda³⁷ , Sofia Samper³⁸ , Igor G Shemyakin³⁹ , Urvashi B Singh⁹ , Akos Somoskovi⁴⁰ , Robin A Skuce⁴¹ , Dick van Soolingen²⁵ , Elisabeth M Streicher²² , Philip N Suffys²⁰ , Enrico Tortoli⁴² , Tatjana Tracevska¹⁰ , Véronique Vincent²¹ , Tommie C Victor²² , Robin M Warren²² , Sook Fan Yap¹⁴ , Khadiza Zaman³⁵ , Françoise Portaels³ , Nalin Rastogi¹ and Christophe Sola¹

¹Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe

²Wadsworth Center, New York State Dept. of Health, Albany, NY, USA

³Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium

⁴Dept. Hygiene Microbiology and Social Medicine, Innsbruck Medical University, Innsbruck, Austria

⁵Dept of Infectious Diseases, Institut of Infectious Diseases, Milano, Italy

⁶Department of Comparative Medicine, King Faisal specialist Hospital and Research Center, Riyadh, Saudi Arabia

⁷Laboratoire de la Tuberculose, Institut Pasteur de Bruxelles, Belgique

⁸Universidad Centrooccidental Lisandro Alvarado, Barquisimeto, Venezuela and Universidad de Zaragoza, Spain

⁹All India Institute of Medical Sciences, New Delhi, India

¹⁰Biomedical Research and Study Center, Riga, Latvia

¹¹Institut for Hygiene, Microbiologie and Tropical Medicine, Austria

¹²Universidade Federal do Rio Grande de Soul, Brazil

¹³Instituto de Biotecnologia INTA, Castelar, Argentina

¹⁴Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health

¹⁵University of Düsseldorf, Heinrich-Heine-University, Düsseldorf

¹⁶Dept of Internal Medicine II, University of Regensbourg, Germany

¹⁷Public Health Laboratory, Hearltlands Hospital, Birmingham, UK

¹⁸Dept of Clinical Microbiology and Infectious Diseases, Hospital Gregorio Marañon, Madrid, Spain

¹⁹Dept. of Experimental Pathology, Medical Biotechnology, Infection and Epidemiology, Pisa University, Pisa, Italy

²⁰Laboratory of Molecular Biology applied to Mycobacteria, Dept. Mycobacteriosis, Oswaldo Cruz Institute, Rio de Janeiro, Brazil

²¹Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France

²²MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa

²³Laboratory Nuclear Medicine Section, Isotope group, Bhabha Atomic Research Centre c/T.M.H. Annexe, Parel, Mumbai-400012, India

²⁴Public Health Research Institute, Newark, NJ, USA

²⁵Mycobacteria reference unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands

²⁶Municipal Institute of Hygiene, Prague, Czech Republic

²⁷Statens Serum Institute, Int. Ref. lab. for Mycobacteriology, Copenhagen Denmark

²⁸Institute of Hygiene and Epidemiology, Hanoi, Vietnam

²⁹Universidad de Zaragoza, Zaragoza, Spain

³⁰Laboratoire de Bactério-virologie-hygiène, CHU Dupuytren, Limoges, France

³¹Institut Pasteur de Saint-Petersbourg, Saint Petersbourg, Russia

³²Bavarian Health and Food Safety Authority, Oberschleissheim, Germany

³³Forschungszentrum, National Reference Center for Mycobacteria, Borstel, Germany

³⁴Dept of Clinical Pathology, Padjadjaran University, Dr. Hasan Sadikin Hospital, Bandung, Indonesia

³⁵Tuberculosis Laboratory, International Centre for Diarrhoeal Research, Dhaka, Bangladesh

³⁶Institut Pasteur de Madagascar, Tananarive, Madagascar

³⁷Dept of Genetics of Microorganisms, University of Lódz, Lodz, Poland

³⁸Servicio Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain

³⁹State Research Center for Applied Microbiology, Obolensk, Russian Federation

⁴⁰Dept. of Respiratory Medicine School of Medicine Semmelweis University, Budapest, Hungary

⁴¹Veterinary Sciences Division, Department of agriculture for Northern Ireland, Belfast, UK

⁴²Centro regionale di Riferimento per i Micobatteri, Laboratorio de Microbiologia e Virologia, Ospedale Careggi, Firenze, Italy