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Volume 8, Number 11—November 2002

Dispatch

Global Distribution of Mycobacterium tuberculosis Spoligotypes

Ingrid Filliol*, Jeffrey R. Driscoll†, Dick van Soolingen‡, Barry N. Kreiswirth§, Kristin Kremer‡, Georges Valétudie*, Dang Duc Anh¶, Rachael Barlow#, Dilip Banerjee**, Pablo J. Bifani§, Karin Brudey*, Angel Cataldi††, Robert C. Cooksey‡‡, Debby V. Cousins§§, Jeremy W. Dale¶¶, Odir A. Dellagostin##, Francis Drobniewski***, Guido Engelmann†††, Séverine Ferdinand*, Deborah Gascoyne-Binzi#, Max Gordon*, M. Cristina Gutierrez‡‡‡, Walter H. Haas§§§, Herre Heersma‡, Gunilla Källenius¶¶¶, Eric Kassa-Kelembho###, Tuija Koivula¶¶¶, Ho Minh Ly¶, Athanasios Makristathis****, Caterina Mammina††††, Gerald Martin‡‡‡‡, Peter Moström*, Igor Mokrousov§§§§, Valérie Narbonne¶¶¶¶, Olga Narvskaya§§§§, Antonino Nastasi####, Sara Ngo Niobe-Eyangoh‡‡‡, Jean W Pape*****†††††, Voahangy Rasolofo-Razanamparany‡‡‡‡‡, Malin Ridell§§§§§, M. Lucia Rossetti¶¶¶¶¶, Fritz Stauffer#####, Philip N. Suffys******, Howard Takiff, Jeanne Texier-Maugein‡‡‡‡‡‡, Véronique Vincent‡‡‡, Jacobus H. de Waard§§§§§§, Christophe Sola*Comments to Author , and Nalin Rastogi*Comments to Author 
Author affiliations: *Institut Pasteur, Pointe-à-Pitre, Guadeloupe, French West Indies; †Wadsworth Center, Albany, New York, USA; ‡National Institute of Public Health and the Environment, Bilthoven, the Netherlands; §Public Health Research Institute, New York, New York, USA; ¶National Institute of Hygiene and Epidemiology, Hanoi, Vietnam; #General Infirmary, Leeds, U.K.; **St. Georges’ Hospital Medical School, London, U.K.; ††Instituto de Biotecnologia, Castelar, Argentina; ‡‡Centers for Disease Control and Prevention, Atlanta, Georgia, USA; §§Australian Reference Laboratory for Bovine Tuberculosis, Department of Agriculture, South Perth, Australia; ¶¶University of Surrey, Guildford, Surrey, U.K.; ##Universidade Federal, Pelotas, Brazil; ***Public Health Laboratory Service, Dulwich Hospital, London, U.K.; †††University Children’s Hospital, Heidelberg, Germany; ‡‡‡Institut Pasteur, Paris, France; §§§Robert Koch Institute, Berlin, Germany; ¶¶¶Swedish Institute for Infectious Disease Control, Solna, Sweden; ###Institut Pasteur, Bangui, Central African Republic; ****Hygiene-Institut der Universität, Wien, Austria; ††††University of Palermo, Palermo, Italy; ‡‡‡‡Bundesinstitut für gesundheitlichenVerbraucherschutz und Veterinärmedizin, Jena, Germany; §§§§Pasteur Institute of Saint Petersburg, Saint Petersburg, Russia; ¶¶¶¶Centre Hospitalier Universitaire, Brest, France; ####University of Firenze, Firenze, Italy; *****Les Centres Gheskio, Institut National de Laboratoire et de Recherche, Port-au- Prince, Haïti; †††††Cornell University, Ithaca, New York, USA; ‡‡‡‡‡Institut Pasteur, Tananarive, Madagascar; §§§§§Göteborg University, Göteborg, Sweden; ¶¶¶¶¶Universidade Federal do Rio Grande do Sul, Brazil; #####Bundesstaatliche bakteriologisch-serologische Untersuchungsanstalt Wien, Austria; ******Oswaldo Cruz Institute, Rio de Janeiro, Brazil; ††††††Caracas, Venezuela; ‡‡‡‡‡‡Centre Hospitalier Universitaire, Bordeaux, France; §§§§§§Instituto de Investigacionas Cientificas, Caracas, Venezuela;

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Table

Excerpt from SpolDB3 database showing prototype spoligotypes, visual recognition rules, and binary and octal descriptiona

Rk ST Classb Total (n)c Rulesd Binary description Octal
1 1 Beijing 1282 ∆1–34 οοοοοοοοοοοοοοοοοοοοοοοοοοοοοοοοοοννννννννν 000000000003771
2 53 T1 864 F ννννννννννννννννννννννννννννννννοοοοννννννν 777777777760771
11 52 T2 163 ∆40 and F ννννννννννννννννννννννννννννννννοοοονννοννν 777777777760731
30 37 T3 71 ∆13 and F ννννννννννννονννννννννννννννννννοοοοννννννν 777737777760771
64 40 T4 26 ∆19 and F ννννννννννννννννννονννννννννννννοοοοννννννν 777777377760771
7 47 Haarlem1 246 ∆26–30 and E νννννννννννννννννννννννννοοοοοονοοοοννννννν 777777774020771
20 2 Haarlem2 104 ∆1–24, ∆26–30 and E οοοοοοοοοοοοοοοοοοοοοοοονοοοοοονοοοοννννννν 000000004020771
3 50 Haarlem3 519 E ννννννννννννννννννννννννννννννονοοοοννννννν 777777777720771
6 119 X1 310 C νννννννννννννννννοννννννννννννννοοοοννννννν 777776777760771
4 137 X2 427 C and ∆39–42 νννννννννννννννννοννννννννννννννοοοοννοοοον 777776777760601
31 92 X3 70 ∆4–12 and C νννοοοοοοοοονννννοννννννννννννννοοοοννννννν 700036777760731
15 48 EAI1 118 A and ∆40 ννννννννννννννννννννννννννννοοοονονννννοννν 777777777413731
13 19 EAI2 130 ∆3, ∆20–21 and A ννοννννννννννννννννοονννννννοοοονοννννννννν 677777477413771
16 11 EAI3 121 ∆2-3, A and ∆37–39 νοονννννννννννννννννννννννννοοοονοννοοονννν 477777777413071
8 139 EAI4 234 ∆26–27 and A νννννννννννννννννννννννννοονοοοονοννννννννν 777777774413771
46 236 EAI5 41 A ννννννννννννννννννννννννννννοοοονοννννννννν 777777777413771
24 181 Afri1 91 ∆7–9 and ∆39 ννννννοοονννννννννννννννννννννννννννννονννν 770777777777671
ND 331 Afri2 9 ∆8–12, ∆21–24 and ∆37–39 νννννννοοοοοννννννννοοοοννννννννννννοοονννν 774077607777071
ND 438 Afri3 3 ∆8–12 and ∆37–39 νννννννοοοοοννννννννννννννννννννννννοοονννν 774077777777071
17 482 M. bovis-BCG 26 ∆3, ∆9, ∆16 and D ννονννννοννννννοννννννννννννννννννννννοοοοο 676773777777600
ND 641 M. microti 8 4-7, 23–24, 37–38 οοοννννοοοοοοοοοοοοοοοννοοοοοοοοοοοοννοοοοο 074000030000600
ND 592 M. canetti 6 30 and 36 οοοοοοοοοοοοοοοοοοοοοοοοοοοοονοοοοονοοοοοοο 000000000101000
21 26 CAS1 102 ∆4–7, ∆23–34 νννοοοονννννννννννννννοοοοοοοοοοοοννννννννν 703777740003771
ND 288 CAS2 6 ∆4–10, ∆23–34 νννοοοοοοοννννννννννννοοοοοοοοοοοοννννννννν 700377740003771
12 20 LAM1 152 ∆3 and B ννονννννννννννννννννοοοοννννννννοοοοννννννν 677777607760771
22 17 LAM2 92 ∆3, ∆13 and B ννονννννννννονννννννοοοοννννννννοοοοννννννν 677737607760771
19 33 LAM3 108 ∆9–11 and B ννννννννοοονννννννννοοοοννννννννοοοοννννννν 776177607760771
49 60 LAM4 37 ∆40 and B ννννννννννννννννννννοοοοννννννννοοοονννοννν 777777607760731
42 93 LAM5 44 ∆13 and B ννννννννννννονννννννοοοοννννννννοοοοννννννν 777737607760771
37 64 LAM6 47 ∆29 and B ννννννννννννννννννννοοοοννννονννοοοοννννννν 777777607560771
36 41 LAM7 48 ∆20, ∆26-27 and B νννννννννννννννννννοοοοονοονννννοοοοννννννν 777777404760771
NA 290 LAM8 9 ∆27 and B ννννννννννννννννννννοοοοννονννννοοοοννννννν 777777606760771
5 42 LAM9e 344 B ννννννννννννννννννννοοοοννννννννοοοοννννννν 777777607760771
9 61 LAM10 202 ∆23–25 and F ννννννννννννννννννννννοοονννννννοοοοννννννν 777777743760771
26 34 Sf 82 ∆9–10 and F ννννννννοοννννννννννννννννννννννοοοοννννννν 776377777760771
28 451 H37Rv 78 ∆20–21 and F νννννννννννννννννννοονννννννννννοοοοννννννν 777777477760771

aRk, ranking no.; ND, not done; ST, arbitrary designation; M., Mycobacterium.
bClass: family definition. See text for the definition of the family acronyms.
cTotal (n), size of the class; binary and octal, description.
dRule A, absence of spacers 29–32, presence of spacer 33 and absence of spacer 34; rule B, absence of spacers 21–24 and spacers 33–36; rule C : absence of spacer 18 and spacers 33–36; rule D, absence of spacers 39–43; rule E, absence of spacer 31 and spacers 3–-36; rule F, absence of spacers 33–36. Clades defined with low sample size, such as Afri2, Afri3, CAS2, and LAM8 are subject to change.
eFormerly LAM1.
fFormerly LAM2.

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