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Volume 7, Number 3—June 2001

Synopsis

Spoligotype Database of Mycobacterium tuberculosis: Biogeographic Distribution of Shared Types and Epidemiologic and Phylogenetic Perspectives

Christophe Sola*Comments to Author , Ingrid Filliol*, Maria Cristina Gutierrez†, Igor Mokrousov*, Véronique Vincent†, and Nalin Rastogi*Comments to Author 
Author affiliations: *Institut Pasteur de Guadeloupe, Pointe à Pitre, Guadeloupe; †Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France

Main Article

Figure A1

Description of the 259 shared types of Mycobacterium tuberculosis with their nomenclatures (for data source, see Table 1). First column (type): number attribution for each spoligotype in our database. Second column (HN): numbers for some patterns described recently in Houston, Texas (12). Third column (spoligotype description): patterns obtained (8). Fourth column (geographic distribution): origin of isolates according to the original publication as ISO-code 3166. Fifth column (total): total num

Figure A1. . Description of the 259 shared types of Mycobacterium tuberculosis with their nomenclatures (for data source, see Table 1). First column (type): number attribution for each spoligotype in our database. Second column (HN): numbers for some patterns described recently in Houston, Texas (12). Third column (spoligotype description): patterns obtained (8). Fourth column (geographic distribution): origin of isolates according to the original publication as ISO-code 3166. Fifth column (total): total number of isolates for each of the shared types. Sixth column (carib): number of shared-type isolates found in the Caribbean by our team. Seventh column (other): number of shared-type isolates found elsewhere than the Caribbean. Note that number of isolates in fifth column for types 69 and 104 to 106 was not available (mentioned as 0). The ISO-codes 3166 are as follows: ARG, Argentina; AUT, Austria; BRB, Barbados; BOL, Bolivia; BRA, Brazil; BDI, Burundi; CAN, Canada; CHL, Chile; CHN, China; COM, Comoros; CIV, Côte d'Ivoire; CUB, Cuba; CZE, Czech Republic; DNK, Denmark; ECU, Ecuador; ETH, Ethiopia; FXX, metropolitan France; GUF, French Guiana; PYF, French Polynesia; GRL, Greenland; GLP, Guadeloupe; GNB, Guinea-Bissau; HND, Honduras; IND, India; ITA, Italy; KOR, Republic of Korea; MTQ, Martinique; MNG, Mongolia; NLD, Netherlands; PER, Peru; PHL, Philippines; ROM, Romania; RUS, Russian Federation; RWA, Rwanda; SAU, Saudi Arabia; SEN, Senegal; SOM, Somalia; ESP, Spain; LKA, Sri Lanka; SUR, Surinam ; TZA, Tanzania; THA, Thaïland; TUN, Tunisia; UGA, Uganda; GBR, United Kingdom; VNM, Vietnam; ZWE, Zimbabwe. Investigators wishing to obtain further information about an upgraded full version of this database may contact the author at csola@pasteur.gp

Main Article

1For this purpose, the independent sampling sizes for Europe and the USA were taken as n1 and n2, the number of individuals within a given shared-type "x" was k1 and k2, and in this case, the representativeness of the two samples was p1=k1/n1 and P2=k2/n2, respectively. To assess if the divergence observed between p1 and p2 was due to sampling bias or the existence of two distinct populations, the percentage of individuals (p0) harboring shared-type "x" in the population studied was estimated by the equation p0= k1+k2/n1+n2=n1p1+n2p2/n1+n2. The distribution of the percentage of shared-type "x" in the sample sizes n1 and n2 follows a normal distribution with a mean p0 and a standard deviation of formula imageand formula imagerespectively, and the difference d=p1-p2 follows a normal distribution of mean p0-p0=0 and of variance σd2p12p22 = p0q0/n1+p0q0/n2 or σd2=p0q0 (1/n1+1/n2). The two samples being independent, the two variances were additive; the standard deviation σd= was calculated, and the homogeneity of the samples tested was assessed using the quotient d/σd=p1-p2/formula image. If the absolute value of the quotient d/σd<2, the two samples were considered to belong to a same population (CI 95%) and the variation observed in the distribution of isolates for given shared types could be due to a sampling bias. Inversely, if d/σd>2, then the differences observed in the distribution of isolates for given shared types were statistically significant and not due to potential sample bias.

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