Emerging Infectious Disease ISSN: 1080-6059

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

Christophe Sola*

, Ingrid Filliol*, Maria Cristina Gutierrez†, Igor Mokrousov*, Véronique Vincent†, and Nalin Rastogi*

Author affiliations: *Institut Pasteur de Guadeloupe, Pointe à Pitre, Guadeloupe; †Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France

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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

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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 image and respectively, and the difference d=p₁-p₂ follows a normal distribution of mean p₀-p₀=0 and of variance σ_d²=σ_p1²+σ_p2² = p₀q₀/n₁+p₀q₀/n₂ or σ_d²=p₀q₀ (1/n₁+1/n₂). The two samples being independent, the two variances were additive; the standard deviation σ_d= was calculated, and the homogeneity of the samples tested was assessed using the quotient d/σ_d=p₁-p₂/ formula image . If the absolute value of the quotient d/σ_d<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/σ_d>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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