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

Main Article

Figure 3

Enlargement of branches A to D from the Mycobacterium tuberculosis phylogenetic tree (Figure 2). Numbers in standard characters refer to spoligotype numbers according to our database; those in boxes describe both the spoligotype number and variable number of tandem DNA repeats (VNTR) allele designations. Italicized numbers refer to spoligotype followed by the Houston spoligotype designation (12), and the major genetic groups 1 to 3 defined on the basis of katG283-gyrA95 allele combination (24).

Figure 3. . Enlargement of branches A to D from the Mycobacterium tuberculosis phylogenetic tree (Figure 2). Numbers in standard characters refer to spoligotype numbers according to our database; those in boxes describe both the spoligotype number and variable number of tandem DNA repeats (VNTR) allele designations. Italicized numbers refer to spoligotype followed by the Houston spoligotype designation (12), and the major genetic groups 1 to 3 defined on the basis of katG283-gyrA95 allele combination (24). A and B show distinct branches belonging essentially to the major genetic group 1 with a high exact tandem repeat (ETR)-A copy number; C and D show branches that include some strains of the "Haarlem family" belonging to the major genetic group 2 with a low ETR-A copy number.

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 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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