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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 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 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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