Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set.

doi:10.1128/JB.188.2.759-772.2006

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Article

Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set.

Journal of bacteriology - 1 Jan 2006

Filliol Ingrid, Motiwala Alifiya S, Cavatore Magali, Qi Weihong, Hazbón Manzour Hernando, Bobadilla del Valle Miriam, Fyfe Janet, García-García Lourdes, Rastogi Nalin, Sola Christophe, Zozio Thierry, Guerrero Marta Inírida, León Clara Inés, Crabtree Jonathan, Angiuoli Sam, Eisenach Kathleen D, Durmaz Riza, Joloba Moses L, Rendón Adrian, Sifuentes-Osornio José, Ponce de León Alfredo, Cave M Donald, Fleischmann Robert, Whittam Thomas S, Alland David

Abstract excerpt

We analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and 96% of the SNP locus pairs were in complete linkage disequilibrium. Cluster analyses identified six deeply branching, phylogenetically distinct SNP cluster groups (SCGs) and five subgroups. The SCGs were strongly...

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PMID: 16385065
DOI: 10.1128/JB.188.2.759-772.2006
PMCID: PMC1347298

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