Chapter 20 : The Evolutionary History, Demography, and Spread of the Mycobacterium tuberculosis Complex

Diagram of the proposed evolutionary pathway of the tubercle bacilli illustrating successive losses of DNA in certain lineages (gray boxes). The diagram is based on the presence or absence of conserved deleted regions and on sequence polymorphisms in five selected genes. The distances between certain branches may not correspond to actual phylogenetic differences calculated by other methods. Blue arrows indicate that strains are characterized by katG463. CTG (Leu), gyrA95 ACC (Thr), typical for group 1 organisms. Green arrows indicate that strains belong to group 2 characterized by katG463 CGG (Arg), gyrA95 ACC (Thr). The red arrow indicates that strains belong to group 3, characterized by katG463 CGG (Arg), gyrA95 AGC (Ser), as defined by Sreevatsan et al. ( 31 ). Adapted from Brosch et al. ( 33 ).

The genome-based phylogeny of MTBC mirrors that of human mitochondrial genomes. Comparison of the MTBC phylogeny (A) and a phylogeny derived from 4,955 mitochondrial genomes (mtDNA) representative of the main human haplogroups (B). Color-coding highlights the similarities in tree topology and geographic distribution between MTBC strains and the main human mitochondrial macrohaplogroups (black, African clades: MTBC lineages 5 and 6, human mitochondrial macrohaplogroups L0 to L3; pink, Southeast Asian and Oceanian clades: MTBC lineage 1, human mitochondrial macrohaplogroup M; blue, Eurasian clades: MTBC lineage 2 to 4, human mitochondrial macrohaplogroup N). Scale bars indicate substitutions per site. Adapted from Comas et al. ( 49 ).

Whole-genome phylogeny of 261 strains belonging to the MTBC. Animal and M. africanum specific deletions are indicated, as well as mutations affecting the PhoPR virulence regulator. Adapted from Bos et al. ( 55 ) and Gonzalo-Asensio et al. ( 34 ).

Biogeographical structure of the M. tuberculosis Beijing lineage. (a) MStree based on 24 MIRU-VNTR markers delineating the clonal complexes (CCs) gathered from a worldwide collection (n = 4,987). Major nodes and associated multilocus variants were grouped into six CCs and a basal sublineage (BL). (b) Genetic variability in the different Beijing lineage CCs and the BL calculated using a rarefaction procedure. Dots correspond to the mean allelic richness; boxes correspond to mean values ± standard error of the mean and error bars correspond to mean values ± standard deviation. (c) Worldwide distribution of the Beijing CCs and BL. Each circle corresponds to a country, and circle sizes are proportional to the number of strains. Adapted from Merker et al. ( 72 ).

Global phylogeny of 1,601 MTBC isolates inferred from a total of 91,648 SNPs spanning the whole genome. All seven main MTBC lineages are indicated in the inner area of the tree. The main sublineages are annotated at the outer arc along with lineage-specific RDs. Identified clades are color-coded. Adapted from Coll et al. ( 86 ).

Consistent with a general pattern for measurably evolving populations, the evolutionary rates of microbial pathogens decrease as a function of the time span over which they are estimated. Data shown are selected representative examples, including one group of RNA viruses and several bacterial pathogens. Adapted from Biek et al. ( 100 ).