China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis

Abstract

A small number of high-burden countries account for the majority of tuberculosis cases worldwide. Detailed data are lacking from these regions. To explore the evolutionary history of Mycobacterium tuberculosis in China-the country with the third highest tuberculosis burden-we analysed a countrywide collection of 4,578 isolates. Little genetic diversity was detected, with 99.4% of the bacterial population belonging to lineage 2 and three sublineages of lineage 4. The deeply rooted phylogenetic positions and geographic restriction of these four genotypes indicate that their populations expanded in situ following a small number of introductions to China. Coalescent analyses suggest that these bacterial subpopulations emerged in China around 1,000 years ago, and expanded in parallel from the twelfth century onwards, and that the whole population peaked in the late eighteenth century. More recently, sublineage L2.3, which is indigenous to China and exhibited relatively high transmissibility and extensive global dissemination, came to dominate the population dynamics of M. tuberculosis in China. Our results indicate that historical expansion of four M. tuberculosis strains shaped the current tuberculosis epidemic in China, and highlight the long-term genetic continuity of the indigenous M. tuberculosis population.

Fig. 1.. Genotyping results of countrywide collected MTBC strains in China.

(a) The prevalence of different MTBC lineages in 32 provinces based on spoligotyping data from 16,221 isolates collected throughout China. (b) The 76 county sites from which MTBC isolates were sampled for this study: “population sites” are counties where MTBC isolates were collected through exhaustive sampling from 2009–2010, and “random sites” are counties where MTBC isolates were randomly sampled in 2007. SNP typing results of L2 strains (c) and L4 strains (d) show the relative proportion of each sublineage in each province. (e) Phylogeny of 301 MTBC isolates reflecting diversity found worldwide. Branches are colored according to the convention described in Comas et al 2010. Sublineages found commonly in China are highlighted, with a notation of their prevalence. Sublineages that were rarely encountered in China are marked with green pentacles; the remaining unmarked sublineages were not identified in China.

Fig. 2.. Low genetic diversity in China’s MTBC population.

(a) Pie charts showing the relative prevalences of MTBC sublineages in different countries, where each sublineage is assigned a color according to a recent defining scheme. Mean pairwise SNP distance between MTBC strains (b), nucleotide diversity (π) in MTBC population (c) from each country/region/population. “SA” refers to South Africa, “SL” refers to Sierra Leone, and 95% confidence intervals are shown. (d) Rarefaction analysis predicted the sublineage diversity of MTBC population in China, India, and Vietnam. Two hundred isolates were randomly sampled from each of the three countries; solid lines show the captured sublineages while the dashed lines show the predicted changes as the sample size is increased.

Fig. 3.. Single origins of the four indigenous genotypes.

The phylogenetic trees of lineage 2 (a) and lineage 4 (b) were reconstructed with 1,242 isolates and 1,569 isolates respectively. To reduce the complexity in both trees, terminal branches with branch length < 0.008 (indicating clusters diversified very recently, e.g. the two Russian clades in L2.3) were automatically collapsed into circles. The circle sizes of those collapsed branches were proportional to the number of leaves that were collapsed. The estimated origin times of indigenous genotypes are shown at the relevant nodes, and their inferred geographic states are shown as pies with the colors indicating the isolates’ country origin. Asia* refers to Asian countries and regions excluding China. The three dominant clades of L4 in China were highlighted.

Fig. 4.. Historical expansions of indigenous MTBC genotypes.

(a) Estimated effective population size changes of the major MTBC sublineages in China. L2.3 was separated from L2.2 in Bayesian Skyline Plot analysis, and the dashed lines represent the 95% HPD. (b) Comparison of Chinese human population growth curve and MTBC N_e curve (all indigenous genotypes). (c) The inferred past population dynamics of each sublineage in China estimated from the effective population growth.

Fig. 5.. Global dispersal of Chinese indigenous genotypes.

(a) A circle plot with ribbons depicting the dispersal flows that led to the global emergence of Chinese indigenous sublineages. All the flows refer to “one-way” outflows and indicate direct or indirect exportation events with the ribbon width at each end proportional to the number of strains sampled in each country. The pie charts next to the country names show the proportion (red sector) of strains in the relative dataset that was found to be descendants of Chinese indigenous genotypes. (b) Global dispersal of Chinese L4.5 strains. Different leaf colors indicate the diverse geographic origins of those isolates. The Chinese L4.5 clade is highlighted in blue, and the branches are colored according to their geographic attributions. The major country transition events are marked with stars, and transition time of each event was estimated under MTBC-6 model. The European specific clades are nested within the Chinese L4.5 clade with the closest branches sampled from Northwest China. The closest branches to the strains sampled from Vietnam were mostly collected in South China.

Fig. 6.. Contour maps show the countrywide prevalence of indigenous sublineages.

(a)-(e) The color ranges showing the prevalence of each sublineage in percentage based on the SNP typing data. (f) A scenario of Maritime Silk Road origins for L4 sublineages in China. The ship symbols mark the major ports on historical sea trade routes. The directions of dispersal of L4.5 and L4.4 are shown.