Origin and Global Expansion of Mycobacterium tuberculosis Complex Lineage 3

Abstract

Mycobacterium tuberculosis complex (MTBC) Lineage 3 (L3) strains are abundant in world regions with the highest tuberculosis burden. To investigate the population structure and the global diversity of this major lineage, we analyzed a dataset comprising 2682 L3 strains from 38 countries over 5 continents, by employing 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats genotyping (MIRU-VNTR) and drug susceptibility testing. We further combined whole-genome sequencing (WGS) and phylogeographic analysis for 373 strains representing the global L3 genetic diversity. Ancestral state reconstruction confirmed that the origin of L3 strains is located in Southern Asia and further revealed multiple independent introduction events into North-East and East Africa. This study provides a systematic understanding of the global diversity of L3 strains and reports phylogenetic variations that could inform clinical trials which evaluate the effectivity of new drugs/regimens or vaccine candidates.

Keywords: Lineage 3; MTBC; Mycobacterium tuberculosis; back to Africa.

Figure 1

Clonal complexes (CCs) of MTBC Lineage 3 strains. Minimum spanning (MS) tree based on 24-loci MIRU-VNTR data of 2682 clinical MTBC L3 strains originating from 38 countries. Five L3 clonal complexes (L3-CCs) and diverse strains representing the L3 background diversity (L3-BG) are color coded. Node size reflects the number of strains with identical 24-loci MIRU-VNTR patterns. Branch length proportional to the number of allele differences between two nodes. Solid lines indicate 1, 2, or 3 allele differences, gray dashed lines represent 4 allele differences, and gray dotted lines represent 5 or more allele differences.

Figure 2

Molecular clusters and drug resistance among L3 clonal complexes (CC). Proportions of clustered strains (A) and rifampicin-resistant (RR) and multidrug-resistant (MDR) strains (B) within L3 clonal complexes (CC) and within diverse strains representing the genetic background (L3-BG).

Figure 3

Global geographical distribution of MTBC Lineage 3 clonal complexes (L3-CCs). Each pie chart represents a country, and the size of each pie chart is proportional to the number of strains. L3-CCs and L3-BG are color coded as in Figure 1.

Figure 4

Global phylogeny of MTBC Lineage 3 strains. Midpoint-rooted maximum-likelihood (ML) tree based on 26,536 concatenated single-nucleotide polymorphisms (SNPs) and 373 L3 strains. The first outer ring provides a color code for the L3 subgroups defined by Napier et al. (18). Subsequent outer rings indicate clades for which we determined signature SNPs. Gray and red dots indicate branches with at least 99% bootstrap support; red dots further indicate branches for which we propose signature SNPs.

Figure 5

Phylogeographic ancestral state reconstruction of MTBC L3 strains. Nodes are color coded by UN regions. Pie charts show likelihoods for ancestral geographic origins for the internal nodes. A South Asian origin for L3 progenitor is supported using the rooted maximum-likelihood phylogeny. The scale bar indicates nucleotide substitutions per site. Four clades with a predicted African common ancestor are indicated and their pie charts are shown enlarged for better visibility, as well as for the root.