Fig 1.
Estimated global burden of MTBC L1 and the proportion of different MTBC lineages worldwide.
The pink heat map indicates the estimated absolute number of L1 TB cases in different countries, while the pie charts indicate the proportion of different MTBC lineages circulating in specific United Nations geoscheme geographical subregions. Data were previously published in a recent review [4]. The map used was created by Frank Bennett, Public Domain, via Wikimedia Commons (https://commons.wikimedia.org/wiki/File:BlankMap-World-Flattened.svg).
Fig 2.
Estimated absolute number of cases of MTBC lineages circulating among L1-endemic high-burden TB, MDR/RR-TB, and TB-HIV countries.
The absolute numbers on the y-axis are scaled by 10,000. The six countries indicated in the figure are L1-endemic countries that are also included in the WHO list of high-burden TB, MDR/RR-TB, and HIV/TB countries. The largest number of TB patients caused by L1 strains are in India and the Philippines, with approximately 1.4 million and 700,000 cases, respectively. Data used were obtained from the 2024 WHO Global TB Report [1] and a recently published review [4].
Fig 3.
The global population structure of MTBC L1.
The phylogenetic tree above consists of 4,171 MTBC L1 genomes originating from 63 countries. The phylogenetic tree indicates the sublineage classification according to L1 SNP barcodes published by Coll and colleagues [12]. Within L1.1.1, there is a clade designated as L1.1.1.1 (labeled in blue curved line). The genomes highlighted in light green (L1.1) and dark green (L1) are examples of genomes that could not be classified by Coll nomenclature, as previously published [5,15]. However, based on their position within the tree, they belong to L1.1.2 and L1.2.2, respectively. The strain’s geographical region of origin is based on the country of birth of the patient or if the country of birth is unknown, the country of isolation. The deeply branching genomes within the L1.2.1 clade, emphasized here with circular tip points, comprise strains from East Africa, Southeast Asia, and Oceania.
Fig 4.
Global distribution of L1 sublineages.
The MTBC genomes included here are the same as the ones represented in Fig 3. The genomes are classified according to the country of birth of the patient source of the isolate, or the country of isolation, when the country of birth is unknown. The size of the pie chart for each country is based on the number of genomes included in the dataset, with the smallest pie chart corresponding to less than five genomes and the largest with more than 20 genomes. The world map was generated from the R package “rnaturalearth” (https://CRAN.R-project.org/package=rnaturalearth).
Table 1.
Comparison of different WGS-based SNP-typing schemes used to classify MTBC L1 strains.