Distribution and identification of Mycobacterium tuberculosis lineage in Kashgar prefecture

Abstract

Objectives Kashgar prefecture is an important transportation and trade hub with a high incidence of tuberculosis. The following study analyzed the composition and differences in Mycobacterium tuberculosis (M.tb) lineage and specific tags to distinguish the lineage of the M.tb in Kashgar prefecture, thus providing a basis for the classification and diagnosis of tuberculosis in this area. Methods Whole-genome sequencing (WGS) of 161 M.tb clinical strains was performed. The phylogenetic tree was constructed using Maximum Likelihood (ML) based on single nucleotide polymorphisms (SNPs) and verified through principal component analysis (PCA). The composition structure of M.tb in different regions was analyzed by combining geographic information. Results M.tb clinical strains were composed of lineage 2 (73/161, 45.34%), lineage 3 (52/161, 32.30%) and lineage 4 (36/161, 22.36%). Moreover, the 3 lineages were subdivided into 11 sublineages, among which lineage 2 included lineage 2.2.2/Asia Ancestral 1 (9/73, 12.33%), lineage 2.2.1-Asia Ancestral 2 (9/73, 12.33%), lineage 2.2.1-Asia Ancestral 3 (18/73, 24.66%), and lineage 2.2.1-Modern Beijing (39/73, 53.42%). Lineage 3 included lineage 3.2 (14/52, 26.92%) and lineage 3.3 (38/52, 73.08%), while lineage 4 included lineage 4.1 (3/36, 8.33%), lineage 4.2 (2/36, 5.66%), lineage 4.4.2 (1/36, 2.78%), lineage 4.5 (28/36, 77.78%) and lineage 4.8 (2/36, 5.66%), all of which were consistent with the PCA results. One hundred thirty-six markers were proposed for discriminating known circulating strains. Reconstruction of a phylogenetic tree using the 136 SNPs resulted in a tree with the same number of delineated clades. Based on geographical location analysis, the composition of Lineage 2 in Kashgar prefecture (45.34%) was lower compared to other regions in China (54.35%-90.27%), while the composition of Lineage 3 (32.30%) was much higher than in other regions of China (0.92%-2.01%), but lower compared to the bordering Pakistan (70.40%). Conclusion Three lineages were identified in M.tb clinical strains from Kashgar prefecture, with 136 branch-specific SNP. Kashgar borders with countries that have a high incidence of tuberculosis, such as Pakistan and India, which results in a large difference between the M.tb lineage and sublineage distribution in this region and other provinces of China.

Comparative Study on Tuberculosis Drug Resistance and Molecular Detection Methods Among Different Mycobacterium Tuberculosis Lineages

“…These were categorized into three major lineages: lineage 2 (73/161, 45.34%), lineage 3 (52/161, 32.30%), and lineage 4 (36/161, 22.36%). 8 A total of 161 strains of M.tb culture underwent pDST using four drugs, and, regrettably, only one of those strains showed resistance to EMB. Given the small sample size, this strain was excluded from the analysis.…”

“…Lineage 3 and Lineage 4 also have a certain presence, particularly in the Kashgar region of Xinjiang, where Lineage 2, Lineage 3, and Lineage 4 are highly prevalent. 8 Therefore, conducting in-depth research on these characteristics holds significant importance for optimizing prevention, control, and treatment strategies for tuberculosis in this specific region.…”

Identification of positively selected genes in Mycobacterium tuberculosis from southern Xinjiang Uygur autonomous region of China

“…Xinjiang Uygur Autonomous Region is one of the areas with a high TB burden, with a morbidity rate of 87.85/100,000 in 2021 ( National Health Commission of the People’s Republic of China, 2022 ). Several studies explored that the characteristics of Mtb in Xinjiang with whole genome sequencing (WGS) have been reported ( Anwaierjiang et al, 2021 ; He et al, 2022 ; Xu et al, 2022 ), including Mtb population structure ( Xu et al, 2022 ), drug resistance ( Anwaierjiang et al, 2021 ), and virulence ( He et al, 2022 ). To date, the report on detailed analysis of the selective evolution of Mtb strains has not been found in this area.…”

Analysis of spatial characteristics and geographic weighted regression of tuberculosis prevalence in Kashgar, China

“…Some factors may influence the development of disease or determine the specificity of the disease and cause damage to the organism. Therefore, analyzing the influencing factors of the disease can provide scientific reference to help preventing the further development of the disease and avoid causing irreversible damage to the body ( Ofori-Anyinam et al, 2020 , Mulholland et al, 2019 , Sapriel et al, 20192019 , Xu et al, 2022 ).…”