Mycobacterium tuberculosis Lineage Distribution in Xinjiang and Gansu Provinces, China

Haixia Chen,Chengmin Shi,Xumin Ni,Liang Ma,Li He,Weimin Li,Hairong Huang,Guangming Dai

doi:10.1038/s41598-017-00720-9

Abstract

Mycobacterium tuberculosis (M. tuberculosis) genotyping has dramatically improved the understanding of the epidemiology of tuberculosis (TB). In this study, 187 M. tuberculosis isolates from Xinjiang Uygur Autonomous Region (Xinjiang) and Gansu province in China were genotyped using large sequence polymorphisms (LSPs) and variable number tandem repeats (VNTR). Ten isolates, which represent major nodes of VNTR-based minimum spanning tree, were selected and subsequently subjected to multi-locus sequence analyses (MLSA) that include 82 genes. Based on a robust lineage assignment, we tested the association between lineages and clinical characteristics by logistic regression. There are three major lineages of M. tuberculosis prevalent in Xinjiang, viz. the East Asian Lineage 2 (42.1%; 56/133), the Euro-American Lineage 4 (33.1%; 44/133), and the Indian and East African Lineage 3 (24.8%; 33/133); two lineages prevalent in Gansu province, which are the Lineage 2 (87%; 47/54) and the Lineage 4 (13%; 7/54). The topological structures of the MLSA-based phylogeny support the LSP-based identification of M. tuberculosis lineages. The statistical results suggest an association between the Lineage 2 and the hemoptysis/bloody sputum symptom, fever in Uygur patients. The pathogenicity of the Lineage 2 remains to be further investigated.

Highlights

Determining M. tuberculosis genotype is critical for designing efforts to control TB due to the impact of genotype on disease outcome, vaccine efficacy and drug resistance[4]
Current trends in genotyping suggest that in strain identification[5], the use of large sequence polymorphisms (LSPs) or single nucleotide polymorphism (SNP) will replace mobile- or repetitive-element based markers, such as spoligotyping and variable number tandem repeats (VNTR), which suffer from problems associated with convergent evolution[6]
M. tuberculosis lineages are identified by detecting LSPs or regions of difference (RDs) that represent a series of well-characterized single-event polymorphisms

Summary

Introduction

Determining M. tuberculosis genotype is critical for designing efforts to control TB due to the impact of genotype on disease outcome, vaccine efficacy and drug resistance[4]. MLSA of these globally distributed strains of MTBC resulted in a single most parsimonious phylogenetic tree with negligible homoplasy[15] This phylogeny was highly congruent with their previous analyses based on large sequence polymorphisms (LSPs)[7]. All three analyses yielded identical tree topologies, which were highly congruent with their previous findings based on maximum parsimony[5] Their results suggest that LSP markers or multi-locus sequence based method yield more robust identification of M. tuberculosis strain lineages as compared to markers based on mobile or repetitive genetic elements, especially spoligotyping. According to the minimum spanning tree based on VNTR result, representative isolates were selected and sequenced to perform multi-locus sequence analysis (MLSA) and further gained insights into the evolution of M. tuberculosis in Xinjiang and Gansu. Our goal is to understand the composition and distributions of the M. tuberculosis lineages in Xinjiang and Gansu, and to explore the association of distinct Lineages of M. tuberculosis with clinical characteristics of infected patients

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Conclusion