학술논문
Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania.
Document Type
Article
Author
Mutayoba, Beatrice Kemilembe; Michael Hoelscher; Heinrich, Norbert; Joloba, Moses L.; Lyamuya, Eligius; Kilale, Andrew Martin; Range, Nyagosya Segere; Ngowi, Bernard James; Ntinginya, Nyanda Elias; Mfaume, Saidi Mwinjuma; Wilfred, Amani; Doulla, Basra; Lyimo, Johnson; Kisonga, Riziki; Kingalu, Amri; Kabahita, Jupiter Marina; Guido, Ocung; Kabugo, Joel; Adam, Isa; Luutu, Moses
Source
Subject
*TUBERCULOSIS
*WHOLE genome sequencing
*MYCOBACTERIUM tuberculosis
*VACCINE effectiveness
*DRUG resistance
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Language
ISSN
1471-2164
Abstract
Background: Mycobacterium tuberculosis presents several lineages each with distinct characteristics of evolutionary status, transmissibility, drug resistance, host interaction, latency, and vaccine efficacy. Whole genome sequencing (WGS) has emerged as a new diagnostic tool to reliably inform the occurrence of phylogenetic lineages of Mycobacterium tuberculosis and examine their relationship with patient demographic characteristics and multidrug-resistance development. Methods: 191 Mycobacterium tuberculosis isolates obtained from a 2017/2018 Tanzanian drug resistance survey were sequenced on the Illumina Miseq platform at Supranational Tuberculosis Reference Laboratory in Uganda. Obtained fast-q files were imported into tools for resistance profiling and lineage inference (Kvarq v0.12.2, Mykrobe v0.8.1 and TBprofiler v3.0.5). Additionally for phylogenetic tree construction, RaxML-NG v1.0.3(25) was used to generate a maximum likelihood phylogeny with 800 bootstrap replicates. The resulting trees were plotted, annotated and visualized using ggtree v2.0.4 Results: Most [172(90.0%)] of the isolates were from newly treated Pulmonary TB patients. Coinfection with HIV was observed in 33(17.3%) TB patients. Of the 191 isolates, 22(11.5%) were resistant to one or more commonly used first line anti-TB drugs (FLD), 9(4.7%) isolates were MDR-TB while 3(1.6%) were resistant to all the drugs. Of the 24 isolates with any resistance conferring mutations, 13(54.2%) and 10(41.6%) had mutations in genes associated with resistance to INH and RIF respectively. The findings also show four major lineages i.e. Lineage 3[81 (42.4%)], followed by Lineage 4 [74 (38.7%)], the Lineage 1 [23 (12.0%)] and Lineages 2 [13 (6.8%)] circulaing in Tanzania. Conclusion: The findings in this study show that Lineage 3 is the most prevalent lineage in Tanzania whereas drug resistant mutations were more frequent among isolates that belonged to Lineage 4. [ABSTRACT FROM AUTHOR]