학술논문
Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania
Document Type
article
Author
Beatrice Kemilembe Mutayoba; Michael Hoelscher; Norbert Heinrich; Moses L. Joloba; Eligius Lyamuya; Andrew Martin Kilale; Nyagosya Segere Range; Bernard James Ngowi; Nyanda Elias Ntinginya; Saidi Mwinjuma Mfaume; Amani Wilfred; Basra Doulla; Johnson Lyimo; Riziki Kisonga; Amri Kingalu; Jupiter Marina Kabahita; Ocung Guido; Joel Kabugo; Isa Adam; Moses Luutu; Maria Magdalene Namaganda; Joanitah Namutebi; George William Kasule; Hasfah Nakato; Henry Byabajungu; Pius Lutaaya; Kenneth Musisi; Denis Oola; Gerald Mboowa; Michel Pletschette
Source
BMC Genomics, Vol 23, Iss 1, Pp 1-9 (2022)
Subject
Language
English
ISSN
1471-2164
Abstract
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.