BMC Genomics (Aug 2022)

Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania

  • 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

DOI
https://doi.org/10.1186/s12864-022-08791-3
Journal volume & issue
Vol. 23, no. 1
pp. 1 – 9

Abstract

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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.

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