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Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania
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 oc...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9356438/ https://www.ncbi.nlm.nih.gov/pubmed/35931954 http://dx.doi.org/10.1186/s12864-022-08791-3 |
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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 Namaganda, Maria Magdalene Namutebi, Joanitah Kasule, George William Nakato, Hasfah Byabajungu, Henry Lutaaya, Pius Musisi, Kenneth Oola, Denis Mboowa, Gerald Pletschette, Michel |
author_facet | 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 Namaganda, Maria Magdalene Namutebi, Joanitah Kasule, George William Nakato, Hasfah Byabajungu, Henry Lutaaya, Pius Musisi, Kenneth Oola, Denis Mboowa, Gerald Pletschette, Michel |
author_sort | Mutayoba, Beatrice Kemilembe |
collection | PubMed |
description | 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08791-3. |
format | Online Article Text |
id | pubmed-9356438 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-93564382022-08-07 Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania 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 Namaganda, Maria Magdalene Namutebi, Joanitah Kasule, George William Nakato, Hasfah Byabajungu, Henry Lutaaya, Pius Musisi, Kenneth Oola, Denis Mboowa, Gerald Pletschette, Michel BMC Genomics Research 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08791-3. BioMed Central 2022-08-05 /pmc/articles/PMC9356438/ /pubmed/35931954 http://dx.doi.org/10.1186/s12864-022-08791-3 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research 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 Namaganda, Maria Magdalene Namutebi, Joanitah Kasule, George William Nakato, Hasfah Byabajungu, Henry Lutaaya, Pius Musisi, Kenneth Oola, Denis Mboowa, Gerald Pletschette, Michel Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania |
title | Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania |
title_full | Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania |
title_fullStr | Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania |
title_full_unstemmed | Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania |
title_short | Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania |
title_sort | phylogenetic lineages of tuberculosis isolates and their association with patient demographics in tanzania |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9356438/ https://www.ncbi.nlm.nih.gov/pubmed/35931954 http://dx.doi.org/10.1186/s12864-022-08791-3 |
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