Published February 25, 2022
| Version v1
Journal article
Open
Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania
Authors/Creators
- Mutayoba Beatrice Kemilembe1
- Hoelscher Michael2
- Heinrich Norbert2
- Joloba L Moses3
- Ershova Julia1
- Lyamuya Eligius4
- Kilale Martin Andrew5
- Range Segere Nyagosya5
- Ngowi James Benard6
- Ntinginya Elias Nyanda7
- Mfaume Mwinjuma Saidi5
- Wilfred Amani
- Basra Doulla8
- Lyimo Johnson
- Kingalu Amri
- Lema Yakobo
- Kabahita Marina Jupiter7
- Guido Ocung7
- Kabugo Joel7
- Adam Isa7
- Luutu Moses3
- Namaganda Magdalene Maria3
- Namutebi Joanitah3
- Kasule William George7
- Nakato Hasfah7
- Byabajungu Henry7
- Lutaaya Pius7
- Musisi Kenneth7
- Oola Denis7
- Pletschette Michel9
-
Mboowa Gerald3
- 1. National AIDS Control Program, Department of Preventive Services, Dodoma, Tanzania
- 2. Department of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany
- 3. Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
- 4. Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences
- 5. US Centers for Disease Control and Prevention (CDC), Division of Global HIV and TB, Global TB Branch, Atlanta, USA
- 6. National Institute for Medical Research (NIMR), Muhimbili Research Centre, Dar es Salaam, Tanzania
- 7. National Tuberculosis Reference Laboratory/Supranational Reference Laboratory, Luzira, Uganda
- 8. MoHCDGEC, NTLP, Central Tuberculosis Reference Laboratory (CTRL), Dar es Salaam, Tanzania
- 9. Muhimbili University of Health and Allied Sciences (MUHAS), Department of Microbiology and Immunology, Dar es Salaam, Tanzania
Description
This study set out to determine the occurrence of phylogenetic lineages of M.tb complex and to examine their relationship with patient demographic characteristics and multidrug-resistant TB (MDR-TB) among pulmonary TB patients enrolled during the second national anti-TB drug resistance survey in Tanzania. A cross-sectional survey was conducted involving a sample of new smear-positive pulmonary TB and previously treated individuals. Sputum samples were collected and transported to the Central TB Reference Laboratory (CTRL) in Dar es Salaam, Tanzania for smear microscopy, culture, strain identification and susceptibility testing following standard National TB and Leprosy Programme (NTLP) guidelines. For WGS, all culture positive isolates were shipped to the National TB Reference Laboratory/Supranational Tuberculosis Reference Laboratory in Uganda. The isolates were sub-cultured on selective Middlebrook 7H11 agar. High quality genomic DNA was extracted using an in-house cetyl trimethylammonium bromide (CTAB) method. Genomic libraries were sequenced using the Illumina MiSeq V3 cartridge. Tools for resistance profiling and lineage inference (Kvarq v0.12.2, Mykrobe v0.8.1 and TBprofiler v3.0.5) were ran. De novo genome assembly of all samples was done using Unicycler v0.4.8. The resulting trees were plotted, annotated and visualized using ggtree v2.0.4.
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md5:a81065c0792c7acb7073d5d89f3f1daf
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4.2 MB | Download |
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md5:c87b90faa6ac1ab55c891bbbc6dcc76b
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4.4 MB | Download |
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md5:772fd8a2a4d67247605922eb6cc3ee6c
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4.2 MB | Download |
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md5:42783f19712422f92fe5e8d9bd268f8c
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4.3 MB | Download |
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md5:346b6d5036df44aa4bc2c2a5c5a99e4a
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3.1 MB | Download |
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md5:787bd737cb5aa87f4a4203d96ece4bf1
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4.3 MB | Download |
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md5:33525c20e3710b1807917086f03b8d15
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4.4 MB | Download |
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md5:3dfebd5e84d3b183643ceedbf0e3e13c
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4.4 MB | Download |
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md5:dbef162be6a95aae1f7b67f854ef8e02
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4.4 MB | Download |
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md5:a927b68c554a2215f064f59fd4d6defc
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4.4 MB | Download |
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md5:72fd4d07c6a483fd01340def3f5eb26e
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4.0 MB | Download |
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md5:d83b54972a859e8cd7bdf33c4619cc90
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4.4 MB | Download |
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md5:c52a7fc64b807a81fb804d85b5c5a279
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2.7 MB | Download |
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md5:dee1465986a4441889dc80bcb036a229
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4.2 MB | Download |
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md5:922bc7807ac7bc21ffd0a56d13e988a0
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4.2 MB | Download |
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md5:75837cada91ee1abb07f11f0bd3e4cd3
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4.3 MB | Download |