High Throughput Sequencing for Clinical Tuberculosis: An Overview
Abstract
:1. Introduction
2. Whole vs. Targeted Sequencing for TB
3. Workflow
4. Sequencing Platforms
5. Sequencing Data Analysis and TB Resistance Platforms
6. Future Directions
7. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Author/Year | Location | tHTS Kit | Index Test Sample | Platform | Reference Standard/Comparisons |
---|---|---|---|---|---|
Cabbibe 2020 [18] | Italy | Deeplex Myc-TB | Sputum | MinION | Deeplex Myc-TB amplicons on MiniSeq |
Kambli 2021 [23] | Mumbai, India | Deeplex Myc-TB | Sputum, isolates | iSeq | pDST from MGIT; LPA; pyrosequencing |
Kayomo 2020 [19] | Congo | Deeplex Myc-TB | Sputum | MiSeq | Xpert MTB/RIF |
Colman 2019 [14] | United States | SMOR assay [24] | Isolates | MiSeq, iSeq | WGS (MiSeq and iSeq) |
Tafess 2020 [13] | Hong Kong, Ethiopia | In-house PCR (19 gene targets) | Isolates | MiSeq, MinION | pDST from MGIT |
Gliddon 2021 [25] | Kwazulu, South Africa | In-house RPA (isothermal) | Isolates | MinION | WGS (HiSeq), pDST from MGIT and solid agar |
Sibandze 2022 [21] | Eswatini, Germany | Deeplex Myc-TB | Stool | NextSeq | pDST from MGIT |
Wang 2019 [26] | Botswana | SMOR assay [24] | Isolates | MiSeq | pDST on MGIT; LPA, Xpert MTB/RIF |
Mariner-Llicer 2021 [27] | Spain | In-house assay (11 gene targets) | Sputum, isolates | MinION | WGS (MiSeq) |
Mesfin 2021 [20] | Eritrea | Deeplex Myc-TB | Sputum | MiniSeq | Xpert MTB/RIF |
Tagliani 2017 [28] | Djibouti | Deeplex Myc-TB | Sputum | MiniSeq | WGS (HiSeq) from isolates |
Song 2022 [24] | China | In house PCR (11 gene targets) | FFPE tissues | Ion Proton | pDST from microtitre plate |
Chan 2020 [15] | Hong Kong | In-house PCR (10 gene targets) | Bronchial aspirate, LN, sputum, bone marrow | MinION, MiSeq | pDST from MGIT; LPA |
Rowneki 2020 [16] | Ghana, Kenya, Uganda, Zambia | In house PCR (17 gene targets) | Sputum | MiSeq | Sanger sequencing on subset of samples |
Colman 2016 [22] | Moldova | SMOR assay | Sputum | MiSeq | pDST from MGIT |
Colman 2015 [29] | Moldova | SMOR assay | Sputum | MiSeq | pDST from MGIT |
Zhao 2022 [17] | Shanghai, China | In-house PCR (7 gene targets) | Sputum | GridION | Sanger sequencing, pDST |
Jouet 2021 [30] | Djibouti, Congo | Deeplex Myc-TB | Sputum | MiSeq | WGS, pDST from Löwenstein–Jensen or Middlebrook 7H11 agar |
Platforms | Characteristics | Pros | Cons | Studies |
---|---|---|---|---|
Illumina iSeq MiniSeq Miseq Nextseq HiSeq NovaSeq | Short-read (2 × 150 bp, MISEQ 2 × 300 bp) Run time 4–72 h | Low error rate (99.9% accuracy) Platforms vary in low to high throughput | Difficulty in sequencing repetitive regions [38] Per base error rate increases with read length (trimming can improve) Long run times | Sibandze 2021 [21]; Kambli 2021 [23]; Kayomo 2020 [19]; Wang 2019 [26]; Colman 2019 [14]; Mesfin 2021 [20]; Tagliani 2017 [28]; Vogel 2021 [11] |
Thermo fisher Ion torrent Proton PGM S5 | Short-read (200–400 bp) Run time 3–24 h | Short run time Low error rate | Low performance on homopolymer regions High cost per sample | Daum 2012 [39]; Pavel 2016 [40] |
Pacbio RSII Sequel | Long-read (10–60 kb) Run time up to 20 h | Short run time, long read length | High cost, high error rate (single base pair deletions most common, can improve with increased depth) | Lee 2019 [41]; Ley 2019 [42] |
Oxford Nanopore Minion Gridion Promethion | Long-read (900 kb +) Run time 30 min to 48 h | Short run time, long read length Increasing portability | Historically higher error rate (>98% reported accuracy with newer technology) [43,44] | Gliddon 2021 [25]; Mariner-Llicer 2021 [27]; Zhao 2022 [17] |
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Ness, T.E.; DiNardo, A.; Farhat, M.R. High Throughput Sequencing for Clinical Tuberculosis: An Overview. Pathogens 2022, 11, 1343. https://doi.org/10.3390/pathogens11111343
Ness TE, DiNardo A, Farhat MR. High Throughput Sequencing for Clinical Tuberculosis: An Overview. Pathogens. 2022; 11(11):1343. https://doi.org/10.3390/pathogens11111343
Chicago/Turabian StyleNess, Tara E., Andrew DiNardo, and Maha R. Farhat. 2022. "High Throughput Sequencing for Clinical Tuberculosis: An Overview" Pathogens 11, no. 11: 1343. https://doi.org/10.3390/pathogens11111343