Targeted next-generation sequencing: a Swiss army knife for mycobacterial diagnostics?

Mohamed, Sagal Y; Köser, Claudio U.; Sougakoff, Wladimir; Heysell, Scott K

doi:10.1183/13993003.04077-2020

Cited by 17 publications

(19 citation statements)

References 30 publications

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“…2 The availability of several new treatment options and strategies is progress, but getting the right drugs to the right patients in time to influence outcomes positively is essential and requires access to rapid and accurate diagnostics that meet the emerging needs. 3,4 WHO set an important but challenging target on universal drug susceptibility testing (DST), which includes testing for the new and repurposed drugs in the WHO revised definition of extensively drug-resistant tuberculosis. 5 Phenotypic DST for Mycobacterium tuberculosis complex (MTBC), although still the reference standard for most drugs, can take over a month to www.thelancet.com/microbe Published online March 8, 2022 https://doi.org/10.1016/ S2666-5247(21)00301-3 complete and requires expensive, complex laboratory capacity.…”

Section: Introductionmentioning

confidence: 99%

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The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

Posey

Walker

Steyn³

et al. 2022

The Lancet Microbe

156

131

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Section: Introductionmentioning

confidence: 99%

“…2 The availability of several new treatment options and strategies for the first time in decades is an advance, but getting the right drugs to the right patients in time to positively impact outcomes is essential, and requires access to rapid and accurate diagnostics that meet the emerging needs. 3 , 4 …”

Section: Introductionmentioning

confidence: 99%

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

Posey

Walker

Steyn³

et al. 2022

The Lancet Microbe

156

131

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“…Although targeted next-generation sequencing (tNGS) can identify species and lineage, predict drug susceptibility, and inform on spoligotype, it is inherently restricted in its resolution in comparative genomics for outbreak investigations compared to WGS. WGS, therefore, remains the ultimate goal (7). Here we explored how close we could get to obtaining useful diagnostic information from sequencing primary clinical samples in two high burden settings; Madagascar, a low-income country, and India, a middle-income country.…”

Section: Introductionmentioning

confidence: 99%

Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination and Drug Susceptibility Prediction

Nilgiriwala

Rabodoarivelo

Hall

et al. 2022

Preprint

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Background Universal access to drug susceptibility testing for newly diagnosed tuberculosis patients is recommended. Access to culture-based diagnostics remains limited and targeted molecular assays are vulnerable to emerging resistance conferring mutations. Improved sample preparation protocols for direct-from-sputum sequencing of Mycobacterium tuberculosis would accelerate access to comprehensive drug susceptibility testing and molecular typing. Methods We assessed a thermo-protection buffer-based direct-from-sample M. tuberculosis whole-genome sequencing protocol. We prospectively processed and analyzed 60 acid-fast bacilli smear-positive sputum samples from tuberculosis patients in India and Madagascar. A diversity of semi-quantitative smear positivity level samples were included. Sequencing was performed using Illumina and MinION (monoplex and multiplex) technologies. We measured the impact of bacterial inoculum and sequencing platforms on M. tuberculosis genomic mean read depth, drug susceptibility prediction performance and typing accuracy. Results M. tuberculosis was identified from 88% (Illumina), 89% (MinION-monoplex) and 83% (MinION-multiplex) of samples for which sufficient DNA could be extracted. The fraction of M. tuberculosis reads from MinION sequencing was lower than from Illumina, but monoplexing grade 3+ sputum samples on MinION produced higher read depth than Illumina (p<0.05) and MinION multiplex (p<0.01). No significant difference in overall sensitivity and specificity of drug susceptibility predictions was seen across these sequencing modalities or within each sequencing technology when stratified by smear grade. Lineage typing agreement percentages between direct and culture-based sequencing were 85% (MinION-monoplex), 88% (Illumina) and 100% (MinION-multiplex) Conclusions M. tuberculosis direct-from-sample whole-genome sequencing remains challenging. Improved and affordable sample treatment protocols are needed prior to clinical deployment.

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“…the most viable option to scale up AST globally [18,19,21]. Between 2011 and 2014, for instance, the WHO-endorsed GenoType MTBDRplus VER 2.0 by Hain Lifescience was designed not to detect rpoB L452P because this mutation was not considered to be a rifampicin resistance mutation at that time [18,19].…”

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confidence: 99%

Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment

Georghiou¹,

Rodwell²,

Korobitsyn³

et al. 2022

Eur Respir J

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Inappropriately high breakpoints have resulted in systematic false-susceptible AST results to anti-TB drugs. MIC, PK/PD and clinical outcome data should be combined when setting breakpoints to minimise the emergence and spread of antimicrobial resistance. https://bit.ly/3i43wb6Cite this article as: Antimycobacterial Susceptibility Testing Group. Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment. Eur

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Targeted next-generation sequencing: a Swiss army knife for mycobacterial diagnostics?

Cited by 17 publications

References 30 publications

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination and Drug Susceptibility Prediction

Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment

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