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Mann BC, Jacobson KR, Ghebrekristos Y, Warren RM, Farhat MR. Assessment and validation of enrichment and target capture approaches to improve Mycobacterium tuberculosis WGS from direct patient samples. J Clin Microbiol 2023; 61:e0038223. [PMID: 37728909 PMCID: PMC10595060 DOI: 10.1128/jcm.00382-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/20/2023] [Indexed: 09/22/2023] Open
Abstract
Within-host Mycobacterium tuberculosis (Mtb) diversity may detect antibiotic resistance or predict tuberculosis treatment failure and is best captured through sequencing directly from sputum. Here, we compared three sample pre-processing steps for DNA decontamination and studied the yield of a new target enrichment protocol for optimal whole-genome sequencing (WGS) from direct patient samples. Mtb-positive NALC-NaOH-treated patient sputum sediments were pooled, and heat inactivated, split in replicates, and treated by either a wash, DNase I, or benzonase digestion. Levels of contaminating host DNA and target Mtb DNA were assessed by quantitative PCR (qPCR), followed by WGS with and without custom dsDNA target enrichment. The pre-treatment sample has a high host-to-target ratio of DNA (6,168 ± 1,638 host copies/ng to 212.3 ± 59.4 Mtb copies/ng) that significantly decreased with all three treatments. Benzonase treatment resulted in the highest enrichment of Mtb DNA at 100-fold compared with control (3,422 ± 2,162 host copies/ng to 11,721 ± 7,096 Mtb copies/ng). The custom dsDNA probe panel successfully enriched libraries from as little as 0.45 pg of Mtb DNA (100 genome copies). Applied to direct sputum the dsDNA target enrichment panel increased the percent of sequencing reads mapping to the Mtb target for all three pre-processing methods. Comparing the results of the benzonase sample sequenced both with and without enrichment, the percent of sequencing reads mapping to the Mtb increased to 90.95% from 1.18%. We demonstrate a low limit of detection for a new custom dsDNA Mtb target enrichment panel that has a favorable cost profile. The results also demonstrate that pre-processing to remove contaminating extracellular DNA prior to cell lysis and DNA extraction improves the host-to-Mtb DNA ratio but is not adequate to support average coverage WGS without target capture.
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Affiliation(s)
- B. C. Mann
- Department of Biomedical Sciences, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - K. R. Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Y. Ghebrekristos
- Department of Biomedical Sciences, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Greenpoint Tuberculosis Laboratory, Cape Town, South Africa
| | - R. M. Warren
- Department of Biomedical Sciences, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - M. R. Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
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Gröschel MI, van den Boom M, Dixit A, Skrahina A, Dodd PJ, Migliori GB, Seddon JA, Farhat MR. Management of childhood MDR-TB in Europe and Central Asia: report of a Regional WHO meeting. Int J Tuberc Lung Dis 2022; 26:433-440. [PMID: 35505487 DOI: 10.5588/ijtld.21.0541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND: As the WHO European Region has the highest proportion of multidrug-resistant TB (MDR-TB) among total incident TB cases, many children and adolescents are at risk of MDR-TB infection and disease.METHODS: We performed an electronic survey of clinicians and TB programme personnel who attended the 2020 Regional Consultation on child and adolescent TB organised by the WHO Regional Office. We characterised access to diagnostics and drugs, and practices in the prevention and management of child and adolescent MDR-TB.RESULTS: Children and adolescents are inconsistently represented in national guidelines and budgets; child-friendly drug formulations for MDR-TB treatment are insufficiently available in 57% of countries, and 32% of countries reported paediatric drug stock-outs. The novel drugs, bedaquiline and delamanid, are accessible by respectively 80% and 60% of respondent countries. Respondents were asked how many children were diagnosed with MDR-TB in 2019, and a comparison of this number to modelled estimates of incidence (to identify the case detection gap) and WHO notifications (to identify the case reporting gap) showed substantial differences in both comparisons.CONCLUSIONS: Better representation of this patient group in guidelines and budgets, greater access to drugs and improved reporting are essential to reach TB elimination in this Region.
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Affiliation(s)
- M I Gröschel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - M van den Boom
- Joint TB, HIV, and Viral Hepatitis Programme, WHO Regional Office for Europe, UN City, Copenhagen, Denmark
| | - A Dixit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA, Division of Infectious Diseases, Boston Children´s Hospital, Boston, MA, USA
| | - A Skrahina
- Republican Scientific and Practical Center for Pulmonology and TB, Minsk, Belarus
| | - P J Dodd
- School of Health and Health-Related Research, University of Sheffield, Sheffield, UK
| | - G B Migliori
- Istituti Clinici Scientifici Maugeri Istituto di Recovero e Cura a Carattere Scientifico, Tradate, Italy
| | - J A Seddon
- Section of Paediatric Infectious Diseases, Department of Infectious Diseases, Imperial College London, London, UK, Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
| | - M R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA, Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
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