A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TB® Assay to Detect in 8 Days Drug Resistance to 13 Antituberculous Drugs and Transmission of Mycobacterium tuberculosis Complex Directly From Clinical Samples
The GeneLEAD VIII (Diagenode, Belgium) is a new, fully automated, sample-to-result precision instrument for the extraction of DNA and PCR detection of Mycobacterium tuberculosis complex (MTBC) directly from clinical samples. The Deeplex Myc-TB® assay (Genoscreen, France) is a diagnostic kit based on...
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| Format: | Article |
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Frontiers Media S.A.
2021-10-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2021.707244/full |
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| author | Isabelle Bonnet Isabelle Bonnet Isabelle Bonnet Vincent Enouf Florence Morel Florence Morel Florence Morel Vichita Ok Vichita Ok Vichita Ok Jérémy Jaffré Jérémy Jaffré Jérémy Jaffré Vincent Jarlier Vincent Jarlier Alexandra Aubry Alexandra Aubry Alexandra Aubry Jérôme Robert Jérôme Robert Jérôme Robert Wladimir Sougakoff Wladimir Sougakoff Wladimir Sougakoff |
| author_facet | Isabelle Bonnet Isabelle Bonnet Isabelle Bonnet Vincent Enouf Florence Morel Florence Morel Florence Morel Vichita Ok Vichita Ok Vichita Ok Jérémy Jaffré Jérémy Jaffré Jérémy Jaffré Vincent Jarlier Vincent Jarlier Alexandra Aubry Alexandra Aubry Alexandra Aubry Jérôme Robert Jérôme Robert Jérôme Robert Wladimir Sougakoff Wladimir Sougakoff Wladimir Sougakoff |
| author_sort | Isabelle Bonnet |
| collection | DOAJ |
| description | The GeneLEAD VIII (Diagenode, Belgium) is a new, fully automated, sample-to-result precision instrument for the extraction of DNA and PCR detection of Mycobacterium tuberculosis complex (MTBC) directly from clinical samples. The Deeplex Myc-TB® assay (Genoscreen, France) is a diagnostic kit based on the deep sequencing of a 24-plexed amplicon mix allowing simultaneously the detection of resistance to 13 antituberculous (antiTB) drugs and the determination of spoligotype. We evaluated the performance of a strategy combining the both mentioned tools to detect directly from clinical samples, in 8 days, MTBC and its resistance to 13 antiTB drugs, and identify potential transmission of strains from patient-to-patient. Using this approach, we screened 112 clinical samples (65 smear-negative) and 94 MTBC cultured strains. The sensitivity and the specificity of the GeneLEAD/Deeplex Myc-TB approach for MTBC detection were 79.3% and 100%, respectively. One hundred forty successful Deeplex Myc-TB results were obtained for 46 clinical samples and 94 strains, a total of 85.4% of which had a Deeplex Myc-TB susceptibility and resistance prediction consistent with phenotypic drug susceptibility testing (DST). Importantly, the Deeplex Myc-TB assay was able to detect 100% of the multidrug-resistant (MDR) MTBC tested. The lowest concordance rates were for pyrazinamide, ethambutol, streptomycin, and ethionamide (84.5%, 81.5%, 73%, and 55%, respectively) for which the determination of susceptibility or resistance is generally difficult with current tools. One of the main difficulties of Deeplex Myc-TB is to interpret the non-synonymous uncharacterized variants that can represent up to 30% of the detected single nucleotide variants. We observed a good level of concordance between Deeplex Myc-TB-spoligotyping and MIRU-VNTR despite a lower discriminatory power for spoligotyping. The median time to obtain complete results from clinical samples was 8 days (IQR 7–13) provided a high-throughput NGS sequencing platform was available. Our results highlight that the GeneLEAD/Deeplex Myc-TB approach could be a breakthrough in rapid diagnosis of MDR TB in routine practice. |
| first_indexed | 2024-12-17T12:44:43Z |
| format | Article |
| id | doaj.art-06807fd58c6c4fd182b91dde7dff0e1f |
| institution | Directory Open Access Journal |
| issn | 2235-2988 |
| language | English |
| last_indexed | 2024-12-17T12:44:43Z |
| publishDate | 2021-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj.art-06807fd58c6c4fd182b91dde7dff0e1f2022-12-21T21:47:46ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882021-10-011110.3389/fcimb.2021.707244707244A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TB® Assay to Detect in 8 Days Drug Resistance to 13 Antituberculous Drugs and Transmission of Mycobacterium tuberculosis Complex Directly From Clinical SamplesIsabelle Bonnet0Isabelle Bonnet1Isabelle Bonnet2Vincent Enouf3Florence Morel4Florence Morel5Florence Morel6Vichita Ok7Vichita Ok8Vichita Ok9Jérémy Jaffré10Jérémy Jaffré11Jérémy Jaffré12Vincent Jarlier13Vincent Jarlier14Alexandra Aubry15Alexandra Aubry16Alexandra Aubry17Jérôme Robert18Jérôme Robert19Jérôme Robert20Wladimir Sougakoff21Wladimir Sougakoff22Wladimir Sougakoff23Assistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, FranceCentre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, FranceSorbonne Université, INSERM, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, FrancePlateforme de Microbiologie Mutualisée (P2M), Pasteur International Bioresources network (PIBnet), Institut Pasteur, Paris, FranceAssistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, FranceCentre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, FranceSorbonne Université, INSERM, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, FranceAssistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, FranceCentre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, FranceSorbonne Université, INSERM, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, FranceAssistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, FranceCentre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, FranceSorbonne Université, INSERM, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, FranceAssistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, FranceCentre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, FranceAssistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, FranceCentre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, FranceSorbonne Université, INSERM, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, FranceAssistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, FranceCentre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, FranceSorbonne Université, INSERM, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, FranceAssistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpêtrière, Service de Bactériologie-Hygiène, Paris, FranceCentre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), Paris, FranceSorbonne Université, INSERM, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Unité Mixte de Recherche (UMR) 1135, Paris, FranceThe GeneLEAD VIII (Diagenode, Belgium) is a new, fully automated, sample-to-result precision instrument for the extraction of DNA and PCR detection of Mycobacterium tuberculosis complex (MTBC) directly from clinical samples. The Deeplex Myc-TB® assay (Genoscreen, France) is a diagnostic kit based on the deep sequencing of a 24-plexed amplicon mix allowing simultaneously the detection of resistance to 13 antituberculous (antiTB) drugs and the determination of spoligotype. We evaluated the performance of a strategy combining the both mentioned tools to detect directly from clinical samples, in 8 days, MTBC and its resistance to 13 antiTB drugs, and identify potential transmission of strains from patient-to-patient. Using this approach, we screened 112 clinical samples (65 smear-negative) and 94 MTBC cultured strains. The sensitivity and the specificity of the GeneLEAD/Deeplex Myc-TB approach for MTBC detection were 79.3% and 100%, respectively. One hundred forty successful Deeplex Myc-TB results were obtained for 46 clinical samples and 94 strains, a total of 85.4% of which had a Deeplex Myc-TB susceptibility and resistance prediction consistent with phenotypic drug susceptibility testing (DST). Importantly, the Deeplex Myc-TB assay was able to detect 100% of the multidrug-resistant (MDR) MTBC tested. The lowest concordance rates were for pyrazinamide, ethambutol, streptomycin, and ethionamide (84.5%, 81.5%, 73%, and 55%, respectively) for which the determination of susceptibility or resistance is generally difficult with current tools. One of the main difficulties of Deeplex Myc-TB is to interpret the non-synonymous uncharacterized variants that can represent up to 30% of the detected single nucleotide variants. We observed a good level of concordance between Deeplex Myc-TB-spoligotyping and MIRU-VNTR despite a lower discriminatory power for spoligotyping. The median time to obtain complete results from clinical samples was 8 days (IQR 7–13) provided a high-throughput NGS sequencing platform was available. Our results highlight that the GeneLEAD/Deeplex Myc-TB approach could be a breakthrough in rapid diagnosis of MDR TB in routine practice.https://www.frontiersin.org/articles/10.3389/fcimb.2021.707244/fullGeneLEAD VIIIDeeplex Myc-TBMycobacterium tuberculosisdiagnosticresistancespoligotype |
| spellingShingle | Isabelle Bonnet Isabelle Bonnet Isabelle Bonnet Vincent Enouf Florence Morel Florence Morel Florence Morel Vichita Ok Vichita Ok Vichita Ok Jérémy Jaffré Jérémy Jaffré Jérémy Jaffré Vincent Jarlier Vincent Jarlier Alexandra Aubry Alexandra Aubry Alexandra Aubry Jérôme Robert Jérôme Robert Jérôme Robert Wladimir Sougakoff Wladimir Sougakoff Wladimir Sougakoff A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TB® Assay to Detect in 8 Days Drug Resistance to 13 Antituberculous Drugs and Transmission of Mycobacterium tuberculosis Complex Directly From Clinical Samples Frontiers in Cellular and Infection Microbiology GeneLEAD VIII Deeplex Myc-TB Mycobacterium tuberculosis diagnostic resistance spoligotype |
| title | A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TB® Assay to Detect in 8 Days Drug Resistance to 13 Antituberculous Drugs and Transmission of Mycobacterium tuberculosis Complex Directly From Clinical Samples |
| title_full | A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TB® Assay to Detect in 8 Days Drug Resistance to 13 Antituberculous Drugs and Transmission of Mycobacterium tuberculosis Complex Directly From Clinical Samples |
| title_fullStr | A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TB® Assay to Detect in 8 Days Drug Resistance to 13 Antituberculous Drugs and Transmission of Mycobacterium tuberculosis Complex Directly From Clinical Samples |
| title_full_unstemmed | A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TB® Assay to Detect in 8 Days Drug Resistance to 13 Antituberculous Drugs and Transmission of Mycobacterium tuberculosis Complex Directly From Clinical Samples |
| title_short | A Comprehensive Evaluation of GeneLEAD VIII DNA Platform Combined to Deeplex Myc-TB® Assay to Detect in 8 Days Drug Resistance to 13 Antituberculous Drugs and Transmission of Mycobacterium tuberculosis Complex Directly From Clinical Samples |
| title_sort | comprehensive evaluation of genelead viii dna platform combined to deeplex myc tb r assay to detect in 8 days drug resistance to 13 antituberculous drugs and transmission of mycobacterium tuberculosis complex directly from clinical samples |
| topic | GeneLEAD VIII Deeplex Myc-TB Mycobacterium tuberculosis diagnostic resistance spoligotype |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2021.707244/full |
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