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Antonello M, Scutari R, Lauricella C, Renica S, Motta V, Torri S, Russo C, Gentile L, Cento V, Colagrossi L, Mattana G, Codecasa LR, Vismara C, Scaglione F, Veronese SM, Bonoldi E, Bandera A, Gori A, Mazzola E, Perno CF, Alteri C. Rapid Detection and Quantification of Mycobacterium tuberculosis DNA in Paraffinized Samples by Droplet Digital PCR: A Preliminary Study. Front Microbiol 2021; 12:727774. [PMID: 34589075 PMCID: PMC8475183 DOI: 10.3389/fmicb.2021.727774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/16/2021] [Indexed: 01/23/2023] Open
Abstract
Background: Rapid and reliable diagnosis of tuberculosis (TB) represents a diagnostic challenge in compartmentalized extrapulmonary TB infection because of the small number of mycobacteria (MTB) and the frequent lack of fresh samples to perform culture. Here, we estimate the performances of homemade droplet digital PCR (ddPCR)-based assays against culture in 89 biopsies, for those fresh and formalin-fixed and paraffin-embedded (FFPE) subsamples were available. Methods: MTB diagnosis in fresh subsamples was performed by culture. Fresh subsamples were also analyzed for acid-fast bacilli smear-microscopy (AFB) and Xpert® MTB/RIF (Xpert). MTB examination was repeated in blind in the 89 FFPE subsamples by in-house ddPCR assays targeting the IS6110 and rpoB. Analytical sensitivity of ddPCR assays was evaluated using serial dilution of H37Rv strain. Limit of detection (LOD) was calculated by probit analysis. Results were expressed in copies/106 cells. Results: IS6110 and rpoB ddPCR assays showed a good linear correlation between expected and observed values (R2: 0.9907 and 0.9743, respectively). Probit analyses predicted a LOD of 17 and 40 copies/106 cells of MTB DNA for IS6110 and rpoB, respectively. Of the 89 biopsies, 68 were culture positive and 21 were culture negative. Considering mycobacterial culture as reference method, IS6110 assay yielded positive results in 67/68 culture-positive samples with a median interquartile range (IQR) of 1,680 (550–8,444) copies/106 cells (sensitivity: 98.5%; accuracy: 98.9). These performances were superior to those reported by the rpoB assay in FFPE subsamples (sensitivity: 66.20%; accuracy: 74.1) and even superior to those reported by Xpert and AFB in fresh subsamples (sensitivity: 79.4 and 33.8%, respectively; accuracy: 84.3 and 49.4, respectively). When Xpert and AFB results were stratified according to mycobacterial load detected by rpoB and IS6110 ddPCR, bacterial load was lower in Xpert and AFB negative with respect to Xpert and AFB-positive samples (p = 0.003 and 0.01 for rpoB and p = 0.01 and 0.11 for IS6110), confirming the poor sensitivity of these methods in paucibacillary disease. Conclusion: ddPCR provides highly sensitive, accurate, and rapid MTB diagnosis in FFPE samples, as defined by the high concordance between IS6110 assay and culture results. This approach can be safely introduced in clinical routine to accelerate MTB diagnosis mainly when culture results remain unavailable.
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Affiliation(s)
- Maria Antonello
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Rossana Scutari
- Department of Experimental Medicine, University of Rome "Tor Vergata,"Rome, Italy
| | - Calogero Lauricella
- Department of Pathology, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Silvia Renica
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Valentina Motta
- Department of Pathology, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Stefania Torri
- Unit of Microbiology, Department of Chemical-Clinical and Microbiology Analyses, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Cristina Russo
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Leonarda Gentile
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valeria Cento
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Luna Colagrossi
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giordana Mattana
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Luigi Ruffo Codecasa
- Regional TB Reference Centre, Villa Marelli Institute, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Chiara Vismara
- Unit of Microbiology, Department of Chemical-Clinical and Microbiology Analyses, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Francesco Scaglione
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Unit of Microbiology, Department of Chemical-Clinical and Microbiology Analyses, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Emanuela Bonoldi
- Department of Pathology, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Alessandra Bandera
- Infectious Disease Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Andrea Gori
- Infectious Disease Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Ester Mazzola
- Unit of Microbiology, Department of Chemical-Clinical and Microbiology Analyses, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Carlo Federico Perno
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Multimodal Medicine Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Claudia Alteri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Multimodal Medicine Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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Mu J, Liu Z, Zhang C, Wang C, Du W, Lin H, Li K, Song J, Che N, Liu H. Performance of the MeltPro MTB Assays in the Diagnosis of Drug-Resistant Tuberculosis Using Formalin-Fixed, Paraffin-Embedded Tissues. Am J Clin Pathol 2021; 156:34-41. [PMID: 33438007 DOI: 10.1093/ajcp/aqaa203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The MeltPro MTB assays for detection of resistance to antituberculosis (TB) drugs perform well in genotypic drug susceptibility testing (DST) of clinical samples, but their effectiveness with formalin-fixed, paraffin-embedded (FFPE) tissues is unknown. METHODS FFPE tissues were obtained from 334 patients with TB. Susceptibility to rifampicin (RIF), isoniazid (INH), and fluoroquinolones was examined using the MeltPro MTB assays, with Xpert MTB/RIF (Xpert) and/or phenotypic DST (pDST) results as references. Samples with discordant results were analyzed by multiplex polymerase chain reaction-targeted amplicon sequencing (MTA-seq). RESULTS With pDST as the reference, the MeltPro MTB assays sensitivity for RIF, INH, levofloxacin (LVX), and moxifloxacin (MXF) was 95.00%, 96.00%, 100%, and 100%, respectively, and the specificity was 95.15%, 95.92%, 94.69%, and 89.92%, respectively. Concordance was 99.08% between the MeltPro MTB and Xpert (κ = 0.956) for RIF and 95.12% (κ = 0.834), 95.93% (κ = 0.880), 95.12% (κ = 0.744), and 90.24% (κ = 0.367) between the MeltPro MTB and pDST for RIF, INH, LVX, and MXF, respectively. MTA-seq confirmed the discordancy between the MeltPro MTB and pDST for 26 (89.66%) of 29 samples. CONCLUSIONS The MeltPro MTB assays rapidly and efficiently predict Mycobacterium tuberculosis resistance to the main first- and second-line anti-TB drugs in FFPE tissues.
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Affiliation(s)
- Jing Mu
- Department of Pathology, Key Laboratory of Head and Neck Molecular Diagnosis Pathology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zichen Liu
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Chen Zhang
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Chongli Wang
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Weili Du
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Haifeng Lin
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Kun Li
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Jing Song
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Nanying Che
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Honggang Liu
- Department of Pathology, Key Laboratory of Head and Neck Molecular Diagnosis Pathology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
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Bielsa S, Bernet A, Civit C, Acosta C, Manonelles A, Porcel JM. FluoroType® MTB in pleural fluid for diagnosing tuberculosis. Rev Clin Esp 2021; 221:139-144. [PMID: 32499060 DOI: 10.1016/j.rce.2020.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/14/2020] [Accepted: 04/02/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVES This work aims to investigate the diagnostic accuracy of a nucleic acid amplification test (FluoroType MTB®) in pleural fluid (PF) and sputum to diagnose tuberculous pleural effusion (TPE). We also analyzed the increase in diagnostic accuracy of a second FluoroType MTB® test on a second thoracentesis sample when the first was negative. METHODS We conducted a prospective single-center study that included 207 patients with pleural effusion (31 tuberculous and 176 due to other causes). Of the 31 cases of TPE, 21 (68%) were confirmed histologically or microbiologically; the other cases were considered probable. RESULTS The operational characteristics of FluoroType MTB® in PF for identifying tuberculosis were a sensitivity of 13%, a specificity of 99%, a positive likelihood ratio of 11, and a negative likelihood ratio of 0.9. The diagnostic efficacy data for sputum samples were 21%, 91%, 2.4, and 0.9, respectively. PF and sputum cultures in solid and liquid media had greater sensitivity (36% and 31%, respectively). A second FluoroType MTB® test in PF was negative for 24 patients who had TPE and for whom the first FluoroType MTB® test was also negative. Only two (6.5%) patients with TPE had a confirmed diagnosis based exclusively on the positive results of the FluoroType MTB® in PF. CONCLUSION Due to its low sensitivity, the FluoroType MTB® test in PF has a limited role in diagnosing tuberculous pleurisy.
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Affiliation(s)
- S Bielsa
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, España
| | - A Bernet
- Servicio de Microbiología, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, España
| | - C Civit
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, España
| | - C Acosta
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, España
| | - A Manonelles
- Servicio de Microbiología, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, España
| | - J M Porcel
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, España.
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Bielsa S, Bernet A, Civit C, Acosta C, Manonelles A, Porcel JM. FluoroType® MTB in pleural fluid for diagnosing tuberculosis. Rev Clin Esp 2021; 221:139-144. [PMID: 33998461 DOI: 10.1016/j.rceng.2020.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/02/2020] [Indexed: 11/24/2022]
Abstract
OBJECTIVES This work aims to investigate the diagnostic accuracy of a nucleic acid amplification test (FluoroType MTB®) in pleural fluid (PF) and sputum to diagnose tuberculous pleural effusion (TPE). We also analyzed the increase in diagnostic accuracy of a second FluoroType MTB® test on a second thoracentesis sample when the first was negative. METHODS We conducted a prospective single-center study that included 207 patients with pleural effusion (31 tuberculous and 176 due to other causes). Of the 31 cases of TPE, 21 (68%) were confirmed histologically or microbiologically; the other cases were considered probable. RESULTS The operational characteristics of FluoroType MTB® in PF for identifying tuberculosis were a sensitivity of 13%, a specificity of 99%, a positive likelihood ratio of 11, and a negative likelihood ratio of 0.9. The diagnostic efficacy data for sputum samples were 21%, 91%, 2.4, and 0.9, respectively. PF and sputum cultures in solid and liquid media had greater sensitivity (36% and 31%, respectively). A second FluoroType MTB® test in PF was negative for 24 patients who had TPE and for whom the first FluoroType MTB® test was also negative. Only two (6.5%) patients with TPE had a confirmed diagnosis based exclusively on the positive results of the FluoroType MTB® in PF. CONCLUSION Due to its low sensitivity, the FluoroType MTB® test in PF has a limited role in diagnosing tuberculous pleurisy.
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Affiliation(s)
- S Bielsa
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, Spain
| | - A Bernet
- Servicio de Microbiología, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, Spain
| | - C Civit
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, Spain
| | - C Acosta
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, Spain
| | - A Manonelles
- Servicio de Microbiología, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, Spain
| | - J M Porcel
- Unidad de Medicina Pleural, Servicio de Medicina Interna, Hospital Universitario Arnau de Vilanova, Instituto de Investigación Biomédica de Lleida, IRBLleida, Lérida, Spain.
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Erkose Genc G, Satana D, Yildirim E, Erturan Z, Yegenoglu Y, Uzun M. Evaluation of FluoroType MTB for direct detection of Mycobacterium tuberculosis complex and GenoType MTBDRplus for determining rifampicin and isoniazid resistance. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1466662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Gonca Erkose Genc
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Dilek Satana
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Esra Yildirim
- Department of Food Engineering, Faculty of Engineering and Natural Sciences, Istanbul Sabahattin Zaim University, Istanbul, Turkey
| | - Zayre Erturan
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Yildiz Yegenoglu
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Meltem Uzun
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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Evaluation of GenoType MTBDR plus by Use of Extracted DNA from Formalin-Fixed Paraffin-Embedded Specimens. J Clin Microbiol 2017; 55:3300-3302. [PMID: 28878006 DOI: 10.1128/jcm.01410-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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