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Schumacher SG, Wells WA, Nicol MP, Steingart KR, Theron G, Dorman SE, Pai M, Churchyard G, Scott L, Stevens W, Nabeta P, Alland D, Weyer K, Denkinger CM, Gilpin C. Guidance for Studies Evaluating the Accuracy of Sputum-Based Tests to Diagnose Tuberculosis. J Infect Dis 2019; 220:S99-S107. [PMID: 31593597 PMCID: PMC6782025 DOI: 10.1093/infdis/jiz258] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Tests that can replace sputum smear microscopy have been identified as a top priority diagnostic need for tuberculosis by the World Health Organization. High-quality evidence on diagnostic accuracy for tests that may meet this need is an essential requirement to inform decisions about policy and scale-up. However, test accuracy studies are often of low and inconsistent quality and poorly reported, leading to uncertainty about true test performance. Here we provide guidance for the design of diagnostic test accuracy studies of sputum smear-replacement tests. Such studies should have a cross-sectional or cohort design, enrolling either a consecutive series or a random sample of patients who require evaluation for tuberculosis. Adults with respiratory symptoms are the target population. The reference standard should at a minimum be a single, automated, liquid culture, but additional cultures, follow-up, clinical case definition, and specific measures to understand discordant results should also be included. Inclusion of smear microscopy and Xpert MTB/RIF (or MTB/RIF Ultra) as comparators is critical to allow broader comparability and generalizability of results, because disease spectrum can vary between studies and affects relative test performance. Given the complex nature of sputum (the primary specimen type used for pulmonary TB), careful design and reporting of the specimen flow is essential. Test characteristics other than accuracy (such as feasibility, implementation considerations, and data on impact on patient, population and health systems outcomes) are also important aspects.
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Affiliation(s)
| | - William A Wells
- United States Agency for International Development, Washington, District of Columbia
| | - Mark P Nicol
- School of Biomedical Sciences, University of Western Australia, Perth, Australia, United Kingdom
| | | | - Grant Theron
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | | | - Madhukar Pai
- McGill International TB Centre and Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada
| | - Gavin Churchyard
- Aurum Institute, Cape Town, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
- Advancing Care and Treatment for TB/HIV, South African Medical Research Council, Parktown, South Africa
| | - Lesley Scott
- University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Wendy Stevens
- University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
| | | | | | - Karin Weyer
- World Health Organization, Geneva, Switzerland
| | - Claudia M Denkinger
- FIND, Geneva, Switzerland
- University Hospital Heidelberg, Division of Tropical Medicine, Centre of Infectious Diseases, Germany
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McNerney R, Clark TG, Campino S, Rodrigues C, Dolinger D, Smith L, Cabibbe AM, Dheda K, Schito M. Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action. Int J Infect Dis 2017; 56:130-135. [PMID: 27986491 DOI: 10.1016/j.ijid.2016.11.422] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 11/15/2022] Open
Abstract
Whole genome sequencing (WGS) can provide a comprehensive analysis of Mycobacterium tuberculosis mutations that cause resistance to anti-tuberculosis drugs. With the deployment of bench-top sequencers and rapid analytical software, WGS is poised to become a useful tool to guide treatment. However, direct sequencing from clinical specimens to provide a full drug resistance profile remains a serious challenge. This article reviews current practices for extracting M. tuberculosis DNA and possible solutions for sampling sputum. Techniques under consideration include enzymatic digestion, physical disruption, chemical degradation, detergent solubilization, solvent extraction, ligand-coated magnetic beads, silica columns, and oligonucleotide pull-down baits. Selective amplification of genomic bacterial DNA in sputum prior to WGS may provide a solution, and differential lysis to reduce the levels of contaminating human DNA is also being explored. To remove this bottleneck and accelerate access to WGS for patients with suspected drug-resistant tuberculosis, it is suggested that a coordinated and collaborative approach be taken to more rapidly optimize, compare, and validate methodologies for sequencing from patient samples.
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Affiliation(s)
- Ruth McNerney
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town, South Africa.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases and Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases and Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Camilla Rodrigues
- Department of Microbiology, P.D. Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | | | - Liezel Smith
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town, South Africa
| | - Andrea M Cabibbe
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town, South Africa
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Prospective cross-sectional evaluation of the small membrane filtration method for diagnosis of pulmonary tuberculosis. J Clin Microbiol 2014; 52:2513-20. [PMID: 24808236 DOI: 10.1128/jcm.00642-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Smear microscopy has suboptimal sensitivity, and there is a need to improve its performance since it is commonly used to diagnose tuberculosis (TB). We prospectively evaluated the diagnostic accuracy of the small membrane filtration (SMF) method, an approach that uses a vacuum manifold and is designed to concentrate bacilli onto a filter that can be examined microscopically. We enrolled hospitalized adults suspected to have pulmonary TB in Kampala, Uganda. We obtained a clinical history and three spontaneously expectorated sputum specimens for smear microscopy (direct, concentrated, and SMF), MGIT (mycobacterial growth indicator tube) 960 and Lowenstein-Jensen (LJ) cultures, and Xpert MTB/RIF testing. We performed per-specimen (primary) and per-patient analyses. From October 2012 to June 2013, we enrolled 212 patients (579 sputum specimens). The participants were mostly female (63.2%), and 81.6% were HIV infected; their median CD4 cell count was 47 cells/μl. Overall, 19.0%, 20.4%, 27.1%, 25.2%, and 25.9% of specimens tested positive by direct smear, concentrated smear, MGIT culture, LJ culture, and Xpert test, respectively. In the per-specimen analysis, the sensitivity of the SMF method (48.5%; 95% confidence interval [CI], 37.4 to 59.6) was lower than those of direct smear (60.9%; 51.4 to 70.5 [P = 0.0001]) and concentrated smear (63.3%; 53.6 to 73.1 [P < 0.0001]). Subgroup analyses showed that SMF performed poorly in specimens having a low volume or low bacterial load. The SMF method performed poorly compared to standard smear techniques and was sensitive to sample preparation techniques. The optimal laboratory SMF protocol may require striking a fine balance between sample dilution and filtration failure rate.
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Sun JR, Cheng YH, Lai PY, Lee SY, Chou YC, Fu YC, Wu CC, Chiueh TS. Ultraviolet light enhances the bovine serum albumin fixation for acid fast bacilli stain. PLoS One 2014; 9:e89370. [PMID: 24586725 PMCID: PMC3931762 DOI: 10.1371/journal.pone.0089370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 01/18/2014] [Indexed: 11/18/2022] Open
Abstract
The use of a liquid culture system such as MGIT broth has greatly improved the sensitivity of isolating mycobacteria in clinical laboratories. Microscopic visualization of acid fast bacilli (AFB) in the culture positive MGIT broth remains the first routine step for rapidly indicating the presence of mycobacteria. We modified an ultraviolet (UV) light fixation process to increase AFB cells adherence to the slide. The retained haze proportion of a 1-cm circle marked area on the smear slide was quantified after the staining procedure indicating the adherence degree of AFB cells. More AFB cells were preserved on the slide after exposure to UV light of either germicidal lamp or UV crosslinker in a time-dependent manner. We demonstrated both the bovine serum albumin (BSA) in MGIT media and UV light exposure were required for enhancing fixation of AFB cells. While applying to AFB stains for 302 AFB positive MGIT broths in clinics, more AFB cells were retained and observed on smear slides prepared by the modified fixation procedure rather than by the conventional method. The modified fixation procedure was thus recommended for improving the sensitivity of microscopic diagnosis of AFB cells in culture positive MGIT broth.
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Affiliation(s)
- Jun-Ren Sun
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan
| | - Yun-Hsiang Cheng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan
| | - Pei-Yin Lai
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan
| | - Shih-Yi Lee
- Division of Clinical Microbiology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Yung-Chieh Fu
- Division of Clinical Microbiology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chen-Cheng Wu
- Division of Clinical Microbiology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Tzong-Shi Chiueh
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan
- * E-mail:
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Ochang E, Collier D, Bode-Sojobi I, Oladele R, Oduyebo O. Car windshield fragments as cheap alternative glass beads for homogenization of Mycobacterium tuberculosis cultures in a resource-limited setting. Int J Mycobacteriol 2014; 3:46-9. [DOI: 10.1016/j.ijmyco.2014.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 01/20/2014] [Indexed: 10/25/2022] Open
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Increased sensitivity in diagnosis of tuberculosis in HIV-positive patients through the small-membrane-filter method of microscopy. J Clin Microbiol 2013; 51:2921-5. [PMID: 23804389 DOI: 10.1128/jcm.00683-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sensitivity of microscopy for the diagnosis of tuberculosis (TB) is around 50% but decreases by about 15% in patients with suspected TB who are coinfected with HIV. Here, we compared the accuracies of three microscopy methods for processing sputum smears (concentration by centrifugation with or without N-acetyl-L-cysteine [NALC] and concentration by filtration on a polycarbonate membrane) to that of culture on Ogawa-Kudoh medium as the gold standard method. Sputum samples were obtained from 432 patients with suspected pulmonary TB, of whom 60% were infected with HIV. Analysis was performed using the first specimen. Compared to the gold standard culture, the small-membrane-filter (SMF) method was the most sensitive microscopic method. In HIV-infected TB patients, the sensitivity of the SMF method was significantly higher than those for centrifugation of sputum samples with or without NALC treatment (61.9%, 47.6%, and 45.2%, respectively; P = 0.001). Similarly, in TB patients without HIV infection, the sensitivity of the SMF method was significantly higher than those for centrifugation of sputum samples with or without NALC treatment (81.8%, 63.6%, and 57.5%, respectively; P = 0.001). In the two study groups, TB patients with or without HIV, no significant differences between the specificities of the three methods were observed. Handling of the second sputum sample similarly by centrifugation with or without NALC and by the SMF method increased positivities by 13%, 11%, and 4%, respectively. The overall agreement between microscopy and culture was above 90% for all groups. Microscopic evaluation of the sputum samples treated with NALC compared to those not treated with NALC did not show any increase in sensitivity. Altogether, the sensitivity of the SMF method is higher than those of the other two microscopic methods studied without a loss of specificity.
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The small membrane filter method of microscopy to diagnose pulmonary tuberculosis. J Clin Microbiol 2012; 50:2096-9. [PMID: 22422854 DOI: 10.1128/jcm.00572-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We modified microscopy for acid-fast bacilli to diagnose tuberculosis (TB) using small membrane filters (SMFs) after special processing and prefiltration. With the first specimen obtained from each of 335 persons suspected of having TB, the sensitivity of the new SMF method using fluorescence microscopy (FM) was 89% (95% confidence interval [CI]: 80%, 95%). This was significantly better (P = 0.0001) than the sensitivity of routine FM of centrifuged specimens of 60% (95% CI: 49%, 71%) or that of direct sputum smears of 56% (95% CI: 40%, 72%).
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