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Chilambi GS, Reiss R, Daivaa N, Banada P, De Vos M, Penn-Nicholson A, Alland D. Optimal processing of tongue swab samples for Mycobacterium tuberculosis detection by the Xpert MTB/RIF Ultra assay. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.20.24309244. [PMID: 38947094 PMCID: PMC11213102 DOI: 10.1101/2024.06.20.24309244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Tongue swabs represent a potential alternative to sputum as a sample type for detecting pulmonary tuberculosis (TB) using molecular diagnostic tests. The methods used to process tongue swabs for testing in the WHO-recommended Xpert MTB/RIF Ultra (Xpert Ultra) assay vary greatly. We aimed to identify the optimal method for processing diagnostic tongue swabs for subsequent testing by Xpert Ultra. We compared four methods for treating dry tongue swabs with Xpert Ultra sample reagent (SR) mixed with various concentrations of Tris-EDTA-Tween (TET), to treatment with SR alone or to a commonly used SR-free heat-inactivation protocol. In each condition, swabs obtained from volunteers without TB were placed into test buffer spiked with known amounts of Mycobacterium tuberculosis ( Mtb ) strain H37Rv-mc 2 6230. Swabs processed with 1:1 diluted SR buffer had the lowest Mtb limit of detection (LOD) at 22.7 CFU/700 µl (95% CI 14.2-31.2), followed by 2:1 diluted SR buffer at 30.3 CFU/700 µl (95% CI 19.9-40.7), neat SR at 30.9 CFU/700 µl (95% CI 21.5-40.3) and SR prefilled in the Xpert Ultra at 57.1 CFU/700 µl (95% CI 42.4-71.7). Swabs processed using the heat-based protocol had the highest LOD (77.6 CFU/700 µl; 95% CI 51.2-104.0). Similar findings were observed for LOD of RIF-susceptibility. Assay sensitivity using the 2:1 diluted SR buffer did not vary considerably in the presence of sputum matrix or phosphate buffer saline. Further studies are needed to assess the performance of this processing protocol in a clinical setting. Importance Xpert MTB/RIF Ultra (Xpert Ultra) is approved by the World Health Organization for the diagnosis of tuberculosis (TB). This test is typically performed using sputum specimens obtained from people with presumptive TB. In order to inactivate Mtb and aid liquefaction, sputum must be mixed with Xpert SR prior to transfer into the Xpert Ultra. However, some people under evaluation for TB are unable to produce sputum. Alternative sample types for TB diagnosis would therefore be of value. Oral-swabs, including tongue-swabs have shown promise, but there are technical challenges associated with sample processing. In this study, several new tongue swab processing conditions were evaluated, utilizing SR, either neat or diluted in buffer. The ability of Xpert Ultra to detect TB was improved under these conditions compared with the previously published heat-processing method (1-3), processing steps were simplified, and technical challenges were overcome.
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Kurtzhals ML, Norman A, Svensson E, Lillebaek T, Folkvardsen DB. Applying whole genome sequencing to predict phenotypic drug resistance in Mycobacterium tuberculosis: leveraging 20 years of nationwide data from Denmark. Antimicrob Agents Chemother 2024:e0043024. [PMID: 38904390 DOI: 10.1128/aac.00430-24] [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: 03/21/2024] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
Infection with Mycobacterium tuberculosis remains one of the biggest causes of death from a single microorganism worldwide, and the continuous emergence of drug resistance aggravates our ability to cure the disease. New improved resistance detection methods are needed to provide adequate treatment, such as whole genome sequencing (WGS), which has been used increasingly to identify resistance-conferring mutations over the last decade. The steadily increasing knowledge of resistance-conferring mutations increases our ability to predict resistance based on genomic data alone. This study evaluates the performance of WGS to predict M. tuberculosis complex resistance. It compares WGS predictions with the phenotypic (culture-based) drug susceptibility results based on 20 years of nationwide Danish data. Analyzing 6,230 WGS-sequenced samples, the sensitivities for isoniazid, rifampicin, ethambutol, and pyrazinamide were 82.5% [78.0%-86.5%, 95% confidence interval (CI)], 97.3% (90.6%-99.7%, 95% CI), 58.0% (43.2%-71.8%, 95% CI), and 60.5% (49.0%-71.2%, 95% CI), respectively, and specificities were 99.8% (99.7%-99.9%, 95% CI), 99.8% (99.7%-99.9%, 95% CI), 99.4% (99.2%-99.6%, 95% CI), and 99.9% (99.7%-99.9%, 95% CI), respectively. A broader range of both sensitivities and specificities was observed for second-line drugs. The results conform with previously reported values and indicate that WGS is reliable for routine resistance detection in resource-rich tuberculosis low-incidence and low-resistance settings such as Denmark.
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Affiliation(s)
- Mads Lindholm Kurtzhals
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Erik Svensson
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
- Global Health Section, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Dorte Bek Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
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Mousavi-Sagharchi SMA, Afrazeh E, Seyyedian-Nikjeh SF, Meskini M, Doroud D, Siadat SD. New insight in molecular detection of Mycobacterium tuberculosis. AMB Express 2024; 14:74. [PMID: 38907086 PMCID: PMC11192714 DOI: 10.1186/s13568-024-01730-3] [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: 11/29/2023] [Accepted: 06/06/2024] [Indexed: 06/23/2024] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, is a pathogenic bacterium that has claimed millions of lives since the Middle Ages. According to the World Health Organization's report, tuberculosis ranks among the ten deadliest diseases worldwide. The presence of an extensive array of genes and diverse proteins within the cellular structure of this bacterium has provided us with a potent tool for diagnosis. While the culture method remains the gold standard for tuberculosis diagnosis, it is possible that molecular diagnostic methods, emphasis on the identification of mutation genes (e.g., rpoB and gyrA) and single nucleotide polymorphisms, could offer a safe and reliable alternative. Over the past few decades, as our understanding of molecular genetics has expanded, methods have been developed based on gene expansion and detection. These methods typically commence with DNA amplification through nucleic acid targeted techniques such as polymerase chain reaction. Various molecular compounds and diverse approaches have been employed in molecular assays. In this review, we endeavor to provide an overview of molecular assays for the diagnosis of tuberculosis with their properties (utilization, challenges, and functions). The ultimate goal is to explore the potential of replacing traditional bacterial methods with these advanced molecular diagnostic techniques.
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Affiliation(s)
| | - Elina Afrazeh
- Department of Marine Biology, Faculty of Marine Science, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
| | | | - Maryam Meskini
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa.
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran.
| | - Delaram Doroud
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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Banik S, Ozay B, Trejo M, Zhu Y, Kanna C, Santellan C, Shaw B, Chandrasekaran S, Chaturvedi S, Vejar L, Chakravorty S, Alland D, Banada P. A simple and sensitive test for Candida auris colonization, surveillance, and infection control suitable for near patient use. J Clin Microbiol 2024:e0052524. [PMID: 38888304 DOI: 10.1128/jcm.00525-24] [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: 04/04/2024] [Accepted: 05/22/2024] [Indexed: 06/20/2024] Open
Abstract
Candida auris is a multidrug-resistant fungal pathogen with a propensity to colonize humans and persist on environmental surfaces. C. auris invasive fungal disease is being increasingly identified in acute and long-term care settings. We have developed a prototype cartridge-based C. auris surveillance assay (CaurisSurV cartridge; "research use only") that includes integrated sample processing and nucleic acid amplification to detect C. auris from surveillance skin swabs in the GeneXpert instrument and is designed for point-of-care use. The assay limit of detection (LoD) in the skin swab matrix was 10.5 and 14.8 CFU/mL for non-aggregative (AR0388) and aggregative (AR0382) strains of C. auris, respectively. All five known clades of C. auris were detected at 2-3-5× (31.5-52.5 CFU/mL) the LoD. The assay was validated using a total of 85 clinical swab samples banked at two different institutions (University of California Los Angeles, CA and Wadsworth Center, NY). Compared to culture, sensitivity was 96.8% (30/31) and 100% (10/10) in the UCLA and Wadsworth cohorts, respectively, providing a combined sensitivity of 97.5% (40/41), and compared to PCR, the combined sensitivity was 92% (46/50). Specificity was 100% with both clinical (C. auris negative matrix, N = 31) and analytical (non-C. auris strains, N = 32) samples. An additional blinded study with N = 60 samples from Wadsworth Center, NY yielded 97% (29/30) sensitivity and 100% (28/28) specificity. We have developed a completely integrated, sensitive, specific, and 58-min prototype test, which can be used for routine surveillance of C. auris and might help prevent colonization and outbreaks in acute and chronic healthcare settings. IMPORTANCE This study has the potential to offer a better solution to healthcare providers at hospitals and long-term care facilities in their ongoing efforts for effective and timely control of Candida auris infection and hence quicker response for any potential future outbreaks.
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Affiliation(s)
- Sukalyani Banik
- Center for Emerging Pathogens, Department of Medicine, Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Burcu Ozay
- Research and Development, Cepheid, Sunnyvale, California, USA
| | - Marisol Trejo
- UCLA DGSOM Pathology & Lab Medicine, UCLA, Los Angeles, California, USA
| | - YanChun Zhu
- Mycology laboratory, Wadsworth Center, Albany, New York, USA
| | - Charan Kanna
- Center for Emerging Pathogens, Department of Medicine, Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Cynthia Santellan
- UCLA DGSOM Pathology & Lab Medicine, UCLA, Los Angeles, California, USA
| | - Bennett Shaw
- UCLA DGSOM Pathology & Lab Medicine, UCLA, Los Angeles, California, USA
| | | | | | - Lindy Vejar
- Research and Development, Cepheid, Sunnyvale, California, USA
| | - Soumitesh Chakravorty
- Center for Emerging Pathogens, Department of Medicine, Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
- Research and Development, Cepheid, Sunnyvale, California, USA
| | - David Alland
- Center for Emerging Pathogens, Department of Medicine, Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Padmapriya Banada
- Center for Emerging Pathogens, Department of Medicine, Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey, USA
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Wu G, Wang J, Xu X, Wei H, Cai L, Liu L. Factors influencing false-positive results of rifampicin resistance detected by Xpert MTB/RIF: A retrospective study in Zhejiang, China. Heliyon 2024; 10:e31680. [PMID: 38841482 PMCID: PMC11152942 DOI: 10.1016/j.heliyon.2024.e31680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
Objective This study aimed to explore the factors influencing false-positive results for rifampicin resistance (RIF-R) detected using Xpert MTB/RIF (Xpert). Methods This retrospective analysis included the clinical data of patients from September 2019 to February 2023. The chi-square and rank sum tests were used to compare differences in patient characteristics between the true-positive and false-positive groups. Logistic regression was used to analyze the factors influencing false positives in the detection of RIF-R by Xpert. Results A total of 384 patients were included. Logistic regression analysis revealed that, with mutation of probe E as the reference, mutations on probe A or C (OR = 72.68, P < 0.001), probe D (OR = 6.44, P < 0.001), and multiple probes (OR = 5.94, P = 0.002) were associated with false-positive results in Xpert detection of RIF-R. Taking probe delay ΔCt <4 as the reference, ΔCt (4-5.9) (OR = 13.54, P < 0.001), ΔCt (6-7.9) (OR = 48.08, P < 0.001) probe delays were associated with false positives in Xpert detection of RIF-R. When very low quantification is accompanied by a probe delay, the probability of false-positive RIF-R detection can reach 80 %. Conclusions Clinicians should consider factors such as probe mutation type, probe delay, and very low quantification accompanied by probe delay when interpreting Xpert results, which can reduce the misdiagnosis of tuberculosis drug resistance.
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Affiliation(s)
- Guihua Wu
- Centre of Laboratory Medicine, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Jing Wang
- Centre of Laboratory Medicine, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Xiaoqun Xu
- Centre of Laboratory Medicine, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Hui Wei
- Centre of Laboratory Medicine, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Long Cai
- Centre of Laboratory Medicine, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Libin Liu
- Centre of Laboratory Medicine, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
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Kim HJ, Kwak N, Yoon SH, Park N, Kim YR, Lee JH, Lee JY, Park Y, Kang YA, Kim S, Mok J, Kim JY, Jeon D, Lee JK, Yim JJ. Artificial intelligence-based radiographic extent analysis to predict tuberculosis treatment outcomes: a multicenter cohort study. Sci Rep 2024; 14:13162. [PMID: 38849439 PMCID: PMC11161500 DOI: 10.1038/s41598-024-63885-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
Predicting outcomes in pulmonary tuberculosis is challenging despite effective treatments. This study aimed to identify factors influencing treatment success and culture conversion, focusing on artificial intelligence (AI)-based chest X-ray analysis and Xpert MTB/RIF assay cycle threshold (Ct) values. In this retrospective study across six South Korean referral centers (January 1 to December 31, 2019), we included adults with rifampicin-susceptible pulmonary tuberculosis confirmed by Xpert assay from sputum samples. We analyzed patient characteristics, AI-based tuberculosis extent scores from chest X-rays, and Xpert Ct values. Of 230 patients, 206 (89.6%) achieved treatment success. The median age was 61 years, predominantly male (76.1%). AI-based radiographic tuberculosis extent scores (median 7.5) significantly correlated with treatment success (odds ratio [OR] 0.938, 95% confidence interval [CI] 0.895-0.983) and culture conversion at 8 weeks (liquid medium: OR 0.911, 95% CI 0.853-0.973; solid medium: OR 0.910, 95% CI 0.850-0.973). Sputum smear positivity was 49.6%, with a median Ct of 26.2. However, Ct values did not significantly correlate with major treatment outcomes. AI-based radiographic scoring at diagnosis is a significant predictor of treatment success and culture conversion in pulmonary tuberculosis, underscoring its potential in personalized patient management.
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Affiliation(s)
- Hyung-Jun Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Nakwon Kwak
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Soon Ho Yoon
- Department of Radiology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Nanhee Park
- Medical Research Collaborating Center, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Ran Kim
- Division of Clinical Research, International Tuberculosis Research Center, Seoul, Republic of Korea
| | - Jae Ho Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ji Yeon Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, National Medical Center, Seoul, Republic of Korea
| | - Youngmok Park
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Young Ae Kang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Saerom Kim
- Division of Pulmonology, Allergy and Critical Care Medicine, Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
| | - Jeongha Mok
- Division of Pulmonology, Allergy and Critical Care Medicine, Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
| | - Joong-Yub Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Doosoo Jeon
- Department of Internal Medicine, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
- Department of Internal Medicine, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Jung-Kyu Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Jae-Joon Yim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
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7
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Adewusi OO, Waldner CL, Hanington PC, Hill JE, Freeman CN, Otto SJG. Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review. J Vet Diagn Invest 2024; 36:400-417. [PMID: 38456288 PMCID: PMC11110769 DOI: 10.1177/10406387241235968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024] Open
Abstract
Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.
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Affiliation(s)
- Olufunto O. Adewusi
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L. Waldner
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Janet E. Hill
- Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N. Freeman
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J. G. Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
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Yerlikaya S, Broger T, Isaacs C, Bell D, Holtgrewe L, Gupta-Wright A, Nahid P, Cattamanchi A, Denkinger CM. Blazing the trail for innovative tuberculosis diagnostics. Infection 2024; 52:29-42. [PMID: 38032537 PMCID: PMC10811035 DOI: 10.1007/s15010-023-02135-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023]
Abstract
The COVID-19 pandemic brought diagnostics into the spotlight in an unprecedented way not only for case management but also for population health, surveillance, and monitoring. The industry saw notable levels of investment and accelerated research which sparked a wave of innovation. Simple non-invasive sampling methods such as nasal swabs have become widely used in settings ranging from tertiary hospitals to the community. Self-testing has also been adopted as standard practice using not only conventional lateral flow tests but novel and affordable point-of-care molecular diagnostics. The use of new technologies, including artificial intelligence-based diagnostics, have rapidly expanded in the clinical setting. The capacity for next-generation sequencing and acceptance of digital health has significantly increased. However, 4 years after the pandemic started, the market for SARS-CoV-2 tests is saturated, and developers may benefit from leveraging their innovations for other diseases; tuberculosis (TB) is a worthwhile portfolio expansion for diagnostics developers given the extremely high disease burden, supportive environment from not-for-profit initiatives and governments, and the urgent need to overcome the long-standing dearth of innovation in the TB diagnostics field. In exchange, the current challenges in TB detection may be resolved by adopting enhanced swab-based molecular methods, instrument-based, higher sensitivity antigen detection technologies, and/or artificial intelligence-based digital health technologies developed for COVID-19. The aim of this article is to review how such innovative approaches for COVID-19 diagnosis can be applied to TB to have a comparable impact.
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Affiliation(s)
- Seda Yerlikaya
- Division of Infectious Diseases and Tropical Medicine, Heidelberg University Hospital and Faculty of Medicine, Heidelberg University, Heidelberg, Germany.
| | - Tobias Broger
- Division of Infectious Diseases and Tropical Medicine, Heidelberg University Hospital and Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | | | - David Bell
- Independent Consultant, Lake Jackson, TX, USA
| | - Lydia Holtgrewe
- Division of Infectious Diseases and Tropical Medicine, Heidelberg University Hospital and Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Ankur Gupta-Wright
- Division of Infectious Diseases and Tropical Medicine, Heidelberg University Hospital and Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Institute for Global Health, University College London, London, UK
| | - Payam Nahid
- UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, CA, USA
| | - Adithya Cattamanchi
- UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, CA, USA
- Division of Pulmonary Diseases and Critical Care Medicine, University of California Irvine, Irvine, CA, USA
| | - Claudia M Denkinger
- Division of Infectious Diseases and Tropical Medicine, Heidelberg University Hospital and Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- German Centre for Infection Research, Partner Site Heidelberg University Hospital, Heidelberg, Germany
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9
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Peng L, Fang T, Cai Q, Li H, Li H, Sun H, Zhu M, Dai L, Shao Y, Cai L. Rapid detection of Mycobacterium tuberculosis in sputum using CRISPR-Cas12b combined with cross-priming amplification in a single reaction. J Clin Microbiol 2024; 62:e0092323. [PMID: 38112450 PMCID: PMC10793277 DOI: 10.1128/jcm.00923-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE In this study, we successfully established a new One-Pot method, named TB One-Pot, for detecting Mtb in sputum by combining CRISPR-cas12b-mediated trans-cleavage with cross-priming amplification (CPA). Our study evaluated the diagnostic performance of TB One-Pot in clinical sputum samples for tuberculosis. The findings provide evidence for the potential of TB One-Pot as a diagnostic tool for tuberculosis.
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Affiliation(s)
- Lijun Peng
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tingting Fang
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qingshan Cai
- Department of Tuberculosis, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Li
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Huanyu Li
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haiqiong Sun
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Mingzhi Zhu
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lingshan Dai
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanqin Shao
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Long Cai
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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10
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Katoch C, Peter DK, Marwah V, Kumar K, Bhati G. Prevalence of isoniazid resistance in cases of rifampicin resistance detected on GeneXpert MTB/RIF assay. Med J Armed Forces India 2023; 79:S1-S5. [PMID: 38144631 PMCID: PMC10746728 DOI: 10.1016/j.mjafi.2021.04.007] [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: 01/05/2020] [Accepted: 04/14/2021] [Indexed: 10/21/2022] Open
Abstract
Background The fight against tuberculosis in our country has taken a new shape with the inclusion of rapid nucleic acid amplification tests like GeneXpert MTB/RIF assay which rapidly detects Mycobacterium tuberculosis and rifampicin resistance. Rifampicin resistance detected on GeneXpert has been considered as a sine qua non for the presence of isoniazid resistance and hence classified as multidrug-resistant tuberculosis (MDR-TB). However treatment of rifampicin-resistant, isoniazid-monoresistance, and MDR-TB are different. Our study was done with the aim of identification of the prevalence of isoniazid resistance on culture, in cases which had rifampicin resistance on GeneXpert. Methods Pulmonary samples of patients of presumptive tuberculosis were subjected to GeneXpert testing and liquid MGIT (mycobacterium growth indicator tube) culture. On detection of rifampicin resistance on MTB/RIF assay, the patients were included in our study and cultures were followed-up for sensitivity to isoniazid. A total of 76 patients were included. Results 76 patients of rifampicin resistance on GeneXpert MTB/RIF assay were followed-up for the sensitivity of isoniazid on culture media. Out of the 76 cases, 62 (81.57%) were found to have isoniazid resistance. Out of the 14 patients, the cultures showed no growth in 6, and in the rest, isoniazid was found to be sensitive. Conclusion GeneXpert MTB/RIF assay is an excellent modality for the detection of M. tuberculosis and rifampicin resistance. The decision to exclude isoniazid from the treatment regimen in patients with rifampicin resistance should be made only after conducting further molecular/phenotypic tests.
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Affiliation(s)
- C.D.S. Katoch
- Director & CEO, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | - Deepu K. Peter
- Graded Specialist (Pulmonary Medicine), Critical Care & Sleep Medicine, Army Institute of Cardiothoracic Sciences (AICTS), Pune, India
| | - Vikas Marwah
- Senior Advisor & Professor (Pulmonary Medicine), Critical Care & Sleep Medicine, Army Institute of Cardiothoracic Sciences (AICTS), Pune, India
| | - Kunal Kumar
- Graded Specialist (Pulmonary Medicine), Critical Care & Sleep Medicine, Military Hospital Namkum, Ranchi, India
| | - Gaurav Bhati
- Graded Specialist (Pulmonary Medicine), Critical Care & Sleep Medicine, Army Institute of Cardiothoracic Sciences (AICTS), Pune, India
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11
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Slail MJ, Booq RY, Al-Ahmad IH, Alharbi AA, Alharbi SF, Alotaibi MZ, Aljubran AM, Aldossary AM, Memish ZA, Alyamani EJ, Tawfik EA, Binjomah AZ. Evaluation of Xpert MTB/RIF Ultra for the Diagnosis of Extrapulmonary Tuberculosis: A Retrospective Analysis in Saudi Arabia. J Epidemiol Glob Health 2023; 13:782-793. [PMID: 37707714 PMCID: PMC10686912 DOI: 10.1007/s44197-023-00150-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
The incidence of extrapulmonary tuberculosis (EPTB) in low- and middle-income countries, as well as, high-income countries has increased over the last two decades. The acid-fast bacillus (AFB) smear test is easy to perform and cost-effective with a quick turnaround time but the test has low sensitivity. Culture remains the gold standard for detecting TB; however, it has low sensitivity and slow bacterial growth patterns, as it may take up to 6 to 8 weeks to grow. Therefore, a rapid detection tool is crucial for the early initiation of treatment and ensuring an improved therapeutic outcome. Here, the Xpert Ultra system was developed as a nucleic acid amplification technique to accelerate the detection of MTB in paucibacillary clinical samples and endorsed by the World Health Organization. From March 2020 to August 2021, Xpert Ultra was evaluated for its sensitivity and specificity against EPTB and compared with those of the routinely used Xpert, culture, and AFB tests in 845 clinical samples in Saudi Arabia. The results indicate the overall sensitivity and specificity of Xpert Ultra to be 91% and 95%, respectively, compared with the Xpert (82% and 99%, respectively) and AFB smear (18% and 100%, respectively) tests. The results also indicated that despite the low microbial loads that were categorized as trace, very low, or low on Xpert Ultra, yet, complete detection was achieved with some sample types (i.e., 100% detection). Consequently, Xpert Ultra has great potential to replace conventional diagnostic approaches as a standard detection method for EPTB.
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Affiliation(s)
- Mousa J Slail
- Tuberculosis Department, Dammam Regional Laboratory, Ministry of Health, Dammam, Saudi Arabia
| | - Rayan Y Booq
- Wellness and Preventive Medicine Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), 11442, Riyadh, Saudi Arabia
| | - Ibrahim H Al-Ahmad
- Tuberculosis Department, Dammam Regional Laboratory, Ministry of Health, Dammam, Saudi Arabia
| | - Arwa A Alharbi
- Mycobacteriology Unit, Riyadh Regional Laboratory, Ministry of Health, 12746, Riyadh, Saudi Arabia
| | - Shafi F Alharbi
- Mycobacteriology Unit, Riyadh Regional Laboratory, Ministry of Health, 12746, Riyadh, Saudi Arabia
| | - Mutlaq Z Alotaibi
- Mycobacteriology Unit, Riyadh Regional Laboratory, Ministry of Health, 12746, Riyadh, Saudi Arabia
| | - Abdulaziz M Aljubran
- Mycobacteriology Unit, Riyadh Regional Laboratory, Ministry of Health, 12746, Riyadh, Saudi Arabia
| | - Ahmad M Aldossary
- Wellness and Preventive Medicine Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), 11442, Riyadh, Saudi Arabia
| | - Ziad A Memish
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia
- Research & Innovation Center, King Saud Medical City, Riyadh, Saudi Arabia
- Hubert Department School of Public Health, Emory University, Atlanta, USA
- Division of Infectious Diseases, Kyung Hee University, Seoul, Korea
| | - Essam J Alyamani
- Wellness and Preventive Medicine Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), 11442, Riyadh, Saudi Arabia
| | - Essam A Tawfik
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), 11442, Riyadh, Saudi Arabia.
| | - Abdulwahab Z Binjomah
- Mycobacteriology Unit, Riyadh Regional Laboratory, Ministry of Health, 12746, Riyadh, Saudi Arabia.
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia.
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12
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Deng Y, Ma Z, Su B, Bai G, Pan J, Wang Q, Cai L, Song Y, Shang Y, Ma P, Li J, Zhou Q, Mulati G, Fan D, Li S, Tan Y, Pang Y. Accuracy of the InnowaveDX MTB/RIF test for detection of Mycobacterium tuberculosis and rifampicin resistance: a prospective multicentre study. Emerg Microbes Infect 2023; 12:2151382. [PMID: 36416478 DOI: 10.1080/22221751.2022.2151382] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Early and accurate diagnosis of tuberculosis (TB) is necessary to initiate proper therapy for the benefit of the patients and to prevent disease transmission in the community. In this study, we developed the InnowaveDX MTB/RIF (InnowaveDX) to detect Mycobacterium tuberculosis (MTB) and rifampicin resistance simultaneously. A prospective multicentre study was conducted to evaluate the diagnostic performance of InnowaveDX for the detection MTB in sputum samples as compared with Xpert and culture. The calculated limit of detection (LOD) for InnowaveDX was 9.6 CFU/ml for TB detection and 374.9 CFU/ml for RIF susceptibility. None of the other bacteria tested produced signals that fulfilled the positive TB criteria, demonstrating a species-specificity of InnowaveDX. Then 951 individuals were enrolled at 7 hospitals, of which 607 were definite TB cases with positive culture and/or Xpert results, including 354 smear-positive and 253 smear-negative cases. InnowaveDX sensitivity was 92.7% versus bacteriologically TB standard. Further follow-up revealed that 61 (91.0%) out of 67 false-positive patients with no bacteriological evidence met the criteria of clinically diagnosed TB. Among 125 RIF-resistant TB patients diagnosed by Xpert, 108 cases were correctly identified by InnowaveDX, yielding a sensitivity of 86.4%. Additionally, the proportion of very low bacterial load in the discordant susceptibility group was significantly higher than in the concordant susceptibility group (P = 0.029). To conclude, we have developed a novel molecular diagnostic with promising detection capabilities of TB and RIF susceptibility. In addition, the discordant RIF susceptibility results between InnowaveDX and Xpert are more frequently observed in samples with very low bacterial load.
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Affiliation(s)
- Yunfeng Deng
- Katharine Hsu International Research Center of Human Infectious Diseases, Shandong Public Health Clinical Center Affiliated to Shandong University, Jinan, People's Republic of China
| | - Zichun Ma
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People's Republic of China
| | - Biyi Su
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, People's Republic of China
| | - Guanghong Bai
- Department of Clinical Laboratory, Shanxi Provincial Tuberculosis Hospital, Xi'an, People's Republic of China
| | - Jianhua Pan
- Department of Clinical Laboratory, Changsha Central Hospital, Changsha, People's Republic of China
| | - Quan Wang
- Department of Clinical Laboratory, The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Long Cai
- Department of Clinical Laboratory, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
| | - Yanhua Song
- Department of Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People's Republic of China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People's Republic of China
| | - Pinyun Ma
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, People's Republic of China
| | - Jing Li
- Department of Clinical Laboratory, Shanxi Provincial Tuberculosis Hospital, Xi'an, People's Republic of China
| | - Qianxuan Zhou
- Department of Clinical Laboratory, Changsha Central Hospital, Changsha, People's Republic of China
| | - Gulibike Mulati
- Department of Clinical Laboratory, The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Dapeng Fan
- Department of Clinical Laboratory, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People's Republic of China
| | - Yaoju Tan
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, People's Republic of China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People's Republic of China
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13
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Sun J, Fan L, Zhao Y, Wu H, Li R, Tian Y, Cheng M, Ma X, Ma Y, Yang X, Shen A, Yu Y, Chen Y. Analysis of Drug-Resistant Tuberculosis in Children in Shenyang, China, 2017-2021. Infect Drug Resist 2023; 16:6983-6998. [PMID: 37933293 PMCID: PMC10625755 DOI: 10.2147/idr.s428720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/19/2023] [Indexed: 11/08/2023] Open
Abstract
Objective Drug-resistant tuberculosis (DR-TB) in children seriously threatens TB control. Information on the epidemiology and characteristics of DR-TB in children in China is limited. We studied data in Shenyang Tenth People's Hospital to understand the DR-TB epidemiology in children in Shenyang. Design or Methods We retrospectively analyzed drug resistance testing data of pediatric TB patients between 2017 and 2021, and included 2976 clinically-diagnosed pediatric TB patients. We described the epidemiology of DR-TB and analyzed the trends of DR-TB incidence. The Kappa value was calculated to assess the agreement between MGIT 960 DST and Xpert MTB/RIF for detecting rifampicin resistance. Multivariate logistic regression was used to identify the risk factors for DR-TB in pediatric patients. Results Of the 2976 TB patients, 1076 were confirmed by MGIT 960 culture and/or Xpert MTB/RIF. Among the 806 patients identified by MGIT 960 culture, 232 cases (28.78%) were DR-TB. Resistance to the six drugs was in the following order: streptomycin (21.09%), isoniazid (9.35%), rifampin (15.01%), levofloxacin (6.20%), ethambutol (4.22%), and amikacin (3.23%). Alarmingly, 12.90% were MDR-TB (104/806), including 28 (3.47%) pre-XDR-TB. Of the 1076 pediatric TB patients, 295 (27.4%) developed DR-TB to any one drug (including 69 rifampicin-resistant cases identified by Xpert MTB/RIF only). No difference was found in the incidence of pediatric DR-TB between 2017 and 2021. Among 376 patients who were positive for both methods, using the MGIT 960 DST results as the gold standard, Xpert MTB/RIF's sensitivity for detecting rifampicin resistance was 91.38% and its specificity was 94.65%. Conclusion Between 2017 and 2021, the DR-TB incidence in children remained unchanged in Shenyang. RR-TB, MDR-TB, and even Pre-XDR-TB require attention in children with drug-resistant TB. Xpert MTB/RIF helped to detect more rifampicin-resistant pediatric patients; thus Xpert MTB/RIF should be widely used as an important complementary tool to detect rifampicin-resistant TB in children.
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Affiliation(s)
- Jiao Sun
- Tuberculosis Laboratory, Shenyang Tenth People’s Hospital/Shenyang Chest Hospital, Shenyang, People’s Republic of China
| | - Lichao Fan
- Department of Tuberculosis, Shenyang Tenth People’s Hospital/Shenyang Chest Hospital, Shenyang, People’s Republic of China
| | - Yanping Zhao
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, People’s Republic of China
| | - Haoyu Wu
- Department of Tuberculosis, Shenyang Tenth People’s Hospital/Shenyang Chest Hospital, Shenyang, People’s Republic of China
| | - Ran Li
- Department of Tuberculosis, Shenyang Tenth People’s Hospital/Shenyang Chest Hospital, Shenyang, People’s Republic of China
| | - Yao Tian
- Department of Tuberculosis, Shenyang Tenth People’s Hospital/Shenyang Chest Hospital, Shenyang, People’s Republic of China
| | - Moxin Cheng
- Department of Tuberculosis, Shenyang Tenth People’s Hospital/Shenyang Chest Hospital, Shenyang, People’s Republic of China
| | - Xin Ma
- Tuberculosis Laboratory, Shenyang Tenth People’s Hospital/Shenyang Chest Hospital, Shenyang, People’s Republic of China
| | - Yingying Ma
- Tuberculosis Laboratory, Shenyang Tenth People’s Hospital/Shenyang Chest Hospital, Shenyang, People’s Republic of China
| | - Xinru Yang
- Tuberculosis Laboratory, Shenyang Tenth People’s Hospital/Shenyang Chest Hospital, Shenyang, People’s Republic of China
| | - Adong Shen
- National Clinical Research Center for Respiratory Disease, Beijing, People’s Republic of China
| | - Yanhong Yu
- Tuberculosis Laboratory, Shenyang Tenth People’s Hospital/Shenyang Chest Hospital, Shenyang, People’s Republic of China
| | - Yu Chen
- Department of Tuberculosis, Shenyang Tenth People’s Hospital/Shenyang Chest Hospital, Shenyang, People’s Republic of China
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14
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Torane VP, Nataraj G, Kanade S, Deshmukh CT. Comparison of gastric lavage/sputum and stool specimens in the diagnosis of pediatric pulmonary tuberculosis- A pilot study. Indian J Tuberc 2023; 70:445-450. [PMID: 37968050 DOI: 10.1016/j.ijtb.2023.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 10/09/2022] [Accepted: 03/29/2023] [Indexed: 11/17/2023]
Abstract
BACKGROUND AND OBJECTIVE Global TB report 2021 mentions 11 % prevalence of pediatric TB, whereas 5.65% of the cases were reported from India in 2020. India features in the list of TB high burden countries, HIV-TB high burden and MDR-TB high burden countries. The diagnosis of pulmonary tuberculosis in children is difficult as they tend to swallow the sputum, invasive techniques of gastric aspirates needs to be followed and the disease itself is paucibacillary. The disease progresses rapidly in young children and hence rapid diagnosis is needed. Obtaining appropriate respiratory samples for diagnosis is difficult especially in primary care settings. Stool sample is easy to obtain and since children swallow sputum, it can be used to diagnose pulmonary tuberculosis. With this background, a pilot study was planned to evaluate the accuracy of the Xpert MTB/RIF assay for the detection of MTB in stool specimens obtained from pediatric pulmonary TB patients confirmed either by gastric lavage(GL) or sputum(SP) Xpert MTB/RIF assay. In addition, the results of microscopy of stool specimen were compared with that of gastric lavage/ sputum (GL/SP) specimen by Ziehl-Neelsen (ZN) and fluorescent light-emitting diode (LED) staining. MATERIAL AND METHODS A prospective study was carried out on 50 GL/SP Xpert MTB/RIF assay positive children (0-14 years). Stool specimens from these children were processed for Xpert MTB/RIF assay. The GL/SP and stool specimens were processed for ZN and Auramine O fluorescent microscopy as well. RESULTS Fluorescent staining detected acid fast bacilli (AFB) in 24 GL/SP and 16 stool specimens as compared to 20 GL/SP and 10 stool specimens by ZN staining. Stool Xpert MTB/ RIF assay was positive in 29 out of 50 children. Rifampicin resistance was detected in 13 of the 50 (26%) GL/SP specimens. Of these 13 children, rifampicin resistance was detected in 7 stool specimens, rifampicin indeterminate resistance was detected in one specimen and in the remaining 5 children, M.tuberculosis was not detected in stool. CONCLUSION Stool is a good non-invasive specimen for the detection of pulmonary TB in children, especially in remote areas, where invasive techniques cannot be performed for sample collection.
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Affiliation(s)
- Vijaya P Torane
- Department of Microbiology, Seth Gordhandas Sunderdas Medical College (GSMC) & King Edward Memorial Hospital (KEMH), Mumbai, Maharashtra, India.
| | - Gita Nataraj
- Department of Microbiology, Seth Gordhandas Sunderdas Medical College (GSMC) & King Edward Memorial Hospital (KEMH), Mumbai, Maharashtra, India
| | - Swapna Kanade
- Department of Microbiology, Seth Gordhandas Sunderdas Medical College (GSMC) & King Edward Memorial Hospital (KEMH), Mumbai, Maharashtra, India
| | - Chandrahas T Deshmukh
- Department of Pediatrics, Seth Gordhandas Sunderdas Medical College (GSMC) & King Edward Memorial Hospital (KEMH), Mumbai, Maharashtra, India
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15
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Nguyen TBN, Nguyen TKD, Trương VH, Tran TTN, Phan VBT, Nguyen TT, Nguyen HB, Ngo VQT, Mai VT, Molicotti P. Drug resistance and the genotypic characteristics of rpoB and katG in rifampicin- and/or isoniazid-resistant Mycobacterium tuberculosis isolates in central Vietnam. Osong Public Health Res Perspect 2023; 14:347-355. [PMID: 37920892 PMCID: PMC10626318 DOI: 10.24171/j.phrp.2023.0124] [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: 05/09/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Tuberculosis (TB) and drug-resistant TB (DR-TB) are national health burdens in Vietnam. In this study, we investigated the prevalence of rifampicin (RIF) and/or isoniazid (isonicotinic acid hydrazide, INH) resistance in patients with suspected TB, and applied appropriate techniques to help rapidly target DR-TB. METHODS In total, 1,547 clinical specimens were collected and cultured using the BACTEC MGIT system (Becton Dickinson and Co.). A resazurin microtiter assay (REMA) was used to determine the proportions of RIF and/or INH resistance. A real-time polymerase chain reaction panel with TaqMan probes was employed to identify the mutations of rpoB and katG associated with DR-TB in clinical isolates. Genotyping of the identified mutations was also performed. RESULTS A total of 468 Mycobacterium tuberculosis isolates were identified using the REMA. Of these isolates, 106 (22.6%) were found to be resistant to 1 or both antibiotics. Of the resistant isolates, 74 isolates (69.8%) were resistant to isoniazid (INH) only, while 1 isolate (0.94%) was resistant to RIF only. Notably, 31 isolates (29.24%) were resistant to both antibiotics. Of the 41 phenotypically INH-resistant isolates, 19 (46.3%) had the Ser315Thr mutation. There were 8 different rpoB mutations in 22 (68.8%) of the RIF-resistant isolates. The most frequently detected mutations were at codons 531 (37.5%), 526 (18.8%), and 516 (6.3%). CONCLUSION To help prevent new cases of DR-TB in Vietnam, it is crucial to gain a comprehensive understanding of the genotypic DR-TB isolates.
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Affiliation(s)
- Thi Binh Nguyen Nguyen
- Department of Infectious Diseases and Tuberculosis, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | | | | | - Thi Tuyet Ngoc Tran
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - van Bao Thang Phan
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Thi Tuyen Nguyen
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Hoang Bach Nguyen
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Viet Quynh Tram Ngo
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Van Tuan Mai
- Department of Microbiology, Hue Central Hospital, Hue, Vietnam
| | - Paola Molicotti
- Department of Biomedical Science, Microbiology and Clinical Microbiology, University of Sassari, Sassari, Italy
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16
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Ouyang X, Li X, Song J, Wang H, Wang S, Fang R, Li Z, Song N. Mycobacteriophages in diagnosis and alternative treatment of mycobacterial infections. Front Microbiol 2023; 14:1277178. [PMID: 37840750 PMCID: PMC10568470 DOI: 10.3389/fmicb.2023.1277178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Antimicrobial resistance is an increasing threat to human populations. The emergence of multidrug-resistant "superbugs" in mycobacterial infections has further complicated the processes of curing patients, thereby resulting in high morbidity and mortality. Early diagnosis and alternative treatment are important for improving the success and cure rates associated with mycobacterial infections and the use of mycobacteriophages is a potentially good option. Since each bacteriophage has its own host range, mycobacteriophages have the capacity to detect specific mycobacterial isolates. The bacteriolysis properties of mycobacteriophages make them more attractive when it comes to treating infectious diseases. In fact, they have been clinically applied in Eastern Europe for several decades. Therefore, mycobacteriophages can also treat mycobacteria infections. This review explores the potential clinical applications of mycobacteriophages, including phage-based diagnosis and phage therapy in mycobacterial infections. Furthermore, this review summarizes the current difficulties in phage therapy, providing insights into new treatment strategies against drug-resistant mycobacteria.
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Affiliation(s)
- Xudong Ouyang
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
| | - Xiaotian Li
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
| | - Jinmiao Song
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
| | - Hui Wang
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
| | - Shuxian Wang
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
| | - Ren Fang
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
| | - Zhaoli Li
- SAFE Pharmaceutical Technology Co. Ltd., Beijing, China
| | - Ningning Song
- School of Life Science and Technology, Weifang Medical University, Weifang, China
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, Weifang, China
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17
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Kaboré OD, Millogo A, Sanogo B, Birba E, Poda A, Nacro B, Marcy O, Godreuil S, Ouédraogo AS. Analytical performances of the Xpert MTB/RIF assay using stool specimens to improve the diagnosis of pulmonary tuberculosis in Burkina Faso, a tuberculosis endemic country. PLoS One 2023; 18:e0288671. [PMID: 37523357 PMCID: PMC10389731 DOI: 10.1371/journal.pone.0288671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 07/01/2023] [Indexed: 08/02/2023] Open
Abstract
Timely diagnosis of Pulmonary Tuberculosis (PTB) is associated with good prognosis, but remains difficult in primary healthcare facilities and particularly in children and patients living with HIV. The aim of this study was to compare the GeneXpert ® MTB/RIF assay (Xpert) performed using a stool sample (3-5 g) and using the first Respiratory Tract Sample (RTS; i.e., sputum, bronchoalveolar or gastric aspirate; as normally done) concomitantly collected from 119 patients with suspected PTB to improve PTB diagnosis in Burkina Faso, a high tuberculosis burden country with limited resources. Overall, microbiological, microscopic and molecular analysis of the 119 first RTS and 119 stool specimens led to Mycobacterium tuberculosis complex detection in 28 patients (23 positive RTS cultures and 5 negative RTS cultures-RTS Xpert positive). When using the 28 clinical confirmed cases as reference standard, the sensitivities of the stool-based and RTS-based Xpert assays were not different (24/28, 85.7%, versus 26/28, 92.86%; p > 0.30), and 22 results were fully concordant. Considering the first RTS culture as the gold standard, the sensitivities of the stool-based and RTS-based Xpert assays to detect PTB in patients with positive RTS culture were 100% (23/23) and 91.3% (21/23), respectively (p >0.05). The stool-based Xpert assay specificity for excluding PTB was 99% (95/96) (compared with 95%, 91/96, when using RTS) and its negative and positive predictive values were 100% (95/95) and 96% (23/24), respectively. Compared with the 23 positive RTS cultures, the incremental yield rates of the RTS-based and stool-based Xpert assays were 4.2% (5/119) and 0.84% (1/119), respectively. Overall, our findings support using the stool-based Xpert assay as an alternative method for earlier PTB diagnosis, when RTS are difficult to obtain.
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Affiliation(s)
- Odilon D Kaboré
- Department of Bacteriology and Virology, Souro Sanou University Hospital, Bobo Dioulasso, Burkina Faso
- Superior Institute of Health Sciences, NAZI BONI University, Bobo-Dioulasso, Burkina Faso
- Laboratory of Emerging and Re-emerging Pathogens, School of Health Sciences Nazi Boni University, Bobo Dioulasso, Burkina Faso
| | - Anselme Millogo
- Department of Bacteriology and Virology, Souro Sanou University Hospital, Bobo Dioulasso, Burkina Faso
| | - Bintou Sanogo
- Superior Institute of Health Sciences, NAZI BONI University, Bobo-Dioulasso, Burkina Faso
- Département de Pédiatrie du Centre Hospitalier Universitaire Sourô Sanou, Bobo-Dioulasso, Burkina Faso
| | - Emile Birba
- Superior Institute of Health Sciences, NAZI BONI University, Bobo-Dioulasso, Burkina Faso
- Service de Pneumologie-Phtisiologie du Centre Hospitalier Universitaire Sourô Sanou, Bobo-Dioulasso, Burkina Faso
| | - Armel Poda
- Superior Institute of Health Sciences, NAZI BONI University, Bobo-Dioulasso, Burkina Faso
- Laboratory of Emerging and Re-emerging Pathogens, School of Health Sciences Nazi Boni University, Bobo Dioulasso, Burkina Faso
- Service des Maladies Infectieuses du Centre Hospitalier Universitaire Sourô Sanou, Bobo-Dioulasso, Burkina Faso
| | - Boubacar Nacro
- Superior Institute of Health Sciences, NAZI BONI University, Bobo-Dioulasso, Burkina Faso
- Département de Pédiatrie du Centre Hospitalier Universitaire Sourô Sanou, Bobo-Dioulasso, Burkina Faso
| | - Olivier Marcy
- Bordeaux Population Health Research Center Inserm U1219, University of Bordeaux, Bordeaux, France
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, CHU de Montpellier, MIVEGEC (IRD, CNRS, Université de Montpellier), Montpellier, France
| | - Abdoul-Salam Ouédraogo
- Department of Bacteriology and Virology, Souro Sanou University Hospital, Bobo Dioulasso, Burkina Faso
- Superior Institute of Health Sciences, NAZI BONI University, Bobo-Dioulasso, Burkina Faso
- Laboratory of Emerging and Re-emerging Pathogens, School of Health Sciences Nazi Boni University, Bobo Dioulasso, Burkina Faso
- Muraz Center, Bobo Dioulasso, Burkina Faso
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18
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Bokop C, Faye LM, Apalata T. Analysis of Discordance between Genotypic and Phenotypic Assays for Rifampicin-Resistant Mycobacterium tuberculosis Isolated from Healthcare Facilities in Mthatha. Pathogens 2023; 12:909. [PMID: 37513756 PMCID: PMC10384316 DOI: 10.3390/pathogens12070909] [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: 04/06/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
The study sought to determine the rate of discordant results between genotypic and phenotypic tests for the diagnosis of drug-resistant tuberculosis (DR-TB). Sputum samples and cultured isolates from suspected DR-TB patients were, respectively, analyzed for Mycobacterium tuberculosis by Xpert® MTB/RIF (Cepheid, Sunnyvale, CA, USA) and line probe assays (LPA) (Hain, Nehren, Germany). Discrepant rifampicin (RMP)-resistant results were confirmed using BACTEC MGIT960 (BD, New York, NY, USA). Of the 224 RMP-resistant results obtained by Xpert MTB/RIF, 5.4% were susceptible to RMP by LPA. MGIT960 showed a 75% agreement with LPA. The discrepancy was attributed to either heteroresistance or DNA contamination during LPA testing in 58.3% of cases. In 25% of the samples showing agreement in RMP resistance between Xpert MTB/RIF and MGIT960, the discrepancy was attributed to laboratory errors causing false RMP susceptible results with LPA. In 16.7% of the cases, the discrepancy was attributed to false RMP susceptible results with Xpert MTB/RIF. Out of the 224 isolates, susceptibility to isoniazid (INH) by LPA was performed in 73.7% RMP-resistant isolates, of which, 80.6% were resistant. All RMP-resistant isolates by Xpert MTB/RIF were confirmed in 98.5% by LPA if TB isolates were resistant to INH, but were only confirmed in 81.3% if TB isolates were susceptible to INH (p < 0.001). In conclusion, laboratory errors should be considered when investigating discordant results.
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Affiliation(s)
- Carine Bokop
- Division of Medical Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University, Mthatha 5099, Eastern Cape, South Africa
| | - Lindiwe M Faye
- Department of Laboratory Medicine and Pathology, Faculty of Health Sciences and National Health Laboratory Services (NHLS), Walter Sisulu University, Mthatha 5099, Eastern Cape, South Africa
| | - Teke Apalata
- Department of Laboratory Medicine and Pathology, Faculty of Health Sciences and National Health Laboratory Services (NHLS), Walter Sisulu University, Mthatha 5099, Eastern Cape, South Africa
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Fan D, Yue Y, Li H, Shang X, Li H, Xiao R, Cai L. Evaluation of the performances of InnowaveDx MTB-RIF assay in the diagnosis of pulmonary tuberculosis using bronchoalveolar lavage fluid. Tuberculosis (Edinb) 2023; 140:102349. [PMID: 37187053 DOI: 10.1016/j.tube.2023.102349] [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: 08/17/2022] [Revised: 03/27/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
OBJECTIVE To evaluate the tuberculosis diagnostic performance of the InnowaveDx MTB-RIF assay (InnowaveDx test) in bronchoalveolar lavage fluid (BALF). METHODS A total of 213 BALF samples from suspected PTB patients were analyzed. AFB smear, culture, Xpert, Innowavedx test, CapitalBio test and simultaneous amplification and testing (SAT) were performed. RESULTS Of the 213 patients included in the study, 163 were diagnosed with PTB, and 50 were TB negative. Using the final clinical diagnosis as the reference, the sensitivity of InnowaveDx assay was 70.6%, which was significantly higher than the values achieved using the other methods (P < 0.05), and the specificity was 88.0%, which was comparable with other methods (P > 0.05). Among the 83 PTB cases with negative culture results, the detection rate of InnowaveDx assay was significantly higher than those of AFB smear, Xpert, CapitalBio test and SAT (P < 0.05). Kappa analysis was used to compare the agreement of InnowaveDx and Xpert in detecting RIF sensitivity, and the result showed the Kappa value was 0.78. CONCLUSIONS The InnowaveDx test is a sensitive, rapid and cost-effective tool for PTB diagnosis. In addition, the sensitivity of InnowaveDx to RIF in samples with low TB load should be interpreted with caution in light of other clinical data.
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Affiliation(s)
- Dapeng Fan
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China
| | - Yongning Yue
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China
| | - Hao Li
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China
| | - Xuechai Shang
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China
| | - Huanyu Li
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China
| | - Rong Xiao
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China.
| | - Long Cai
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China.
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20
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Yezli S, Yassin Y, Mushi A, Maashi F, Abdelmalek NM, Awam AH, Alotaibi BM. Undiagnosed and missed active pulmonary tuberculosis during mass gatherings: a prospective cross-sectional study from the Hajj pilgrimage. Eur J Clin Microbiol Infect Dis 2023; 42:727-740. [PMID: 37074544 PMCID: PMC10113968 DOI: 10.1007/s10096-023-04596-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/10/2023] [Indexed: 04/20/2023]
Abstract
Mass gatherings increase the risk of infectious diseases transmission including tuberculosis (TB). The Hajj pilgrimage to Mecca, Saudi Arabia, is attended by over 2 million pilgrims many of whom are from high TB-burden countries, and has been linked to increased risk of TB acquisition among travellers. We investigated the burden of undiagnosed and missed active pulmonary TB (PTB) among Hajj pilgrims symptomatic for cough. The study was conducted among hospitalised and non-hospitalised travellers attending the Hajj pilgrimage in 2016 and 2017. Questionnaires were used to collect relevant data and sputum samples were collected from participants and processed using the Xpert MTB-RIF assay. Non-hospitalised pilgrims (n = 1510) originating from 16 high and medium TB-burden countries were enrolled. Undiagnosed, rifampicin-sensitive, active PTB was identified in 0.7%. Comorbidities (adjOR = 5.9 [95% CI = 1.2-27.8]), close contact with a TB case (adjOR = 5.9 [95% CI = 1.2-27.8]), cough in household (adjOR = 4.46 [95% CI = 1.1-19.5]), and previous TB treatment (adjOR = 10.1 [95% CI = 4.1-98.1]) were independent risk factors for TB. Of the hospitalised pilgrims (n = 304), 2.9% were positive for PTB, and 2.3% were missed, including a rifampicin-resistant case. History of TB treatment was associated with increased risk of TB (adjOR = 8.1 [95% CI = 1.3-48.7]). International mass gatherings may play an important role in the global epidemiology of TB. Preventive measures should be directed to reducing the risk of TB importation and transmission during Hajj and other similar events.
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Affiliation(s)
- Saber Yezli
- Global Centre for Mass Gathering Medicine, Ministry of Health, Riyadh, Saudi Arabia.
- Biostatistics, Epidemiology and Scientific Computing Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11564, Saudi Arabia.
| | - Yara Yassin
- Global Centre for Mass Gathering Medicine, Ministry of Health, Riyadh, Saudi Arabia
- Federation of Saudi Chambers Institute, Federation of Saudi Chambers, Riyadh, Saudi Arabia
| | - Abdulaziz Mushi
- Global Centre for Mass Gathering Medicine, Ministry of Health, Riyadh, Saudi Arabia
- Infection Prevention and Control Department, Jazan Health Affairs, Jazan, Saudi Arabia
| | - Fuad Maashi
- Global Centre for Mass Gathering Medicine, Ministry of Health, Riyadh, Saudi Arabia
- Public Health Laboratory, Public Health Authority, Riyadh, Saudi Arabia
| | - Nour M Abdelmalek
- Global Centre for Mass Gathering Medicine, Ministry of Health, Riyadh, Saudi Arabia
- Academic and Training Affairs Department, Riyadh Third Health Cluster, Riyadh, Saudi Arabia
| | - Amnah H Awam
- Global Centre for Mass Gathering Medicine, Ministry of Health, Riyadh, Saudi Arabia
- Communicable Disease Department, Public Health Authority, Riyadh, Saudi Arabia
| | - Badriah M Alotaibi
- Global Centre for Mass Gathering Medicine, Ministry of Health, Riyadh, Saudi Arabia
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21
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Wang J, Zhang X, Huo F, Qin L, Liu R, Shang Y, Yao C, Ma L, Pang Y. Analysis of Xpert MTB/RIF results in retested patients with very low initial bacterial loads: A retrospective study in China. J Infect Public Health 2023; 16:911-916. [PMID: 37068397 DOI: 10.1016/j.jiph.2023.04.004] [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: 09/03/2022] [Revised: 02/18/2023] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND The Xpert MTB/RIF (Xpert) assay has been widely used to diagnose suspected active tuberculosis (TB) and rifampicin-resistant TB cases. Despite its excellent performance record, false-positive Xpert rifampicin (RIF) resistance results are obtained for specimens with extremely low bacterial loads. OBJECTIVE We aimed to study the feasibility of repeat Xpert testing as a strategy for reducing the odds of obtaining false-positive results when testing paucibacillary TB patients. METHODS We enrolled previously tested TB patients with very low initial bacterial loads from May 2016 to February 2022 for Xpert retesting. A total of 251 TB patients were retested using the Xpert assay. RESULTS RIF resistance was noted in 65 (25.9 %) patients when tested by Xpert at initial diagnosis. Only 107 (42.6 %) of 251 patients tested positive for MTB when retested via Xpert. The majority (98.6 %) of RIF-susceptible cases were still susceptible to RIF when retested. Initial Xpert testing yielded 35 positive results for MTB in the RIF-resistant group, of whom 25 (71.4 %) still exhibited RIF resistance when retested. All culture-positive MTB isolates in the RIF-susceptible group were also RIF-susceptible by phenotypic DST. In the RIF-resistant group, 10 of 14 culture-positive MTB isolates exhibited RIF resistance, of which 4 isolates were deemed RIF-susceptible by phenotypic DST. The proportion of double mutations within the MTB rpoB RRDR sequence, as detected by hybridization of Xpert D and E probes, was significantly higher in the RIF-susceptible group than in the RIF-susceptible group. CONCLUSIONS Our results demonstrated that initial RIF-susceptible results were more accurate than RIF-resistant results. Additionally, patients with double mutations that delayed probe D/E hybridization were more likely to have false-positive Xpert results. Our findings emphasize that repeat Xpert MTB/RIF testing is necessary for TB patients with extremely low bacterial loads who are at high risk for RIF-resistant TB.
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Affiliation(s)
- Jun Wang
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Xuxia Zhang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Fengmin Huo
- National Clinical Laboratory on Tuberculosis, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Lin Qin
- Department of Endoscopic Diagnosis & Treatment, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Rongmei Liu
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Cong Yao
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Liping Ma
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China.
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China.
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22
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Santos VS, Allgayer MF, Kontogianni K, Rocha JE, Pimentel BJ, Amorim MTP, Duarte MVSC, de Melo Ferreira P, Moura LCL, de Lima VPS, Guimarães LC, Dodd J, Creswell J, Cuevas LE. Pooling of sputum samples to increase tuberculosis diagnostic capacity in Brazil during the COVID-19 pandemic. Int J Infect Dis 2023; 129:10-14. [PMID: 36642209 PMCID: PMC9834119 DOI: 10.1016/j.ijid.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/17/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES We assessed whether combining (pooling) four individual's samples and testing with Xpert Ultra has the same accuracy as testing samples individually as a more efficient testing method. METHODS We conducted a cross-sectional study of individuals with presumptive tuberculosis attending primary health care or general hospital facilities in Alagoas, Brazil. The sputum samples of four consecutive individuals were pooled and the pool and individual samples were tested with Xpert Ultra. The agreement of the tests was compared using kappa statistics. We estimated the sensitivity and specificity of pooling using the individual test as the reference standard and potential cartridge savings. RESULTS A total of 396 participants were tested. A total of 95 (24.0%) individual samples were Mycobacterium tuberculosis (MTB)-positive, 300 (75.8%) "MTB not detected", including 20 "MTB trace", and one reported an error. A total of 99 pools of four samples were tested, of which 62 (62.6%) had MTB detected and 37 (37.4%) MTB not detected, including six (6.1%) with MTB trace. The agreement between individual and pooled testing was 96.0%. Pooling had a sensitivity of 95.0% (95% confidence interval 86.9-99%), specificity of 97.1% (95% confidence interval 85.1-99.9%), and kappa of 0.913. The method saved 12.4% of cartridge costs. CONCLUSION The pooled testing of specimens had a high level of agreement with individual testing. The pooling of samples for testing improves the efficiency of testing, potentially enabling the screening and testing of larger numbers of individuals more cost-effectively.
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Affiliation(s)
- Victor Santana Santos
- Department of Nursing. Centre for Epidemiology and Public Health. Federal University of Alagoas, Arapiraca, Brazil; Graduate Program in Health Sciences. Federal University of Alagoas, Maceió, Brazil; Graduate Program in Health Sciences. Federal University of Sergipe, Aracaju, Brazil
| | - Manuela Filter Allgayer
- Department of Nursing. Centre for Epidemiology and Public Health. Federal University of Alagoas, Arapiraca, Brazil
| | | | - José Erinaldo Rocha
- Laboratório de Diagnóstico, Pesquisa e Controle de Tuberculose, Maceió, Brazil
| | | | | | | | | | | | | | | | - James Dodd
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Jacob Creswell
- Stop TB Partnership, Innovations and Grants, Geneva, Switzerland
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23
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Sharma M, Broor S, Maheshwari M, Sudan DPS. Comparison of conventional diagnostic methods with molecular method for the diagnosis of pulmonary tuberculosis. Indian J Tuberc 2023; 70:182-189. [PMID: 37100575 DOI: 10.1016/j.ijtb.2022.04.006] [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: 10/19/2021] [Accepted: 04/24/2022] [Indexed: 04/28/2023]
Abstract
BACKGROUND Tuberculosis remains one of the deadliest communicable diseases. Prompt diagnosis of active tuberculosis cases facilitates timely therapeutic intervention and minimizes the community transmission. Although conventional microscopy has low sensitivity, still it remains the corner stone for the diagnosis of pulmonary tuberculosis in high burden countries like India. On the other hand, Nucleic acid amplification techniques due to their rapidity and sensitivity, not only help in early diagnosis and management of tuberculosis but also curtail the transmission of the disease. This study therefore was aimed at assessing the diagnostic performance of Microscopy by Ziehl Neelsen (ZN) and Auramine Staining (AO) with Gene Xpert/CBNAAT (Cartridge based nucleic acid amplification test) in the diagnosis of Pulmonary Tuberculosis. METHODS A prospective comparative study was done on the sputum samples of 1583 adult patients from November 2018 to May 2020 suspected of having pulmonary tuberculosis as per NTEP criteria visiting the Designated Microscopic Centre of SGT Medical College, Budhera, Gurugram. Each sample was subjected to ZN staining, AO staining, and was run on CBNAAT as per National Tuberculosis Elimination Program (NTEP) guidelines. The sensitivity, specificity, PPV and NPV and Area under the curve of ZN microscopy and Fluorescent Microscopy were calculated taking CBNAAT as reference in absence of culture. RESULTS Out of the 1583 samples studied, 145 (9.15%) and 197 (12.44%) were positive by ZN and AO staining methods respectively. By CBNAAT 246 (15.54%) samples were positive for M. tuberculosis. AO was also able to detect more pauci-bacillary cases than ZN. While CBNAAT detected M. tuberculosis in 49 sputum samples which were missed by both methods of microscopy. On the other hand there were 9 samples which were positive for AFB by both the smear microscopy techniques but M. tuberculosis was not detected by CBNAAT, these were considered as Non-Tuberculous Mycobacteria. Seventeen samples were resistant to rifampicin. CONCLUSION Auramine Staining technique is more sensitive and less time consuming for the diagnosis of pulmonary tuberculosis as compared to the conventional ZN Staining. CBNAAT can be a useful tool for early diagnosis of patients with high clinical suspicion of pulmonary tuberculosis and detecting rifampicin resistance.
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Affiliation(s)
- Monika Sharma
- Department of Microbiology, SGT Medical College, Hospital and Research Institute, SGT University, Budhera, Gurugram, India.
| | | | - Megha Maheshwari
- Department of Microbiology, B Block, Dr Babasaheb Ambedkar Medical College, Rohini, Sector 6, New Delhi, India.
| | - Dharam Pal Singh Sudan
- Department of Pulmonary Medicine, SGT Medical College, Hospital and Research Institute, SGT University, Budhera, Gurugram, India.
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24
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Kanade S, Mohammed Z, Kulkarni A, Nataraj G. Comparison of xpert MTB/RIF assay, line probe assay, and culture in diagnosis of pulmonary tuberculosis on bronchoscopic specimen. Int J Mycobacteriol 2023; 12:151-156. [PMID: 37338476 DOI: 10.4103/ijmy.ijmy_86_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Background In patients unable to expectorate good quality sputum or with minimal to none sputum production, bronchoscopic specimens may be collected. The objective of the study is to determine the use of Xpert MTB/RIF assay and line probe assay (LPA) in the diagnosis of pulmonary TB (PTB) using specimens collected by bronchoscopy in a tertiary care center. Methods Bronchoscopy specimens received in the TB laboratory were processed by microscopy, Xpert MTB/RIF assay, LPA, and mycobacteria growth indicator tube (MGIT) culture. Results of MGIT culture are considered gold standard. Results Of the 173 specimens tested, MTB was detected in 48 (27.74%) samples by any of the above methods. Positivity in bronchoalveolar lavage was 31.4% (44/140) and in bronchial wash was 12.1% (4/33). Detection by microscopy, Xpert assay, and culture was 20 (11.56%), 45 (26.01%), and 38 (21.96%), respectively. Culture detected MTB in three additional specimens compared to Xpert assay. Xpert assay detected MTB in 45 (26%) specimens which include 10 specimens which were negative by culture. LPA detected MTB in 18 (90%) out of 20 smear-positive specimens. RIF resistance was detected in 20 (41.7%) specimens by Xpert and/or MGIT culture drug susceptibility testing (DST). Isoniazid (INH) resistance was detected in 19 specimens by LPA and MGIT culture DST. Conclusion Bronchoscopy can provide alternative respiratory specimens for diagnosing PTB in patients with difficulty to expectorate sputum. The utility of Xpert MTB/RIF as a rapid, sensitive, and specific test should always be supplemented with culture in difficult-to-obtain and precious respiratory specimens. LPA plays an important role in rapid detection of INH monoresistance.
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Affiliation(s)
- Swapna Kanade
- Department of Microbiology, Seth G.S. Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Zakiuddin Mohammed
- Department of Microbiology, Seth G.S. Medical College and KEM Hospital, Mumbai, Maharashtra; Telangana Diagnostics Central Laboratory, Hyderabad, Telangana, India
| | - Anisha Kulkarni
- Department of Microbiology, Seth G.S. Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Gita Nataraj
- Department of Microbiology, Seth G.S. Medical College and KEM Hospital, Mumbai, Maharashtra, India
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25
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Kanade S, Solanki M, Thombare S, Nataraj G. Utility of laboratory diagnostic tests in women suspected of genital tuberculosis attending a tertiary care teaching hospital. Int J Mycobacteriol 2023; 12:135-138. [PMID: 37338473 DOI: 10.4103/ijmy.ijmy_75_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Background Genital Tuberculosis is a form of extrapulmonary tuberculosis, which if not diagnosed early can lead to complications. The objective of this study was to determine the sensitivity and specificity of Xpert Mycobacterium tuberculosis/rifampin (MTB/RIF) assay in genital tuberculosis (TB) in comparison with culture as a gold standard. Methods The results of the Xpert MTB/RIF assay performed from January 2020 to August 2021 were compared with the results of culture by Mycobacterium Growth Indicator Tube (MGIT) 960. Results Out of 75 specimens, fluorescent microscopy and liquid culture using MGIT and Xpert assay were positive in 3 (4%), 21 (28%), and 14 (18%), respectively. The sensitivity and specificity of the Xpert MTB/RIF assay were 66.67% and 100%. All smear-positive specimens were positive by culture and Xpert assay. Three specimens were positive by all the tests, i.e., microscopy, culture, and Xpert assay. Fifty-four specimens were negative by microscopy, culture, and Xpert assay. Discordance between the results of culture and Xpert assay was observed in seven specimens which were culture positive and Xpert assay negative. Three (21.42%) out of 21 culture-positive specimens showed monoresistance to rifampicin by Xpert MTB/RIF assay and culture drug susceptibility testing. Conclusion Xpert MTB/RIF assay showed good sensitivity and specificity compared to liquid culture in genital TB. This test is easy to perform, provides results in 2 h, and can also detect rifampicin resistance, which is a surrogate marker for multidrug-resistant TB. Hence, the Xpert assay can be used under the National TB Elimination Program for early and rapid diagnosis of TB in endometrial specimens to prevent complications like infertility.
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Affiliation(s)
- Swapna Kanade
- Department of Microbiology, Seth G. S. Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Mitali Solanki
- Department of Microbiology, Seth G. S. Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Swapnil Thombare
- Department of Microbiology, Seth G. S. Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Gita Nataraj
- Department of Microbiology, Seth G. S. Medical College and KEM Hospital, Mumbai, Maharashtra, India
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26
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Guan Z, Han X, Huang W, Wang X, Wang H, Fan Y. Construction and application of a heterogeneous quality control library for the Xpert MTB/RIF assay in tuberculosis diagnosis. Front Cell Infect Microbiol 2023; 13:1128337. [PMID: 37009507 PMCID: PMC10063913 DOI: 10.3389/fcimb.2023.1128337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Proficiency testing based on quality control materials is an important component of the quality assurance system for detection methods. However, in the detection of infectious diseases, it is a challenge to use quality control materials derived from clinical samples or pathogens owing to their infectious nature. The Xpert MTB/RIF assay, endorsed by the World Health Organization, is one of the most widely implemented assays in the detection of Mycobacterium tuberculosis along with rifampicin resistance and its heterogeneity. Clinical isolates are typically used as quality controls for this assay, leading to concerns about biosafety, constrained target sequence polymorphisms, and time-consuming preparation. In this study, a heterogeneous quality control library for the Xpert MTB/RIF assay was constructed based on DNA synthesis and site-directed mutation, which provides sufficient rifampicin resistance polymorphisms, enabling monitoring all five probes of Xpert MTB/RIF and its combinations. Escherichia coli and Bacillus subtilis were used as heterogeneous hosts rather than the pathogen itself to eliminate biosafety risks; thus, preparation does not require a biosafety level III laboratory and the production time is reduced from a few months to a few days. The panel was stable for more than 15 months stored at 4°C and could be distributed at room temperature. All 11 laboratories in Shanghai participating in a pilot survey identified the specimens with corresponding probe patterns, and discordant results highlighted inappropriate operations in the process. Collectively, we show, for the first time, that this library, based on heterogeneous hosts, is an appropriate alternative for M. tuberculosis detection.
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Affiliation(s)
- Zehao Guan
- R&D Laboratory of Quality Control Material, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Xuefei Han
- R&D Laboratory of Quality Control Material, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Weigang Huang
- R&D Laboratory of Quality Control Material, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Xueliang Wang
- R&D Laboratory of Quality Control Material, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Hualiang Wang
- R&D Laboratory of Quality Control Material, Shanghai Center for Clinical Laboratory, Shanghai, China
- Shanghai Academy of Experimental Medicine, Shanghai, China
| | - Yun Fan
- R&D Laboratory of Quality Control Material, Shanghai Center for Clinical Laboratory, Shanghai, China
- *Correspondence: Yun Fan,
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27
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Kim T, Kim J, Kim T, Oak CH, Ryoo S. Transrenal DNA detection of Mycobacterium tuberculosis in patients with pulmonary tuberculosis. Int J Mycobacteriol 2023; 12:66-72. [PMID: 36926765 DOI: 10.4103/ijmy.ijmy_12_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
Background Multiple attempts have been made to use biological samples other than sputum to diagnose tuberculosis (TB). Sputum acid-fast bacillus (AFB) microscopy is the fastest, most straightforward, and most inexpensive method for diagnosing pulmonary TB. However, urine can be used in place of sputum owing to its various advantages, such as a noninvasive method of collection, convenient handling and storage, and minimal risk of infection in health-care workers involved in sample collection. In this study, we aimed to assess the suitability of urine as a sample to obtain transrenal DNA (trDNA) to diagnose TB. This study involved several patients with TB undergoing inpatient treatment, whose AFB microscopy showed negative inversion. Methods Here, 51 urine samples were collected from 40 patients with TB and examined to confirm the presence of trDNA. First, we compared the efficiency of two trDNA extraction methods. An automated magnetic bead-based method and a more efficient anchoring extraction method. Statistical analyses were performed using Excel software (Microsoft Office Professional Plus 2019). Results Although molecular diagnosis using GeneXpert yielded negative results, a peculiarity was observed. There was no significant difference between GeneXpert findings and our results nor was there any difference in the sequential trDNA samples obtained. However, even when GeneXpert results were negative, trDNA was detected in seven out of ten samples using the anchor extraction method. Conclusions Further studies are needed to establish biomarkers for the progression of TB treatment.
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Affiliation(s)
- Taeyoon Kim
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon, Republic of Korea
| | - Jehun Kim
- Department of Internal Medicine, Division of Pulmonology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Republic of Korea
| | - Taeyun Kim
- Department of Internal Medicine, Division of Pulmonology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Republic of Korea
| | - Chul-Ho Oak
- Department of Internal Medicine, Division of Pulmonology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Republic of Korea
| | - Sungweon Ryoo
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon, Republic of Korea
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Host biomarker-based quantitative rapid tests for detection and treatment monitoring of tuberculosis and COVID-19. iScience 2022; 26:105873. [PMID: 36590898 PMCID: PMC9791715 DOI: 10.1016/j.isci.2022.105873] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/24/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022] Open
Abstract
Diagnostic services for tuberculosis (TB) are not sufficiently accessible in low-resource settings, where most cases occur, which was aggravated by the COVID-19 pandemic. Early diagnosis of pulmonary TB can reduce transmission. Current TB-diagnostics rely on detection of Mycobacterium tuberculosis (Mtb) in sputum requiring costly, time-consuming methods, and trained staff. In this study, quantitative lateral flow (LF) assays were used to measure levels of seven host proteins in sera from pre-COVID-19 TB patients diagnosed in Europe and latently Mtb-infected individuals (LTBI), and from COVID-19 patients and healthy controls. Analysis of host proteins showed significantly lower levels in LTBI versus TB (AUC:0 · 94) and discriminated healthy individuals from COVID-19 patients (0 · 99) and severe COVID-19 from TB. Importantly, these host proteins allowed treatment monitoring of both respiratory diseases. This study demonstrates the potential of non-sputum LF assays as adjunct diagnostics and treatment monitoring for COVID-19 and TB based on quantitative detection of multiple host biomarkers.
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Gargava A, Raghuwanshi S, Verma P, Jaiswal S. To Study the Role of Cartridge-Based Nucleic Acid Amplification Test (CBNAAT) in Early Diagnosis of Extra Pulmonary Tuberculosis. Indian J Otolaryngol Head Neck Surg 2022; 74:5412-5415. [PMID: 36742905 PMCID: PMC9895136 DOI: 10.1007/s12070-021-02673-y] [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: 04/26/2021] [Accepted: 05/31/2021] [Indexed: 02/07/2023] Open
Abstract
Diagnosing EPTB is difficult as various clinical presentations are seen with paucibacillary nature of the disease. Maurya AK et al. (J Postgrad Med 58(3):185-189) AFB smear hasn't been much effective in diagnosing of EPTB. Tuberculosis of head and neck diagnosis can be missed due to large number of smear negative cases, leading false negative cases increase. CBNAAT is cartridge-based nucleic acid amplification test which detects the presence of TB bacilli this study we have examined the effectiveness of CBNAAT for diagnosing EPTB with cervical lymphadenitis and compared with Sputum AFB Microscopy smear. Aims and objective 1.To study the role of cartridge-based nucleic acid amplification test (CBNAAT) in early diagnosis of extra pulmonary tuberculosis. 2 Comparative analysis of CBNAAT with AFB smears in EPTB. Type of Study Descriptive retrospective observational study was done at the department of ENT and Head & surgery, A.B.V. Govt medical college, Vidisha, M.P, India. Result Out of 184 patients 43 samples were AFB smear positive and 141 were negative. In CBNAAT 88 out of 184 and 96 were found to be negative.32 patients were negative on Sputum microscopy AFB analysis but found to be positive on CBNAAT. Sensitivity of CBNAAT was 86% AFB 64%, Specificity of CBNAAT, AFB is 91% and 89% respectively. Our study finds that CBNAAT is much more effective in diagnosis of EPTB with cervical lymphadenitis when compared to AFB smear microscopy alone.
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Affiliation(s)
- Aditya Gargava
- A.B.V Govt Medical College, Vidisha, Madhya Pradesh India
| | | | - Priyanka Verma
- A.B.V Govt Medical College, Vidisha, Madhya Pradesh India
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Sailo CV, Lalremruata R, Sanga Z, Fela V, Kharkongor F, Chhakchhuak Z, Chhakchhuak L, Nemi L, Zothanzama J, Kumar NS. Distribution and frequency of common mutations in rpoB gene of Mycobacterium tuberculosis detected by Xpert MTB/RIF and identification of residential areas of Rifampicin Resistant-TB cases: A first retrospective study from Mizoram, Northeast India. J Clin Tuberc Other Mycobact Dis 2022; 29:100342. [DOI: 10.1016/j.jctube.2022.100342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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31
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Byanyima P, Kaswabuli S, Musisi E, Nabakiibi C, Zawedde J, Sanyu I, Sessolo A, Andama A, Worodria W, Huang L, Davis JL. Feasibility and Sensitivity of Saliva GeneXpert MTB/RIF Ultra for Tuberculosis Diagnosis in Adults in Uganda. Microbiol Spectr 2022; 10:e0086022. [PMID: 36154664 PMCID: PMC9603304 DOI: 10.1128/spectrum.00860-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/30/2022] [Indexed: 12/30/2022] Open
Abstract
The objective of this prospective observational study carried out at China-Uganda Friendship Hospital-Naguru in Kampala, Uganda, was to determine the performance of GeneXpert MTB/RIF Ultra (Xpert Ultra) molecular testing on saliva for active tuberculosis (TB) disease among consecutive adults undergoing TB diagnostic evaluation who were Xpert Ultra positive on sputum. We calculated sensitivity to determine TB diagnostic performance in comparison to a composite reference standard of Mycobacterium tuberculosis liquid and solid cultures on two spot sputum specimens. Xpert Ultra on a single saliva sample had a sensitivity of 90% (95% confidence interval [CI], 81 to 95%) relative to the composite sputum culture-based reference standard, similar to the composite sensitivity of 87% (95% CI, 77 to 94%) for fluorescence microscopy (FM) for acid-fast bacilli on two sputum smears. The sensitivity of salivary Xpert Ultra was 24% lower (95% CI for difference, 2 to 48%; P = 0.003) among persons living with HIV (71%; 95% CI, 44 to 90%) than among persons living without HIV (95%; 95% CI, 86 to 99%) and 46% higher (95% CI, 14 to 77%; P < 0.0001) among FM-positive (96%; 95% CI, 87 to 99%) than among FM-negative (50%; 95% CI, 19 to 81%) patients. The semiquantitative Xpert Ultra grade was systematically higher in sputum than in a paired saliva sample from the same patient. In conclusion, molecular testing of saliva for active TB diagnosis was feasible and almost as sensitive as molecular testing of sputum in a high TB burden setting. IMPORTANCE Tuberculosis is among the leading causes of morbidity and mortality worldwide, in large part because >3 million people go undiagnosed and untreated each year. Sputum has been the mainstay for TB diagnosis for over a century but can be difficult for patients to produce. In addition, the vigorous coughing required during sputum collection can lead to infection of nearby individuals and health workers. In this case-only study, applying the ultra-sensitive GeneXpert MTB/RIF Ultra molecular diagnostic assay to saliva detected 90% of culture-confirmed TB cases among 81 adults who were undergoing TB evaluation at the outpatient department of a general hospital in Uganda and tested sputum GeneXpert MTB/RIF Ultra positive. These results suggest that saliva may be a feasible and sensitive alternative to sputum for TB diagnosis, thereby meeting two key metrics proposed by the World Health Organization in its target performance profile for a nonsputum test for TB.
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Affiliation(s)
| | | | - Emmanuel Musisi
- Division of Infection and Global Health, School of Medicine, University of St. Andrews, United Kingdom
| | | | | | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Abdul Sessolo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Alfred Andama
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - William Worodria
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, USA
- Division of HIV, Infectious Diseases, and Global Medicine, University of California San Francisco, San Francisco, California, USA
| | - J. Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Pulmonary, Critical Care, and Sleep Medicine Section, Yale School of Medicine, New Haven, Connecticut, USA
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Li Z. The Value of GeneXpert MTB/RIF for Detection in Tuberculosis: A Bibliometrics-Based Analysis and Review. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2022; 2022:2915018. [PMID: 36284547 PMCID: PMC9588380 DOI: 10.1155/2022/2915018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/26/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
With the continuous development of medical science and technology, especially with the advent of the era of precision diagnosis and treatment, molecular biology detection technology is widely valued and applied as an aid to early diagnosis of tuberculosis. The GeneXpert Mycobacterium tuberculosis Branching (MTB) technology is a suite of semi-nested real-time fluorescent quantitative PCR in vitro diagnostic technologies developed by Cepheid Inc. It targets the rifampicin resistance gene, rpoB, and can detect both MTB and resistance to rifampicin within 2 h. This review analyzed the papers related to GeneXpert using bibliometric software CiteSpace and Bibliometrix. A total of 151 articles were analyzed, spanning from 2011 to 2021. This bibliometrics-based review summarizes the history of the development of GeneXpert in tuberculosis diagnosis and its current status. Contributions of different countries to the topic, journal analysis, key paper analysis, and clustering of keywords were used to analyze this topic.
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Affiliation(s)
- Zhiyi Li
- Laboratory Medicine, Nanan Hospital, Nanan, Quanzhou 362300, Fujian, China
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Kay AW, Ness T, Verkuijl SE, Viney K, Brands A, Masini T, González Fernández L, Eisenhut M, Detjen AK, Mandalakas AM, Steingart KR, Takwoingi Y. Xpert MTB/RIF Ultra assay for tuberculosis disease and rifampicin resistance in children. Cochrane Database Syst Rev 2022; 9:CD013359. [PMID: 36065889 PMCID: PMC9446385 DOI: 10.1002/14651858.cd013359.pub3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Every year, an estimated one million children and young adolescents become ill with tuberculosis, and around 226,000 of those children die. Xpert MTB/RIF Ultra (Xpert Ultra) is a molecular World Health Organization (WHO)-recommended rapid diagnostic test that simultaneously detects Mycobacterium tuberculosis complex and rifampicin resistance. We previously published a Cochrane Review 'Xpert MTB/RIF and Xpert MTB/RIF Ultra assays for tuberculosis disease and rifampicin resistance in children'. The current review updates evidence on the diagnostic accuracy of Xpert Ultra in children presumed to have tuberculosis disease. Parts of this review update informed the 2022 WHO updated guidance on management of tuberculosis in children and adolescents. OBJECTIVES To assess the diagnostic accuracy of Xpert Ultra for detecting: pulmonary tuberculosis, tuberculous meningitis, lymph node tuberculosis, and rifampicin resistance, in children with presumed tuberculosis. Secondary objectives To investigate potential sources of heterogeneity in accuracy estimates. For detection of tuberculosis, we considered age, comorbidity (HIV, severe pneumonia, and severe malnutrition), and specimen type as potential sources. To summarize the frequency of Xpert Ultra trace results. SEARCH METHODS We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, three other databases, and three trial registers without language restrictions to 9 March 2021. SELECTION CRITERIA Cross-sectional and cohort studies and randomized trials that evaluated Xpert Ultra in HIV-positive and HIV-negative children under 15 years of age. We included ongoing studies that helped us address the review objectives. We included studies evaluating sputum, gastric, stool, or nasopharyngeal specimens (pulmonary tuberculosis), cerebrospinal fluid (tuberculous meningitis), and fine needle aspirate or surgical biopsy tissue (lymph node tuberculosis). For detecting tuberculosis, reference standards were microbiological (culture) or composite reference standard; for stool, we also included Xpert Ultra performed on a routine respiratory specimen. For detecting rifampicin resistance, reference standards were drug susceptibility testing or MTBDRplus. DATA COLLECTION AND ANALYSIS Two review authors independently extracted data and, using QUADAS-2, assessed methodological quality judging risk of bias separately for each target condition and reference standard. For each target condition, we used the bivariate model to estimate summary sensitivity and specificity with 95% confidence intervals (CIs). We stratified all analyses by type of reference standard. We summarized the frequency of Xpert Ultra trace results; trace represents detection of a very low quantity of Mycobacterium tuberculosis DNA. We assessed certainty of evidence using GRADE. MAIN RESULTS We identified 14 studies (11 new studies since the previous review). For detection of pulmonary tuberculosis, 335 data sets (25,937 participants) were available for analysis. We did not identify any studies that evaluated Xpert Ultra accuracy for tuberculous meningitis or lymph node tuberculosis. Three studies evaluated Xpert Ultra for detection of rifampicin resistance. Ten studies (71%) took place in countries with a high tuberculosis burden based on WHO classification. Overall, risk of bias was low. Detection of pulmonary tuberculosis Sputum, 5 studies Xpert Ultra summary sensitivity verified by culture was 75.3% (95% CI 64.3 to 83.8; 127 participants; high-certainty evidence), and specificity was 97.1% (95% CI 94.7 to 98.5; 1054 participants; high-certainty evidence). Gastric aspirate, 7 studies Xpert Ultra summary sensitivity verified by culture was 70.4% (95% CI 53.9 to 82.9; 120 participants; moderate-certainty evidence), and specificity was 94.1% (95% CI 84.8 to 97.8; 870 participants; moderate-certainty evidence). Stool, 6 studies Xpert Ultra summary sensitivity verified by culture was 56.1% (95% CI 39.1 to 71.7; 200 participants; moderate-certainty evidence), and specificity was 98.0% (95% CI 93.3 to 99.4; 1232 participants; high certainty-evidence). Nasopharyngeal aspirate, 4 studies Xpert Ultra summary sensitivity verified by culture was 43.7% (95% CI 26.7 to 62.2; 46 participants; very low-certainty evidence), and specificity was 97.5% (95% CI 93.6 to 99.0; 489 participants; high-certainty evidence). Xpert Ultra sensitivity was lower against a composite than a culture reference standard for all specimen types other than nasopharyngeal aspirate, while specificity was similar against both reference standards. Interpretation of results In theory, for a population of 1000 children: • where 100 have pulmonary tuberculosis in sputum (by culture): - 101 would be Xpert Ultra-positive, and of these, 26 (26%) would not have pulmonary tuberculosis (false positive); and - 899 would be Xpert Ultra-negative, and of these, 25 (3%) would have tuberculosis (false negative). • where 100 have pulmonary tuberculosis in gastric aspirate (by culture): - 123 would be Xpert Ultra-positive, and of these, 53 (43%) would not have pulmonary tuberculosis (false positive); and - 877 would be Xpert Ultra-negative, and of these, 30 (3%) would have tuberculosis (false negative). • where 100 have pulmonary tuberculosis in stool (by culture): - 74 would be Xpert Ultra-positive, and of these, 18 (24%) would not have pulmonary tuberculosis (false positive); and - 926 would be Xpert Ultra-negative, and of these, 44 (5%) would have tuberculosis (false negative). • where 100 have pulmonary tuberculosis in nasopharyngeal aspirate (by culture): - 66 would be Xpert Ultra-positive, and of these, 22 (33%) would not have pulmonary tuberculosis (false positive); and - 934 would be Xpert Ultra-negative, and of these, 56 (6%) would have tuberculosis (false negative). Detection of rifampicin resistance Xpert Ultra sensitivity was 100% (3 studies, 3 participants; very low-certainty evidence), and specificity range was 97% to 100% (3 studies, 128 participants; low-certainty evidence). Trace results Xpert Ultra trace results, regarded as positive in children by WHO standards, were common. Xpert Ultra specificity remained high in children, despite the frequency of trace results. AUTHORS' CONCLUSIONS We found Xpert Ultra sensitivity to vary by specimen type, with sputum having the highest sensitivity, followed by gastric aspirate and stool. Nasopharyngeal aspirate had the lowest sensitivity. Xpert Ultra specificity was high against both microbiological and composite reference standards. However, the evidence base is still limited, and findings may be imprecise and vary by study setting. Although we found Xpert Ultra accurate for detection of rifampicin resistance, results were based on a very small number of studies that included only three children with rifampicin resistance. Therefore, findings should be interpreted with caution. Our findings provide support for the use of Xpert Ultra as an initial rapid molecular diagnostic in children being evaluated for tuberculosis.
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Affiliation(s)
- Alexander W Kay
- The Global Tuberculosis Program, Texas Children's Hospital, Section of Global and Immigrant Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Tara Ness
- The Global Tuberculosis Program, Texas Children's Hospital, Section of Global and Immigrant Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Kerri Viney
- Global TB Programme, World Health Organization, Geneva, Switzerland
| | - Annemieke Brands
- Global TB Programme, World Health Organization, Geneva, Switzerland
| | - Tiziana Masini
- Global TB Programme, World Health Organization, Geneva, Switzerland
| | - Lucia González Fernández
- The Global Tuberculosis Program, Texas Children's Hospital, Section of Global and Immigrant Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Michael Eisenhut
- Paediatric Department, Luton & Dunstable University Hospital NHS Foundation Trust, Luton, UK
| | | | - Anna M Mandalakas
- The Global Tuberculosis Program, Texas Children's Hospital, Section of Global and Immigrant Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Karen R Steingart
- Honorary Research Fellow, Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Yemisi Takwoingi
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
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Mukhida S, Vyawahare CR, Mirza SB, Gandham NR, Khan S, Kannuri S, Bhaumi S. Role of GeneXpert MTB/RIF assay for the diagnosis of cervical lymph node tuberculosis and rifampicin resistance. Tzu Chi Med J 2022; 34:418-422. [PMID: 36578636 PMCID: PMC9791852 DOI: 10.4103/tcmj.tcmj_86_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/03/2022] [Accepted: 07/20/2022] [Indexed: 12/31/2022] Open
Abstract
Objectives Tuberculosis (TB) of lymph node (TB lymphadenitis) is one of the most common forms of extrapulmonary TB (EPTB) whose diagnosis is critically challenging. Although new diagnostic methods have been developed, especially in patients without a history of TB, the cervical tuberculous lymphadenitis diagnosis is still elusive. This study assessed the applicability of GeneXpert in early diagnosis of EPTB, especially cervical lymphadenopathy. Materials and Methods The study was conducted in a tertiary care hospital from January 2018 to December 2020 at the department of microbiology. All the samples of cervical lymph node tissue and lymph node aspirate were followed as per the routine protocol for mycobacterial identification. The sample was divided into two parts: one was used for the new molecular-based GeneXpert MTB/RIF assay and the second one was tested by direct and concentrated acid-fast bacilli microscopy by Z-N staining and culture for the detection of MTB. Results Among the 145 samples tested, the GeneXpert detected the DNA of MTB in 89 samples (61.37%), whereas the culture test was positive in 42 (28.93%) specimens. GeneXpert also detected 7 rifampicin resistance cases. GeneXpert sensitivity and specificity results were assessed according to culture results. The sensitivity and specificity of the GeneXpert assay were 85.71% and 48.54%, respectively. Conclusion GeneXpert MTB/RIF should be used in conjunction with clinical presentation and other molecular investigation in nonrespiratory specimens.
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Affiliation(s)
- Sahjid Mukhida
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India
| | - Chanda R. Vyawahare
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India,Address for correspondence: Dr. Chanda R. Vyawahare, Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pimpri, Pune - 411 018, Maharashtra, India. E-mail:
| | - Shahzad Beg Mirza
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India
| | - Nageswari R. Gandham
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India
| | - Sameena Khan
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India
| | - Sriram Kannuri
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India
| | - Shalini Bhaumi
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India
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Hameed HMA, Fang C, Liu Z, Ju Y, Han X, Gao Y, Wang S, Chiwala G, Tan Y, Guan P, Hu J, Xiong X, Peng J, Lin Y, Hussain M, Zhong N, Maslov DA, Cook GM, Liu J, Zhang T. Characterization of Genetic Variants Associated with Rifampicin Resistance Level in Mycobacterium tuberculosis Clinical Isolates Collected in Guangzhou Chest Hospital, China. Infect Drug Resist 2022; 15:5655-5666. [PMID: 36193294 PMCID: PMC9526423 DOI: 10.2147/idr.s375869] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/11/2022] [Indexed: 11/23/2022] Open
Abstract
Objective Rifampicin (RIF)-resistance, a surrogate marker for multidrug-resistant tuberculosis (TB), is mediated by mutations in the rpoB gene. We aimed to investigate the prevalence of mutations pattern in the entire rpoB gene of Mycobacterium tuberculosis clinical isolates and their association with resistance level to RIF. Methods Among 465 clinical isolates collected from the Guangzhou Chest Hospital, drug-susceptibility of 175 confirmed Mtb strains was performed via the proportion method and Bactec MGIT 960 system. GeneXpert MTB/RIF and sanger sequencing facilitated in genetic characterization, whereas the MICs of RIF were determined by Alamar blue assay. Results We found 150/175 (85.71%) RIF-resistant strains (MIC: 4 to >64 µg/mL) of which 57 were MDR and 81 pre-XDR TB. Genetic analysis identified 17 types of mutations 146/150 (97.33%) within RRDR (codons 426–452) of rpoB, mainly at L430 (P), D435 (V, E, G, N), H445 (N, D, Y, R, L), S450 (L, F) and L452 (P). D435V 12/146 (8.2%), H445N 16/146 (10.9%), and S450L 70/146 (47.94%) were the most frequently encountered mutations. Mutations Q432K, M434V, and N437D are rarely identified in RRDR. Deletions at (1284–1289 CCAGCT), (1295–1303 AATTCATGG), and insertion at (1300–1302 TTC) were detected within RRDR of three RIFR strains for the first time. We detected 47 types of mutations and insertions/deletions (indels) outside the RRDR. Four RIFR strains were detected with only novel mutations/indels outside the RRDR. Two of the four had (K274Q + C897 del + I491M) and (A286V + L494P), respectively. The other two had (G1687del + P454L) and (TT1835-6 ins + I491L) individually. Compared with phenotypic characterization, diagnostic sensitivities of GeneXpert MTB/RIF and sequencing analysis were 95.33% (143/150), and 100% (150/150) respectively. Conclusion Our findings underscore the key role of RRDR mutations and the contribution of non-RRDR mutations in rapid molecular diagnosis of RIFR clinical isolates. Such insights will support early detection of disease and recommend the appropriate anti-TB regimens in high-burden settings.
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Affiliation(s)
- H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
- University of Chinese Academy of Sciences (UCAS), Beijing, People’s Republic of China
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
- University of Chinese Academy of Sciences (UCAS), Beijing, People’s Republic of China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
| | - Yanan Ju
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
| | - Xingli Han
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
- University of Chinese Academy of Sciences (UCAS), Beijing, People’s Republic of China
| | - Yamin Gao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
- University of Chinese Academy of Sciences (UCAS), Beijing, People’s Republic of China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People’s Hospital, Shenzhen, People’s Republic of China
| | - Gift Chiwala
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
- University of Chinese Academy of Sciences (UCAS), Beijing, People’s Republic of China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, People’s Republic of China
| | - Ping Guan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, People’s Republic of China
| | - Jinxing Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, People’s Republic of China
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
| | - Jiacong Peng
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yongping Lin
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Muzammal Hussain
- University of Chinese Academy of Sciences (UCAS), Beijing, People’s Republic of China
| | - Nanshan Zhong
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Dmitry A Maslov
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, People’s Republic of China
- Jianxiong Liu, Guangzhou Chest Hospital, 62 Hengzhigang Road, Yuexiu District, Guangzhou, People’s Republic of China, Tel +86-2083595977, Email
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, People’s Republic of China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, People’s Republic of China
- University of Chinese Academy of Sciences (UCAS), Beijing, People’s Republic of China
- Correspondence: Tianyu Zhang, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Room A207, 190 Kaiyuan Ave, Science Park, Huangpu District, Guangzhou, 510530, People’s Republic of China, Tel +86-2032015270, Email
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Worku G, Gumi B, Girma M, Mohammedbirhan B, Diriba G, Seid G, Getu M, Amare M, Sinshaw W, Ashagre W, Tschopp R, Carruth L, Ameni G. Drug sensitivity of clinical isolates of Mycobacterium tuberculosis and its association with bacterial genotype in the Somali region, Eastern Ethiopia. Front Public Health 2022; 10:942618. [PMID: 36062084 PMCID: PMC9428271 DOI: 10.3389/fpubh.2022.942618] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/25/2022] [Indexed: 01/21/2023] Open
Abstract
Background Drug resistance is becoming a major bottleneck for tuberculosis (TB) control programs in countries with high TB burdens. Although several studies were conducted on the drug sensitivity of Mycobacterium tuberculosis (M. tuberculosis) in central Ethiopia, there is a lack of data on the drug sensitivity of M. tuberculosis in the peripheral regions of the country including in the Somali region. Therefore, the objective of this study was to evaluate the drug sensitivity of M. tuberculosis and its association with bacterial genotype and evaluate the performance of Xpert MTB/RIF (Xpert) in detecting resistance to rifampicin (RIF). Methods A total of 302 M. tuberculosis were tested using the BD BACTEC-Mycobacteria Growth Indicator Tube 960 (MGIT 960) system for their drug sensitivity to the first-line anti-TB drugs. Besides, the drug sensitivity of 10 multidrug-resistant (MDR) M. tuberculosis isolates was evaluated for the second-line anti-TB drugs. Additionally, 177 of the 302 isolates were tested for genotypic drug resistance using Xpert. Chi-square and Fisher's exact tests were used for the evaluation of the association between variables and drug sensitivity. Results The overall prevalence of resistance to at least one drug was 11.6% (95% CI: 7.9-15.2%), while the prevalence of MDR was 3.3% (95% CI: 1.3-5.3%). Two of the 10 MDR isolates were resistant to capreomycin. The spoligotype Shared International Type (SIT) 149 was significantly associated with either monoresistance or MDR (p < 0.05). Of the 177 isolates tested by Xpert, 6.2% (11/177) were RIF-resistant. Discordant between Xpert and MGIT 960 was observed in one isolate and linked with probe-binding delay (ΔCT max = 5.8). The sensitivity and specificity of the Xpert assay were 100 and 99.4%, respectively, while its positive and negative predictive values were 90.9 and 100%, respectively. Conclusion The magnitude of MDR M. tuberculosis in the Somali region of Ethiopia was higher than the national prevalence of MDR-TB warranting the strengthening of the TB control program in the Somali region. Besides, drug resistance was associated with SIT 149 spoligotype (genotype). The Xpert assay was observed to have high sensitivity and specificity in detecting RIF-resistant M. tuberculosis, which is encouraging for its application widely.
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Affiliation(s)
- Getnet Worku
- College of Medicine and Health Sciences, Jigjiga University, Jigjiga, Ethiopia,Animal Health and Zoonotic Unit, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Balako Gumi
- Animal Health and Zoonotic Unit, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Musse Girma
- Animal Health and Zoonotic Unit, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Getu Diriba
- Ethiopian Public Health Institute, National Tuberculosis Reference Laboratory, Addis Ababa, Ethiopia
| | - Getachew Seid
- Ethiopian Public Health Institute, National Tuberculosis Reference Laboratory, Addis Ababa, Ethiopia
| | - Melak Getu
- Ethiopian Public Health Institute, National Tuberculosis Reference Laboratory, Addis Ababa, Ethiopia
| | - Misikir Amare
- Ethiopian Public Health Institute, National Tuberculosis Reference Laboratory, Addis Ababa, Ethiopia
| | - Waganeh Sinshaw
- Ethiopian Public Health Institute, National Tuberculosis Reference Laboratory, Addis Ababa, Ethiopia
| | - Wondimu Ashagre
- One-Health Unit, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Rea Tschopp
- One-Health Unit, Armauer Hansen Research Institute, Addis Ababa, Ethiopia,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Lauren Carruth
- School of International Service, American University, Washington DC, DC, United States
| | - Gobena Ameni
- Animal Health and Zoonotic Unit, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates,*Correspondence: Gobena Ameni ;
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Islam MA, Kundu S, Hanis TM, Hajissa K, Musa KI. A Global Bibliometric Analysis on Antibiotic-Resistant Active Pulmonary Tuberculosis over the Last 25 Years (1996–2020). Antibiotics (Basel) 2022; 11:antibiotics11081012. [PMID: 36009881 PMCID: PMC9405510 DOI: 10.3390/antibiotics11081012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Tuberculosis (TB) is still a leading global cause of mortality and an increasingly crucial problem in fighting TB is antibiotic resistance. We aimed to conduct a bibliometric analysis on the articles of the past 25 years on antibiotic-resistant active pulmonary TB. Methods: Appropriate keywords were combined using the Boolean and wildcard operators and searched in Scopus database for articles published between 1996 and 2020 in English language. For all the bibliometric analyses, the Bibliometrix package in RStudio and Biblioshiny web apps were used. We identified the publication and citation trends, topmost cited documents, most productive authors, countries and institutions and most influential journals and funding agencies. We constructed collaborative networks of countries and co-citations. In addition, we developed a Three-Fields plot and a Thematic Map to explore different publication themes. Results: We included 7024 articles (88.9% research articles) and a persistently increasing publication and citation trends were evident throughout the past 25 years. Boehme 2010 was the most cited paper (1609 times cited), Stefan Niemann was the most productive author (86 papers), and ‘International Journal of Tuberculosis and Lung Disease’ was the leading journal. Centers for Disease Control and Prevention was the top contributing institution (3.7% papers) and both US- and UK-based funders were leading. The most productive countries were the USA, India, the UK, South Africa, and China and most of the collaborations took place between the USA, the UK, and South Africa. Conclusion: Undoubtedly, researchers and funders from the USA dominated followed by the UK in most of the fields in antibiotic-resistant TB research. The outcomes of antibiotic-resistant TB research would be more productive and translational if researchers from low- or middle-income countries (especially from Africa, South America and Asia) with high research productivity and TB burden could be in collaboration with high-income countries exhibiting low TB burden.
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Affiliation(s)
- Md Asiful Islam
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK
- Correspondence: or (M.A.I.); (K.I.M.)
| | - Shoumik Kundu
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh;
| | - Tengku Muhammad Hanis
- Department of Community Medicine, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Khalid Hajissa
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia;
- Department of Zoology, Faculty of Science and Technology, Omdurman Islamic University, P.O. Box 382, Omdurman 14415, Sudan
| | - Kamarul Imran Musa
- Department of Community Medicine, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia;
- Correspondence: or (M.A.I.); (K.I.M.)
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Accuracy of Tongue Swab Testing Using Xpert MTB-RIF Ultra for Tuberculosis Diagnosis. J Clin Microbiol 2022; 60:e0042122. [PMID: 35758702 PMCID: PMC9297831 DOI: 10.1128/jcm.00421-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tongue dorsum swabs have shown promise as alternatives to sputum for detecting Mycobacterium tuberculosis (MTB) in patients with pulmonary tuberculosis (TB). Some of the most encouraging results have come from studies that used manual quantitative PCR (qPCR) to analyze swabs. Studies using the automated Cepheid Xpert MTB/RIF Ultra qPCR test (Xpert Ultra) have exhibited less sensitivity with tongue swabs, possibly because Xpert Ultra is optimized for testing sputum, not tongue swab samples. Using two new sample preprocessing methods that demonstrated good sensitivity in preliminary experiments, we assessed diagnostic accuracy and semi-quantitative signals of Xpert Ultra performed on tongue swabs collected from 183 adults with presumed TB in Kampala, Uganda. Relative to a sputum Xpert Ultra reference standard, the sensitivity of tongue swab Xpert Ultra was 77.8% (95% confidence interval [CI] 64.4-88.0) and specificity was 100.0% (95% CI, 97.2-100.0). When compared to a microbiological reference standard (MRS) incorporating both sputum Xpert Ultra and sputum mycobacterial culture, sensitivity was 72.4% (95% CI, 59.1-83.3) and specificity remained the same. Semi-quantitative Xpert Ultra results were generally lower with tongue swabs than with sputum, and cycle threshold values were higher. None of the eight sputum Xpert Ultra "trace" or "very low" results were detected using tongue swabs. Tongue swabs should be considered when sputum cannot be collected for Xpert Ultra testing, or in certain mass-screening settings. Further optimization of tongue swab analysis is needed to achieve parity with sputum-based molecular testing for TB.
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Diagnostic Yield of Xpert MTB/RIF Assay Using Bronchoalveolar Lavage Fluid in Detecting Mycobacterium tuberculosis among the Sputum-Scarce Suspected Pulmonary TB Patients. Diagnostics (Basel) 2022; 12:diagnostics12071676. [PMID: 35885580 PMCID: PMC9324532 DOI: 10.3390/diagnostics12071676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) remains one of the leading causes of death worldwide and is caused by the single infectious agent Mycobacterium tuberculosis (Mtb). Although sputum is the most common specimen for pulmonary TB detection, some other respiratory specimens, such as bronchoalveolar lavage (BAL) fluid, gastric lavage (GL), and induced sputum (IS), are also collected from patients who are unable to deliver sputum. In this study, we aimed to evaluate the diagnostic performances of different test methods for TB diagnosis using BAL fluid specimens from sputum-scarce pulmonary TB patients. In this current study, a total of 210 BAL fluid specimens were collected and subjected to culture on Lowenstein–Jensen (L-J) medium, using an N-acetyl-L-cysteine-Sodium Hydroxide decontamination and digestion method, Xpert MTB/RIF (Xpert, Cepheid, Sunnyvale, CA, USA) assay, and acid-fast bacilli (AFB) microscopy with a Ziehl–Neelsen staining method for the detection of pulmonary TB. The sensitivity and specificity of these methods were then analyzed against the composite reference standard (CRS). Additionally, the receiver operating characteristic (ROC) curve was used to evaluate the diagnostic value of these assays. Among the 210 specimens, 39 (18.6%), 27 (12.8%), and 12 (5.7%) were found positive with Xpert assay, culture, and AFB microscopy, respectively. Considering the CRS, 42 (20%) were positive as the final diagnosis. The Xpert assay had a significantly higher sensitivity (92.9%, 95% CI: 80.5–98.5) compared to culture (64.3%, 95% CI: 48.0–78.4) and AFB microscopy (28.6%, 95% CI: 15.7–44.6) against the CRS. Additionally, the area under the ROC curve (AUC) for the Xpert assay, culture, and AFB microscopy accounted for 0.964, 0.821, and 0.655, respectively, when using CRS as the reference. In conclusion, our study findings demonstrated that the Xpert assay conferred a considerable diagnostic potential compared to other conventional methods for the diagnosis of pulmonary TB from BAL fluid specimens.
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Merchant SA, Shaikh MJS, Nadkarni P. Tuberculosis conundrum - current and future scenarios: A proposed comprehensive approach combining laboratory, imaging, and computing advances. World J Radiol 2022; 14:114-136. [PMID: 35978978 PMCID: PMC9258306 DOI: 10.4329/wjr.v14.i6.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/17/2022] [Accepted: 05/28/2022] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB) remains a global threat, with the rise of multiple and extensively drug resistant TB posing additional challenges. The International health community has set various 5-yearly targets for TB elimination: mathematical modelling suggests that a 2050 target is feasible with a strategy combining better diagnostics, drugs, and vaccines to detect and treat both latent and active infection. The availability of rapid and highly sensitive diagnostic tools (Gene-Xpert, TB-Quick) will vastly facilitate population-level identification of TB (including rifampicin resistance and through it, multi-drug-resistant TB). Basic-research advances have illuminated molecular mechanisms in TB, including the protective role of Vitamin D. Also, Mycobacterium tuberculosis impairs the host immune response through epigenetic mechanisms (histone-binding modulation). Imaging will continue to be key, both for initial diagnosis and follow-up. We discuss advances in multiple imaging modalities to evaluate TB tissue changes, such as molecular imaging techniques (including pathogen-specific positron emission tomography imaging agents), non-invasive temporal monitoring, and computing enhancements to improve data acquisition and reduce scan times. Big data analysis and Artificial Intelligence (AI) algorithms, notably in the AI sub-field called “Deep Learning”, can potentially increase the speed and accuracy of diagnosis. Additionally, Federated learning makes multi-institutional/multi-city AI-based collaborations possible without sharing identifiable patient data. More powerful hardware designs - e.g., Edge and Quantum Computing- will facilitate the role of computing applications in TB. However, “Artificial Intelligence needs real Intelligence to guide it!” To have maximal impact, AI must use a holistic approach that incorporates time tested human wisdom gained over decades from the full gamut of TB, i.e., key imaging and clinical parameters, including prognostic indicators, plus bacterial and epidemiologic data. We propose a similar holistic approach at the level of national/international policy formulation and implementation, to enable effective culmination of TB’s endgame, summarizing it with the acronym “TB - REVISITED”.
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Affiliation(s)
- Suleman Adam Merchant
- Lokmanya Tilak Municipal Medical College and General Hospital, Mumbai 400022, Maharashtra, India
| | - Mohd Javed Saifullah Shaikh
- Department of Radiology, North Bengal Neuro Centre, Jupiter magnetic resonance imaging, Diagnostic Centre, Siliguri 734003, West Bengal, India
| | - Prakash Nadkarni
- College of Nursing, University of Iowa, Iowa 52242, IA, United States
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Nadkarni P, Merchant SA. Enhancing medical-imaging artificial intelligence through holistic use of time-tested key imaging and clinical parameters: Future insights. Artif Intell Med Imaging 2022; 3:55-69. [DOI: 10.35711/aimi.v3.i3.55] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/12/2022] [Accepted: 06/17/2022] [Indexed: 02/06/2023] Open
Abstract
Much of the published literature in Radiology-related Artificial Intelligence (AI) focuses on single tasks, such as identifying the presence or absence or severity of specific lesions. Progress comparable to that achieved for general-purpose computer vision has been hampered by the unavailability of large and diverse radiology datasets containing different types of lesions with possibly multiple kinds of abnormalities in the same image. Also, since a diagnosis is rarely achieved through an image alone, radiology AI must be able to employ diverse strategies that consider all available evidence, not just imaging information. Using key imaging and clinical signs will help improve their accuracy and utility tremendously. Employing strategies that consider all available evidence will be a formidable task; we believe that the combination of human and computer intelligence will be superior to either one alone. Further, unless an AI application is explainable, radiologists will not trust it to be either reliable or bias-free; we discuss some approaches aimed at providing better explanations, as well as regulatory concerns regarding explainability (“transparency”). Finally, we look at federated learning, which allows pooling data from multiple locales while maintaining data privacy to create more generalizable and reliable models, and quantum computing, still prototypical but potentially revolutionary in its computing impact.
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Affiliation(s)
- Prakash Nadkarni
- College of Nursing, University of Iowa, Iowa City, IA 52242, United States
| | - Suleman Adam Merchant
- Department of Radiology, LTM Medical College & LTM General Hospital, Mumbai 400022, Maharashtra, India
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Xie NG, Zhang K, Song P, Li R, Luo J, Zhang DY. High-Throughput Variant Detection Using a Color-Mixing Strategy. J Mol Diagn 2022; 24:878-892. [PMID: 35718091 PMCID: PMC9379672 DOI: 10.1016/j.jmoldx.2022.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 04/04/2022] [Accepted: 04/25/2022] [Indexed: 11/16/2022] Open
Abstract
Many diseases are related to multiple genetic alterations along a single gene. Probing for highly multiple (>10) variants in a single quantitative PCR tube is not possible because of a limited number of fluorescence channels and one variant per channel, so many more tubes are needed. Herein, a novel color-mixing strategy that uses fluorescence combinations as digital color codes to probe multiple variants simultaneously was experimentally validated. The color-mixing strategy relies on a simple intratube assay that can probe for 15 variants as part of an intertube assay that can probe for an exponentially increased number of variants. This strategy is achieved by using multiplex double-stranded toehold probes modified with fluorophores and quenchers; the probes are designed to be quenched or luminous after binding to wild-type or variant templates. The color-mixing strategy was used to probe for 21 pathogenic variants in thalassemia and to distinguish between heterozygous and homozygous variants in six tubes, with a specificity of 99% and a sensitivity of 94%. To support tuberculosis diagnosis, the same strategy was applied to simultaneously probe in Mycobacterium tuberculosis for rifampicin-resistance mutations occurring within one 81-bp region and one 48-bp region in the rpoB gene, plus five isoniazid-resistance mutations in the inhA and katG genes.
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Affiliation(s)
- Nina Guanyi Xie
- Department of Bioengineering, Rice University, Houston, Texas
| | - Kerou Zhang
- Department of Bioengineering, Rice University, Houston, Texas
| | - Ping Song
- Department of Bioengineering, Rice University, Houston, Texas
| | | | | | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, Texas.
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Jabber Benellam YK, Ozkan O, Saadoon Aziz Z. Diagnosis of Mycobacterium tuberculosis using GeneXpert MTB / RIF and TB-LAMP techniques from pulmonary and extra-pulmonary TB patients in Iraq. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.02.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Tuberculosis is considered one globally public health problem, particularly in unindustrialized countries. The disease has an increasing threat to public health, causing high morbidity and mortality rates. So, rapid diagnosis is critical to diminish the death and interfere with transmission. In this study, GeneXpert MTB/RIF and Loop-Mediated Isothermal Amplification (TB-LAMP) assays were utilized for the rapid molecular diagnosis of Mycobacterium tuberculosis bacteria and compared sensitivity and specificity of Mycobacterium tuberculosis bacteria; these tests with acid-fast bacilli staining in pulmonary and extra-pulmonary clinical specimens from Iraqi patients in Baghdad capital. 141 pulmonary and extra-pulmonary samples were collected and tested for tuberculosis detection. Acid-fast bacilli, TB-LAMP and GeneXpert MTB/RIF methods were used to diagnose tuberculosis. Of 141 tuberculosis specimens, 58 were acid-fast bacilli smear-positive, while 90 samples were positive for Mycobacterium tuberculosis by GeneXpert MTB/RIF assay and 78 by TB-LAMP assay. The results reported a high sensitivity rate of GeneXpert MTB/RIF assay compared to the TB-LAMP and bacilli staining method. The sensitivity of GeneXpert was 63.83%, specificity 50%; positive and negative predictive values were 58.36% to 68.96% and 42.73% to 57.27%, respectively. TB-LAMP sensitivity was 55.32%, specificity 50%; positive and negative predictive values were 49.61% to 60.89% and 43.70% to 56.30%, respectively, while the sensitivity of bacilli staining was 41.13%, specificity 50%; positive and negative predictive values were 35.26% to 47.27% and 44.88% to 55.12%, respectively, these values are dependent on disease prevalence. We concluded that the GeneXpert MTB/RIF test is more sensitive and specific than the TB-LAMP and both techniques are more sensitive and specific than the conventional acid-fast staining method for both pulmonary and extra-pulmonary specimens. Despite culture remaining the gold standard for laboratory confirmation of TB, GeneXpert MTB/RIF and TB-LAMP should become standard practice for patients with suspected TB, and all clinicians and public health programs for TB control should have access to molecular testing for TB to shorten diagnosis time.
Keywords. Mycobacterium tuberculosis; Pulmonary TB; Extrapulmonary TB; GeneXpert MTB/RIF; TB-LAMP; A.F.B
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Affiliation(s)
| | - Ozcan Ozkan
- Department of Biology, Faculty of Science, Cankiri Karatekin University, Cankiri, Turkey
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Engel N, Ochodo EA, Karanja PW, Schmidt BM, Janssen R, Steingart KR, Oliver S. Rapid molecular tests for tuberculosis and tuberculosis drug resistance: a qualitative evidence synthesis of recipient and provider views. Cochrane Database Syst Rev 2022; 4:CD014877. [PMID: 35470432 PMCID: PMC9038447 DOI: 10.1002/14651858.cd014877.pub2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Programmes that introduce rapid molecular tests for tuberculosis and tuberculosis drug resistance aim to bring tests closer to the community, and thereby cut delay in diagnosis, ensure early treatment, and improve health outcomes, as well as overcome problems with poor laboratory infrastructure and inadequately trained personnel. Yet, diagnostic technologies only have an impact if they are put to use in a correct and timely manner. Views of the intended beneficiaries are important in uptake of diagnostics, and their effective use also depends on those implementing testing programmes, including providers, laboratory professionals, and staff in health ministries. Otherwise, there is a risk these technologies will not fit their intended use and setting, cannot be made to work and scale up, and are not used by, or not accessible to, those in need. OBJECTIVES To synthesize end-user and professional user perspectives and experiences with low-complexity nucleic acid amplification tests (NAATs) for detection of tuberculosis and tuberculosis drug resistance; and to identify implications for effective implementation and health equity. SEARCH METHODS We searched MEDLINE, Embase, CINAHL, PsycInfo and Science Citation Index Expanded databases for eligible studies from 1 January 2007 up to 20 October 2021. We limited all searches to 2007 onward because the development of Xpert MTB/RIF, the first rapid molecular test in this review, was completed in 2009. SELECTION CRITERIA We included studies that used qualitative methods for data collection and analysis, and were focused on perspectives and experiences of users and potential users of low-complexity NAATs to diagnose tuberculosis and drug-resistant tuberculosis. NAATs included Xpert MTB/RIF, Xpert MTB/RIF Ultra, Xpert MTB/XDR, and the Truenat assays. Users were people with presumptive or confirmed tuberculosis and drug-resistant tuberculosis (including multidrug-resistant (MDR-TB)) and their caregivers, healthcare providers, laboratory technicians and managers, and programme officers and staff; and were from any type of health facility and setting globally. MDR-TB is tuberculosis caused by resistance to at least rifampicin and isoniazid, the two most effective first-line drugs used to treat tuberculosis. DATA COLLECTION AND ANALYSIS We used a thematic analysis approach for data extraction and synthesis, and assessed confidence in the findings using GRADE CERQual approach. We developed a conceptual framework to illustrate how the findings relate. MAIN RESULTS We found 32 studies. All studies were conducted in low- and middle-income countries. Twenty-seven studies were conducted in high-tuberculosis burden countries and 21 studies in high-MDR-TB burden countries. Only one study was from an Eastern European country. While the studies covered a diverse use of low-complexity NAATs, in only a minority of studies was it used as the initial diagnostic test for all people with presumptive tuberculosis. We identified 18 review findings and grouped them into three overarching categories. Critical aspects users value People with tuberculosis valued reaching diagnostic closure with an accurate diagnosis, avoiding diagnostic delays, and keeping diagnostic-associated cost low. Similarly, healthcare providers valued aspects of accuracy and the resulting confidence in low-complexity NAAT results, rapid turnaround times, and keeping cost to people seeking a diagnosis low. In addition, providers valued diversity of sample types (for example, gastric aspirate specimens and stool in children) and drug resistance information. Laboratory professionals appreciated the improved ease of use, ergonomics, and biosafety of low-complexity NAATs compared to sputum microscopy, and increased staff satisfaction. Challenges reported to realizing those values People with tuberculosis and healthcare workers were reluctant to test for tuberculosis (including MDR-TB) due to fears, stigma, or cost concerns. Thus, low-complexity NAAT testing is not implemented with sufficient support or discretion to overcome barriers that are common to other approaches to testing for tuberculosis. Delays were reported at many steps of the diagnostic pathway owing to poor sample quality; difficulties with transporting specimens; lack of sufficient resources; maintenance of low-complexity NAATs; increased workload; inefficient work and patient flows; over-reliance on low-complexity NAAT results in lieu of clinical judgement; and lack of data-driven and inclusive implementation processes. These challenges were reported to lead to underutilization. Concerns for access and equity The reported concerns included sustainable funding and maintenance and equitable use of resources to access low-complexity NAATs, as well as conflicts of interest between donors and people implementing the tests. Also, lengthy diagnostic delays, underutilization of low-complexity NAATs, lack of tuberculosis diagnostic facilities in the community, and too many eligibility restrictions hampered access to prompt and accurate testing and treatment. This was particularly the case for vulnerable groups, such as children, people with MDR-TB, or people with limited ability to pay. We had high confidence in most of our findings. AUTHORS' CONCLUSIONS Low-complexity diagnostics have been presented as a solution to overcome deficiencies in laboratory infrastructure and lack of skilled professionals. This review indicates this is misleading. The lack of infrastructure and human resources undermine the added value new diagnostics of low complexity have for recipients and providers. We had high confidence in the evidence contributing to these review findings. Implementation of new diagnostic technologies, like those considered in this review, will need to tackle the challenges identified in this review including weak infrastructure and systems, and insufficient data on ground level realities prior and during implementation, as well as problems of conflicts of interest in order to ensure equitable use of resources.
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Affiliation(s)
- Nora Engel
- Department of Health, Ethics & Society, School of Public Health and Primary Care (CAPHRI), Maastricht University, Maastricht, Netherlands
| | - Eleanor A Ochodo
- Centre for Evidence-based Health Care, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Bey-Marrié Schmidt
- School of Public Health, University of the Western Cape, Cape Town, South Africa
| | - Ricky Janssen
- Department of Health, Ethics & Society, School of Public Health and Primary Care (CAPHRI), Maastricht University, Maastricht, Netherlands
| | - Karen R Steingart
- Honorary Research Fellow, Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Sandy Oliver
- EPPI-Centre, Social Science Research Unit, UCL Institute of Education, University College London, London, UK
- Africa Centre for Evidence, Faculty of Humanities, University of Johannesburg, Johannesburg, South Africa
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Iem V, Chittamany P, Suthepmany S, Siphanthong S, Somphavong S, Kontogianni K, Dodd J, Khan JAM, Dominguez J, Wingfield T, Creswell J, Cuevas LE. Pooling sputum for Xpert MTB/RIF and Xpert Ultra testing during the Covid-19 pandemic in Lao People's Democratic Republic. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000116. [PMID: 36962200 PMCID: PMC10022270 DOI: 10.1371/journal.pgph.0000116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/19/2022] [Indexed: 11/18/2022]
Abstract
The global Covid-19 pandemic has limited access to molecular TB diagnostics and National Programmes are struggling to maintain essential services. The pooling method (testing several samples together) could reduce the number of cartridges and staff time needed for TB diagnosis but has not been tested within the pandemic. We conducted two independent cross-sectional surveys. Pools composed of four sputum samples were tested using either Xpert-MTB/RIF or Xpert-Ultra. Pooled and individual results were compared to determine the level of agreement. Each survey included 840 participants and 210 pools. In the Xpert MTB/RIF survey, 77/81 (sensitivity 95.1%, 95%CI 87.8%-98.6%) pools containing ≥1 positive sample tested MTB-positive and 4/81 (4.9%, 95%CI 1.4%-12.2%) tested MTB-negative. All 129/129 pools containing MTB-negative samples tested MTB-negative (specificity 100%, 95%CI 97.2%-100%), with 98.1% agreement (Kappa: 0.959). In the Xpert-Ultra survey, 70/70 (sensitivity 100%, 95%CI 94.9%-100%) pools containing ≥ 1 MTB-positive sample tested MTB-positive and 140/140 (specificity 100%, 95%CI 97.4%-100%) pools containing only MTB-negative samples tested MTB-negative, with 100% agreement (Kappa: 1). Pooled testing with Xpert-MTB/RIF and Xpert-Ultra saved 38.3% and 41.7% (322/840 and 350/840, respectively) in cartridge costs alone. The pooling method with Xpert-MTB/RIF and Xpert-Ultra has similar performance to individual testing and can reduce the number of cartridges needed. These efficiencies can facilitate maintenance of stocks and sustain essential services as countries face difficulties for laboratory procurement during the pandemic and will provide cost and time savings post-pandemic.
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Affiliation(s)
- Vibol Iem
- National Tuberculosis Control Center, Vientiane, Lao People’s Democratic Republic
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Phonenaly Chittamany
- National Tuberculosis Control Center, Vientiane, Lao People’s Democratic Republic
| | - Sakhone Suthepmany
- National Tuberculosis Control Center, Vientiane, Lao People’s Democratic Republic
| | | | - Silaphet Somphavong
- Center of Infectiology Lao Christophe Mérieux, Vientiane, Lao People’s Democratic Republic
| | | | - James Dodd
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Jahangir Akber Mahmud Khan
- University of Gothenburg, Health Economics and Policy Unit, School of Public Health and Community Medicine, Gothenburg, Sweden
| | - Jose Dominguez
- Institut d’Investigació Germans Trias i Pujol, CIBER Enfermedades Respiratorias, and Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Tom Wingfield
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- WHO Collaborating Centre for Tuberculosis and Social Medicine, Department of Global Public Health, Karolinska Institutet, Solna, Sweden
| | - Jacob Creswell
- Stop TB Partnership, Innovations and Grants, Geneva, Switzerland
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Li Y, Jiao M, Liu Y, Ren Z, Li A. Application of Metagenomic Next-Generation Sequencing in Mycobacterium tuberculosis Infection. Front Med (Lausanne) 2022; 9:802719. [PMID: 35433724 PMCID: PMC9010669 DOI: 10.3389/fmed.2022.802719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The fight against Mycobacterium tuberculosis (MTB) has been going on for thousands of years, while it still poses a threat to human health. In addition to routine detections, metagenomic next-generation sequencing (mNGS) has begun to show presence as a comprehensive and hypothesis-free test. It can not only detect MTB without isolating specific pathogens but also suggest the co-infection pathogens or underlying tumor simultaneously, which is of benefit to assist in comprehensive clinical diagnosis. It also shows the potential to detect multiple drug resistance sites for precise treatment. However, considering the cost performance compared with conventional assays (especially Xpert MTB/RIF), mNGS seems to be overqualified for patients with mild and typical symptoms. Technology optimization of sequencing and analyzing should be conducted to improve the positive rate and broaden the applicable fields.
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Affiliation(s)
- Yaoguang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mengfan Jiao
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Zhigang Ren,
| | - Ang Li
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Ang Li,
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Wakode P, Siddaiah N, Manjunath N, Bahubali VKH. GeneXpert: A Rapid and Supplementary Diagnostic Tool for Tuberculous Meningitis, Experience from Tertiary Neurocenter. J Neurosci Rural Pract 2022; 13:204-210. [PMID: 35694081 PMCID: PMC9187421 DOI: 10.1055/s-0041-1742138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background
Tuberculous meningitis (TBM) is a highly lethal form of central nervous system tuberculosis (CNS TB) that causes high mortality and morbidity in children and adults. Nonspecific clinical presentation and fewer TB bacilli challenge clinicians resulting in delays in diagnosis and treatment.
Aim
This study aimed to evaluate the utility of GeneXpert alone and in combination with culture using 1 mL of cerebrospinal fluid (CSF) in a volume constraint situation.
Methods
A total of 125 clinically confirmed TBM and 110 non-TBM cases, comprised of both infectious and noninfectious diseases. were included in the study. Patient details including clinical signs and symptoms, CSF, and imaging data were collected from the case records. CSF samples were obtained from all the patients and were tested by the mycobacterial culture method and GeneXpert test. The performance of both the tests was statistically calculated and reported in the form of sensitivity and specificity.
Results
Out of 125 TBM cases, 40 were detected positive by culture and 26 by GeneXpert. All 110 non-TBM cases were identified negative by both methods. The sensitivity and specificity of GeneXpert in comparison with culture were 27 and 100%, respectively. The culture was found to be more sensitive (32%) than GeneXpert. But the assay was able to detect a considerable number of clinically confirmed culture-negative TBM cases.
Conclusion
GeneXpert is a rapid test and including this as an adjunctive test along with the culture in routine clinical practice can improve the diagnosis of TBM in volume constraint scenario.
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Affiliation(s)
- Priyanka Wakode
- Department of Neuromicrobiology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Nagarathna Siddaiah
- Department of Neuromicrobiology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Netravathi Manjunath
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
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Rahman SMM, Ather MF, Nasrin R, Hoque MA, Khatun R, Rahman T, Uddin MKM, Ahmed S, Banu S. Performance of WHO-Endorsed Rapid Tests for Detection of Susceptibility to First-Line Drugs in Patients with Pulmonary Tuberculosis in Bangladesh. Diagnostics (Basel) 2022; 12:diagnostics12020410. [PMID: 35204501 PMCID: PMC8870910 DOI: 10.3390/diagnostics12020410] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/05/2022] [Accepted: 01/25/2022] [Indexed: 12/10/2022] Open
Abstract
The fast and accurate detection of susceptibility in drugs is a major challenge for a successful tuberculosis (TB) control programme. This study evaluated the performance of WHO-endorsed rapid diagnostic tools, such as BACTEC MGIT 960 SIRE (MGIT SIRE), GenoType MTBDRplus (MTBDRplus) and Xpert MTB/RIF (Xpert), for detecting susceptibility to first-line anti-TB drugs among pulmonary TB patients in Bangladesh. A total of 825 sputum samples with results from drug susceptibility testing (DST) against first-line anti-TB drugs in the MGIT SIRE, MTBDRplus and Xpert assays were evaluated and compared with the gold standard proportion susceptibility method of the Lowenstein–Jensen (LJ) medium. The overall sensitivities of MGIT SIRE were 97.6%, 90.0%, 61.3% and 44.9%, while specificities were 89.9%, 94.5%, 91.3% and 92.2% for detection of susceptibility to isoniazid (INH), rifampicin (RIF), streptomycin (STR) and ethambutol (EMB), respectively. For MTBDRplus, the sensitivities were 88.0% and 88.7%, and the specificities were 97.4% and 97.8% for the detection of susceptibility to INH and RIF, respectively. Xpert demonstrated a sensitivity and specificity of 94.8% and 99.5%, respectively, for the detection of RIF susceptibility. All tests performed significantly better in retreated TB patients compared with primary TB cases. For detection of RIF and INH susceptibility, all three assays showed almost perfect agreement with the LJ method, although MGIT SIRE exhibited low agreement for STR and EMB. Considering the high performance, shorter turnaround time and ease of use, molecular-based approaches Xpert and MTBDRplus can be widely implemented throughout the country for the rapid detection of drug-resistant TB.
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Simieneh A, Tadesse M, Kebede W, Gashaw M, Abebe G. Combination of Xpert® MTB/RIF and DetermineTM TB-LAM Ag improves the diagnosis of extrapulmonary tuberculosis at Jimma University Medical Center, Oromia, Ethiopia. PLoS One 2022; 17:e0263172. [PMID: 35113917 PMCID: PMC8812938 DOI: 10.1371/journal.pone.0263172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 01/14/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Ethiopia is one of the high burden countries for extrapulmonary tuberculosis (EPTB); however, the prompt diagnosis of EPTB remains challenging. This study is aimed to evaluate the diagnostic performance of Xpert MTB/RIF and DetermineTM TB-LAM Ag (TB-LAM) for the prompt diagnosis of EPTB in Ethiopia. METHODS A total of 147 presumptive EPTB patients, including 23 HIV- positive participants were enrolled. Extra-pulmonary samples were collected from all presumptive EPTB cases and tested for Mycobacterium tuberculosis complex (MTBC) using fluorescent microscopy, Xpert MTB/RIF, and culture. Additionally, urine samples were also collected from 126 participants and were tested by DetermineTM TB-LAM Ag (Alere Inc, Waltham, USA). The Sensitivity and specificity of Xpert and TB- LAM tests were calculated by comparing with a composite reference standard (CRS), which comprises smear microscopy, culture and response to empirical anti-TB treatment. RESULTS Of 147 patients, 23 (15.6%) were confirmed EPTB cases (culture-positive), 14 (9.5%) were probable EPTB (clinically, radiologically or cytologically positive and received anti-TB treatment with good response), and 110 (74.8%) were classified as "non- TB" cases. Compared to the composite reference standard (CRS), the overall sensitivity and specificity of Xpert MTB/RIF were 43.2% and 100%, respectively with the highest sensitivity for Lymph node aspirate (85.7%) and lower sensitivity for pleural fluid (14.3%) and 100% specificity for all specimen types. The sensitivity and specificity of TB-LAM were 33.3% and 94.4% respectively with the highest sensitivity for HIV co-infected participants (83.3%). The sensitivity of the combination of Xpert MTB/RIF and TB-LAM tests regardless of HIV status was 61.1% whereas the sensitivity was improved to 83.3% for HIV-positive cases. CONCLUSION TB-LAM alone has low sensitivity for EPTB diagnosis; however, the combination of TB-LAM and Xpert MTB/RIF improves the diagnosis of EPTB particularly for countries with high EPTB and HIV cases.
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Affiliation(s)
- Asnake Simieneh
- Mycobacteriology Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
- Department of Medical Laboratory Sciences, Mizan-Tepi University, Mizan, Ethiopia
| | - Mulualem Tadesse
- Mycobacteriology Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Wakjira Kebede
- Mycobacteriology Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Mulatu Gashaw
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Gemeda Abebe
- Mycobacteriology Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
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Dastgir G, Majeed MI, Nawaz H, Rashid N, Raza A, Ali MZ, Shakeel M, Javed M, Ehsan U, Ishtiaq S, Fatima R, Abdulraheem A. Surface-enhanced Raman spectroscopy of polymerase chain reaction (PCR) products of Rifampin resistant and susceptible tuberculosis patients. Photodiagnosis Photodyn Ther 2022; 38:102758. [DOI: 10.1016/j.pdpdt.2022.102758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 10/19/2022]
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