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Leo S, Narasimhan M, Rathinam S, Banerjee A. Biomarkers in diagnosing and therapeutic monitoring of tuberculosis: a review. Ann Med 2024; 56:2386030. [PMID: 39097795 PMCID: PMC11299445 DOI: 10.1080/07853890.2024.2386030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/06/2024] [Accepted: 06/12/2024] [Indexed: 08/05/2024] Open
Abstract
Tuberculosis (TB) continues to pose a significant health challenge worldwide, emphasizing the importance of prompt diagnosis and efficient monitoring of treatment outcomes for effective disease control. Biomarkers have become increasingly important in the realm of TB diagnoses and treatment. The objective of this comprehensive review is to examine the present state of biomarkers employed in the diagnosis of TB, monitoring the response to treatment, and predicting treatment outcomes. In this study, we undertake a comprehensive examination of the diverse biomarkers utilized in TB diagnoses, spanning molecular, immunological, and other novel methodologies. Furthermore, we examine the potential of biomarkers in the context of therapeutic monitoring, assessment of treatment effectiveness, and anticipation of drug resistance. Additionally, this paper presents future prospects regarding the utilization of biomarkers in the therapy of tuberculosis.
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Affiliation(s)
- Sneha Leo
- Department of Respiratory Medicine, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Meenakshi Narasimhan
- Department of Respiratory Medicine, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Sridhar Rathinam
- Department of Respiratory Medicine, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - Antara Banerjee
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
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Nasrin R, Uddin MKM, Kabir SN, Rahman T, Biswas S, Hossain A, Rahman SMM, Ahmed S, Pouzol S, Hoffmann J, Banu S. Xpert MTB/RIF Ultra for the rapid diagnosis of extrapulmonary tuberculosis in a clinical setting of high tuberculosis prevalence country and interpretation of 'trace' results. Tuberculosis (Edinb) 2024; 145:102478. [PMID: 38218133 DOI: 10.1016/j.tube.2024.102478] [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: 10/13/2023] [Revised: 12/12/2023] [Accepted: 01/06/2024] [Indexed: 01/15/2024]
Abstract
To evaluate the diagnostic performance of Xpert MTB/RIF Ultra (Ultra) for the diagnosis of extrapulmonary tuberculosis (EPTB) from different types of extrapulmonary specimens in comparison with culture and composite microbiological reference standard (CRS). A total of 240 specimens were prospectively collected from presumptive EPTB patients between July 2021-January 2022 and tested by Ultra, Xpert, culture and acid-fast bacilli (AFB) smear microscopy. Out of 240 specimens, 35.8 %, 20.8 %, 11.3 %, and 7.1 % were detected as Mycobacterium tuberculosis complex by Ultra, Xpert, culture and AFB microscopy, respectively. An additional 15.0 % cases were detected by Ultra compared to Xpert MTB/RIF (Xpert) assay. A total of 28 (11.7 %) cases were identified as 'trace' category by Ultra with indeterminate rifampicin resistance result; of which 36.4 % were clinically confirmed as EPTB. Compared to culture, the sensitivity and specificity of Ultra and Xpert were 100 % and 72.3 %; 92.6 % and 88.3 %, respectively. In comparison with CRS, these were respectively: 98.9 % and 100 %; 57.5 % and 100 %. For individual category of specimens, sensitivity of Ultra was 100 % with varying specificity. We found that Ultra was highly sensitive for the rapid diagnosis of EPTB and has extensive potential over current diagnostics in high TB burden countries, but 'trace' results should be interpreted with caution.
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Affiliation(s)
- Rumana Nasrin
- Infectious Diseases Division, Icddr,b, Dhaka, 1212, Bangladesh
| | | | - Sk Nazmul Kabir
- Infectious Diseases Division, Icddr,b, Dhaka, 1212, Bangladesh
| | - Tanjina Rahman
- Infectious Diseases Division, Icddr,b, Dhaka, 1212, Bangladesh
| | - Samanta Biswas
- Infectious Diseases Division, Icddr,b, Dhaka, 1212, Bangladesh
| | - Aazia Hossain
- Infectious Diseases Division, Icddr,b, Dhaka, 1212, Bangladesh
| | | | - Shahriar Ahmed
- Infectious Diseases Division, Icddr,b, Dhaka, 1212, Bangladesh
| | - Stephane Pouzol
- Scientific and Medical Department, Fondation Mérieux (Lyon), France
| | | | - Sayera Banu
- Infectious Diseases Division, Icddr,b, Dhaka, 1212, Bangladesh.
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Bouzouita I, Ghariani A, Dhaou KB, Jemaeil S, Essaalah L, Bejaoui S, Draoui H, El Marzouk N, Mehiri E, Slim-Saidi L. Usefulness of Xpert MTB/RIF Ultra for rapid diagnosis of extrapulmonary tuberculosis in Tunisia. Sci Rep 2024; 14:2217. [PMID: 38278853 PMCID: PMC10817909 DOI: 10.1038/s41598-024-52130-3] [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: 06/17/2023] [Accepted: 01/14/2024] [Indexed: 01/28/2024] Open
Abstract
Extrapulmonary tuberculosis (EPTB) remains a challenging diagnosis. The purpose of this study was to assess the accuracy of Xpert MTB/RIF Ultra (Cepheid, USA) for rapid diagnosis of EPTB in Tunisia. Eight hundred and forty-seven extrapulmonary samples collected from 2017 to 2021, were subjected to Xpert MTB/RIF Ultra. Microscopy and culture were performed for all the specimens. The accuracy of Xpert Ultra was evaluated in comparison to the culture. Xpert Ultra diagnosed EPTB with a global sensitivity of 80.66% (74.3-85.75) and specificity of 70.87% (67.31-74.20). The molecular test was most accurate when performed in cerebrospinal fluids, bones and joints and cutaneous specimens showing a sensitivity of 100% and a specificity ranging from 70.60 to 91.11%. In lymph node samples comprising aspirates and biopsies, the sensitivity of Xpert Ultra was high 87.50% (77.23-93.53), however, the specificity was 51.08% (44.67-57.46). For pleural samples, the Xpert Ultra sensitivity was 77.50% (68.34-84.68) ranging from 71.43 to 80% in pleural biopsies and fluids respectively. The specificity in all pleural specimens was 79.56% (74.40-83.91). Xpert Ultra showed promise in the diagnosis of EPTB. The performances varied according to the site of the disease. The test may be more valuable if used in combination with other diagnostic modalities.
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Affiliation(s)
- Imen Bouzouita
- National Reference Laboratory for Mycobacteria, LR19SP02, Abderahmane Mami pneumology hospital, Rue de l'hôpital, 2080, Ariana, Tunisia.
- Faculty of Mathematical, Physical and Natural Sciences of Tunis, University of Tunis El Manar, Campus Universitaire El Manar, 1068, Tunis, Tunisia.
| | - Asma Ghariani
- National Reference Laboratory for Mycobacteria, LR19SP02, Abderahmane Mami pneumology hospital, Rue de l'hôpital, 2080, Ariana, Tunisia
- Faculty of Pharmacy, University of Monastir, Rue Ibn Sina 5000, Monastir, Tunisia
| | - Khouloud Ben Dhaou
- National Reference Laboratory for Mycobacteria, LR19SP02, Abderahmane Mami pneumology hospital, Rue de l'hôpital, 2080, Ariana, Tunisia
- Faculty of Pharmacy, University of Monastir, Rue Ibn Sina 5000, Monastir, Tunisia
| | - Sabrine Jemaeil
- National Reference Laboratory for Mycobacteria, LR19SP02, Abderahmane Mami pneumology hospital, Rue de l'hôpital, 2080, Ariana, Tunisia
| | - Leila Essaalah
- National Reference Laboratory for Mycobacteria, LR19SP02, Abderahmane Mami pneumology hospital, Rue de l'hôpital, 2080, Ariana, Tunisia
| | - Sana Bejaoui
- National Reference Laboratory for Mycobacteria, LR19SP02, Abderahmane Mami pneumology hospital, Rue de l'hôpital, 2080, Ariana, Tunisia
| | - Henda Draoui
- National Reference Laboratory for Mycobacteria, LR19SP02, Abderahmane Mami pneumology hospital, Rue de l'hôpital, 2080, Ariana, Tunisia
| | - Naceur El Marzouk
- National Reference Laboratory for Mycobacteria, LR19SP02, Abderahmane Mami pneumology hospital, Rue de l'hôpital, 2080, Ariana, Tunisia
| | - Emna Mehiri
- National Reference Laboratory for Mycobacteria, LR19SP02, Abderahmane Mami pneumology hospital, Rue de l'hôpital, 2080, Ariana, Tunisia
- Faculty of Pharmacy, University of Monastir, Rue Ibn Sina 5000, Monastir, Tunisia
| | - Leila Slim-Saidi
- National Reference Laboratory for Mycobacteria, LR19SP02, Abderahmane Mami pneumology hospital, Rue de l'hôpital, 2080, Ariana, Tunisia
- Faculty of Pharmacy, University of Monastir, Rue Ibn Sina 5000, Monastir, Tunisia
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Zahid QUA, Khursheed N, Adnan F, Zafar A. Concordance and discordance of GeneXpert MTB/RIF and conventional culture method for diagnosis of Extra-Pulmonary Tuberculosis at a tertiary care hospital in Pakistan. Pak J Med Sci 2024; 40:S64-S69. [PMID: 38328643 PMCID: PMC10844911 DOI: 10.12669/pjms.40.2(icon).8967] [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: 10/14/2023] [Revised: 10/16/2023] [Accepted: 11/12/2023] [Indexed: 02/09/2024] Open
Abstract
Objective To identify concordance and discordance between GeneXpert MTB/RIF assay and gold standard bacteriologic culture for the diagnosis of Mycobacterium tuberculosis (MTB) in Extra-Pulmonary tuberculosis (EPTB) specimens in our region. Methods This is a retrospective cross-sectional study conducted at the Indus Hospital and Health Network. Data from 1st January, 2020 to 31st December, 2021 was analyzed. A total of 1499 EPTB specimens were included for which GeneXpert was requested along with acid-fast bacteria (AFB) culture from the same specimen. Specimens were processed according to specimen type following standard operating procedures of the laboratory. Fluorescent staining was performed on all specimens along with bacteriologic culture. The GeneXpert MTB/RIF assay was carried out in exact accordance with the manufacturer's instructions. Results Out of 1499 EPTB specimens, 1370 (91.39%) specimens exhibited concordance between GeneXpert and conventional culture method, while 129 (8.60%) specimens showed discordance. GeneXpert exhibited sensitivity and specificity of 69.4% and 94.3% respectively in comparison to culture. Conclusion GeneXpert sensitivity for the diagnosis of EPTB varied with the site involved. Lower sensitivity was observed in ascitic and pleural fluids as compared to higher sensitivity observed among urine samples and pus aspirates. However, given the quick turnaround time and ease of use, it is a helpful tool in the diagnosis of EPTB when utilized in the appropriate clinical context. Caution is advised while interpreting negative GeneXpert results in endemic settings and should be interpreted along with other supporting clinical and diagnostic features.
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Affiliation(s)
- Qurat-ul-Ain Zahid
- Dr. Qurat-ul-Ain Zahid, Department of Pathology, Section of Microbiology Indus Hospital and Health Network, Karachi, Pakistan
| | - Nazia Khursheed
- Dr. Nazia Khursheed, FCPS. Department of Pathology, Section of Microbiology Indus Hospital and Health Network, Karachi, Pakistan
| | - Fareeha Adnan
- Dr. Fareeha Adnana, FCPS. Department of Pathology, Section of Microbiology Indus Hospital and Health Network, Karachi, Pakistan
| | - Adeel Zafar
- Dr. Adeel Zafar, Department of Pathology, Section of Microbiology Indus Hospital and Health Network, Karachi, Pakistan
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Bekoulis T, Christodoulou P, Dogramatzis K, Markopoulou E, Antonogiannakis E, Kokkinakis E, Apostolopoulos AP, Manimanaki A. The Need for Persistence in the Diagnosis of Mycobacterium Tuberculosis Mono-arthritis: A Unique Case Presentation. J Long Term Eff Med Implants 2024; 34:35-40. [PMID: 37938203 DOI: 10.1615/jlongtermeffmedimplants.2022044642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Although tuberculosis (TB) is considered to be a common disease confined to undeveloped or developing countries, it may also appear in countries that accept great migrant influx from endemic areas. In terms of the skeletal system, it can be involved in 1-6% of tuberculosis patients while the knee joint is the third most frequently affected site after spine and hip. Given that systemic symptoms are present in only one-third of patients with skeletal tuberculosis and secondary septic arthritis, TB is often indolent and diagnosis can hence be missed or delayed. As a result, a high index of suspicion is imperative. Here, we aim to report a case of mono-arthritis caused by Mycobacterium tuberculosis in a native 77-year-old man who was suffering from low-grade knee pain for six months and despite multiple presentations to the Accident and Emergency department, diagnosis had not been established.
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Affiliation(s)
- T Bekoulis
- Trauma and Orthopedic Department, Inverclyde Royal Hospital, Royal Alexandra Hospital Greater Glasgow and Clyde, NHS, Glasgow, UK
| | - P Christodoulou
- Trauma and Orthopaedic Department, St. George Hospital, Chania, Greece; cTrauma and Orthopaedic Department, Great Western Hospital, NHS, UK
| | - K Dogramatzis
- Trauma and Orthopaedic Department, Great Western Hospital, NHS, UK
| | - E Markopoulou
- Commanding Officer, Special Operation Forces Training Centre, Athens, Greece
| | | | - E Kokkinakis
- Trauma and Orthopaedic Department, Royal Alexandra Hospital, NHS, UK
| | - Alexandros P Apostolopoulos
- Trauma and Orthopaedic Department, "Korgialenio-Benakio" Hellenic Red Cross Hospital, Athens, Greece; Trauma and Orthopaedic Department, Ealing Hospital, North West University Healthcare NHS Trust, London, United Kingdom
| | - A Manimanaki
- Trauma and Orthopaedic Department, St. George Hospital, Chania, Greece
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Makhubela PCK, Rohwer ER, Naudé Y. Detection of tuberculosis-associated compounds from human skin by GCxGC-TOFMS. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1231:123937. [PMID: 37995549 DOI: 10.1016/j.jchromb.2023.123937] [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: 07/07/2023] [Revised: 09/28/2023] [Accepted: 10/10/2023] [Indexed: 11/25/2023]
Abstract
Tuberculosis (TB) remains a global health concern. This study aimed to investigate the potential of human skin volatile organic compounds (VOCs) as prospective biomarkers for TB diagnosis. It employed a non-invasive approach using a wearable silicone rubber band for VOC sampling, comprehensive gas chromatography - time of flight mass spectrometry (GCxGC-TOFMS), and chemometric techniques. Both targeted and untargeted biochemical screening was utilized to explore biochemical differences between healthy individuals and those with TB infection. Results confirmed a correlation between compounds found in this study, and those reported for TB from other biofluids. In a comparison to known TB-associated compounds from other biofluids our analysis established the presence of 27 of these compounds emanating from human skin. Additionally, 16 previously unreported compounds were found as potential biomarkers. The diagnostic ability of the VOCs selected by statistical methods was investigated using predictive modelling techniques. Artificial neural network multi-layered perceptron (ANN) yielded two compounds, 1H-indene, 2,3 dihydro-1,1,3-trimethyl-3-phenyl; and heptane-3-ethyl-2-methyl, as the most discriminatory, and could differentiate between TB-positive (n = 15) and TB-negative (n = 23) individuals with an area under the receiver operating characteristic curve (AUROC) of 92 %, a sensitivity of 100 % and a specificity of 94 % for six targeted features. For untargeted analysis, ANN assigned 3-methylhexane as the most discriminatory between TB-positive and TB- negative individuals. An AUROC of 98.5 %, a sensitivity of 83 %, and a specificity of 88 % were obtained for 16 untargeted features as chosen by high performance variable selection. The obtained values compare highly favourable to alternative diagnostic methods such as breath analysis and GeneXpert. Consequently, human skin VOCs hold considerable potential as a TB diagnostic screening test.
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Affiliation(s)
- Portia C K Makhubela
- Department of Chemistry, University of Pretoria, Private Bag X20, Hatfield, 0028 Pretoria, South Africa
| | - Egmont R Rohwer
- Department of Chemistry, University of Pretoria, Private Bag X20, Hatfield, 0028 Pretoria, South Africa
| | - Yvette Naudé
- Department of Chemistry, University of Pretoria, Private Bag X20, Hatfield, 0028 Pretoria, South Africa.
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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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Ealand CS, Sewcharran A, Peters JS, Gordhan BG, Kamariza M, Bertozzi CR, Waja Z, Martinson NA, Kana BD. The performance of tongue swabs for detection of pulmonary tuberculosis. Front Cell Infect Microbiol 2023; 13:1186191. [PMID: 37743867 PMCID: PMC10512057 DOI: 10.3389/fcimb.2023.1186191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction Oral and/or tongue swabs have demonstrated ability to detect Mycobacterium tuberculosis (Mtb) in adults with pulmonary tuberculosis (TB). Swabs provide useful alternative specimens for diagnosis of TB using molecular assays however, the diagnostic pickup by culture requires further improvement and development. Several studies identified the presence of differentially culturable tubercle bacilli (DCTB) populations in a variety of clinical specimens. These organisms do not grow in routine laboratory media and require growth factors in the form of culture filtrate (CF) from logarithmic phase cultures of Mtb H37Rv. Methods Herein, we compared the diagnostic performance of sputum and tongue swabs using Mycobacterial Growth Indicator Tube (MGIT) assays, Auramine smear, GeneXpert and DCTB assays supplemented with or without CF. Results From 89 eligible participants, 83 (93%), 66 (74%) and 79 (89%) were sputum positive by MGIT, smear and GeneXpert, respectively. The corresponding tongue swabs displayed a lower sensitivity with 39 (44%), 2 (2.0%) and 18 (20%) participants respectively for the same tests. We aimed to improve the diagnostic yield by utilizing DCTB assays. Sputum samples were associated with a higher positivity rate for CF-augmented DCTB at 82/89 (92%) relative to tongue swabs at 36/89 (40%). Similarly, sputum samples had a higher positivity rate for DCTB populations that were CF-independent at 64/89 (72%) relative to tongue swabs at 26/89 (29%). DCTB positivity increased significantly, relative to MGIT culture, for tongue swabs taken from HIV-positive participants. We next tested whether the use of an alternative smear stain, DMN-Trehalose, would improve diagnostic yield but noted no substantial increase. Discussion Collectively, our data show that while tongue swabs yield lower bacterial numbers for diagnostic testing, the use of growth supplementation may improve detection of TB particularly in HIV-positive people but this requires further interrogation in larger studies.
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Affiliation(s)
- Christopher S. Ealand
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Astika Sewcharran
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Julian S. Peters
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Bhavna G. Gordhan
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Mireille Kamariza
- Department of Biology, Stanford University, Stanford, CA, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
- Department of Chemistry, Stanford University, Stanford, CA, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Ziyaad Waja
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Neil A. Martinson
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University, Centre for Tuberculosis Research, Baltimore, MD, United States
| | - Bavesh D. Kana
- Department of Science and Innovation/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
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Dahiya B, Mehta N, Soni A, Mehta PK. Diagnosis of extrapulmonary tuberculosis by GeneXpert MTB/RIF Ultra assay. Expert Rev Mol Diagn 2023; 23:561-582. [PMID: 37318829 DOI: 10.1080/14737159.2023.2223980] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Diagnosis of extrapulmonary tuberculosis (EPTB) is an arduous task owing to different anatomical locations, unusual clinical presentations, and sparse bacillary load in clinical specimens. Although GeneXpert® MTB/RIF is a windfall in TB diagnostics including EPTB, it yields low sensitivities but high specificities in many EPTB specimens. To further improve the sensitivity of GeneXpert®, GeneXpert® Ultra, a fully nested real-time PCR targeting IS6110, IS1081 and rpoB (Rv0664) has been endorsed by the WHO (2017), wherein melt curve analysis is utilized to detect rifampicin-resistance (RIF-R). AREA COVERED We described the assay chemistry/work design of Xpert Ultra and evaluated its performance in several EPTB types, that is, TB lymphadenitis, TB pleuritis, TB meningitis, and so on, against the microbiological reference standard or composite reference standard. Notably, Xpert Ultra exhibited better sensitivities than Xpert, but mostly at the compensation of specificity values. Moreover, Xpert Ultra exhibited low false-negative and false-positive RIF-R results, compared with Xpert. We also detailed other molecular tests, that is, Truenat MTBTM/TruPlus, commercial real-time PCR, line probe assay, and so on, for EPTB diagnosis. EXPERT OPINION A combination of clinical features, imaging, histopathological findings, and Xpert Ultra are adequate for definite EPTB diagnosis so as to initiate an early anti-tubercular therapy.
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Affiliation(s)
- Bhawna Dahiya
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Neeru Mehta
- Department of Medical Electronics, Ambedkar Delhi Skill & Entrepreneurship University, Shakarpur, New Delhi, India
| | - Aishwarya Soni
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonipat, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
- Microbiology Department, Faculty of Allied Health Sciences, SGT University, Budhera, Gurgaon, India
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Echeverria G, Rueda V, Espinoza W, Rosero C, Zumárraga MJ, de Waard JH. First Case Reports of Nontuberculous Mycobacterial (NTM) Lung Disease in Ecuador: Important Lessons to Learn. Pathogens 2023; 12:pathogens12040507. [PMID: 37111393 PMCID: PMC10142742 DOI: 10.3390/pathogens12040507] [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: 02/09/2023] [Revised: 03/12/2023] [Accepted: 03/16/2023] [Indexed: 04/29/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) lung infections are often misdiagnosed as tuberculosis, which can lead to ineffective antibiotic treatments. In this report, we present three cases of NTM lung infections in Ecuador that were initially diagnosed and treated as tuberculosis based on the results of sputum smear microscopy. The patients, all male, included two immunocompetent individuals and one HIV-positive subject. Unfortunately, sputum culture was not initiated until late in the course of the disease and the cause of the lung infection, Mycobacterium avium complex (MAC), was only identified after the patients had either passed away or were lost to follow-up. These cases are the first documented cases of NTM lung infections in the English medical literature from Ecuador. We emphasize the importance of accurate diagnosis of NTM infections by culture and identification to species level. Sputum smear staining alone cannot differentiate between mycobacterial species, which can lead to misidentification and ineffective treatments. Additionally, reporting NTM pulmonary disease as a notifiable disease to national TB control programs is recommended to obtain accurate prevalence data. These data are critical in determining the importance of this public health problem and the necessary actions needed to address it.
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Affiliation(s)
- Gustavo Echeverria
- Instituto de Investigación en Zoonosis-CIZ, Universidad Central del Ecuador, Quito 170518, Ecuador
- Programa de Doctorado, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires C1063ACV, Argentina
- División Investigación y Desarrollo, BioGENA, Quito 170509, Ecuador
| | - Veronica Rueda
- Instituto de Investigación en Zoonosis-CIZ, Universidad Central del Ecuador, Quito 170518, Ecuador
| | - Wilson Espinoza
- Departamento de Tuberculosis, Hospital de Especialidades Eugenio Espejo, Quito 170401, Ecuador
| | - Carlos Rosero
- Departamento de Tuberculosis, Hospital de Especialidades Eugenio Espejo, Quito 170401, Ecuador
| | - Martín J Zumárraga
- Instituto de Agrobiotecnología y Biología Molecular, IABIMO, INTA-CONICET, Buenos Aires C1063ACV, Argentina
| | - Jacobus H de Waard
- Departamento de Tuberculosis, Instituto de Biomedicina "Jacinto Convit", Universidad Central de Venezuela, Caracas 1010, Venezuela
- One Health Research Group, Facultad de Ciencias de la Salud, Universidad de Las Américas (UDLA), Quito 180602, Ecuador
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11
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Nogueira BMF, Krishnan S, Barreto‐Duarte B, Araújo‐Pereira M, Queiroz ATL, Ellner JJ, Salgame P, Scriba TJ, Sterling TR, Gupta A, Andrade BB. Diagnostic biomarkers for active tuberculosis: progress and challenges. EMBO Mol Med 2022; 14:e14088. [PMID: 36314872 PMCID: PMC9728055 DOI: 10.15252/emmm.202114088] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB) is a leading cause of morbidity and mortality from a single infectious agent, despite being preventable and curable. Early and accurate diagnosis of active TB is critical to both enhance patient care, improve patient outcomes, and break Mycobacterium tuberculosis (Mtb) transmission cycles. In 2020 an estimated 9.9 million people fell ill from Mtb, but only a little over half (5.8 million) received an active TB diagnosis and treatment. The World Health Organization has proposed target product profiles for biomarker- or biosignature-based diagnostics using point-of-care tests from easily accessible specimens such as urine or blood. Here we review and summarize progress made in the development of pathogen- and host-based biomarkers for active TB diagnosis. We describe several unique patient populations that have posed challenges to development of a universal diagnostic TB biomarker, such as people living with HIV, extrapulmonary TB, and children. We also review additional limitations to widespread validation and utilization of published biomarkers. We conclude with proposed solutions to enhance TB diagnostic biomarker validation and uptake.
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Affiliation(s)
- Betânia M F Nogueira
- Programa de Pós‐graduação em Ciências da SaúdeUniversidade Federal da BahiaSalvadorBrazil,Instituto Couto MaiaSalvadorBrazil,Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil
| | - Sonya Krishnan
- Division of Infectious Diseases, Department of MedicineJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Beatriz Barreto‐Duarte
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil,Curso de MedicinaUniversidade Salvador (UNIFACS)SalvadorBrazil,Programa de Pós‐Graduação em Clínica MédicaUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil,Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil
| | - Mariana Araújo‐Pereira
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil,Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil,Faculdade de MedicinaUniversidade Federal da BahiaSalvadorBrazil
| | - Artur T L Queiroz
- Instituto Couto MaiaSalvadorBrazil,Center of Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil
| | - Jerrold J Ellner
- Department of Medicine, Centre for Emerging PathogensRutgers‐New Jersey Medical SchoolNewarkNJUSA
| | - Padmini Salgame
- Department of Medicine, Centre for Emerging PathogensRutgers‐New Jersey Medical SchoolNewarkNJUSA
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of PathologyUniversity of Cape TownCape TownSouth Africa
| | - Timothy R Sterling
- Division of Infectious Diseases, Department of MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Amita Gupta
- Division of Infectious Diseases, Department of MedicineJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Bruno B Andrade
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) InitiativeSalvadorBrazil,Curso de MedicinaUniversidade Salvador (UNIFACS)SalvadorBrazil,Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo MonizFundação Oswaldo CruzSalvadorBrazil,Faculdade de MedicinaUniversidade Federal da BahiaSalvadorBrazil,Curso de MedicinaFaculdade de Tecnologia e Ciências (FTC)SalvadorBrazil,Curso de MedicinaEscola Bahiana de Medicina e Saúde Pública (EBMSP)SalvadorBrazil
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12
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Comparative Performance of Line Probe Assay and GeneXpert in the Detection of Rifampicin Monoresistance in a TB-Endemic African Country. Antibiotics (Basel) 2022; 11:antibiotics11111489. [PMID: 36358145 PMCID: PMC9686643 DOI: 10.3390/antibiotics11111489] [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: 09/13/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
Rapid, accurate and reliable assays are required for timely detection of drug-resistant tuberculosis and early initiation of second-line TB treatment as well as to minimize transmission of resistant strains. This study assessed diagnostic performance characteristics of two rapid molecular assays, line probe assay (LPA) and GeneXpert (MTB/RIF), in the detection rifampicin monoresistance using the phenotypic proportion method on Lowenstein−Jensen media as the gold standard. This study involved a total of 357 isolates, 74 rifampicin-resistant and 283 rifampicin-susceptible, collected at the Central Tuberculosis Reference Laboratory (CTRL) in Dar es Salaam, Tanzania, between 2016 and 2019. Sensitivity, specificity and positive and negative predictive values were used to assess the performance characteristics of the two assays while kappa coefficient was used to determine agreement of test results. The receiver operating curve (ROC) was used to determine the discriminatory ability of the test in distinguishing resistant and susceptible TB isolates. Our results showed that GeneXpert had sensitivity, specificity and positive and negative predictive values of 93.2, 82.7, 58.5 and 97.9%, respectively; the corresponding performance for LPA was 86.5, 97.5, 90.1 and 96.5%, respectively. Compared with conventional phenotypic DST results, GeneXpert had a moderate agreement (kappa 0.621, p < 0.001), while LPA had high agreement (0.853, p < 0.001). LPA showed an accuracy of 95.2% compared to GeneXpert’s 84.9%. ROC curve depicted the ability of the tests to distinguish rifampicin-sensitive and rifampicin-resistant strains to be 87.9% for GeneXpert and 92.0% for LPA. Our results indicate the superiority of LPA over GeneXpert regarding detection of rifampicin monoresistance. However, logistic challenges such as longer turnaround time and need for skilled laboratory personnel may limit its use.
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13
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Burger Z, Aung HT, Seifert M, Mar TT, Harris V, Colman RE, Rodwell TC, Aung ST. Contributions of GeneXpert ® to TB diagnosis in Myanmar. Int J Tuberc Lung Dis 2022; 26:875-879. [PMID: 35996278 PMCID: PMC9423018 DOI: 10.5588/ijtld.22.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND: Xpert® MTB/RIF, a rapid, molecular TB diagnostic assay, can detect Mycobacterium tuberculosis and rifampin resistance directly from clinical sputum samples in <2 h with high sensitivity and specificity. The added diagnostic value of Xpert over smear microscopy at a national level in Myanmar has not been previously reported.METHODS: We evaluated 339,358 Xpert and demographic records captured from January 2015 to December 2018 as part of the Myanmar National TB Program Data Utilization and Connectivity Project to examine the additional diagnostic yield of Xpert relative to smear for the detection of M. tuberculosis for TB diagnosis in Myanmar, with a focus on people living with HIV (PLHIV) and sample type.RESULTS: Use of Xpert increased TB case detection by 40% compared to smear microscopy results. Among PLHIV, use of Xpert increased TB case detection by almost 100% compared to smear microscopy results.CONCLUSION: Xpert testing identified more patients with TB than smear microscopy alone, particularly in cohorts with significant proportions of PLHIV. The use of Xpert as a screening tool in countries with a high burden of TB could lead to significantly increased diagnosis of TB at a regional and national level.
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Affiliation(s)
- Z Burger
- University of California San Diego, La Jolla, CA, USA
| | - H T Aung
- Clinton Health Access Initiative, Yangon, Myanmar
| | - M Seifert
- University of California San Diego, La Jolla, CA, USA
| | - T T Mar
- Ministry of Health and Sports, Naypyitaw, Myanmar
| | - V Harris
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - R E Colman
- University of California San Diego, La Jolla, CA, USA
| | - T C Rodwell
- University of California San Diego, La Jolla, CA, USA
| | - S T Aung
- Ministry of Health and Sports, Naypyitaw, Myanmar
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14
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Systematic Evaluation of Line Probe Assays for the diagnosis of Tuberculosis and Drug-resistant Tuberculosis. Clin Chim Acta 2022; 533:183-218. [DOI: 10.1016/j.cca.2022.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/22/2022] [Accepted: 06/17/2022] [Indexed: 11/19/2022]
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15
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Mansfield M, McLaughlin AM, Roycroft E, Montgomery L, Keane J, Fitzgibbon MM, Rogers TR. Diagnostic Performance of Xpert MTB/RIF Ultra Compared with Predecessor Test, Xpert MTB/RIF, in a Low TB Incidence Setting: a Retrospective Service Evaluation. Microbiol Spectr 2022; 10:e0234521. [PMID: 35471095 PMCID: PMC9241712 DOI: 10.1128/spectrum.02345-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/06/2022] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to evaluate the performance of Xpert MTB/RIF Ultra (Ultra) compared with its predecessor, Xpert MTB/RIF (Xpert), in the diagnosis of tuberculosis (TB) in a low TB incidence country. Retrospective analysis was performed on 689 clinical samples received between 2015 and 2018, on which Xpert was performed, and on 715 samples, received between 2018 and 2020, on which Ultra was performed. Samples were pulmonary (n = 830) and extrapulmonary (n = 574) in nature, and a total of 264 were culture positive for Mycobacterium tuberculosis complex (MTBC). The diagnostic performance of both assays was analyzed using culture as the reference standard. The sensitivity of Ultra for culture positive (smear positive and smear negative) MTBC samples, was 93.2% (110/118) compared with 82.2% (120/146) for Xpert (P = 0.0078). In smear negative-culture positive samples, Ultra had a sensitivity of 74.2% (23/31) versus 36.11% (13/36) for Xpert (P = 0.0018). Specificity of both assays was comparable at 94.8% (566/597) for Ultra and 95.8% (520/543) for Xpert (P = 0.4475). The sensitivity of Ultra and Xpert assays among exclusively pulmonary samples was 95.3% (82/86) and 90.3% (84/93), respectively (P = 0.1955), and 87.5% (28/32) and 67.9% (36/53), respectively, among extrapulmonary samples (P = 0.0426). Ultra showed improved performance compared with Xpert in a low TB incidence setting, particularly in smear negative and extrapulmonary MTBC disease. The specificity of Ultra was lower than Xpert, however, this was not statistically significant. IMPORTANCE The study demonstrates the improved sensitivity of the Ultra compared with the Xpert, particularly in smear negative TB disease, for both pulmonary and extrapulmonary samples in a low TB incidence setting. Cycle threshold (Ct) value for both assays was found to positively correlate with time to TB culture positivity, suggesting that Ct and semiquantitative results could be used as indicators of sample MTBC bacillary burden, and thus, perhaps, of transmission potential. This may have implications for the designation of patient isolation precautions.
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Affiliation(s)
- Mary Mansfield
- Department of Clinical Microbiology, Trinity College Dublin, St James’s Hospital Campus, Dublin, Ireland
| | | | - Emma Roycroft
- Department of Clinical Microbiology, Trinity College Dublin, St James’s Hospital Campus, Dublin, Ireland
- Irish Mycobacteria Reference Laboratory, St. James’s Hospital, Dublin, Ireland
| | - Lorraine Montgomery
- Irish Mycobacteria Reference Laboratory, St. James’s Hospital, Dublin, Ireland
| | - Joseph Keane
- Department of Respiratory Medicine, St. James’s Hospital, Dublin, Ireland
| | - Margaret M. Fitzgibbon
- Department of Clinical Microbiology, Trinity College Dublin, St James’s Hospital Campus, Dublin, Ireland
- Irish Mycobacteria Reference Laboratory, St. James’s Hospital, Dublin, Ireland
| | - Thomas R. Rogers
- Department of Clinical Microbiology, Trinity College Dublin, St James’s Hospital Campus, Dublin, Ireland
- Irish Mycobacteria Reference Laboratory, St. James’s Hospital, Dublin, Ireland
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16
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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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17
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Yu W, Shen Y, Zhu P, Chen D. Head-to-head comparison of the efficacy of Xpert MTB/RIF Ultra and Xpert MTB/RIF for the diagnosis of tuberculous pleurisy: A systematic review and meta-analysis. Medicine (Baltimore) 2022; 101:e29363. [PMID: 35608435 PMCID: PMC9276415 DOI: 10.1097/md.0000000000029363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/08/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The aim of this study was to evaluate the diagnostic accuracy of Xpert MTB/RIF Ultra (Xpert Ultra) and Xpert MTB/RIF (Xpert) for the diagnosis of tuberculous pleurisy (TBP) head-to-head using meta-analysis method. METHODS On May 12, 2021, we searched multiple databases for reports that used Xpert Ultra and Xpert for TBP diagnosis head-to-head and screened eligible studies for inclusion. Accuracy of Xpert Ultra and Xpert were compared to that of the composite reference standard (CRS) and culture. When heterogeneity was evident, sources of heterogeneity were explored using subgroup analyses, sensitivity analysis, and meta-regression analyses. RESULTS Five articles met the inclusion criteria for meta-analysis. When results from different specimens or different reference standards were reported in the same article, we analyzed them as separate studies. Thus, 6 studies compared Xpert Ultra and Xpert with CRS, 5 studies compared Xpert Ultra and Xpert with culture. Pooled sensitivity and specificity of Xpert Ultra were 52% and 98% compared to CRS, and 82% and 77% compared to culture. Pooled sensitivity and specificity of Xpert were 22% and 99% compared to CRS, and 48% and 94% compared to culture. Significant heterogeneity in sensitivity was observed compared to CRS. CONCLUSION The sensitivity of Xpert Ultra was moderate but better than that of the Xpert; however, its specificity was lower. The role of Xpert Ultra and Xpert in the early and rapid diagnosis of TBP was limited.
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Affiliation(s)
- Wenfeng Yu
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Zhejiang Chinese Medicine and Western Medicine Integrated Hospital, Hangzhou, Zhejiang, China
| | - Yanqin Shen
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Zhejiang Chinese Medicine and Western Medicine Integrated Hospital, Hangzhou, Zhejiang, China
| | - Pengfei Zhu
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Zhejiang Chinese Medicine and Western Medicine Integrated Hospital, Hangzhou, Zhejiang, China
| | - Da Chen
- Department of Thoracic Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
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18
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Pradhan NN, Paradkar MS, Kagal A, Valvi C, Kinikar A, Khwaja S, Dhage R, Chandane J, Ithape M, Bendre M, Madewar R, Nadgeri V, Nijampurkar A, Jain D, Gupte N, Gupta A, Mave V, Dooley KE, Thakur KT. Performance of Xpert ® MTB/RIF and Xpert ® Ultra for the diagnosis of tuberculous meningitis in children. Int J Tuberc Lung Dis 2022; 26:317-325. [PMID: 35351236 PMCID: PMC9592112 DOI: 10.5588/ijtld.21.0388] [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: 01/01/2023] Open
Abstract
OBJECTIVE: To assess Xpert® MTB/RIF (Xpert) and Xpert® MTB/RIF Ultra (Ultra) performance in diagnosing pediatric tuberculous meningitis (TBM).METHODS: We conducted a study among children with suspected meningoencephalitis in Pune, India. Clinical, radiological, laboratory, and treatment data were analyzed to classify disease as definite, probable, possible or no TBM, using microbiologic or composite reference standards. We tested cerebrospinal fluid (CSF) either using Xpert or Ultra and estimated test performance characteristics.RESULTS: Of 341 participants, 149 (43.7%) were tested using Ultra and 192 (56.3%) with Xpert. Ultra had higher sensitivity (50% vs. 18%), lower specificity (91% vs. 99%), poor positive predictive value (PPV) (13% vs. 75%), and higher negative predictive value (NPV) (99% vs. 93%) than Xpert using the composite reference standard, with similar results by the microbiologic reference standard. Of 10 participants with trace positivity on Ultra, none met clinical TBM definitions.CONCLUSION: This is the first study to report on diagnostic performance of Ultra in pediatric TBM, which showed higher sensitivity and NPV than Xpert. For children presenting with nonspecific clinical features, Ultra is a promising diagnostic test. Further studies are required to define its optimal clinical use, including interpretation of trace positive results.
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Affiliation(s)
- N. N. Pradhan
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India;,Johns Hopkins India, Pune, India
| | - M. S. Paradkar
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India;,Johns Hopkins India, Pune, India
| | - A. Kagal
- BJ Government Medical College and Sassoon General Hospitals, Pune, India
| | - C. Valvi
- BJ Government Medical College and Sassoon General Hospitals, Pune, India
| | - A. Kinikar
- BJ Government Medical College and Sassoon General Hospitals, Pune, India
| | - S. Khwaja
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India
| | - R. Dhage
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India
| | - J. Chandane
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India
| | - M. Ithape
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India
| | - M. Bendre
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India
| | - R. Madewar
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India
| | - V. Nadgeri
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India
| | - A. Nijampurkar
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India;,Johns Hopkins India, Pune, India
| | - D. Jain
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India
| | - N. Gupte
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India;,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - A. Gupta
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - V. Mave
- BJ Government Medical College-Johns Hopkins Clinical Research Site, Pune, India;,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - K. E. Dooley
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - K. T. Thakur
- Department of Neurology, Columbia University Irving Medical Center and the New York Presbyterian Hospital, New York, NY, USA
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19
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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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20
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Mbelele PM, Sabiiti W, Heysell SK, Sauli E, Mpolya EA, Mfinanga S, Gillespie SH, Addo KK, Kibiki G, Sloan DJ, Mpagama SG. Use of a molecular bacterial load assay to distinguish between active TB and post-TB lung disease. Int J Tuberc Lung Dis 2022; 26:276-278. [PMID: 35197168 PMCID: PMC8886960 DOI: 10.5588/ijtld.21.0459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- P M Mbelele
- Kibong´oto Infectious Diseases Hospital, Sanya Juu, Siha, Kilimanjaro, Tanzania, Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - W Sabiiti
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, Scotland, UK
| | - S K Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - E Sauli
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - E A Mpolya
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - S Mfinanga
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania, National Institute for Medical Research (NIMR), Muhimbili Center, Dar es salaam, Tanzania
| | - S H Gillespie
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, Scotland, UK
| | - K K Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - G Kibiki
- Kibong´oto Infectious Diseases Hospital, Sanya Juu, Siha, Kilimanjaro, Tanzania, East African Health Research Commission (EAHRC), Bujumbura, Burundi
| | - D J Sloan
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, Scotland, UK
| | - S G Mpagama
- Kibong´oto Infectious Diseases Hospital, Sanya Juu, Siha, Kilimanjaro, Tanzania, Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
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21
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Grønningen E, Nanyaro M, Sviland L, Ngadaya E, Muller W, Torres L, Mfinanga S, Mustafa T. Improved diagnosis of extrapulmonary tuberculosis in adults with and without HIV in Mbeya, Tanzania using the MPT64 antigen detection test. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0001317. [PMID: 36962852 PMCID: PMC10021170 DOI: 10.1371/journal.pgph.0001317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022]
Abstract
Extrapulmonary tuberculosis (EPTB) in People Living with HIV (PLWHIV) is a diagnostic challenge. Our immunochemistry based MPT64 antigen detection test has shown improved sensitivity compared to current laboratory tests in the resource limited diagnostic setting. The aim of this study was to validate the implementability and diagnostic performance of the test in PLWHIV and HIV negative adults in a HIV endemic Tanzanian setting. Adult (>18 y) presumptive EPTB patients were prospectively enrolled at Mbeya Zonal Referral Hospital and followed to the end of treatment or until an alternative diagnosis was reached. Suspected sites of infection were sampled and were subject to routine diagnostics, GeneXpert MTB/RIF assay and the MPT64 test. The performance of the diagnostics tests was assessed using a composite reference standard that included clinical suspicion, mycobacterial culture, response to anti-tuberculosis (TB) therapy, cytological and radiological findings. Patients (N = 168) were categorized as 21 confirmed TB, 23 probable TB and 44 possible TB cases, 69 patients were categorized as non-TB cases and 11 were uncategorized. In the TB group, the three most common infections were adenitis (41%), peritonitis (19%) and pleuritis (14%). The TB and non-TB groups did not differ in HIV seropositivity (46% vs 42%) Among HIV negative and PLWHIV, the MPT64 test had a sensitivity of (91% vs 78%), specificity (75% vs 86%), positive predictive value (80% vs 88%), negative predictive value (89% vs 74%), and accuracy (84% vs 81%), respectively. Performance was not significantly reduced in PLWHIV, and sensitivity was higher than in the currently used tests, including the GeneXpert MTB/RIF assay. The MPT64 test improved the diagnosis of EPTB, irrespective of HIV status. The test performed better than currently used diagnostic test. The test was implementable in a tertiary level hospital with basic pathology services in a HIV endemic Tanzanian setting.
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Affiliation(s)
- Erlend Grønningen
- Department of Global Public Health and Primary Care, Centre for International Health, University of Bergen, Bergen, Vestland, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Vestland, Norway
| | - Marywinnie Nanyaro
- National Institute for Medical Research, Dar es Salaam, The United Republic of Tanzania
| | - Lisbet Sviland
- Faculty of Medicine, Department of Clinical Medicine, University of Bergen, Bergen, Vestland, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Vestland, Norway
| | - Esther Ngadaya
- National Institute for Medical Research, Dar es Salaam, The United Republic of Tanzania
| | - William Muller
- National Institute for Medical Research, Dar es Salaam, The United Republic of Tanzania
- Mbeya Zonal Referral Hospital, Mbeya, The United Republic of Tanzania
| | - Lisete Torres
- National Institute for Medical Research, Dar es Salaam, The United Republic of Tanzania
- Mbeya Zonal Referral Hospital, Mbeya, The United Republic of Tanzania
| | - Sayoki Mfinanga
- National Institute for Medical Research, Dar es Salaam, The United Republic of Tanzania
| | - Tehmina Mustafa
- Department of Global Public Health and Primary Care, Centre for International Health, University of Bergen, Bergen, Vestland, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Vestland, Norway
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22
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Mariner-Llicer C, Goig GA, Zaragoza-Infante L, Torres-Puente M, Villamayor L, Navarro D, Borras R, Chiner-Oms Á, Comas I. Accuracy of an amplicon-sequencing nanopore approach to identify variants in tuberculosis drug-resistance-associated genes. Microb Genom 2021; 7:000740. [PMID: 34919513 PMCID: PMC8767343 DOI: 10.1099/mgen.0.000740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A rapid and accurate diagnostic assay represents an important means to detect Mycobacterium tuberculosis, identify drug-resistant strains and ensure treatment success. Currently employed techniques to diagnose drug-resistant tuberculosis include slow phenotypic tests or more rapid molecular assays that evaluate a limited range of drugs. Whole-genome-sequencing-based approaches can detect known drug-resistance-conferring mutations and novel variations; however, the dependence on growing samples in culture, and the associated delays in achieving results, represents a significant limitation. As an alternative, targeted sequencing strategies can be directly performed on clinical samples at high throughput. This study proposes a targeted sequencing assay to rapidly detect drug-resistant strains of M. tuberculosis using the Nanopore MinION sequencing platform. We designed a single-tube assay that targets nine genes associated with drug resistance to seven drugs and two phylogenetic-determining regions to determine strain lineage and tested it in nine clinical isolates and six sputa. The study's main aim is to calibrate MinNION variant calling to detect drug-resistance-associated mutations with different frequencies to match the accuracy of Illumina (the current gold-standard sequencing technology) from both culture and sputum samples. After calibrating Nanopore MinION variant calling, we demonstrated 100% agreement between Illumina WGS and our MinION set up to detect known drug resistance and phylogenetic variants in our dataset. Importantly, other variants in the amplicons are also detected, decreasing the recall. We identify minority variants and insertions/deletions as crucial bioinformatics challenges to fully reproduce Illumina WGS results.
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Affiliation(s)
| | - Galo A. Goig
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland,University of Basel, Basel, Switzerland
| | - Laura Zaragoza-Infante
- Institute of Applied Biosciences Centre for Research and Technology Hellas, Thessaloniki, Greece
| | | | | | - David Navarro
- Hospital Clínico Universitario de València, València, Spain,Department of Microbiology and Ecology, School of Medicine, University of València, València, Spain
| | - Rafael Borras
- Hospital Clínico Universitario de València, València, Spain,Department of Microbiology and Ecology, School of Medicine, University of València, València, Spain
| | | | - Iñaki Comas
- Instituto de Biomedicina de València (CSIC), València, Spain,CIBER in Epidemiology and Public Health, València, Spain,*Correspondence: Iñaki Comas,
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Saba Villarroel PM, Castro Soto MDR, Melendres Flores O, Peralta Landívar A, Calderón ME, Loayza R, Boucraut J, Thirion L, Dubot-Pérès A, Ninove L, de Lamballerie X. A clinical, aetiological, and public health perspective on central nervous system infections in Bolivia, 2017-2018. Sci Rep 2021; 11:23235. [PMID: 34853372 PMCID: PMC8636643 DOI: 10.1038/s41598-021-02592-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
Central nervous system (CNS) infections are important causes of morbidity and mortality worldwide. In Bolivia, aetiologies, case fatality, and determinants of outcome are poorly characterised. We attempted to investigate such parameters to guide diagnosis, treatment, prevention, and health policy. From Nov-2017 to Oct-2018, we prospectively enrolled 257 inpatients (20.2% HIV-positive patients) of all ages from healthcare centers of Cochabamba and Santa Cruz, Bolivia with a suspected CNS infection and a lumbar puncture performed. Biological diagnosis included classical microbiology, molecular, serological and immunohistochemical tests. An infectious aetiology was confirmed in 128/257 (49.8%) inpatients, including, notably among confirmed single and co-infections, Cryptococcus spp. (41.7%) and Mycobacterium tuberculosis (27.8%) in HIV-positive patients, and Mycobacterium tuberculosis (26.1%) and Streptococcus pneumoniae (18.5%) in HIV-negative patients. The total mortality rate was high (94/223, 42.1%), including six rabies cases. In multivariate logistic regression analysis, mortality was associated with thrombocytopenia (Odds ratio (OR) 5.40, 95%-CI 2.40-11.83) and hydrocephalus (OR 4.07, 95%-CI 1.35-12.23). The proportion of untreated HIV patients, late presentations of neurotuberculosis, the rate of pneumococcal cases, and rabies patients who did not benefit from a post-exposure prophylaxis, suggest that decreasing the burden of CNS infections requires reinforcing health policy regarding tuberculosis, rabies, S. pneumoniae vaccination, and HIV-infections.
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Affiliation(s)
- Paola Mariela Saba Villarroel
- Unité des Virus Émergents (UVE: Aix-Marseille Univ.-IRD 190-INSERM 1207-IHU Méditerranée Infection), 13005, Marseille, France.
- Molecular Biology Unit, Centro Nacional de Enfermedades Tropicales (CENETROP), Santa Cruz de la Sierra, Bolivia.
| | | | | | | | - María E Calderón
- Infectology Department, Manuel Ascencio Villarroel Hospital, Cochabamba, Bolivia
| | - Roxana Loayza
- Molecular Biology Unit, Centro Nacional de Enfermedades Tropicales (CENETROP), Santa Cruz de la Sierra, Bolivia
| | - José Boucraut
- Immunology Laboratory, Conception Hospital, 13005, Marseille, France
- Timone Neuroscience Institute, Aix-Marseille University, 13005, Marseille, France
| | - Laurence Thirion
- Unité des Virus Émergents (UVE: Aix-Marseille Univ.-IRD 190-INSERM 1207-IHU Méditerranée Infection), 13005, Marseille, France
| | - Audrey Dubot-Pérès
- Unité des Virus Émergents (UVE: Aix-Marseille Univ.-IRD 190-INSERM 1207-IHU Méditerranée Infection), 13005, Marseille, France
| | - Laetitia Ninove
- Unité des Virus Émergents (UVE: Aix-Marseille Univ.-IRD 190-INSERM 1207-IHU Méditerranée Infection), 13005, Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ.-IRD 190-INSERM 1207-IHU Méditerranée Infection), 13005, Marseille, France
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Shield CG, Swift BMC, McHugh TD, Dedrick RM, Hatfull GF, Satta G. Application of Bacteriophages for Mycobacterial Infections, from Diagnosis to Treatment. Microorganisms 2021; 9:2366. [PMID: 34835491 PMCID: PMC8617706 DOI: 10.3390/microorganisms9112366] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium tuberculosis and other non-tuberculous mycobacteria are responsible for a variety of different infections affecting millions of patients worldwide. Their diagnosis is often problematic and delayed until late in the course of disease, requiring a high index of suspicion and the combined efforts of clinical and laboratory colleagues. Molecular methods, such as PCR platforms, are available, but expensive, and with limited sensitivity in the case of paucibacillary disease. Treatment of mycobacterial infections is also challenging, typically requiring months of multiple and combined antibiotics, with associated side effects and toxicities. The presence of innate and acquired drug resistance further complicates the picture, with dramatic cases without effective treatment options. Bacteriophages (viruses that infect bacteria) have been used for decades in Eastern Europe for the treatment of common bacterial infections, but there is limited clinical experience of their use in mycobacterial infections. More recently, bacteriophages' clinical utility has been re-visited and their use has been successfully demonstrated both as diagnostic and treatment options. This review will focus specifically on how mycobacteriophages have been used recently in the diagnosis and treatment of different mycobacterial infections, as potential emerging technologies, and as an alternative treatment option.
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Affiliation(s)
- Christopher G. Shield
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield AL9 7TA, UK;
| | - Benjamin M. C. Swift
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield AL9 7TA, UK;
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, University College London, London NW3 2PF, UK; (T.D.M.); (G.S.)
| | - Rebekah M. Dedrick
- Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.M.D.); (G.F.H.)
| | - Graham F. Hatfull
- Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.M.D.); (G.F.H.)
| | - Giovanni Satta
- Centre for Clinical Microbiology, University College London, London NW3 2PF, UK; (T.D.M.); (G.S.)
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Anthwal D, Gupta RK, Singhal R, Bhalla M, Verma AK, Khayyam KU, Myneedu VP, Sarin R, Gupta A, Gupta NK, Singh M, Sivaswami Tyagi J, Haldar S. Compatibility of a novel filter paper-based bio-safe sputum transport kit with line probe assay for diagnosing drug-resistant tuberculosis: a single-site evaluation study. ERJ Open Res 2021; 7:00137-2021. [PMID: 34350282 PMCID: PMC8326685 DOI: 10.1183/23120541.00137-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/08/2021] [Indexed: 01/29/2023] Open
Abstract
Background Near-patient access to appropriate tests is a major obstacle for the efficient diagnosis of tuberculosis (TB) and associated drug resistance. Methods We recently developed the “TB Concentration & Transport” kit for bio-safe, ambient-temperature transportation of dried sputum on Trans-Filter, and the “TB DNA Extraction” kit for DNA extraction from Trans-Filter for determining drug resistance by DNA sequencing. In the present study, we evaluated the compatibility of Kit-extracted DNA with Hain's line probe assays (LPAs), which are endorsed by National TB programmes for the detection of drug resistance in sputum collected from presumptive multidrug-resistant TB patients (n=207). Results Trans-Filter-extracted DNA was seamlessly integrated with the LPA protocol (Kit-LPA). The sensitivity of Kit-LPA for determining drug resistance was 83.3% for rifampicin (95% CI 52–98%), 77.7% for isoniazid (95% CI 52–94%), 85.7% for fluoroquinolones (95% CI 42–100%) and 66.6% for aminoglycosides (95% CI 9–99%), with a specificity range of 93.7% (95% CI 87–97) to 99.1% (95% CI 95–100) using phenotypic drug susceptibility testing (DST) as a reference standard. A high degree of concordance was noted between results obtained from Kit-LPA and LPA (99% to 100% (κ value: 0.83–1.0)). Conclusions This study demonstrates successful integration of our developed kits with LPA. The adoption of these kits across Designated Microscopy Centres in India can potentially overcome the existing challenge of transporting infectious sputum at controlled temperature to centralised testing laboratories and can provide rapid near-patient cost-effective “Universal DST” services to TB subjects residing in remote areas. The adoption of bio-safe “TB Concentration & Transport” kit by Microscopy Centres can potentially overcome the challenge of transporting infectious sputum to central laboratories and provide universal DST services to TB subjects residing in remote areas.https://bit.ly/2QrQ5qL
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Affiliation(s)
- Divya Anthwal
- Dept of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.,Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Rakesh Kumar Gupta
- Dept of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.,Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Ritu Singhal
- Dept of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Manpreet Bhalla
- Dept of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Ajoy Kumar Verma
- Dept of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Khalid Umar Khayyam
- Dept of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Vithal Prasad Myneedu
- Dept of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Rohit Sarin
- Dept of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | | | | | - Manjula Singh
- India TB Research Consortium, Indian Council of Medical Research, New Delhi, India
| | - Jaya Sivaswami Tyagi
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India.,Dept of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Sagarika Haldar
- Dept of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.,Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
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Rapid Molecular Diagnosis of Tuberculosis and Its Resistance to Rifampicin and Isoniazid with Automated MDR/MTB ELITe MGB ® Assay. Antibiotics (Basel) 2021; 10:antibiotics10070797. [PMID: 34208899 PMCID: PMC8300793 DOI: 10.3390/antibiotics10070797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/22/2022] Open
Abstract
The MDR/MTB ELITe MGB® kit (ELITech) carried on the ELITe InGenius® platform is a new real-time PCR assay allowing automated extraction and detection of DNA of the Mycobacterium tuberculosis complex (MTB) and mutations in the rpoB and katG genes and inhA promoter region (pro-inhA) associated to resistance to rifampicin and isoniazid, the two markers of multidrug-resistant TB (MDR). We assessed the performances of the test on a collection of strains (n = 54) and a set of clinical samples (n = 242) from routine practice, comparatively to TB diagnosis and genotypic drug susceptibility testing (gDST) as references. Regarding the 242 clinical samples, the sensitivity and specificity of MTB detection by ELITe were 90.9% and 97.5%, respectively. For the detection of resistance-conferring mutations on positive clinical samples, we observed perfect agreement with gDST for katG and pro-inhA (κ = 1.0) and two discordant results for rpoB (κ = 0.82). Considering the 54 cultured strains, very good agreement with gDST was observed for the detection of the 25 distinct mutations in rpoB, katG, and pro-inhA, (κ = 0.95, 0.88, and 0.95, respectively). In conclusion, the automated MDR/MTB ELITe MGB® assay shows great promise and appears to be a valuable tool for rapid detection of pre-MDR- and MDR-TB directly from clinical specimens.
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Study Designs: Diagnostic Studies. Indian Pediatr 2021. [DOI: 10.1007/s13312-022-2449-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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28
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Kohli M, Schiller I, Dendukuri N, Yao M, Dheda K, Denkinger CM, Schumacher SG, Steingart KR. Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev 2021; 1:CD012768. [PMID: 33448348 PMCID: PMC8078545 DOI: 10.1002/14651858.cd012768.pub3] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Xpert MTB/RIF Ultra (Xpert Ultra) and Xpert MTB/RIF are World Health Organization (WHO)-recommended rapid nucleic acid amplification tests (NAATs) widely used for simultaneous detection of Mycobacterium tuberculosis complex and rifampicin resistance in sputum. To extend our previous review on extrapulmonary tuberculosis (Kohli 2018), we performed this update to inform updated WHO policy (WHO Consolidated Guidelines (Module 3) 2020). OBJECTIVES To estimate diagnostic accuracy of Xpert Ultra and Xpert MTB/RIF for extrapulmonary tuberculosis and rifampicin resistance in adults with presumptive extrapulmonary tuberculosis. SEARCH METHODS Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature, Scopus, ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number Registry, and ProQuest, 2 August 2019 and 28 January 2020 (Xpert Ultra studies), without language restriction. SELECTION CRITERIA Cross-sectional and cohort studies using non-respiratory specimens. Forms of extrapulmonary tuberculosis: tuberculous meningitis and pleural, lymph node, bone or joint, genitourinary, peritoneal, pericardial, disseminated tuberculosis. Reference standards were culture and a study-defined composite reference standard (tuberculosis detection); phenotypic drug susceptibility testing and line probe assays (rifampicin resistance detection). DATA COLLECTION AND ANALYSIS Two review authors independently extracted data and assessed risk of bias and applicability using QUADAS-2. For tuberculosis detection, we performed separate analyses by specimen type and reference standard using the bivariate model to estimate pooled sensitivity and specificity with 95% credible intervals (CrIs). We applied a latent class meta-analysis model to three forms of extrapulmonary tuberculosis. We assessed certainty of evidence using GRADE. MAIN RESULTS 69 studies: 67 evaluated Xpert MTB/RIF and 11 evaluated Xpert Ultra, of which nine evaluated both tests. Most studies were conducted in China, India, South Africa, and Uganda. Overall, risk of bias was low for patient selection, index test, and flow and timing domains, and low (49%) or unclear (43%) for the reference standard domain. Applicability for the patient selection domain was unclear for most studies because we were unsure of the clinical settings. Cerebrospinal fluid Xpert Ultra (6 studies) Xpert Ultra pooled sensitivity and specificity (95% CrI) against culture were 89.4% (79.1 to 95.6) (89 participants; low-certainty evidence) and 91.2% (83.2 to 95.7) (386 participants; moderate-certainty evidence). Of 1000 people where 100 have tuberculous meningitis, 168 would be Xpert Ultra-positive: of these, 79 (47%) would not have tuberculosis (false-positives) and 832 would be Xpert Ultra-negative: of these, 11 (1%) would have tuberculosis (false-negatives). Xpert MTB/RIF (30 studies) Xpert MTB/RIF pooled sensitivity and specificity against culture were 71.1% (62.8 to 79.1) (571 participants; moderate-certainty evidence) and 96.9% (95.4 to 98.0) (2824 participants; high-certainty evidence). Of 1000 people where 100 have tuberculous meningitis, 99 would be Xpert MTB/RIF-positive: of these, 28 (28%) would not have tuberculosis; and 901 would be Xpert MTB/RIF-negative: of these, 29 (3%) would have tuberculosis. Pleural fluid Xpert Ultra (4 studies) Xpert Ultra pooled sensitivity and specificity against culture were 75.0% (58.0 to 86.4) (158 participants; very low-certainty evidence) and 87.0% (63.1 to 97.9) (240 participants; very low-certainty evidence). Of 1000 people where 100 have pleural tuberculosis, 192 would be Xpert Ultra-positive: of these, 117 (61%) would not have tuberculosis; and 808 would be Xpert Ultra-negative: of these, 25 (3%) would have tuberculosis. Xpert MTB/RIF (25 studies) Xpert MTB/RIF pooled sensitivity and specificity against culture were 49.5% (39.8 to 59.9) (644 participants; low-certainty evidence) and 98.9% (97.6 to 99.7) (2421 participants; high-certainty evidence). Of 1000 people where 100 have pleural tuberculosis, 60 would be Xpert MTB/RIF-positive: of these, 10 (17%) would not have tuberculosis; and 940 would be Xpert MTB/RIF-negative: of these, 50 (5%) would have tuberculosis. Lymph node aspirate Xpert Ultra (1 study) Xpert Ultra sensitivity and specificity (95% confidence interval) against composite reference standard were 70% (51 to 85) (30 participants; very low-certainty evidence) and 100% (92 to 100) (43 participants; low-certainty evidence). Of 1000 people where 100 have lymph node tuberculosis, 70 would be Xpert Ultra-positive and 0 (0%) would not have tuberculosis; 930 would be Xpert Ultra-negative and 30 (3%) would have tuberculosis. Xpert MTB/RIF (4 studies) Xpert MTB/RIF pooled sensitivity and specificity against composite reference standard were 81.6% (61.9 to 93.3) (377 participants; low-certainty evidence) and 96.4% (91.3 to 98.6) (302 participants; low-certainty evidence). Of 1000 people where 100 have lymph node tuberculosis, 118 would be Xpert MTB/RIF-positive and 37 (31%) would not have tuberculosis; 882 would be Xpert MTB/RIF-negative and 19 (2%) would have tuberculosis. In lymph node aspirate, Xpert MTB/RIF pooled specificity against culture was 86.2% (78.0 to 92.3), lower than that against a composite reference standard. Using the latent class model, Xpert MTB/RIF pooled specificity was 99.5% (99.1 to 99.7), similar to that observed with a composite reference standard. Rifampicin resistance Xpert Ultra (4 studies) Xpert Ultra pooled sensitivity and specificity were 100.0% (95.1 to 100.0), (24 participants; low-certainty evidence) and 100.0% (99.0 to 100.0) (105 participants; moderate-certainty evidence). Of 1000 people where 100 have rifampicin resistance, 100 would be Xpert Ultra-positive (resistant): of these, zero (0%) would not have rifampicin resistance; and 900 would be Xpert Ultra-negative (susceptible): of these, zero (0%) would have rifampicin resistance. Xpert MTB/RIF (19 studies) Xpert MTB/RIF pooled sensitivity and specificity were 96.5% (91.9 to 98.8) (148 participants; high-certainty evidence) and 99.1% (98.0 to 99.7) (822 participants; high-certainty evidence). Of 1000 people where 100 have rifampicin resistance, 105 would be Xpert MTB/RIF-positive (resistant): of these, 8 (8%) would not have rifampicin resistance; and 895 would be Xpert MTB/RIF-negative (susceptible): of these, 3 (0.3%) would have rifampicin resistance. AUTHORS' CONCLUSIONS Xpert Ultra and Xpert MTB/RIF may be helpful in diagnosing extrapulmonary tuberculosis. Sensitivity varies across different extrapulmonary specimens: while for most specimens specificity is high, the tests rarely yield a positive result for people without tuberculosis. For tuberculous meningitis, Xpert Ultra had higher sensitivity and lower specificity than Xpert MTB/RIF against culture. Xpert Ultra and Xpert MTB/RIF had similar sensitivity and specificity for rifampicin resistance. Future research should acknowledge the concern associated with culture as a reference standard in paucibacillary specimens and consider ways to address this limitation.
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MESH Headings
- Adult
- Antibiotics, Antitubercular/therapeutic use
- Bias
- Drug Resistance, Bacterial
- False Negative Reactions
- False Positive Reactions
- Humans
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/isolation & purification
- Nucleic Acid Amplification Techniques/methods
- Nucleic Acid Amplification Techniques/statistics & numerical data
- Reagent Kits, Diagnostic
- Rifampin/therapeutic use
- Sensitivity and Specificity
- Tuberculosis/cerebrospinal fluid
- Tuberculosis/diagnosis
- Tuberculosis/drug therapy
- Tuberculosis, Lymph Node/cerebrospinal fluid
- Tuberculosis, Lymph Node/diagnosis
- Tuberculosis, Lymph Node/drug therapy
- Tuberculosis, Meningeal/cerebrospinal fluid
- Tuberculosis, Meningeal/diagnosis
- Tuberculosis, Meningeal/drug therapy
- Tuberculosis, Multidrug-Resistant/cerebrospinal fluid
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Pleural/cerebrospinal fluid
- Tuberculosis, Pleural/diagnosis
- Tuberculosis, Pleural/drug therapy
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Affiliation(s)
- Mikashmi Kohli
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada
| | - Ian Schiller
- Centre for Outcomes Research, McGill University Health Centre - Research Institute, Montreal, Canada
| | - Nandini Dendukuri
- Centre for Outcomes Research, McGill University Health Centre - Research Institute, Montreal, Canada
| | - Mandy Yao
- Centre for Outcomes Research, McGill University Health Centre - Research Institute, Montreal, Canada
| | - Keertan Dheda
- Centre for Lung Infection and Immunity Unit, Department of Medicine and UCT Lung Institute, University of Cape Town, Cape Town, South Africa
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK
| | - Claudia M Denkinger
- FIND, Geneva , Switzerland
- Division of Tropical Medicine, Centre for Infectious Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Karen R Steingart
- Honorary Research Fellow, Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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Mokaddas E, Ahmad S, Eldeen H. Performance Comparison of GeneXpert MTB/RIF and ProbeTec ET Tests for Rapid Molecular Diagnosis of Extrapulmonary Tuberculosis in a Low TB/MDR-TB Incidence Country. Med Princ Pract 2021; 30:277-284. [PMID: 33592621 PMCID: PMC8280443 DOI: 10.1159/000515254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/15/2021] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE This study evaluated the performance of GeneXpert MTB/RIF (Xpert) and ProbeTec ET (PTec-ET) assays in diagnosing extrapulmonary tuberculosis (EPTB) in Kuwait. MATERIALS AND METHODS We tested nonrespiratory clinical specimens (n = 3,995) collected from 3,995 patients suspected to have EPTB. These included cavitary fluids (n = 2,054), fine-needle aspirate (FNA)/pus/tissue biopsy (n = 1,461), urine (n = 302), cerebrospinal fluid (CSF, n = 118), and others (n = 60). All specimens were processed for acid-fast bacilli (AFB), culture in mycobacteria growth indicator tube 960 system, and nucleic acid detection by Xpert and PTec-ET according to manufacturer's instructions. RESULTS Of 3,995 specimens, 95 were AFB-positive, 403 were culture-positive, and an additional 86 samples had histopathology suggestive of TB. Using culture as reference, the sensitivity and specificity values were 88.33 and 97.3% for Xpert and 72.95 and 97.80% for PTec-ET, respectively. Although performance of both tests was comparable in AFB-positive samples, Xpert detected significantly more cases in culture-positive samples. Among culture-negative samples, Xpert detected 18 more cases including 16 with histopathological evidence of TB. Lowest positivity was detected for both tests in cavitary fluids. Xpert performed better than PTec-ET in culture-positive FNA/pus/tissue biopsy and CSF samples. CONCLUSIONS Although performance of both tests was suboptimal for AFB-negative/culture-positive samples, Xpert performed better than PTec-ET and also detected more cases of AFB-negative/culture-negative/histopathology-positive samples. PTec-ET was positive in 3, while Xpert was positive in all 6 culture-positive CSF specimens for rapid diagnosis of TB meningitis. Xpert was thus superior to PTec-ET or smear microscopy in rapid diagnosis of EPTB.
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Affiliation(s)
- Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- *Correspondence to: Suhail Ahmad,
| | - Hanaa Eldeen
- Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
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Chopra KK, Singh S. Tuberculosis: Newer diagnostic tests: Applications and limitations. Indian J Tuberc 2020; 67:S86-S90. [PMID: 33308677 DOI: 10.1016/j.ijtb.2020.09.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 01/29/2023]
Abstract
A public health worry as is Tuberculosis (TB) has been making more than 10 million people globally suffer from its terror and causing more than 2 million people worldwide to lose their lives every year. Mankind is putting all its efforts, since the discovery of the causative bacilli, to come up with some dramatic improvements in providing high-quality TB diagnostic services. Nevertheless, it poses a challenge and many people with TB remain use only smear microscopy for diagnosis. In an environment where transmission is becoming easier by the day the challenge becomes burdensome once disease gets associated with drug resistance, HIV, other diseases, etc. It becomes of paramount importance to address this biggest public health challenge delivering timely diagnosis using advanced technologies. Initial microscopic examination forms the backbone of TB diagnosis since 100 years along with clinical confirmations. Newer advanced diagnostic tools coming into play are genotypic assays (LPA, CBNAAT, LAMP) that are rapid molecular tests, and culture methods (liquid culture media) with standard drug susceptibility testing assays. Program ideates to correlate these rapid molecular diagnostics with turn-around time (TAT) as low as around 2 hours, with conventional standard methods. These help in reinforcing the diagnostic capacities and also provide identification of drug resistance patterns for few most important first line and second line drugs. The present day developments have brought these tests to near-patient point of care. Culture tests (liquid culture media) are gold standard technique for the analysis of TB with its increased sensitivity and highest quality over all others. An on-going search under TB diagnostics is to find an efficient, reproducible, cost effective tool with minimal infrastructure requirements. This review conveys the advances made over the past decades in the diagnosis of the disease and drug resistance.
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Affiliation(s)
- K K Chopra
- New Delhi Tuberculosis Centre, Jawaharlal Nehru Marg, Delhi Gate, New Delhi, 110002, India.
| | - Shweta Singh
- Preventive and Social Medicine, Government Institute of Medical Sciences, Greater Noida, Gautam Buddha Nagar, 201013, India.
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Hashmi AA, Naz S, Yaqeen SR, Ahmed O, Ali SI, Irfan M, Kamal A, Faridi N. Utility of the GeneXpert Mycobacterium tuberculosis/Rifampin (MTB/RIF) Assay on Paraffin-Embedded Biopsy Tissue Samples for Detecting Tuberculosis: Comparison With Histopathology. Cureus 2020; 12:e12048. [PMID: 33447478 PMCID: PMC7802736 DOI: 10.7759/cureus.12048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Introduction The Xpert Mycobacterium tuberculosis/Rifampin (MTB/RIF) assay is a qualitative nested real-time polymerase chain reaction (PCR) performed on the GeneXpert instrument system. Although, the utility of this technique for detecting tuberculosis (TB) in sputum and pus samples is well established, however, the usefulness of GeneXpert on biopsy samples is still a matter of debate. Therefore, in this study, we evaluated the utility of GeneXpert for detecting MTB in biopsy specimens diagnosed with TB. Methods A retrospective observational study was conducted at the Department of Pathology, Liaquat National Hospital and Medical College. The data collection period was between January 2016 and December 2018 over a period of three years. Specimens included trucut/incisional biopsies and lymph node excisions. Cases with a favoured histopathological diagnosis of TB were included in the study. The Xpert MTB/RIF assay was performed on the samples obtained from paraffin-embedded biopsy tissue material, and comparison of histological features with Xpert MTB/RIF assay was performed. Results A total of 114 cases were included in the study. The mean age of the patients was 40.53±16.83 years, and 57.9% of patients were male. 68.4% of cases were extra-nodal with the lung being the most common extra-nodal site. On histopathological analysis, caseation necrosis, epithelioid granulomas and Langhan's giant cells were present in 64.9%, 70.2%, and 59.6% cases, respectively. On GeneXpert PCR assay, MTB was detected in 26.3% cases. A significant association of MTB detection on Xpert PCR assay was noted with the presence of necrosis on histopathology. Conclusion In our study, we noted that the MTB detection rate by GeneXpert assay on histopathologically diagnosed cases of TB was only 26.3%, and the detection rate was significantly increased in the presence of caseation necrosis on a biopsy tissue sample. Despite the low detection rate due to rapid turnover time, GeneXpert assay is an excellent adjunctive tool for detecting MTB in paraffin-embedded tissue samples.
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Affiliation(s)
- Atif A Hashmi
- Pathology, Liaquat National Hospital and Medical College, Karachi, PAK
| | - Samreen Naz
- Pathology, Liaquat National Hospital and Medical College, Karachi, PAK
| | | | - Omer Ahmed
- Internal Medicine, Liaquat National Hospital and Medical College, Karachi, PAK
| | | | - Muhammad Irfan
- Statistics, Liaquat National Hospital and Medical College, Karachi, PAK
| | - Anwar Kamal
- Pathology, Liaquat National Hospital and Medical College, Karachi, PAK
| | - Naveen Faridi
- Pathology, Liaquat National Hospital and Medical College, Karachi, PAK
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Chien JY, Lin CK, Yu CJ, Hsueh PR. Usefulness of Xpert MTB/RIF Ultra to Rapidly Diagnose Sputum Smear-Negative Pulmonary Tuberculosis Using Bronchial Washing Fluid. Front Microbiol 2020; 11:588963. [PMID: 33072058 PMCID: PMC7536285 DOI: 10.3389/fmicb.2020.588963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/01/2020] [Indexed: 11/13/2022] Open
Abstract
This study evaluated the performance of the Xpert MTB/RIF Ultra assay (Xpert Ultra) to detect smear-negative pulmonary tuberculosis (PTB). Xpert Ultra assay was prospectively performed using bronchial washing fluid (BWF) in comparison to COBAS TaqMan MTB (COBAS) assay and mycobacterial culture. Of the 165 enrolled participants, 27 (16.4%) had PTB based on composite reference standard and 16 (9.7%) had culture-confirmed PTB. By the composite reference standard of PTB, the sensitivity of Xpert Ultra (63.0, 95% confidence interval, CI, 42.4–80.6%) was higher than the COBAS assay (25.9%, P = 0.006), BWF-culture (33.3%, P = 0.029) and sputum-culture (37.0%, P = 0.057). Meanwhile, the specificity of Xpert Ultra was 99.3% which was slightly lower than the 100.0% specificity of the COBAS assay (P = 1.000) and cultures (P = 1.000). Against the reference standard of culture-confirmed PTB, Xpert Ultra also had a higher sensitivity (62.5, 95% CI, 35.4–84.8%) than the COBAS assay (31.3%, P = 0.077) and was similar to BWF-culture (56.3%, P = 0.719) and sputum-culture (62.5%, P = 1.000). However, one subject with previously treated old PTB had a false-positive result on the Xpert Ultra assay. This prospective study showed Xpert Ultra assay using BWF had better sensitivity than COBAS assay and mycobacterial cultures but could represent a false positive in patients with inactive old PTB.
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Affiliation(s)
- Jung-Yien Chien
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ching-Kai Lin
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
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Park M, Kon OM. Use of Xpert MTB/RIF and Xpert Ultra in extrapulmonary tuberculosis. Expert Rev Anti Infect Ther 2020; 19:65-77. [PMID: 32806986 DOI: 10.1080/14787210.2020.1810565] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Tuberculosis (TB) remains a major global health burden. There still remains a large gap between the notified and estimated incident cases. Extrapulmonary (EP) TB represents 15% of all TB cases and the diagnosis is more challenging due to the paucity of the organism. Smear microscopy is often insensitive and culture methods are prolonged. With the introduction of Xpert MTB/RIF and more recently Xpert Ultra, this has changed TB diagnostics by providing a rapid accessible platform to diagnose TB and identify rifampicin resistance within 2 h. AREAS COVERED The diagnostic accuracy and the clinical role of Xpert MTB/RIF and Xpert Ultra in the different forms of EPTB. EXPERT OPINION Whilst significant advances have been made in TB diagnostics, there is still a need to optimize the diagnostic yield of Xpert MTB/RIF and Xpert Ultra in EPTB samples. Research is needed to facilitate standardization and optimal preparation of samples as well as understanding the role of Xpert MTB/RIF and Xpert Ultra in different burden settings. Alongside the current GeneXpert platform, the launch of rapid second-line drug resistance polymerase chain reactions and whole genome sequencing may help tackle the global health burden with a more comprehensive diagnostic approach and appropriate treatment.
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Affiliation(s)
- Mirae Park
- Imperial College Healthcare NHS Trust, St Mary's Hospital , London, UK.,National Heart and Lung Institute, Imperial College London , London, UK
| | - Onn Min Kon
- Imperial College Healthcare NHS Trust, St Mary's Hospital , London, UK.,National Heart and Lung Institute, Imperial College London , London, UK
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Which sample type is better for Xpert MTB/RIF to diagnose adult and pediatric pulmonary tuberculosis? Biosci Rep 2020; 40:225865. [PMID: 32701147 PMCID: PMC7403955 DOI: 10.1042/bsr20200308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 02/05/2023] Open
Abstract
Objective: This review aimed to identify proper respiratory-related sample types for adult and pediatric pulmonary tuberculosis (PTB), respectively, by comparing performance of Xpert MTB/RIF when using bronchoalveolar lavage (BAL), induced sputum (IS), expectorated sputum (ES), nasopharyngeal aspirates (NPAs), and gastric aspiration (GA) as sample. Methods: Articles were searched in Web of Science, PubMed, and Ovid from inception up to 29 June 2020. Pooled sensitivity and specificity were calculated, each with a 95% confidence interval (CI). Quality assessment and heterogeneity evaluation across included studies were performed. Results: A total of 50 articles were included. The respective sensitivity and specificity were 87% (95% CI: 0.84–0.89), 91% (95% CI: 0.90–0.92) and 95% (95% CI: 0.93–0.97) in the adult BAL group; 90% (95% CI: 0.88–0.91), 98% (95% CI: 0.97–0.98) and 97% (95% CI: 0.95–0.99) in the adult ES group; 86% (95% CI: 0.84–0.89) and 97% (95% CI: 0.96–0.98) in the adult IS group. Xpert MTB/RIF showed the sensitivity and specificity of 14% (95% CI: 0.10–0.19) and 99% (95% CI: 0.97–1.00) in the pediatric ES group; 80% (95% CI: 0.72–0.87) and 94% (95% CI: 0.92–0.95) in the pediatric GA group; 67% (95% CI: 0.62–0.72) and 99% (95% CI: 0.98–0.99) in the pediatric IS group; and 54% (95% CI: 0.43–0.64) and 99% (95% CI: 0.97–0.99) in the pediatric NPA group. The heterogeneity across included studies was deemed acceptable. Conclusion: Considering diagnostic accuracy, cost and sampling process, ES was a better choice than other sample types for diagnosing adult PTB, especially HIV-associated PTB. GA might be more suitable than other sample types for diagnosing pediatric PTB. The actual choice of sample types should also consider the needs of specific situations.
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Agashe VM, Johari AN, Shah M, Anjum R, Romano C, Drago L, Sharma HK, Benzakour T. Diagnosis of Osteoarticular Tuberculosis: Perceptions, Protocols, Practices, and Priorities in the Endemic and Non-Endemic Areas of the World-A WAIOT View. Microorganisms 2020; 8:microorganisms8091312. [PMID: 32872175 PMCID: PMC7563388 DOI: 10.3390/microorganisms8091312] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/18/2020] [Accepted: 08/23/2020] [Indexed: 02/07/2023] Open
Abstract
There has been a major resurgence of tuberculosis (TB) and drug-resistant tuberculosis in the last few decades. Although it has been brought under control in most Western countries, it is still a major cause of death in endemic regions like India. Osteoarticular tuberculosis (OA TB) forms a small proportion of the total cases of tuberculosis. Perceptions and practices of orthopedic surgeons are entirely different in endemic and non-endemic regions around the world, due to the vast difference in exposure. Literature from endemic areas puts stress on clinico-radiological diagnosis and empirical anti-tubercular treatment (ATT). Such practices, although non-invasive, simple to implement, and economical, carry a significant risk of missing TB mimics and developing drug resistance. However, OA TB is still perceived as a “diagnostic enigma” in non-endemic regions, leading to a delay in diagnosis. Hence, a high index of suspicion, especially in a high-risk population, is needed to improve the diagnosis. Evolving drug resistance continues to thwart efforts to control the disease globally. This review article discusses the perceptions and practices in different parts of the world, with India as an example of the endemic world, and lays down priorities for overcoming the challenges of diagnosing osteoarticular TB.
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Affiliation(s)
| | - Ashok N. Johari
- ENABLE International Centre for Paediatric Musculoskeletal Care, Mumbai 400016, India;
| | - Mudit Shah
- Dr. Agashe’s Maternity and Surgical Nursing Home, 116 Bazar ward, MN, Road Kurla, Mumbai 400070, India;
| | - Rashid Anjum
- Department of Orthopaedics, ASCOMS and Hospital, J and K, Jammu 180017, India
- Correspondence:
| | - Carlo Romano
- Studio Medico Associato Cecca-Romanò, 20121 Milano, Italy;
| | - Lorenzo Drago
- Clinical Microbiology, University of Milan, 20100 Milan, Italy;
| | - Hemant K. Sharma
- Hull University Teaching Hospitals, Anlaby Road, Hull HU3 2JZ, UK;
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Saeed M, Hussain S, Riaz S, Rasheed F, Ahmad M, Iram S, Arif M, Rahmani TH, Anwar AI. GeneXpert Technology for the diagnosis of HIV-associated tuberculosis: Is scale-up worth it? Open Life Sci 2020; 15:458-465. [PMID: 33817234 PMCID: PMC7874587 DOI: 10.1515/biol-2020-0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/15/2020] [Accepted: 05/21/2020] [Indexed: 11/15/2022] Open
Abstract
Recent evaluations of the GeneXpert MTB/RIF assay for the simultaneous detection of Mycobacterium tuberculosis and drug resistance in less than 2 h have stimulated tremendous enthusiasm. This is the breakthrough that tuberculosis (TB) control has been waiting for. In this (retrospective review) case study, sputum samples from strongly suspected pulmonary tuberculosis patients were collected and assessed for the GeneXpert MTB/RIF assay for diagnosing TB and drug resistance in comparison with other tests, including Ziehl–Neelsen smear and Löwenstein–Jensen test. Of 3,784 cases, 5.7% (216/3,784) were human immunodeficiency virus (HIV)-positive and TB co-infected patients. In diagnosing HIV-positive and TB co-infected cases, the sensitivity and specificity of GeneXpert were 76.4% and 100%. While in HIV-negative and TB suspected cases, the sensitivity and specificity were 95.6% and 100%. This new test represents a major milestone for global TB diagnosis and care. It also represents new hope for the millions of people who are at the highest risk of TB and drug-resistant disease. GeneXpert is World Health Organization-endorsed technology representing the gold standard for TB testing despite attaining less sensitivity for HIV and TB co-infected patients as compared to HIV-negative patients.
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Affiliation(s)
- Muhammad Saeed
- Department of Pathology, Medical Lab Technologist-Manager Pathology & Transfusion Medicine, District Head Quarter Hospital Mandi Bahauddin, Lahore, Punjab, 50400, Pakistan
| | - Shahida Hussain
- Department of Microbiology and Molecular Genetics (MMG), Punjab University Lahore, Lahore, Punjab, 54590, Pakistan
| | - Saba Riaz
- Department of Microbiology and Molecular Genetics (MMG), Punjab University Lahore, Lahore, Punjab, 54590, Pakistan
| | - Farhan Rasheed
- Department of Pathology, Microbiology Section, Allama Iqbal Medical College & Jinnah Hospital (AIMC&JHL) Lahore, Lahore, Punjab, 54590, Pakistan
| | - Maqsood Ahmad
- Government College University Faisalabad, Lahore, Punjab, 38000, Pakistan
| | - Shagufta Iram
- Microbiology Section, Department of Pathology, Allama Iqbal Medical College, Lahore, Punjab, 54590, Pakistan
| | - Mizna Arif
- Postgraduate Medical Institute Lahore, Lahore, Punjab, 54590, Pakistan
| | - Tariq Hamid Rahmani
- Department of Pathology, Ameer Iqbal Medical College Lahore, Lahore, Punjab, 54590, Pakistan
| | - Ambereen Imran Anwar
- Department of Pathology, Allama Iqbal Medical College, Lahore, Punjab, 54590, Pakistan
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Shekar PA, Kumar PS. Microbiological diagnosis in urogenital tuberculosis: the Holy Grail still Eludes. World J Urol 2020; 39:3693-3694. [PMID: 32504316 DOI: 10.1007/s00345-020-03293-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 10/24/2022] Open
Affiliation(s)
- P Ashwin Shekar
- Department of Urology, Sri Sathya Sai Institute of Higher Medical Sciences, Prashantigram, Puttaparthi, Andhra Pradesh, 515134, India.
| | - P Satish Kumar
- Department of Urology, Sri Sathya Sai Institute of Higher Medical Sciences, Prashantigram, Puttaparthi, Andhra Pradesh, 515134, India
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Menichini M, Lari N, Lupetti A, Rindi L. Evaluation of Xpert MTB/RIF Ultra assay for rapid diagnosis of pulmonary and extra-pulmonary tuberculosis in an Italian center. Eur J Clin Microbiol Infect Dis 2020; 39:1597-1600. [PMID: 32232690 DOI: 10.1007/s10096-020-03867-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/12/2020] [Indexed: 10/23/2022]
Affiliation(s)
| | - Nicoletta Lari
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Via San Zeno, 35/39, 56127, Pisa, Italy
| | - Antonella Lupetti
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Via San Zeno, 35/39, 56127, Pisa, Italy
| | - Laura Rindi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Via San Zeno, 35/39, 56127, Pisa, Italy.
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Chumpa N, Kawkitinarong K, Rotcheewaphan S, Sawatpanich A, Petsong S, Tumwasorn S, Suwanpimolkul G. Evaluation of Anyplex™ II MTB/MDR kit's performance to rapidly detect isoniazid and rifampicin resistant Mycobacterium tuberculosis from various clinical specimens. Mol Biol Rep 2020; 47:2501-2508. [PMID: 32124172 DOI: 10.1007/s11033-020-05331-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/15/2020] [Indexed: 12/30/2022]
Abstract
To determine the accuracy of multiplex real-time PCR (Anyplex™ II MTB/MDR kit) in detecting Isoniazid (INH)- and Rifampin (RIF)-resistant Mycobacterium tuberculosis strains from various clinical specimens. The performance of Anyplex™ II MTB/MDR kit in detecting INH- and RIF-resistant M. tuberculosis compared to the conventional drug susceptibility tests by Mycobacterial Growth Indicator Tube (MGIT). A total of 430 clinical samples had positive results for M. tuberculosis from both Anyplex™ II MTB/MDR kit assay and mycobacterial cultures by MGIT method. When compared to MGITs, the sensitivity and specificity of Anyplex™ II MTB/MDR kit in detecting INH-resistant TB were 85.71% and 99.75%, respectively. For the detection of MDR-TB, the sensitivity and specificity of the test were 82.35% and 99.76%, respectively. The positive predictive values and negative predictive values to detect INH-resistant TB were 96.77% and 98.75%, respectively. Anyplex™ II MTB/MDR kit can be used to rapidly detect isoniazid and rifampicin resistances. It has a high sensitivity, specificity and PPV in detecting INH-resistant TB and MDR-TB. This test can be used as an alternative test to Xpert MTB/RIF because it can rapidly detect both INH-resistant TB and RIF-resistant TB.
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Affiliation(s)
- Nuntana Chumpa
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Kamon Kawkitinarong
- Division of Pulmonary and Critical Care, Department of Medicine, Faculty of Medicine, Chulalongkorn Hospital, Thai Red Cross Society, Bangkok, Thailand
- Tuberculosis Research Unit, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Suwatchareeporn Rotcheewaphan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Ajcharaporn Sawatpanich
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Suthidee Petsong
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Somying Tumwasorn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Gompol Suwanpimolkul
- Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand.
- Tuberculosis Research Unit, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand.
- Department of Medicine, Faculty of Medicine, Thai Red Cross Emerging Infectious Diseases Clinical Center, Chulalongkorn University, Bangkok, Thailand.
- Division of Infectious Diseases, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV Road, Pathum Wan, Bangkok, 10330, Thailand.
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