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Xie YL, Eichberg C, Hapeela N, Nakabugo E, Anyango I, Arora K, Korte JE, Odero R, van Heerden J, Zemanay W, Kennedy S, Nabeta P, Hanif M, Rodrigues C, Skrahina A, Stevens W, Dietze R, Liu X, Ellner JJ, Alland D, Joloba ML, Schumacher SG, McCarthy KD, Nakiyingi L, Dorman SE. Xpert MTB/RIF Ultra versus mycobacterial growth indicator tube liquid culture for detection of Mycobacterium tuberculosis in symptomatic adults: a diagnostic accuracy study. THE LANCET. MICROBE 2024; 5:e520-e528. [PMID: 38608680 DOI: 10.1016/s2666-5247(24)00001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 04/14/2024]
Abstract
BACKGROUND Xpert MTB/RIF Ultra (Ultra) is an automated molecular test for the detection of Mycobacterium tuberculosis in sputum. We compared the sensitivity of Ultra to that of mycobacterial growth indicator tube (MGIT) liquid culture, considered the most sensitive assay in routine clinical use. METHODS In this prospective, multicentre, cross-sectional diagnostic accuracy study, we used a non-inferiority design to assess whether the sensitivity of a single Ultra test was non-inferior to that of a single liquid culture for detection of M tuberculosis in sputum. We enrolled adults (age ≥18 years) with pulmonary tuberculosis symptoms in 11 countries and each adult provided three sputum specimens with a minimum volume of 2 mL over 2 days. Ultra was done directly on sputum 1, and Ultra and MGIT liquid culture were done on resuspended pellet from sputum 2. Results of MGIT and solid media cultures done on sputum 3 were considered the reference standard. The pre-defined non-inferiority margin was 5·0%. FINDINGS Between Feb 18, 2016, and Dec 4, 2019, we enrolled 2906 participants. 2600 (89%) participants were analysed, including 639 (25%) of 2600 who were positive for tuberculosis by the reference standard. Of the 2357 included in the non-inferiority analysis, 877 (37%) were HIV-positive and 984 (42%) were female. Sensitivity of Ultra performed directly on sputum 1 was non-inferior to that of sputum 2 MGIT culture (MGIT 91·1% vs Ultra 91·9%; difference -0·8 percentage points; 95% CI -2·8 to 1·1). Sensitivity of Ultra performed on sputum 2 pellet was also non-inferior to that of sputum 2 MGIT (MGIT 91·1% vs Ultra 91·9%; difference -0·8 percentage points; -2·7 to 1·0). INTERPRETATION For the detection of M tuberculosis in sputum from adults with respiratory symptoms, there was no difference in sensitivity of a single Ultra test to that of a single MGIT culture. Highly sensitive, rapid molecular approaches for M tuberculosis detection, combined with advances in genotypic methods for drug resistance detection, have potential to replace culture. FUNDING US National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Yingda L Xie
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | | | - Nchimunya Hapeela
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Irene Anyango
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - Kiranjot Arora
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | | | - Ronald Odero
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - Judi van Heerden
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Widaad Zemanay
- Division of Medical Microbiology and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Samuel Kennedy
- Medical University of South Carolina, Charleston, SC, USA
| | | | - Mahmud Hanif
- State TB Training and Demonstration Centre, New Delhi, India
| | | | - Alena Skrahina
- National Reference Laboratory, Republican Scientific and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Wendy Stevens
- Department of Molecular Medicine and Hematology, Faculty of Health Science, School of Pathology, and the National Priority Program of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Xin Liu
- Henan Provincial Chest Hospital, Zhengzhou, China
| | - Jerrold J Ellner
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - David Alland
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Moses L Joloba
- Mycobacteriology Laboratory, Department of Microbiology, School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | | | | | - Lydia Nakiyingi
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Susan E Dorman
- Medical University of South Carolina, Charleston, SC, USA.
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Zaporojan N, Negrean RA, Hodișan R, Zaporojan C, Csep A, Zaha DC. Evolution of Laboratory Diagnosis of Tuberculosis. Clin Pract 2024; 14:388-416. [PMID: 38525709 PMCID: PMC10961697 DOI: 10.3390/clinpract14020030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/26/2024] Open
Abstract
Tuberculosis (TB) is an infectious disease of global public health importance caused by the Mycobacterium tuberculosis complex. Despite advances in diagnosis and treatment, this disease has worsened with the emergence of multidrug-resistant strains of tuberculosis. We aim to present and review the history, progress, and future directions in the diagnosis of tuberculosis by evaluating the current methods of laboratory diagnosis of tuberculosis, with a special emphasis on microscopic examination and cultivation on solid and liquid media, as well as an approach to molecular assays. The microscopic method, although widely used, has its limitations, and the use and evaluation of other techniques are essential for a complete and accurate diagnosis. Bacterial cultures, both in solid and liquid media, are essential methods in the diagnosis of TB. Culture on a solid medium provides specificity and accuracy, while culture on a liquid medium brings rapidity and increased sensitivity. Molecular tests such as LPA and Xpert MTB/RIF have been found to offer significant benefits in the rapid and accurate diagnosis of TB, including drug-resistant forms. These tests allow the identification of resistance mutations and provide essential information for choosing the right treatment. We conclude that combined diagnostic methods, using several techniques and approaches, provide the best result in the laboratory diagnosis of TB. Improving the quality and accessibility of tests, as well as the implementation of advanced technologies, is essential to help improve the sensitivity, efficiency, and accuracy of TB diagnosis.
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Affiliation(s)
- Natalia Zaporojan
- Doctoral School of Biomedical Sciences, University of Oradea, Str. Universitatii 1, 410087 Oradea, Romania; (N.Z.)
| | - Rodica Anamaria Negrean
- Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 December 10, 410087 Oradea, Romania
| | - Ramona Hodișan
- Doctoral School of Biomedical Sciences, University of Oradea, Str. Universitatii 1, 410087 Oradea, Romania; (N.Z.)
- Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 December 10, 410087 Oradea, Romania
| | - Claudiu Zaporojan
- Emergency County Hospital Bihor, Str. Republicii 37, 410167 Oradea, Romania
| | - Andrei Csep
- Department of Psycho-Neurosciences and Recovery, Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 December 10, 410087 Oradea, Romania
| | - Dana Carmen Zaha
- Doctoral School of Biomedical Sciences, University of Oradea, Str. Universitatii 1, 410087 Oradea, Romania; (N.Z.)
- Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 December 10, 410087 Oradea, Romania
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Naidoo K, Perumal R, Ngema SL, Shunmugam L, Somboro AM. Rapid Diagnosis of Drug-Resistant Tuberculosis-Opportunities and Challenges. Pathogens 2023; 13:27. [PMID: 38251335 PMCID: PMC10819693 DOI: 10.3390/pathogens13010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
Global tuberculosis (TB) eradication is undermined by increasing prevalence of emerging resistance to available drugs, fuelling ongoing demand for more complex diagnostic and treatment strategies. Early detection of TB drug resistance coupled with therapeutic decision making guided by rapid characterisation of pre-treatment and treatment emergent resistance remains the most effective strategy for averting Drug-Resistant TB (DR-TB) transmission, reducing DR-TB associated mortality, and improving patient outcomes. Solid- and liquid-based mycobacterial culture methods remain the gold standard for Mycobacterium tuberculosis (MTB) detection and drug susceptibility testing (DST). Unfortunately, delays to result return, and associated technical challenges from requirements for specialised resource and capacity, have limited DST use and availability in many high TB burden resource-limited countries. There is increasing availability of a variety of rapid nucleic acid-based diagnostic assays with adequate sensitivity and specificity to detect gene mutations associated with resistance to one or more drugs. While a few of these assays produce comprehensive calls for resistance to several first- and second-line drugs, there is still no endorsed genotypic drug susceptibility test assay for bedaquiline, pretomanid, and delamanid. The global implementation of regimens comprising these novel drugs in the absence of rapid phenotypic drug resistance profiling has generated a new set of diagnostic challenges and heralded a return to culture-based phenotypic DST. In this review, we describe the available tools for rapid diagnosis of drug-resistant tuberculosis and discuss the associated opportunities and challenges.
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Affiliation(s)
- Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Rubeshan Perumal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Senamile L. Ngema
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Letitia Shunmugam
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Anou M. Somboro
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa (S.L.N.); (L.S.); (A.M.S.)
- SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa
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Zhang Y, Tian X, Fan F, Wang X, Dong S. The dynamic evolution and IS26-mediated interspecies transfer of a bla NDM-1-bearing fusion plasmid leading to a hypervirulent carbapenem-resistant Klebsiella pneumoniae strain harbouring bla KPC-2 in a single patient. J Glob Antimicrob Resist 2023; 35:181-189. [PMID: 37734657 DOI: 10.1016/j.jgar.2023.08.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/03/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023] Open
Abstract
OBJECTIVES To characterize the evolution and interspecies transfer of plasmids between Klebsiella pneumoniae and Escherichia coli within a single patient. METHODS Minimum inhibitory concentrations were measured using broth microdilution assays. Conjugation assays, string tests, and Galleria mellonella infection model experiments were also conducted. Whole-genome sequencing was performed on the Illumina and Nanopore platforms. Antimicrobial resistance determinants, insertion sequences, and virulence factors were identified using ABRicate/ResFinder database, ISFinder, and virulence factor database. Wzi and capsular polysaccharide (KL) were typed using Kleborate and Kaptive. Multi-locus sequence typing (MLST), replicon typing, and single nucleotide polymorphism analyses were conducted using the BacWGSTdb server. RESULTS The carbapenem-resistant K. pneumoniae 2111KP was characterized as ST11, wzi64, and KL64, with a positive string test result and a relatively high virulence phenotype. Analysis of the 2111KP genome revealed that blaNDM-1 was located in a 268,400-bp IncFIB/IncHI1B/IncX3 conjugative plasmid (p2111KP-1), regulated by IS26, IS5, and ISKox3. p2111KP-1 was also a rmpA2-associated virulence plasmid with an iutA-iucABCD gene cluster and a IS26-mediated multidrug-resistant fusion plasmid, which contained 8-bp (AGCTGCAC or GGCCTTTG) target site duplications. Segments flanked by IS26 of p2111KP-1 were 99.99% identical to a 49,016-bp E. coli plasmid. CONCLUSIONS This study provided direct evidence of plasmid fusion via IS26 between two different bacterial species within one patient and revealed the process by which genetic elements conferring carbapenem resistance and virulence were simultaneously transferred between these species. It highlights the need for strategic antibiotic use and rigorous monitoring to prevent the plasmid-mediated fusion and transmission of drug-resistance/virulence factors.
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Affiliation(s)
- Yapei Zhang
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, People's Republic of China
| | - Xuebin Tian
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Fanghua Fan
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, People's Republic of China
| | - Xuan Wang
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, People's Republic of China
| | - Shilei Dong
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, People's Republic of China.
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Quan S, Zou T, Duan L, Tian X, Wang Y, Zhu Y, Fang M, Shi Y, Wan C, Sun L, Shen A. Clinical Characteristics of Pulmonary Tuberculosis in Children Tested by Xpert MTB/RIF Ultra. Pediatr Infect Dis J 2023; 42:389-395. [PMID: 36854100 DOI: 10.1097/inf.0000000000003866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
BACKGROUND The Xpert MTB/rifampicin Ultra (Xpert Ultra) assay improves the early diagnosis of active tuberculosis (TB) in children. Clinical evaluation is paramount for the interpretation of any positive Xpert Ultra test, especially those with low quantities of DNA. METHODS In this study, 391 children with suspected TB who were tested with Xpert Ultra were enrolled. The clinical characteristics and Xpert Ultra results were further analyzed. RESULTS The sensitivity and specificity of Xpert Ultra were 45.0% (149/331) and 96.7% (58/60), respectively. Children with higher semiquantitative scales of Xpert Ultra showed higher percentages of a positive MTB culture, positive acid-fast bacilli staining, severe type of disease, fever, cough and expectoration, a higher white blood cell count and higher C-reactive protein concentrations (all P < 0.01). Among 44 children with an Xpert Ultra trace result, there were no differences in clinical characteristics between confirmed cases and unconfirmed TB cases. CONCLUSIONS The prevalence of trace is relatively high and can be considered positive in paucibacillary children. Clinical presentations are associated with bacterial load quantified by Xpert Ultra. The interpretation of Xpert Ultra trace results based on clinical information is important for the diagnosis of TB.
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Affiliation(s)
- Shuting Quan
- From the National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Tingting Zou
- Department of Pediatrics Infectious Diseases, West China Second Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Chengdu, China
| | - Li Duan
- Department of Pediatrics Infectious Diseases, The No. 1 People's Hospital of Liangshan Yizu Autonomous Prefecture, Liangshan, China
| | - Xue Tian
- From the National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yacui Wang
- From the National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yu Zhu
- Department of Pediatrics Infectious Diseases, West China Second Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Chengdu, China
| | - Min Fang
- Department of Pediatrics Infectious Diseases, The No. 1 People's Hospital of Liangshan Yizu Autonomous Prefecture, Liangshan, China
| | - Yan Shi
- Department of Pediatrics Infectious Diseases, The No. 1 People's Hospital of Liangshan Yizu Autonomous Prefecture, Liangshan, China
| | - Chaomin Wan
- Department of Pediatrics Infectious Diseases, West China Second Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Chengdu, China
| | - Lin Sun
- From the National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Adong Shen
- From the National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
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Mapamba DA, Sauli E, Lalashowi J, Buza J, John J, Mwaisango Z, Tarmo P, Sabi I, Rachow A, Ntinginya NE, Mtafya B. Performance of Tuberculosis Molecular Bacterial Load Assay Compared to Alere TB-LAM in Urine of Pulmonary Tuberculosis Patients with HIV Co-Infections. Int J Mol Sci 2023; 24:ijms24043715. [PMID: 36835127 PMCID: PMC9965206 DOI: 10.3390/ijms24043715] [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: 12/19/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
Alternative tools are needed to improve the detection of M. tuberculosis (M. tb) in HIV co-infections. We evaluated the utility of Tuberculosis Molecular Bacterial Load Assay (TB-MBLA) compared to lipoarabinomannan (LAM) to detect M. tb in urine. Sputum Xpert MTB/RIF-positive patients were consented to provide urine at baseline, weeks 2, 8, 16, and 24 of treatment for TB-MBLA, culture, and LAM. Results were compared with sputum cultures and microscopy. Initial M. tb. H37Rv spiking experiments were performed to validate the tests. A total of 63 urine samples from 47 patients were analyzed. The median age (IQR) was 38 (30-41) years; 25 (53.2%) were male, 3 (6.5%) had urine for all visits, 45 (95.7%) were HIV positive, of whom 18 (40%) had CD4 cell counts below 200 cells/µL, and 33 (73.3%) were on ART at enrollment. Overall urine LAM positivity was 14.3% compared to 4.8% with TB-MBLA. Culture and microscopy of their sputum counterparts were positive in 20.6% and 12.7% of patients, respectively. Of the three patients with urine and sputum at baseline, one (33.33%) had urine TB-MBLA and LAM positive compared to 100% with sputum MGIT culture positive. Spearman's rank correction coefficient (r) between TB-MBLA and MGIT was -0.85 and 0.89 with a solid culture, p > 0.05. TB-MBLA has the promising potential to improve M. tb detection in urine of HIV-co-infected patients and complement current TB diagnostics.
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Affiliation(s)
- Daniel Adon Mapamba
- National Institute for Medical Research—Mbeya Medical Research Centre (NIM-MMRC), Mbeya P.O. Box 2410, Tanzania
- The Nelson Mandela African Institution of Science and Technology, Arusha P.O. Box 447, Tanzania
- Correspondence: ; Tel.: +255-25-250-3364
| | - Elingarami Sauli
- The Nelson Mandela African Institution of Science and Technology, Arusha P.O. Box 447, Tanzania
| | - Julieth Lalashowi
- National Institute for Medical Research—Mbeya Medical Research Centre (NIM-MMRC), Mbeya P.O. Box 2410, Tanzania
| | - Joram Buza
- The Nelson Mandela African Institution of Science and Technology, Arusha P.O. Box 447, Tanzania
| | - Joseph John
- National Institute for Medical Research—Mbeya Medical Research Centre (NIM-MMRC), Mbeya P.O. Box 2410, Tanzania
| | - Zawadi Mwaisango
- National Institute for Medical Research—Mbeya Medical Research Centre (NIM-MMRC), Mbeya P.O. Box 2410, Tanzania
| | - Peter Tarmo
- National Institute for Medical Research—Mbeya Medical Research Centre (NIM-MMRC), Mbeya P.O. Box 2410, Tanzania
| | - Issa Sabi
- National Institute for Medical Research—Mbeya Medical Research Centre (NIM-MMRC), Mbeya P.O. Box 2410, Tanzania
| | - Andrea Rachow
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich (LMU), 80802 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
| | - Nyanda Elias Ntinginya
- National Institute for Medical Research—Mbeya Medical Research Centre (NIM-MMRC), Mbeya P.O. Box 2410, Tanzania
| | - Bariki Mtafya
- National Institute for Medical Research—Mbeya Medical Research Centre (NIM-MMRC), Mbeya P.O. Box 2410, Tanzania
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Prajwal P, Neary T, Rohrbach K, Bittel P, Göller PC, Buch T, Dümcke S, Keller PM. Optimizing mycobacteria molecular diagnostics: No decontamination! Human DNA depletion? Greener storage at 4 °C! Front Microbiol 2023; 14:1104752. [PMID: 37113238 PMCID: PMC10126496 DOI: 10.3389/fmicb.2023.1104752] [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: 11/22/2022] [Accepted: 03/06/2023] [Indexed: 04/29/2023] Open
Abstract
Introduction Tuberculosis (TB) is an infectious disease caused by the group of bacterial pathogens Mycobacterium tuberculosis complex (MTBC) and is one of the leading causes of death worldwide. Timely diagnosis and treatment of drug-resistant TB is a key pillar of WHO's strategy to combat global TB. The time required to carry out drug susceptibility testing (DST) for MTBC via the classic culture method is in the range of weeks and such delays have a detrimental effect on treatment outcomes. Given that molecular testing is in the range of hours to 1 or 2 days its value in treating drug resistant TB cannot be overstated. When developing such tests, one wants to optimize each step so that tests are successful even when confronted with samples that have a low MTBC load or contain large amounts of host DNA. This could improve the performance of the popular rapid molecular tests, especially for samples with mycobacterial loads close to the limits of detection. Where optimizations could have a more significant impact is for tests based on targeted next generation sequencing (tNGS) which typically require higher quantities of DNA. This would be significant as tNGS can provide more comprehensive drug resistance profiles than the relatively limited resistance information provided by rapid tests. In this work we endeavor to optimize pre-treatment and extraction steps for molecular testing. Methods We begin by choosing the best DNA extraction device by comparing the amount of DNA extracted by five commonly used devices from identical samples. Following this, the effect that decontamination and human DNA depletion have on extraction efficiency is explored. Results The best results were achieved (i.e., the lowest Ct values) when neither decontamination nor human DNA depletion were used. As expected, in all tested scenarios the addition of decontamination to our workflow substantially reduced the yield of DNA extracted. This illustrates that the standard TB laboratory practice of applying decontamination, although being vital for culture-based testing, can negatively impact the performance of molecular testing. As a complement to the above experiments, we also considered the best Mycobacterium tuberculosis DNA storage method to optimize molecular testing carried out in the near- to medium-term. Comparing Ct values following three-month storage at 4 °C and at -20 °C and showed little difference between the two. Discussion In summary, for molecular diagnostics aimed at mycobacteria this work highlights the importance of choosing the right DNA extraction device, indicates that decontamination causes significant loss of mycobacterial DNA, and shows that samples preserved for further molecular testing can be stored at 4 °C, just as well at -20 °C. Under our experimental settings, human DNA depletion gave no significant improvement in Ct values for the detection of MTBC.
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Affiliation(s)
- Prajwal Prajwal
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute of Laboratory Animal Science, University of Zurich, Zurich, Switzerland
- Clemedi AG, Schlieren, Switzerland
| | - Turlough Neary
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Katja Rohrbach
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Pauline C. Göller
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Thorsten Buch
- Institute of Laboratory Animal Science, University of Zurich, Zurich, Switzerland
| | | | - Peter M. Keller
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- *Correspondence: Peter M. Keller,
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A practical approach to render tuberculosis samples safe for application of tuberculosis molecular bacterial load assay in clinical settings without a biosafety level 3 laboratory. Tuberculosis (Edinb) 2023; 138:102275. [PMID: 36434867 DOI: 10.1016/j.tube.2022.102275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/05/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Mycobacterium tuberculosis is a category B infectious pathogen requiring level-3-containment laboratories for handling. We assessed the efficacy of heat and Guanidine thiocyanate (GTC) to inactivate M. tuberculosis prior to performance of tuberculosis Molecular Bacterial Load Assay (TB-MBLA). METHOD We performed in vitro experiments using M.tb, H37Rv reference strain and replicated in sputum specimens. A 0.5 MacFarland standard of M. tuberculosis was serially diluted to 1x101 CFU/mL and pooled sputum was homogenised prior to serial dilutions and Xpert MTB/RIF Ultra. Three replicates for each containing 1 mL for M. tuberculosis and sputum were inactivated at 80 °C for 20 min and with GTC for 15 min. Inactivated samples were processed for culture and TB-MBLA. RESULTS No M. tuberculosis growth was observed in MGIT for GTC or heat treated H37Rv cultures. All untreated H37Rv dilutions were MGIT positive except the most diluted specimens. Heat and GTC treatment of H37Rv reduced TB-MBLA load by 2.1log10 (P = 0.7) and 1.8log10 (P = 0.7) respectively, compared to controls. In contrast, heat treated sputum had TB-MBLA bacterial load of 3.47 ± 3.53 log10 compared to 5.4 ± 3.1 log10 eCFU/mL for GTC (p = 0.57). All heat and GTC treated sputum were culture negative. CONCLUSION Heat or GTC renders M. tuberculosis non-viable and eliminates the need for BSL3 laboratory for performing TB-MBLA in routine healthcare settings.
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Xu JC, Shi X, Ma X, Gu WF, Fang ZX, Zhang H, Fan XY. Diagnosis of extrapulmonary tuberculosis by ultrasound-guided biopsy: A retrospective comparison study. Front Cell Infect Microbiol 2023; 13:1154939. [PMID: 37033480 PMCID: PMC10075254 DOI: 10.3389/fcimb.2023.1154939] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/07/2023] [Indexed: 04/11/2023] Open
Abstract
Objective To compare the diagnostic performance of laboratory assays on the ultrasound-guided core needle biopsy samples for diagnosis of extra-pulmonary tuberculosis (EPTB) in HIV-positive and HIV-negative patients. Methods A total of 217 patients suspected to have EPTB underwent lesion biopsy from 2017 to 2020. Results of laboratory tests on the biopsy and non-biopsy samples were collected with clinical data for retrospective analysis of test utility. The calculated diagnostic accuracy of the tests was stratified according to the specimen types and HIV status. Results The cohort contained 118 patients with a final positive diagnosis of extrapulmonary tuberculosis (EPTB group, 54.4%) and 99 finally diagnosed as without TB (non-EPTB group, 45.6%). The risk factor for EPTB was HIV co-infection (OR 2.22, 95% CI 1.17-4.28, p = 0.014). In biopsy samples, GeneXpert (Xpert) showed higher sensitivity (96.6% [91.6-98.7], p < 0.0001) than culture (56.1% [47.0-64.9]). Regardless of HIV status, Xpert had the highest sensitivity (>95%) and specificity (nearly 100%) of any methods. In non-biopsy samples, only T-SPOT.TB (T-SPOT) showed higher sensitivity than culture (90.9% [62.3-99.5] vs 35.3% [17.3-58.7], p = 0.0037). Furthermore, the sensitivities of Xpert were lower in non-biopsy samples (60.0% [23.1-92.9], p = 0.022) than in biopsy samples (100% [86.7-100]). Even in smear-negative biopsy samples, Xpert still had higher sensitivity than culture and retained high specificity (100% [95.7-100]). Conclusion Superior performance of Xpert in diagnosing EPTB was observed regardless of HIV status and specimen types. Nevertheless, the biopsy samples still substantially facilitated the accurate diagnosis of extrapulmonary tuberculosis.
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Affiliation(s)
- Jin-Chuan Xu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xia Shi
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xin Ma
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Wen-fei Gu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Zhi-xiong Fang
- Department of Infectious Diseases and Public Health, Central Hospital of Xiangtan, Xiangtan, China
| | - Hui Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- *Correspondence: Xiao-Yong Fan, ; Hui Zhang,
| | - Xiao-Yong Fan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Xiao-Yong Fan, ; Hui Zhang,
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10
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Zainabadi K, Lee MH, Walsh KF, Vilbrun SC, Mathurin LD, Ocheretina O, Pape JW, Fitzgerald DW. An optimized method for purifying, detecting and quantifying Mycobacterium tuberculosis RNA from sputum for monitoring treatment response in TB patients. Sci Rep 2022; 12:17382. [PMID: 36253384 PMCID: PMC9574834 DOI: 10.1038/s41598-022-19985-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/07/2022] [Indexed: 02/05/2023] Open
Abstract
Diagnostics that more accurately detect and quantify viable Mycobacterium tuberculosis (Mtb) in the sputum of patients undergoing therapy are needed. Current culture- and molecular-based tests have shown limited efficacy for monitoring treatment response in TB patients, either due to the presence of viable sub-populations of Mtb which fail to grow under standard culture conditions (termed differentially detectable/culturable Mtb, DD Mtb) or the prolonged half-life of Mtb DNA in sputum. Here, we report an optimized RNA-based method for detecting and quantifying viable Mtb from patient sputum during the course of therapy. We first empirically derived a novel RNA extraction protocol from sputum that improves recovery of Mtb RNA while almost completely eliminating contamination from Mtb DNA and host nucleic acids. Next, we identified five Mtb 16S rRNA primer sets with varying limits of detection that were capable of distinguishing between live versus dead H37Rv Mtb. This combined protocol was then tested on sputa from a longitudinal cohort of patients receiving therapy for drug sensitive (DS) or drug resistant (DR) TB with first-line or second-line regimens, respectively. Results were compared with that of culture, including CFU, BACTEC MGIT, and a limiting dilution assay capable of detecting DD Mtb. The five 16S rRNA primer sets positively identified nearly all (range 94-100%) culture positive sputa, and a portion (19-37%) of culture negative sputa. In comparison, ten highly expressed Mtb mRNAs showed positivity in 72-86% of culture positive sputa, and in 0-13% of culture negative sputa. Two of the five 16S rRNA primer sets were able to positively identify 100% of culture positive sputa, and when tested on culture negative sputa from the DS cohort at 2 months post-initiation of therapy, identified 40% of samples as positive; a percentage that is in line with expected treatment failure rates when first-line therapy is discontinued early. These two primer sets also detected 16S rRNA in 13-20% of sputa at 6 months post-initiation of therapy in the DR cohort. Cycle threshold values for 16S rRNA showed a strong correlation with Mtb numbers as determined by culture (R > 0.87), including as Mtb numbers declined during the course of treatment with first-line and second-line regimens. The optimized molecular assay outlined here may have utility for monitoring treatment response in TB patients.
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Affiliation(s)
- Kayvan Zainabadi
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA.
| | - Myung Hee Lee
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA
| | - Kathleen Frances Walsh
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | - Jean William Pape
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA
- Les Centres GHESKIO, Port-au-Prince, Haiti
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11
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Heyckendorf J, Georghiou SB, Frahm N, Heinrich N, Kontsevaya I, Reimann M, Holtzman D, Imperial M, Cirillo DM, Gillespie SH, Ruhwald M. Tuberculosis Treatment Monitoring and Outcome Measures: New Interest and New Strategies. Clin Microbiol Rev 2022; 35:e0022721. [PMID: 35311552 PMCID: PMC9491169 DOI: 10.1128/cmr.00227-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Despite the advent of new diagnostics, drugs and regimens, tuberculosis (TB) remains a global public health threat. A significant challenge for TB control efforts has been the monitoring of TB therapy and determination of TB treatment success. Current recommendations for TB treatment monitoring rely on sputum and culture conversion, which have low sensitivity and long turnaround times, present biohazard risk, and are prone to contamination, undermining their usefulness as clinical treatment monitoring tools and for drug development. We review the pipeline of molecular technologies and assays that serve as suitable substitutes for current culture-based readouts for treatment response and outcome with the potential to change TB therapy monitoring and accelerate drug development.
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Affiliation(s)
- Jan Heyckendorf
- Department of Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | | | - Nicole Frahm
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, USA
| | - Norbert Heinrich
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich (LMU), Munich, Germany
| | - Irina Kontsevaya
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Maja Reimann
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - David Holtzman
- FIND, the Global Alliance for Diagnostics, Geneva, Switzerland
| | - Marjorie Imperial
- University of California San Francisco, San Francisco, California, USA, United States
| | - Daniela M. Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stephen H. Gillespie
- School of Medicine, University of St Andrewsgrid.11914.3c, St Andrews, Fife, Scotland
| | - Morten Ruhwald
- FIND, the Global Alliance for Diagnostics, Geneva, Switzerland
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12
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Gupta T, Somanna N, Rowe T, LaGatta M, Helms S, Owino SO, Jelesijevic T, Harvey S, Jacobs W, Voss T, Sakamoto K, Day C, Whalen C, Karls R, He B, Tompkins SM, Bakre A, Ross T, Quinn FD. Ferrets as a model for tuberculosis transmission. Front Cell Infect Microbiol 2022; 12:873416. [PMID: 36051240 PMCID: PMC9425069 DOI: 10.3389/fcimb.2022.873416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/11/2022] [Indexed: 11/26/2022] Open
Abstract
Even with the COVID-19 pandemic, tuberculosis remains a leading cause of human death due to a single infectious agent. Until successfully treated, infected individuals may continue to transmit Mycobacterium tuberculosis bacilli to contacts. As with other respiratory pathogens, such as SARS-CoV-2, modeling the process of person-to-person transmission will inform efforts to develop vaccines and therapies that specifically impede disease transmission. The ferret (Mustela furo), a relatively inexpensive, small animal has been successfully employed to model transmissibility, pathogenicity, and tropism of influenza and other respiratory disease agents. Ferrets can become naturally infected with Mycobacterium bovis and are closely related to badgers, well known in Great Britain and elsewhere as a natural transmission vehicle for bovine tuberculosis. Herein, we report results of a study demonstrating that within 7 weeks of intratracheal infection with a high dose (>5 x 103 CFU) of M. tuberculosis bacilli, ferrets develop clinical signs and pathological features similar to acute disease reported in larger animals, and ferrets infected with very-high doses (>5 x 104 CFU) develop severe signs within two to four weeks, with loss of body weight as high as 30%. Natural transmission of this pathogen was also examined. Acutely-infected ferrets transmitted M. tuberculosis bacilli to co-housed naïve sentinels; most of the sentinels tested positive for M. tuberculosis in nasal washes, while several developed variable disease symptomologies similar to those reported for humans exposed to an active tuberculosis patient in a closed setting. Transmission was more efficient when the transmitting animal had a well-established acute infection. The findings support further assessment of this model system for tuberculosis transmission including the testing of prevention measures and vaccine efficacy.
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Affiliation(s)
- Tuhina Gupta
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Naveen Somanna
- Molecular Analytics R&D, GlaxoSmithKline Vaccines, Rockville, MD, United States
| | - Thomas Rowe
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Monica LaGatta
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Shelly Helms
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Simon Odera Owino
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Tomislav Jelesijevic
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Stephen Harvey
- Animal Resources Program, University of Georgia, Athens, GA, United States
| | - Wayne Jacobs
- Animal Resources Program, University of Georgia, Athens, GA, United States
| | - Thomas Voss
- Merck Research Laboratories, West Point, PA, United States
| | - Kaori Sakamoto
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Cheryl Day
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, United States
| | - Christopher Whalen
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, United States
| | - Russell Karls
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Biao He
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - S. Mark Tompkins
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Abhijeet Bakre
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Ted Ross
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Frederick D. Quinn
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- *Correspondence: Frederick D. Quinn,
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13
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Kotrbová L, Lara AC, Corretto E, Scharfen J, Ulmann V, Petříčková K, Chroňáková A. Evaluation and comparison of antibiotic susceptibility profiles of Streptomyces spp. from clinical specimens revealed common and region-dependent resistance patterns. Sci Rep 2022; 12:9353. [PMID: 35672429 PMCID: PMC9174267 DOI: 10.1038/s41598-022-13094-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/20/2022] [Indexed: 12/02/2022] Open
Abstract
Notwithstanding the fact that streptomycetes are overlooked in clinical laboratories, studies describing their occurrence in disease and potential pathogenicity are emerging. Information on their species diversity in clinical specimens, aetiology and appropriate therapeutic treatment is scarce. We identified and evaluated the antibiotic susceptibility profile of 84 Streptomyces clinical isolates from the Czech Republic. In the absence of appropriate disk diffusion (DD) breakpoints for antibiotic susceptibility testing (AST) of Streptomyces spp., we determined DD breakpoints by correlation with the broth microdilution method and by the distribution of zone diameters among isolates. Correlation accuracy was high for 9 antibiotics, leading to the establishment of the most valid DD breakpoints for Streptomyces antibiotic susceptibility evaluation so far. Clinical strains belonged to 17 different phylotypes dominated by a cluster of strains sharing the same percentage of 16S rRNA gene sequence identity with more than one species (S. albidoflavus group, S. hydrogenans, S. resistomycificus, S. griseochromogenes; 70% of isolates). AST results showed that Streptomyces exhibited intrinsic resistance to penicillin, general susceptibility to amikacin, gentamycin, vancomycin and linezolid, and high percentage of susceptibility to tetracyclines and clarithromycin. For the remaining antibiotics, AST showed inter- and intra-species variations when compared to available literature (erythromycin, trimethoprim-sulfamethoxazole), indicating a region-dependent rather than species-specific patterns.
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14
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Detection and Quantification of Viable Mycobacterium tuberculosis Bacilli in Saline-Processed Stool Samples by Tuberculosis Molecular Bacterial Load Assay: a Potential Alternative for Processing Stool. Microbiol Spectr 2022; 10:e0027422. [PMID: 35546535 PMCID: PMC9241876 DOI: 10.1128/spectrum.00274-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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15
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High Mycobacterium tuberculosis Bacillary Loads Detected by Tuberculosis Molecular Bacterial Load Assay in Patient Stool: a Potential Alternative for Nonsputum Diagnosis and Treatment Response Monitoring of Tuberculosis. Microbiol Spectr 2022; 10:e0210021. [PMID: 35019686 PMCID: PMC8754106 DOI: 10.1128/spectrum.02100-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Not all patients produce sputum, yet most available TB tests use sputum. We investigated the utility of a novel RNA-based quantitative test, the tuberculosis molecular bacterial load assay (TB-MBLA), for the detection and quantification of Mycobacterium tuberculosis in stool. Stools from 100 adult individuals were treated with OMNIgene-sputum reagent and tested using Xpert MTB/RIF ultra (Xpert ultra), auramine O smear microscopy (smear), mycobacterial growth indicator tube (MGIT), and Lowenstein-Jensen (LJ) cultures. The remaining portions were frozen at −20°C and later tested by TB-MBLA. MGIT sputum culture was used as a TB confirmatory test and reference for stool tests. Sixty-one of 100 participants were already confirmed TB positive by MGIT sputum culture, 20 (33%) of whom were HIV coinfected. TB-MBLA detected M. tuberculosis in 57/100 stool samples, including 49 already confirmed for TB. The mean bacterial load measured by stool TB-MBLA was 5.67 ± 1.7 log10 estimated CFU (eCFU) per mL in HIV-coinfected participants, which was higher than the 4.83 ± 1.59 log10 eCFU per mL among the HIV-negative participants (P = 0.04). The sensitivities (95% confidence intervals [CI]) of stool assays were 80% (68 to 89) and 90% (79 to 98) for TB-MBLA and Xpert ultra, which were both higher than the 44% (32 to 58), 64% (51 to 76), and 62% (45 to 77) for smear, MGIT, and Lowenstein-Jensen (LJ) stool cultures, respectively. The specificity (95% CI) of stool assays was highest for smear, at 97% (87 to 100), followed by Xpert ultra at 91% (76 to 98), TB-MBLA at 79% (63 to 90), LJ at 80% (64 to 91), and MGIT at 62% (45 to 77). Twenty-six percent of MGIT and 21% of LJ stool cultures were indeterminate due to contamination. Detection and quantification of viable M. tuberculosis bacilli in stool raises its utility as an alternative to sputum as a sample type for TB diagnosis. IMPORTANCE This paper highlights the value of stool as a sample type for diagnosis of tuberculosis. While other studies have used DNA-based assays like the Xpert MTB/RIF and culture to detect Mycobacterium tuberculosis in stool, this is the first study that has applied TB-MBLA, an RNA-based assay, to quantify TB bacteria in stool. The high microbial density and diversity in stool compromises the specificity and sensitivity of culture-based tests due to overgrowth of non-M. tuberculosis flora. Consequently, TB-MBLA becomes the most sensitive and specific test for the detection and quantification of viable TB bacteria in stool. Most crucially, this study raises the possibility of a nonsputum alternative sample type for diagnosis of TB among people who have difficulty in producing sputum.
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16
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Dippenaar A, Ismail N, Grobbelaar M, Oostvogels S, de Vos M, Streicher EM, Heupink TH, van Rie A, Warren RM. Optimizing liquefaction and decontamination of sputum for DNA extraction from Mycobacterium tuberculosis. Tuberculosis (Edinb) 2022; 132:102159. [PMID: 34906896 DOI: 10.1016/j.tube.2021.102159] [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: 08/27/2021] [Revised: 11/21/2021] [Accepted: 12/02/2021] [Indexed: 10/19/2022]
Abstract
Whole genome sequencing (WGS) can investigate the entire Mycobacterium tuberculosis (Mtb) genome but currently requires large amounts of mycobacterial DNA, necessitating culture. Culture-free Mtb WGS could revolutionize the clinical use of WGS but is hampered by the high viscosity, low mycobacterial load, and high contamination with bacterial and human DNA in sputum samples. To improve the sputum liquefaction and decontamination step prior to DNA extraction, we assessed the efficiency of Myco-TB, MycoPrep, and Sputolysin with/without TiKa-Kic in liquefying and decontaminating sputum and aimed to evaluate the effect of these approaches on mycobacterial viability, and Mtb DNA quality and quantity. Experiments using spiked sputum samples showed that Myco-TB and BD MycoPrep with standard (15 min) or increased (30 min) incubation time, but not reduced (7,5 min) incubation time performed well in liquefying and decontaminating sputum. No difference in DNA quality or quantity, contamination, or the amount of human DNA present was observed. In comparison, Sputolysin with/without TiKa-Kic was less effective for liquefaction and decontamination of sputum. PCR amplification of the human GAPDH gene after sputum treatment, showed the presence of human DNA in all samples, regardless of sputum treatment. Focused efforts are needed to deplete contaminating DNA for culture-free Mtb WGS.
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Affiliation(s)
- Anzaan Dippenaar
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa; Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.
| | - Nabila Ismail
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Melanie Grobbelaar
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Selien Oostvogels
- Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Margaretha de Vos
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Elizabeth M Streicher
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Tim H Heupink
- Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Annelies van Rie
- Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Robin M Warren
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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17
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Goosen WJ, Kleynhans L, Kerr TJ, van Helden PD, Buss P, Warren RM, Miller MA. Improved detection of Mycobacterium tuberculosis and M. bovis in African wildlife samples using cationic peptide decontamination and mycobacterial culture supplementation. J Vet Diagn Invest 2021; 34:61-67. [PMID: 34510986 PMCID: PMC8688974 DOI: 10.1177/10406387211044192] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In South Africa, mycobacterial culture is regarded as the gold standard for the detection of Mycobacterium tuberculosis complex (MTBC) infection in wildlife even though it is regarded as “imperfect.” We compared a novel decontamination and mycobacterial culture technique (TiKa) to the conventional mycobacterium growth indicator tube (MGIT) system using known amounts of bacilli and clinical samples from MTBC-infected African buffaloes (Syncerus caffer), white rhinoceros (Ceratotherium simum), and African elephants (Loxodonta africana). Use of the TiKa-KiC decontamination agent on samples spiked with 10,000 to 10 colony forming units (cfu) of M. bovis (SB0121) and M. tuberculosis (H37Rv) had no effect on isolate recovery in culture. In contrast, decontamination with MGIT MycoPrep resulted in no growth of M. bovis samples at concentrations < 1,000 cfu and M. tuberculosis samples < 100 cfu. Subsequently, we used the TiKa system with stored clinical samples (various lymphatic tissues) collected from wildlife and paucibacillary bronchoalveolar lavage fluid, trunk washes, and endotracheal tube washes from 3 species with known MTBC infections. Overall, MTBC recovery by culture was improved significantly (p < 0.01) by using TiKa compared to conventional MGIT, with 54 of 57 positive specimens versus 25 of 57 positive specimens, respectively. The TiKa mycobacterial growth system appears to significantly enhance the recovery of MTBC members from tissue and paucibacillary respiratory samples collected from African buffaloes, African elephants, and white rhinoceros. Moreover, the TiKa system may improve success of MTBC culture from various sample types previously deemed unculturable from other species.
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Affiliation(s)
- Wynand J Goosen
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Léanie Kleynhans
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tanya J Kerr
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Paul D van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Peter Buss
- Veterinary Wildlife Services, Kruger National Park, South African National Parks, Skukuza, South Africa
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Michele A Miller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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18
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Said B, Charlie L, Getachew E, Wanjiru CL, Abebe M, Manyazewal T. Molecular bacterial load assay versus culture for monitoring treatment response in adults with tuberculosis. SAGE Open Med 2021; 9:20503121211033470. [PMID: 34349999 PMCID: PMC8287413 DOI: 10.1177/20503121211033470] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022] Open
Abstract
The lack of rapid, sensitive, and deployable tuberculosis diagnostic tools is
hampering the early diagnosis of tuberculosis and early detection of treatment
failures. The conventional sputum smear microscopy or Xpert MTB/RIF assay cannot
distinguish between alive and dead bacilli and the culture method delays
providing results. Tuberculosis molecular bacterial load assay is a reverse
transcriptase real-time quantitative polymerase chain reaction that quantifies
viable tuberculosis bacillary load as a marker of treatment response for
patients on anti-tuberculosis therapy. However, results are not synthesized
enough to inform its comparative advantage to tuberculosis culture technique
which is yet the gold standard of care. With this review, we searched electronic
databases, including PubMed, Embase, and Web of Science, from March 2011 up to
February 2021 for clinical trials or prospective cohort studies that compared
tuberculosis molecular bacterial load assay with tuberculosis culture in adults.
We included eight studies that meet the inclusion criteria. Tuberculosis
molecular bacterial load assay surpasses culture in monitoring patients with
tuberculosis during the first few weeks of anti-tuberculosis treatment. It is
more desirable over culture for its shorter time to results, almost zero rates
of contamination, need for less expertise on the method, early rate of decline,
lower running cost, and reproducibility. Its rapid and specific tuberculosis
treatment monitoring competency benefits patients and healthcare providers to
monitor changes of bacillary load among isolates with drug-susceptible or
resistance to anti-tuberculosis regimens. Despite of the high installing cost of
the tuberculosis molecular bacterial load assay method, molecular expertise, and
a well-equipped laboratory, tuberculosis molecular bacterial load assay is a
cost-effective method with comparison to culture in operational running. To
achieve maximum utility in high tuberculosis burden settings, an intensive
initial investment in nucleic acid extraction and polymerase chain reaction
equipment, training in procedures, and streamlining laboratory supply
procurement systems are crucial. More evidence is needed to demonstrate the
potential large-scale and sustainable use of tuberculosis molecular bacterial
load assay over culture in resource-constrained settings.
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Affiliation(s)
- Bibie Said
- Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.,Kibong'oto National Tuberculosis Hospital, Kilimanjaro, Tanzania
| | - Loveness Charlie
- Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Emnet Getachew
- Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.,Department of Public Health, College of Health Science, Arsi University, Asella, Ethiopia
| | - Catherine Lydiah Wanjiru
- Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mekdelawit Abebe
- Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.,St. Peter Tuberculosis Specialized Hospital, Addis Ababa, Ethiopia
| | - Tsegahun Manyazewal
- Center for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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19
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Hai HT, Sabiiti W, Thu DDA, Phu NH, Gillespie SH, Thwaites GE, Thuong NTT. Evaluation of the molecular bacterial load assay for detecting viable Mycobacterium tuberculosis in cerebrospinal fluid before and during tuberculous meningitis treatment. Tuberculosis (Edinb) 2021; 128:102084. [PMID: 33965677 PMCID: PMC8204225 DOI: 10.1016/j.tube.2021.102084] [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: 02/17/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 12/03/2022]
Abstract
New tools to monitor treatment response and predict outcome from tuberculous meningitis (TBM) are urgently required. We retrospectively evaluated the 16S rRNA-based molecular bacterial load assay (MBLA) to quantify viable Mycobacterium tuberculosis in serial cerebrospinal fluid (CSF) from adults with TBM. 187 CSF samples were collected before and during the first two months of treatment from 99 adults TBM, comprising 56 definite, 43 probable or possible TBM, and 18 non-TBM and preserved at −80°C prior to MBLA. We compared MBLA against MGIT culture, GeneXpert MTB/RIF (Xpert) and Ziehl-Neelsen (ZN) smear. Before treatment, MBLA was positive in 34/99 (34.3%), significantly lower than MGIT 47/99 (47.5%), Xpert 51/99 (51.5%) and ZN smear 55/99 (55.5%). After one month of treatment, MBLA and MGIT were positive in 3/38 (7.9%) and 4/38 (10.5%), respectively, whereas Xpert and ZN smear remained positive in 19/38 (50.0%) and 18/38 (47.4%). In summary, MBLA was less likely to detect CSF bacteria before the start of treatment compared with MGIT culture, Xpert and ZN smear. MBLA and MGIT positivity fell during treatment because of detecting only viable bacteria, whereas Xpert and ZN smear remained positive for longer because of detecting both live and dead bacteria. Sample storage and processing may have reduced MBLA-detectable viable bacteria; and sampling earlier in treatment may yield more useful results. Prospective studies with CSF sampling after 1–2 weeks are warranted.
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Affiliation(s)
- Hoang Thanh Hai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Wilber Sabiiti
- School of Medicine, Division of Infection and Global Health, University of St Andrews, United Kingdom
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Nguyen Hoan Phu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
| | - Stephen H Gillespie
- School of Medicine, Division of Infection and Global Health, University of St Andrews, United Kingdom
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Nuffield Department of Medicine, University of Oxford, United Kingdom.
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20
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Mycobactericidal Effects of Different Regimens Measured by Molecular Bacterial Load Assay among People Treated for Multidrug-Resistant Tuberculosis in Tanzania. J Clin Microbiol 2021; 59:JCM.02927-20. [PMID: 33536294 PMCID: PMC8092737 DOI: 10.1128/jcm.02927-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Rifampin or multidrug-resistant tuberculosis (RR/MDR-TB) treatment has largely transitioned to regimens free of the injectable aminoglycoside component, despite the drug class’ purported bactericidal activity early in treatment. We tested whether Mycobacterium tuberculosis Rifampin or multidrug-resistant tuberculosis (RR/MDR-TB) treatment has largely transitioned to regimens free of the injectable aminoglycoside component, despite the drug class’ purported bactericidal activity early in treatment. We tested whether Mycobacterium tuberculosis killing rates measured by tuberculosis molecular bacterial load assay (TB-MBLA) in sputa correlate with composition of the RR/MDR-TB regimen. Serial sputa were collected from patients with RR/MDR- and drug-sensitive TB at days 0, 3, 7, and 14, and then monthly for 4 months of anti-TB treatment. TB-MBLA was used to quantify viable M. tuberculosis 16S rRNA in sputum for estimation of colony forming units per ml (eCFU/ml). M. tuberculosis killing rates were compared among regimens using nonlinear-mixed-effects modeling of repeated measures. Thirty-seven patients produced 296 serial sputa and received treatment as follows: 13 patients received an injectable bedaquiline-free reference regimen, 9 received an injectable bedaquiline-containing regimen, 8 received an all-oral bedaquiline-based regimen, and 7 patients were treated for drug-sensitive TB with conventional rifampin/isoniazid/pyrazinamide/ethambutol (RHZE). Compared to the adjusted M. tuberculosis killing of −0.17 (95% confidence interval [CI] −0.23 to −0.12) for the injectable bedaquiline-free reference regimen, the killing rates were −0.62 (95% CI −1.05 to −0.20) log10 eCFU/ml for the injectable bedaquiline-containing regimen (P = 0.019), −0.35 (95% CI −0.65 to −0.13) log10 eCFU/ml for the all-oral bedaquiline-based regimen (P = 0.054), and −0.29 (95% CI −0.78 to +0.22) log10 eCFU/ml for the RHZE regimen (P = 0.332). Thus, M. tuberculosis killing rates from sputa were higher among patients who received bedaquiline but were further improved with the addition of an injectable aminoglycoside.
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21
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Mycobacteriophage SWU1-Functionalized magnetic particles for facile bioluminescent detection of Mycobacterium smegmatis. Anal Chim Acta 2020; 1145:17-25. [PMID: 33453875 DOI: 10.1016/j.aca.2020.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/12/2020] [Accepted: 12/05/2020] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis, ranks one of the most dangerous pathogens for its large deaths toll. Due to its characteristic extremely slow growth, the conventional culture-based protocol cannot meet the requirement for the efficient diagnosis of M. tuberculosis-induced tuberculosis. With our previously isolated mycobacteriophage SWU1, we tried to develop a mycobacteriophage-based protocol for detecting Mycobacterium genus. In this work, Mycobacterium smegmatis (M. smegmatis) was used as a model due to its similar physiological features as pathogenic M. tuberculosis, much faster growth and nonpathogenic property. Mycobacteriophage SWU1-functionalized magnetic particles (SWU1-MPs) were used as highly efficient separation carriers for the viable host M. smegmatis. After a replication cycle of approximate 60 min, the cells of M. smegmatis were disrupted by the progeny mycobacteriophages to release intracellular adenosine triphosphate (ATP). The bioluminescent (BL) signal of released ATP was collected to quantitate the amount of M. smegmatis. For the developed protocol, the detection range is 5.0 × 102 to 5.0 × 105 CFU mL-1, and the detection limit is 3.8 × 102 CFU mL-1 (S/N = 3). Furthermore, the protocol can exclude the potential interference of 3 non-pathogenic mycobacteria and 6 other bacterial species. It has been successfully applied to quantitate M. smegmatis in human urine, human saliva, and human serum. The results demonstrate its application potential for a simple, fast, and specific diagnosis of M. tuberculosis infection.
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22
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Wang WH, Takeuchi R, Jain SH, Jiang YH, Watanuki S, Ohtaki Y, Nakaishi K, Watabe S, Lu PL, Ito E. A novel, rapid (within hours) culture-free diagnostic method for detecting live Mycobacterium tuberculosis with high sensitivity. EBioMedicine 2020; 60:103007. [PMID: 32949995 PMCID: PMC7501073 DOI: 10.1016/j.ebiom.2020.103007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Nucleic acid amplification tests (NAATs) are widely used to diagnose tuberculosis (TB), but cannot discriminate live bacilli from dead bacilli. Live bacilli can be isolated by culture methods, but this is time-consuming. We developed a de novo TB diagnostic method that detects only live bacilli with high sensitivity within hours. METHODS A prospective study was performed in Taiwan from 2017 to 2018. Sputum was collected consecutively from 1102 patients with suspected TB infection. The sputum was pretreated and heated at 46°C for 1 h to induce the secretion of MPT64 protein from live Mycobacterium tuberculosis. MPT64 was detected with our ultrasensitive enzyme-linked immunosorbent assay (ELISA) coupled with thionicotinamide-adenine dinucleotide (thio-NAD) cycling. We compared our data with those obtained using a culture test (MGIT), a smear test (Kinyoun staining), and a NAAT (Xpert). FINDINGS The limit of detection for MPT64 in our culture-free ultrasensitive ELISA was 2.0 × 10-19 moles/assay. When the criterion for a positive response was set as an absorbance value ≥17 mAbs, this value corresponded to ca. 330 CFU/mL in the culture method - almost the same high-detection sensitivity as the culture method. To confirm that MPT64 is secreted from only live bacilli, M. bovis BCG was killed using 8 μg/mL rifampicin and then heated. Following this procedure, our method detected no MPT64. Our rapid ultra-sensitive ELISA-based method required only 5 h to complete. Comparing the results of our method with those of culture tests for 944 specimens revealed a sensitivity of 86.9% (93/107, 95% CI: 79.0-92.7%) and a specificity of 92.0% (770/837, 95% CI: 89.9-93.7%). The performance data were not significantly different (McNemar's test, P = 0.887) from those of the Xpert tests. In addition, at a ≥1+ titer in the smear test, the positive predictive value of our culture-free ultrasensitive ELISA tests was in a good agreement with that of the culture tests. Furthermore, our culture-free ultrasensitive ELISA test had better validity for drug effectiveness examination than Xpert tests because our test detected only live bacilli. INTERPRETATION Our culture-free ultrasensitive ELISA method detects only live TB bacilli with high sensitivity within hours, allowing for rapid diagnosis of TB and monitoring drug efficacy. FUNDING Matching Planner Program from JST (VP29117939087), the A-STEP Program from JST (AS3015096U), Waseda University grants for Specific Research Projects (2017A-015 and 2019C-123), the Precise Measurement Technology Promotion Foundation to E.I.
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Affiliation(s)
- Wen-Hung Wang
- Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical University Hospital, 100 TzYou 1st Rd., Kaohsiung 80756, Taiwan
| | - Rikiya Takeuchi
- R&D Department, TAUNS Laboratories, Inc., 761-1 Kamishima, Izunokuni, Shizuoka 410-2325, Japan
| | - Shu-Huei Jain
- Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical University Hospital, 100 TzYou 1st Rd., Kaohsiung 80756, Taiwan
| | - Yong-Huang Jiang
- R&D Department, TAUNS Laboratories, Inc., 761-1 Kamishima, Izunokuni, Shizuoka 410-2325, Japan
| | - Sonoko Watanuki
- R&D Department, TAUNS Laboratories, Inc., 761-1 Kamishima, Izunokuni, Shizuoka 410-2325, Japan
| | - Yoshiharu Ohtaki
- R&D Department, TAUNS Laboratories, Inc., 761-1 Kamishima, Izunokuni, Shizuoka 410-2325, Japan
| | - Kazunari Nakaishi
- R&D Headquarters, TAUNS Laboratories, Inc., 761-1 Kamishima, Izunokuni, Shizuoka 410-2325, Japan; Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Satoshi Watabe
- R&D Headquarters, TAUNS Laboratories, Inc., 761-1 Kamishima, Izunokuni, Shizuoka 410-2325, Japan; Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Po-Liang Lu
- Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Medical University Hospital, 100 TzYou 1st Rd., Kaohsiung 80756, Taiwan; College of Medicine, Kaohsiung Medical University, 100 Shih-Chuan 1st Rd., Kaohsiung 80756, Taiwan.
| | - Etsuro Ito
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan; Graduate Institute of Medicine, Kaohsiung Medical University, 100 Shih-Chuan 1st Rd., Kaohsiung 80756, Taiwan; Department of Biology, Waseda University, 2-2 Wakamatsucho, Shinjuku, Tokyo 162-8480, Japan.
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23
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Hai HT, Vinh DN, Thu DDA, Hanh NT, Phu NH, Srinivasan V, Thwaites GE, T T Thuong N. Comparison of the Mycobacterium tuberculosis molecular bacterial load assay, microscopy and GeneXpert versus liquid culture for viable bacterial load quantification before and after starting pulmonary tuberculosis treatment. Tuberculosis (Edinb) 2019; 119:101864. [PMID: 31568973 PMCID: PMC6899431 DOI: 10.1016/j.tube.2019.101864] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/23/2019] [Accepted: 09/20/2019] [Indexed: 01/02/2023]
Abstract
Molecular bacterial load assay (MBLA) rapidly quantifies viable Mycobacterium tuberculosis (Mtb) and may be useful for monitoring treatment response and treatment efficacy. We conducted a prospective study in 56 adults with pulmonary tuberculosis from whom 244 sputum samples were collected before and during the first month of treatment. We evaluated MBLA for early monitoring of bacterial burden and investigated bactericidal activities of first-line therapy in patients infected with drug susceptible and resistant isolates. Mtb loads measured by MBLA and culture were correlated after one-week (r = 0.56) and one-month (r = 0.73) of treatment. Correlations between culture and GeneXpert or microscopy were weaker during treatment. Mtb load by MBLA declined more rapidly than GeneXpert after one-week (2.73 Ct, P < 0.001; 0.95 Ct, P = 0.297, respectively) and one-month (8.94 Ct, P < 0.001; 6.78 Ct, P < 0.001). Mtb loads in multidrug resistant (MDR) infections were significantly greater than in both sensitive and poly/mono-resistance after one-week (P < 0.02) and one-month treatment (P = 0.001). MBLA performed better than GeneXpert and microscopy in comparison to culture for quantifying viable Mtb during treatment. It can be used for monitoring bacterial load during TB treatment, facilitating early detection of treatment failure thus improving outcomes.
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Affiliation(s)
- Hoang T Hai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Dao N Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Do D A Thu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Nguyen T Hanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Nguyen H Phu
- Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
| | - Vijay Srinivasan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Nguyen T T Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam.
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