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Vijay S, Bao NLH, Vinh DN, Nhat LTH, Thu DDA, Quang NL, Trieu LPT, Nhung HN, Ha VTN, Thai PVK, Ha DTM, Lan NH, Caws M, Thwaites GE, Javid B, Thuong NTT. Rifampicin tolerance and growth fitness among isoniazid-resistant clinical Mycobacterium tuberculosis isolates: an in-vitro longitudinal study. bioRxiv 2024:2023.11.22.568240. [PMID: 38045287 PMCID: PMC10690245 DOI: 10.1101/2023.11.22.568240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Antibiotic tolerance in Mycobacterium tuberculosis leads to less effective bacterial killing, poor treatment responses and resistant emergence. Therefore, we investigated the rifampicin tolerance of M. tuberculosis isolates, with or without pre-existing isoniazid-resistance. We determined the in-vitro rifampicin survival fraction by minimum duration of killing assay in isoniazid susceptible (IS, n=119) and resistant (IR, n=84) M. tuberculosis isolates. Then we correlated the rifampicin tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs) and isoniazid-resistant mutations. The longitudinal IR isolates collected from patients were analyzed for changes in rifampicin tolerance and associated emergence of genetic variants. The median duration of rifampicin exposure reducing the M. tuberculosis surviving fraction by 90% (minimum duration of killing-MDK90) increased from 1.23 (95%CI 1.11; 1.37) and 1.31 (95%CI 1.14; 1.48) to 2.55 (95%CI 2.04; 2.97) and 1.98 (95%CI 1.69; 2.56) days, for IS and IR respectively, during 15 to 60 days of incubation. This indicated the presence of fast and slow growing tolerant sub-populations. A range of 6 log 10 -fold survival fraction enabled classification of tolerance as low, medium or high and revealed IR association with increased tolerance with faster growth (OR=2.68 for low vs. medium, OR=4.42 for low vs. high, P -trend=0.0003). The high tolerance in IR isolates was specific to those collected during rifampicin treatment in patients and associated with bacterial genetic microvariants. Furthermore, the high rifampicin tolerant IR isolates have survival potential similar to multi-drug resistant isolates. These findings suggest that IR tuberculosis needs to be evaluated for high rifampicin tolerance to improve treatment regimen and prevent the risk of MDR-TB emergence.
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Tram TTB, Trieu LPT, Nhat LTH, Thu DDA, Quang NL, Bang ND, Chau TTH, Thwaites GE, Walker TM, Ha VTN, Thuong NTT. Targeted sequencing from cerebrospinal fluid for rapid identification of drug-resistant tuberculous meningitis. J Clin Microbiol 2024; 62:e0128723. [PMID: 38466092 PMCID: PMC11005362 DOI: 10.1128/jcm.01287-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/03/2024] [Indexed: 03/12/2024] Open
Abstract
Mortality from tuberculous meningitis (TBM) remains around 30%, with most deaths occurring within 2 months of starting treatment. Mortality from drug-resistant strains is higher still, making early detection of drug resistance (DR) essential. Targeted next-generation sequencing (tNGS) produces high read depths, allowing the detection of DR-associated alleles with low frequencies. We applied Deeplex Myc-TB-a tNGS assay-to cerebrospinal fluid (CSF) samples from 72 adults with microbiologically confirmed TBM and compared its genomic drug susceptibility predictions to a composite reference standard of phenotypic susceptibility testing (pDST) and whole genome sequencing, as well as to clinical outcomes. Deeplex detected Mycobacterium tuberculosis complex DNA in 24/72 (33.3%) CSF samples and generated full DR reports for 22/24 (91.7%). The read depth generated by Deeplex correlated with semi-quantitative results from MTB/RIF Xpert. Alleles with <20% frequency were seen at canonical loci associated with first-line DR. Disregarding these low-frequency alleles, Deeplex had 100% concordance with the composite reference standard for all drugs except pyrazinamide and streptomycin. Three patients had positive CSF cultures after 30 days of treatment; reference tests and Deeplex identified isoniazid resistance in two, and Deeplex alone identified low-frequency rifampin resistance alleles in one. Five patients died, of whom one had pDST-identified pyrazinamide resistance. tNGS on CSF can rapidly and accurately detect drug-resistant TBM, but its application is limited to those with higher bacterial loads. In those with lower bacterial burdens, alternative approaches need to be developed for both diagnosis and resistance detection.
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Affiliation(s)
| | | | | | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Le Quang
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | | | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Timothy M. Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Spatola M, Nziza N, Irvine EB, Cizmeci D, Jung W, Van LH, Nhat LTH, Ha VTN, Phu NH, Nghia HDT, Thwaites G, Lauffenburger DA, Fortune S, Thuong NTT, Alter G. Distinctive antibody responses to Mycobacterium tuberculosis in pulmonary and brain infection. Brain 2024:awae066. [PMID: 38442687 DOI: 10.1093/brain/awae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 02/07/2024] [Accepted: 02/24/2024] [Indexed: 03/07/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), remains a global health burden. While Mtb is primarily a respiratory pathogen, it can spread to other organs, including the brain and meninges, causing TB meningitis (TBM). However, little is known about the immunological mechanisms that leads to differential disease across organs. Attention has focused on differences in T cell responses in the control of Mtb in the lungs, but emerging data point to a role for antibodies, as both biomarkers of disease control and as antimicrobial molecules. Given an increasing appreciation for compartmentalized antibody responses across the blood brain barrier, here we characterized the antibody profiles across the blood and brain compartments during TBM, and determined whether Mtb-specific humoral immune responses differed between Mtb infection of the lung (pulmonary TB) and TBM. Using a high throughput systems serology approach, we deeply profiled the antibody responses against 10 different Mtb antigens, including lipoarabinomannan (LAM) and purified protein derivative (PPD), in HIV-negative adults with pulmonary TB (n=10) vs TBM (n=60). Antibody studies included analysis of immunoglobulin isotypes (IgG, IgM, IgA) and subclass levels (IgG1-4), the capacity of Mtb-specific antibodies to bind to Fc receptors or C1q, and to activate innate immune effectors functions (complement and NK cells activation, monocyte or neutrophil phagocytosis). Machine learning methods were applied to characterize serum and CSF responses in TBM, identify prognostic factors associated with disease severity, and define the key antibody features that distinguish TBM from pulmonary TB. In individuals with TBM, we identified CSF-specific antibody profiles that marked a unique and compartmentalized humoral response against Mtb, characterized by an enrichment of Mtb-specific antibodies able to robustly activate complement and drive phagocytosis by monocytes and neutrophils, all of which were associated with milder TBM severity at presentation. Moreover, individuals with TBM exhibited Mtb-specific antibodies in the serum with an increased capacity to activate phagocytosis by monocytes, compared to individuals with pulmonary TB, despite having lower IgG titers and Fcγ receptors (FcγR)-binding capacity. Collectively, these data point to functionally divergent humoral responses depending on the site of infection (i.e. lungs vs brain), and demonstrate a highly compartmentalized Mtb-specific antibody response within the CSF during TBM. Moreover, our results suggest that phagocytosis- and complement-mediating antibodies may promote attenuated neuropathology and milder TBM disease.
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Affiliation(s)
- Marianna Spatola
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Nadège Nziza
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Edward B Irvine
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Deniz Cizmeci
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA0 2139, USA
| | - Wonyeong Jung
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA0 2139, USA
| | - Le Hong Van
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, 700000 Ho Chi Minh City, Vietnam
| | - Le Thanh Hoang Nhat
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, 700000 Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, 700000 Ho Chi Minh City, Vietnam
| | - Nguyen Hoan Phu
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, 700000 Ho Chi Minh City, Vietnam
- Vietnam National University School of Medicine, 700000 Ho Chi Minh City, Vietnam
| | - Ho Dang Trung Nghia
- Hospital for Tropical Diseases, 700000 Ho Chi Minh City, Vietnam
- Pham Ngoc Thach University of Medicine, 700000 Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, 700000 Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7LG, UK
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA0 2139, USA
| | - Sarah Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, 700000 Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7LG, UK
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
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Silcocks M, Chang X, Thuong Thuong NT, Qin Y, Minh Ha DT, Khac Thai PV, Vijay S, Anh Thu DD, Ngoc Ha VT, Ngoc Nhung H, Huu Lan N, Quynh Nhu NT, Edwards D, Nath A, Pham K, Duc Bang N, Hong Chau TT, Thwaites G, Heemskerk AD, Chuen Khor C, Teo YY, Inouye M, Ong RTH, Caws M, Holt KE, Dunstan SJ. Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam. Microbiol Spectr 2023; 11:e0256223. [PMID: 37971428 PMCID: PMC10714959 DOI: 10.1128/spectrum.02562-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Xuling Chang
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Youwen Qin
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Phan Vuong Khac Thai
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Srinivasan Vijay
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Theoretical Microbial Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Hoang Ngoc Nhung
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Lan
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Quynh Nhu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - David Edwards
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Artika Nath
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kym Pham
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Tran Thi Hong Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - A. Dorothee Heemskerk
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | | | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Public Health and Primary Care, Cambridge Baker Systems Genomics Initiative, University of Cambridge, Cambridge, United Kingdom
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Birat Nepal Medical Trust, Kathmandu, Nepal
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sarah J. Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
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Tram TTB, Ha VTN, Trieu LPT, Ashton PM, Crawford ED, Thu DDA, Quang NL, Thwaites GE, Walker TM, Anscombe C, Thuong NTT. FLASH-TB: an Application of Next-Generation CRISPR to Detect Drug Resistant Tuberculosis from Direct Sputum. J Clin Microbiol 2023; 61:e0163422. [PMID: 37010411 PMCID: PMC10117099 DOI: 10.1128/jcm.01634-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Offering patients with tuberculosis (TB) an optimal and timely treatment regimen depends on the rapid detection of Mycobacterium tuberculosis (Mtb) drug resistance from clinical samples. Finding Low Abundance Sequences by Hybridization (FLASH) is a technique that harnesses the efficiency, specificity, and flexibility of the Cas9 enzyme to enrich targeted sequences. Here, we used FLASH to amplify 52 candidate genes probably associated with resistance to first- and second-line drugs in the Mtb reference strain (H37Rv), then detect drug resistance mutations in cultured Mtb isolates, and in sputum samples. 92% of H37Rv reads mapped to Mtb targets, with 97.8% of target regions covered at a depth ≥ 10X. Among cultured isolates, FLASH-TB detected the same 17 drug resistance mutations as whole genome sequencing (WGS) did, but with much greater depth. Among the 16 sputum samples, FLASH-TB increased recovery of Mtb DNA compared with WGS (from 1.4% [IQR 0.5-7.5] to 33% [IQR 4.6-66.3]) and average depth reads of targets (from 6.3 [IQR 3.8-10.5] to 1991 [IQR 254.4-3623.7]). FLASH-TB identified Mtb complex in all 16 samples based on IS1081 and IS6110 copies. Drug resistance predictions for 15/16 (93.7%) clinical samples were highly concordant with phenotypic DST for isoniazid, rifampicin, amikacin, and kanamycin [15/15 (100%)], ethambutol [12/15 (80%)] and moxifloxacin [14/15 (93.3%)]. These results highlighted the potential of FLASH-TB for detecting Mtb drug resistance from sputum samples.
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Affiliation(s)
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Philip M Ashton
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Emily D Crawford
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Le Quang
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Timothy M Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Catherine Anscombe
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Donovan J, Thu DDA, Phu NH, Dung VTM, Quang TP, Nghia HDT, Oanh PKN, Nhu TB, Chau NVV, Ha VTN, Hang VTT, Trinh DHK, Geskus RB, Tan LV, Thuong NTT, Thwaites GE. Xpert MTB/RIF Ultra versus Xpert MTB/RIF for the diagnosis of tuberculous meningitis: a prospective, randomised, diagnostic accuracy study. Lancet Infect Dis 2020; 20:299-307. [PMID: 31924551 PMCID: PMC7045088 DOI: 10.1016/s1473-3099(19)30649-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/24/2019] [Accepted: 11/12/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Xpert MTB/RIF Ultra (Xpert Ultra) might have higher sensitivity than its predecessor, Xpert MTB/RIF (Xpert), but its role in tuberculous meningitis diagnosis is uncertain. We aimed to compare Xpert Ultra with Xpert for the diagnosis of tuberculous meningitis in HIV-uninfected and HIV-infected adults. METHODS In this prospective, randomised, diagnostic accuracy study, adults (≥16 years) with suspected tuberculous meningitis from a single centre in Vietnam were randomly assigned to cerebrospinal fluid testing by either Xpert Ultra or Xpert at baseline and, if treated for tuberculous meningitis, after 3-4 weeks of treatment. Test performance (sensitivity, specificity, and positive and negative predictive values) was calculated for Xpert Ultra and Xpert and compared against clinical and mycobacterial culture reference standards. Analyses were done for all patients and by HIV status. FINDINGS Between Oct 16, 2017, and Feb 10, 2019, 205 patients were randomly assigned to Xpert Ultra (n=103) or Xpert (n=102). The sensitivities of Xpert Ultra and Xpert for tuberculous meningitis diagnosis against a reference standard of definite, probable, and possible tuberculous meningitis were 47·2% (95% CI 34·4-60·3; 25 of 53 patients) for Xpert Ultra and 39·6% (27·6-53·1; 21 of 53) for Xpert (p=0·56); specificities were 100·0% (95% CI 92·0-100·0; 44 of 44) and 100·0% (92·6-100·0; 48 of 48), respectively. In HIV-negative patients, the sensitivity of Xpert Ultra was 38·9% (24·8-55·1; 14 of 36) versus 22·9% (12·1-39·0; eight of 35) by Xpert (p=0·23). In HIV co-infected patients, the sensitivities were 64·3% (38·8-83·7; nine of 14) for Xpert Ultra and 76·9% (49·7-91·8; ten of 13) for Xpert (p=0·77). Negative predictive values were 61·1% (49·6-71·5) for Xpert Ultra and 60·0% (49·0-70·0) for Xpert. Against a reference standard of mycobacterial culture, sensitivities were 90·9% (72·2-97·5; 20 of 22 patients) for Xpert Ultra and 81·8% (61·5-92·7; 18 of 22) for Xpert (p=0·66); specificities were 93·9% (85·4-97·6; 62 of 66) and 96·9% (89·5-91·2; 63 of 65), respectively. Six (22%) of 27 patients had a positive test by Xpert Ultra after 4 weeks of treatment versus two (9%) of 22 patients by Xpert. INTERPRETATION Xpert Ultra was not statistically superior to Xpert for the diagnosis of tuberculous meningitis in HIV-uninfected and HIV-infected adults. A negative Xpert Ultra or Xpert test does not rule out tuberculous meningitis. New diagnostic strategies are urgently required. FUNDING Wellcome Trust and the Foundation for Innovative New Diagnostics.
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Affiliation(s)
- Joseph Donovan
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam
| | - Nguyen Hoan Phu
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam; Viet Anh Ward, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Vu Thi Mong Dung
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam
| | - Tran Phu Quang
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam
| | - Ho Dang Trung Nghia
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam; Viet Anh Ward, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Pham Kieu Nguyet Oanh
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam; Viet Anh Ward, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Tran Bao Nhu
- Viet Anh Ward, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Nguyen Van Vinh Chau
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam; Viet Anh Ward, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam
| | - Vu Thi Ty Hang
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam
| | - Dong Huu Khanh Trinh
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam
| | - Ronald B Geskus
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Le Van Tan
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Centre for Tropical Medicine, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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7
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Heemskerk AD, Donovan J, Thu DDA, Marais S, Chaidir L, Dung VTM, Centner CM, Ha VTN, Annisa J, Dian S, Bovijn L, Mai NTH, Phu NH, Chau NVV, Ganiem AR, Van CT, Geskus RB, Thuong NTT, Ruslami R, Meintjes G, van Crevel R, Wilkinson RJ, Thwaites GE. Improving the microbiological diagnosis of tuberculous meningitis: A prospective, international, multicentre comparison of conventional and modified Ziehl-Neelsen stain, GeneXpert, and culture of cerebrospinal fluid. J Infect 2018; 77:509-515. [PMID: 30217659 PMCID: PMC6293313 DOI: 10.1016/j.jinf.2018.09.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/07/2018] [Accepted: 09/07/2018] [Indexed: 01/23/2023]
Abstract
OBJECTIVES Tuberculous meningitis (TBM) is the severest form of tuberculosis, but current diagnostic tests are insensitive. Recent reports suggest simple modifications to conventional cerebrospinal fluid (CSF) Ziehl-Neelsen (ZN) staining may greatly improve sensitivity. We sought to define the performance of modified and conventional ZN stain for TBM diagnosis. METHODS In hospitals in Vietnam, South Africa and Indonesia we conducted a prospective study of modified ZN with or without cytospin, conventional ZN smear, GeneXpert, and culture on CSF in adults with suspected TBM. RESULTS A total of 618 individuals were enrolled across 3 sites. Compared with the TBM clinical diagnostic gold standard for research (definite probable or possible TBM), sensitivity of conventional ZN and modified ZN with cytospin were 33.9% and 34.5% respectively (p = 1.0 for the difference between tests), compared with culture 31.8% and Xpert 25.1%. Using culture as a reference, sensitivities of conventional ZN, modified ZN with cytospin, and Xpert were 66.4%, 67.5%, and 72.3%, respectively. Higher CSF volume and lactate, and lower CSF:blood glucose ratio were independently associated with microbiologically confirmed TBM. CONCLUSIONS Modified ZN stain does not improve diagnosis of TBM. Currently available tests are insensitive, but testing large CSF volumes improves performance. New diagnostic tests for TBM are urgently required.
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Affiliation(s)
- A Dorothee Heemskerk
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Joseph Donovan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Suzaan Marais
- Wellcome Center for Infectious Diseases Research in Africa and Department of Medicine, University of Cape Town, Observatory 7925, South Africa; Department of Neurology, Inkosi Albert Luthuli Central Hospital and University of KwaZulu-Natal, Durban, South Africa
| | - Lidya Chaidir
- Infectious Disease Research Center, Faculty of Medicine, Universitas Padjadjaran/Hasan Sadikin Hospital, Bandung, Indonesia
| | - Vu Thi Mong Dung
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Chad M Centner
- Division of Medical Microbiology, University of Cape Town and National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Jessi Annisa
- Infectious Disease Research Center, Faculty of Medicine, Universitas Padjadjaran/Hasan Sadikin Hospital, Bandung, Indonesia
| | - Sofiati Dian
- Infectious Disease Research Center, Faculty of Medicine, Universitas Padjadjaran/Hasan Sadikin Hospital, Bandung, Indonesia; Department of Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Louise Bovijn
- Wellcome Center for Infectious Diseases Research in Africa and Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Nguyen Thi Hoang Mai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Nguyen Hoan Phu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Nguyen Van Vinh Chau
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Ahmad Rizal Ganiem
- Infectious Disease Research Center, Faculty of Medicine, Universitas Padjadjaran/Hasan Sadikin Hospital, Bandung, Indonesia
| | - Cao Thao Van
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ronald B Geskus
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Rovina Ruslami
- Infectious Disease Research Center, Faculty of Medicine, Universitas Padjadjaran/Hasan Sadikin Hospital, Bandung, Indonesia
| | - Graeme Meintjes
- Wellcome Center for Infectious Diseases Research in Africa and Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Reinout van Crevel
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Department of Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Robert J Wilkinson
- Wellcome Center for Infectious Diseases Research in Africa and Department of Medicine, University of Cape Town, Observatory 7925, South Africa; Department of Medicine, Imperial College London, W2 1PG, United Kingdom; Francis Crick Institute, NW1 1AT, United Kingdom
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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8
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Holt KE, McAdam P, Thai PVK, Thuong NTT, Ha DTM, Lan NN, Lan NH, Nhu NTQ, Hai HT, Ha VTN, Thwaites G, Edwards DJ, Nath AP, Pham K, Ascher DB, Farrar J, Khor CC, Teo YY, Inouye M, Caws M, Dunstan SJ. Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nat Genet 2018; 50:849-856. [PMID: 29785015 PMCID: PMC6143168 DOI: 10.1038/s41588-018-0117-9] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/22/2018] [Indexed: 12/19/2022]
Abstract
To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data identify an underlying burden of disease caused by the endemic Mtb lineage 1 associated with the activation of long-term latent infection, and a threefold higher burden associated with the more recently introduced Beijing lineage and lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than the endemic lineage 1 Mtb. Screening for parallel evolution of Beijing lineage-associated SNPs in other Mtb lineages as a signal of positive selection, we identify an alteration in the ESX-5 type VII-secreted protein EsxW, which could potentially contribute to the enhanced transmission of Beijing lineage Mtb in Vietnamese and other host populations.
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Affiliation(s)
- Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
| | - Paul McAdam
- Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Phan Vuong Khac Thai
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | | | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Nguyen Ngoc Lan
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Lan
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | | | - Hoang Thanh Hai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - David J Edwards
- Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Artika P Nath
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia.,Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kym Pham
- Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Singapore, Singapore.,Singapore Eye Research Institute, Singapore, Singapore
| | - Yik Ying Teo
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Michael Inouye
- Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia.,Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
| | - Maxine Caws
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK.,Birat-Nepal Medical Trust, Kathmandu, Nepal
| | - Sarah J Dunstan
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.
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