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Kebede W, Abebe G, De Boeck I, Gudina EK, Cauwenberghs E, Lebeer S, Van Rie A. Bacterial pathogens in Xpert MTB/RIF Ultra-negative sputum samples of patients with presumptive tuberculosis in a high TB burden setting: a 16S rRNA analysis. Microbiol Spectr 2024; 12:e0293123. [PMID: 38189296 PMCID: PMC10845949 DOI: 10.1128/spectrum.02931-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
In patients with presumptive tuberculosis (TB) in whom the diagnosis of TB was excluded, understanding the bacterial etiology of lower respiratory tract infections (LRTIs) is important for optimal patient management. A secondary analysis was performed on a cohort of 250 hospitalized patients with symptoms of TB. Bacterial DNA was extracted from sputum samples for Illumina 16S rRNA sequencing to identify bacterial species based on amplicon sequence variant level. The bacterial pathogen most likely to be responsible for the patients' LRTI could only be identified in a minority (6.0%, 13/215) of cases based on 16S rRNA amplicon sequencing: Mycoplasma pneumoniae (n = 7), Bordetella pertussis (n = 2), Acinetobacter baumanii (n = 2), and Pseudomonas aeruginosa (n = 2). Other putative pathogens were present in similar proportions of Xpert Ultra-positive and Xpert Ultra-negative sputum samples. The presence of Streptococcus (pseudo)pneumoniae appeared to increase the odds of radiological abnormalities (aOR 2.5, 95% CI 1.12-6.16) and the presence of S. (pseudo)pneumoniae (aOR 5.31, 95% CI 1.29-26.6) and Moraxella catarrhalis/nonliquefaciens (aOR 12.1, 95% CI 2.67-72.8) increased the odds of 6-month mortality, suggesting that these pathogens might have clinical relevance. M. pneumoniae, B. pertussis, and A. baumanii appeared to be the possible causes of TB-like symptoms. S. (pseudo)pneumoniae and M. catarrhalis/nonliquefaciens also appeared of clinical relevance based on 16S rRNA amplicon sequencing. Further research using tools with higher discriminatory power than 16S rRNA sequencing is required to develop optimal diagnostic and treatment strategies for this population.IMPORTANCEThe objective of this study was to identify possible bacterial lower respiratory tract infection (LRTI) pathogens in hospitalized patients who were initially suspected to have TB but later tested negative using the Xpert Ultra test. Although 16S rRNA was able to identify some less common or difficult-to-culture pathogens such as Mycoplasma pneumoniae and Bordetella pertussis, one of the main findings of the study is that, in contrast to what we had hypothesized, 16S rRNA is not a method that can be used to assist in the management of patients with presumptive TB having a negative Xpert Ultra test. Even though this could be considered a negative finding, we believe it is an important finding to report as it highlights the need for further research using different approaches.
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Affiliation(s)
- Wakjira Kebede
- Department of Epidemiology and Social Medicine, Faculty of Medicine and Health sciences, University of Antwerp, Antwerp, Belgium
- Mycobacteriology Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Science, Jimma University, Jimma, Ethiopia
| | - Gemeda Abebe
- Mycobacteriology Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Science, Jimma University, Jimma, Ethiopia
| | - Ilke De Boeck
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Esayas Kebede Gudina
- Department of Internal Medicine, Jimma University Medical Center, Jimma University, Jimma, Ethiopia
| | - Eline Cauwenberghs
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Annelies Van Rie
- Department of Epidemiology and Social Medicine, Faculty of Medicine and Health sciences, University of Antwerp, Antwerp, Belgium
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Divala TH, Fielding KL, Kandulu C, Nliwasa M, Sloan DJ, Gupta-Wright A, Corbett EL. Utility of broad-spectrum antibiotics for diagnosing pulmonary tuberculosis in adults: a systematic review and meta-analysis. THE LANCET. INFECTIOUS DISEASES 2020; 20:1089-1098. [PMID: 32437700 PMCID: PMC7456780 DOI: 10.1016/s1473-3099(20)30143-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 01/15/2020] [Accepted: 02/18/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Suboptimal diagnostics for pulmonary tuberculosis drive the use of the so-called trial of antibiotics, a course of broad-spectrum antibiotics without activity against Mycobacterium tuberculosis that is given to patients who are mycobacteriology negative but symptomatic, with the aim of distinguishing pulmonary tuberculosis from bacterial lower respiratory tract infection. The underlying assumption-that patients with lower respiratory tract infection will improve, whereas those with pulmonary tuberculosis will not-has an unclear evidence base for such a widely used intervention (at least 26·5 million courses are prescribed per year). We aimed to collate available evidence on the diagnostic performance of the trial of antibiotics. METHODS In this systematic review and meta-analysis we searched the MEDLINE, Embase, and Global Health databases for studies published up to March 15, 2019, that investigated the sensitivity and specificity of the trial of antibiotics against mycobacteriology tests in adults (≥15 years) with tuberculosis symptoms. We used the QUADAS-2 tool to assess the risk of bias. We estimated pooled values for sensitivity and specificity of trial of antibiotics (as the index text) versus mycobacteriology tests (as the reference standard) using random-effects bivariate modelling, and we used the I2 statistic to assess heterogeneity between studies contributing to these estimates. This study is registered with PROSPERO, number CRD42017083915. FINDINGS Of the 9410 articles identified by our search, eight studies were eligible for inclusion. The studies were from seven countries in Africa, South America, and Asia, and involved 2786 participants. Six studies used mycobacterial culture as the reference standard, and six used penicillins for the trial of antibiotics. The treatment duration, number of antimicrobial courses, and definition of what constituted response to treatment varied substantially between studies. The pooled sensitivity (67%, 95% CI 42-85) and specificity (73%, 58-85) of the trial of antibiotics versus mycobacteriology tests were below internationally defined minimum performance profiles for tuberculosis diagnostics and had substantial heterogeneity (I2 was 96% for sensitivity and 99% for specificity). Each included study failed on one or more domain of the QUADAS-2 tool. INTERPRETATION Current policy and practice regarding the trial of antibiotics appear inappropriate, given the weak evidence base, poor diagnostic performance, potential contribution to the global antimicrobial resistance crisis, and adverse individual and public health consequences from the misclassification of tuberculosis status. Antibiotic strategies during tuberculosis investigations should instead optimise clinical outcomes, ideally guided by clinical trials in both inpatient and outpatient groups. FUNDING Helse Nord RHF, Wellcome Trust, and the UK Commonwealth Scholarship Commission.
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Affiliation(s)
- Titus H Divala
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK; Helse Nord Tuberculosis Initiative, University of Malawi College of Medicine, Blantyre, Malawi; Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi.
| | - Katherine L Fielding
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK; School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Chikondi Kandulu
- Helse Nord Tuberculosis Initiative, University of Malawi College of Medicine, Blantyre, Malawi; Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Marriott Nliwasa
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK; Helse Nord Tuberculosis Initiative, University of Malawi College of Medicine, Blantyre, Malawi; Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Derek J Sloan
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Ankur Gupta-Wright
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK; Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Elizabeth L Corbett
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK; Helse Nord Tuberculosis Initiative, University of Malawi College of Medicine, Blantyre, Malawi; Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
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Boyd AT, Oboho I, Paulin H, Ali H, Godfrey C, Date A, Sean Cavanaugh J. Addressing advanced HIV disease and mortality in global HIV programming. AIDS Res Ther 2020; 17:40. [PMID: 32650797 PMCID: PMC7348123 DOI: 10.1186/s12981-020-00296-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/02/2020] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION The US President's Emergency Plan for AIDS Relief (PEPFAR) was launched to increase access to antiretroviral treatment (ART) among people living with HIV (PLHIV) and to prevent new HIV infections globally. As new infections have decreased in many PEPFAR-supported countries, PEPFAR is increasingly focusing on understanding and decreasing mortality among PLHIV, specifically by addressing advanced HIV disease (AHD) and its attendant opportunistic infections (OIs). Several developments in identifying AHD, in preventing, diagnosing, and treating selected OIs, and in PEPFAR's support for mortality surveillance make this an opportune moment for PEPFAR to address HIV-related mortality. DISCUSSION AHD upon diagnosis or re-engagement in HIV care is not uncommon, and it substantially increases risk of death from OIs. The World Health Organization provides evidence-based guidelines for a package of interventions for preventing, diagnosing, and treating common OIs, including tuberculosis (TB), cryptococcal meningitis, and severe bacterial infections. PEPFAR facilitates implementation of these guidelines. To identify PLHIV with low CD4, PEPFAR plans to support expanded access to CD4 testing, including a point-of-care assay that differentiates CD4 cell count as a binary of greater than or less than 200 cells/µL. To prevent AHD-related mortality, PEPFAR supports rapid ART initiation with integrase inhibitor-based regimens and implementation and documentation of TB preventive treatment. To diagnose selected OIs, PEPFAR is implementing urine lateral flow lipoarabinomannan use to identify TB among PLHIV who have a CD4 cell count < 200 cells/µL. To treat selected OIs, PEPFAR has focused on improving patient-centered care in TB/HIV co-infection services and scaling up implementation of new drug regimens for cryptococcal meningitis. To better understand mortality, PEPFAR has introduced an indicator, TX_ML, to routinely and systematically categorize outcomes, including deaths, among PLHIV on ART. CONCLUSIONS PEPFAR is increasing its efforts to identify AHD; to prevent, diagnose, and treat OIs; and to track mortality in its programs. These ongoing efforts, done in collaboration with other stakeholders, seek to decrease mortality among PLHIV.
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Datta S, Evans CA. The uncertainty of tuberculosis diagnosis. THE LANCET. INFECTIOUS DISEASES 2020; 20:1002-1004. [PMID: 32437698 PMCID: PMC7234790 DOI: 10.1016/s1473-3099(20)30400-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/24/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Sumona Datta
- Liverpool School of Tropical Medicine, Liverpool, UK; Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Innovation For Health And Development, Laboratory of Research and Development, Universidad Peruana Cayetano Heredia, Lima, Peru; Innovación Por la Salud Y Desarrollo, Asociación Benéfica PRISMA, Lima, Peru
| | - Carlton A Evans
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK; Innovation For Health And Development, Laboratory of Research and Development, Universidad Peruana Cayetano Heredia, Lima, Peru; Innovación Por la Salud Y Desarrollo, Asociación Benéfica PRISMA, Lima, Peru.
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Mthiyane T, Peter J, Allen J, Connolly C, Davids M, Rustomjee R, Holtz TH, Malinga L, Dheda K. Urine lipoarabinomannan (LAM) and antimicrobial usage in seriously-ill HIV-infected patients with sputum smear-negative pulmonary tuberculosis. J Thorac Dis 2019; 11:3505-3514. [PMID: 31559057 DOI: 10.21037/jtd.2019.07.69] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Based on current WHO guidelines, hospitalized tuberculosis (TB) and HIV co-infected patients with CD4 count <100 cells/mm3 who are urine lipoarabinomannan (LAM) positive should be initiated on TB treatment. This recommendation is conditional, and data are limited in sputum smear-negative patients from TB endemic countries where the LAM test is largely inaccessible. Other potential benefits of LAM, including reduction in antibiotic usage have, hitherto, not been explored. Methods We consecutively enrolled newly-admitted seriously-ill HIV-infected patients (n=187) with suspected TB from three hospitals in KwaZulu-Natal, South Africa. All patients were empirically treated for TB as per the WHO 2007 smear-negative TB algorithm (patients untreated for TB were not recruited). Bio-banked urine, donated prior to anti-TB treatment, was tested for TB-infection using a commercially available LAM-ELISA test. TB sputum and blood cultures were performed. Results Data from 156 patients containing CD4 count, urine-LAM, sputum and blood culture results were analysed. Mean age was 37 years, median CD4-count was 75 cells/mm3 [interquartile range (IQR), 34-169 cells/mm3], 54/156 (34.6%) were sputum culture-positive, 12/54 (22.2%) blood-culture positive, and 53/156 (34.0%) LAM-positive. Thus, LAM sensitivity was 55.6% (30/54). The study design did not allow for calculation of specificity. Urine-LAM positivity was associated with low CD4 count (P=0.002). Ninety-point-six percent (48/53) of LAM-positive patients received antibiotics [15/48 (31.3%), 23/48 (47.9%) and 10/48 (20.8%) received one, two or three different antibiotics respectively], while the duration of antibiotic therapy was more than 5 days in 26 of 46 (56.5%) patients. Conclusions Urine LAM testing in sputum smear-negative severely-ill hospitalized patients with TB-HIV co-infection and advanced immunosuppression, offered an immediate rule-in diagnosis in one-third of empirically treated patients. Moreover, LAM, by providing a rapid alternative diagnosis, could potentially reduce antibiotic overusage in such patients thereby reducing health-care costs and facilitating antibiotic stewardship.
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Affiliation(s)
- Thuli Mthiyane
- Tuberculosis Platform, South African Medical Research Council, Pretoria, South Africa
| | - Jonny Peter
- Division of Allergology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Jenny Allen
- Tuberculosis Platform, South African Medical Research Council, Pretoria, South Africa.,Queensland Audit of Surgical Mortality, East Brisbane, Queensland, Australia
| | - Cathy Connolly
- Biostatistics Department, South African Medical Research Council, Durban, South Africa
| | - Malika Davids
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Roxana Rustomjee
- Tuberculosis Platform, South African Medical Research Council, Pretoria, South Africa.,Division of AIDS/NIAID/NIH/DHHS, Therapeutics Research Program, Tuberculosis Clinical Research Branch, Rockville, MD, USA
| | - Timothy H Holtz
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lesibana Malinga
- Tuberculosis Platform, South African Medical Research Council, Pretoria, South Africa
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa.,Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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