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Musisi E, Wamutu S, Ssengooba W, Kasiinga S, Sessolo A, Sanyu I, Kaswabuli S, Zawedde J, Byanyima P, Kia P, Muwambi W, Toskin DT, Kigozi E, Walbaum N, Dombay E, Legrady MB, Ssemambo KDM, Joloba M, Kuchaka D, Worodria W, Huang L, Gillespie SH, Sabiiti W. Accuracy of the tuberculosis molecular bacterial load assay to diagnose and monitor response to anti-tuberculosis therapy: a longitudinal comparative study with standard-of-care smear microscopy, Xpert MTB/RIF Ultra, and culture in Uganda. Lancet Microbe 2024; 5:e345-e354. [PMID: 38458206 DOI: 10.1016/s2666-5247(23)00367-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/18/2023] [Accepted: 10/31/2023] [Indexed: 03/10/2024]
Abstract
BACKGROUND In 2018, the tuberculosis molecular bacterial load assay (TB-MBLA), a ribosomal RNA-based test, was acknowledged by WHO as a molecular assay that could replace smear microscopy and culture for monitoring tuberculosis treatment response. In this study, we evaluated the accuracy of TB-MBLA for diagnosis and monitoring of treatment response in comparison with standard-of-care tests. METHODS For this longitudinal prospective study, patients aged 18 years or older with presumptive tuberculosis (coughing for at least 2 weeks, night sweats, and weight loss) were enrolled at China-Uganda Friendship Hospital Naguru (Kampala, Uganda). Participants were evaluated for tuberculosis by TB-MBLA in comparison with Xpert MTB/RIF Ultra (Xpert-Ultra) and smear microscopy, with Mycobacteria Growth Indicator Tube (MGIT) culture as a reference test. Participants who were positive on Xpert-Ultra were enrolled on a standard 6-month anti-tuberculosis regimen, and monitored for treatment response at weeks 2, 8, 17, and 26 after initiation of treatment and then 3 months after treatment. FINDINGS Between Nov 15, 2019, and June 15, 2022, 210 participants (median age 35 years [IQR 27-44]) were enrolled. 135 (64%) participants were male and 72 (34%) were HIV positive. The pretreatment diagnostic sensitivities of TB-MBLA and Xpert-Ultra were similar (both 99% [95% CI 95-100]) but the specificity was higher for TB-MBLA (90% [83-96]) than for Xpert-Ultra (78% [68-86]). Ten participants were Xpert-Ultra trace positive, eight (80%) of whom were negative by TB-MBLA and MGIT culture. Smear microscopy had lower diagnostic sensitivity (75% [65-83]) but higher specificity (98% [93-100]) than TB-MBLA and Xpert-Ultra. Among participants who were smear microscopy negative, the sensitivity of TB-MBLA was 96% (95 CI 80-100) and was 100% (95% CI 86-100) in those who were HIV positive. 129 (61%) participants were identified as tuberculosis positive by Xpert-Ultra and these individuals were enrolled in the treatment group and monitored for treatment response. According to TB-MBLA, 19 of these patients cleared bacillary load to zero by week 2 of treatment and remained negative throughout the 6-month treatment follow-up. Positivity for tuberculosis decreased with treatment as measured by all tests, but the rate was slower with Xpert-Ultra. Consequently, 31 (33%) of 95 participants were still Xpert-Ultra positive at the end of treatment but were clinically well and negative on TB-MBLA and culture at 6 months of treatment. Two patients were still Xpert-Ultra positive with a further 3 months of post-treatment follow-up. The rate of conversion to negative of the DNA-based Xpert-Ultra was 3·3-times slower than that of the rRNA-based TB-MBLA. Consequently for the same patient, it would take 13 weeks and 52 weeks to reach complete tuberculosis negativity by TB-MBLA and Xpert-Ultra, respectively. Participants who were positive on smear microscopy at 8 weeks, who received an extra month of intensive treatment, had a similar TB-MBLA-measured bacillary load at 8 weeks to those who were smear microscopy negative. INTERPRETATION TB-MBLA has a similar performance to Xpert-Ultra for pretreatment diagnosis of tuberculosis, but is more accurate at detecting and characterising the response to treatment than Xpert-Ultra and standard-of-care smear microscopy. FUNDING European and Developing Countries Clinical Trials Partnership, Makerere University Research and Innovation Fund, US National Institutes of Health.
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Affiliation(s)
- Emmanuel Musisi
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK; Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Samuel Wamutu
- Department of Biochemistry and Sports Sciences, Makerere University, Kampala, Uganda
| | - Willy Ssengooba
- BSL-3 Mycobacteriology Laboratory, Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda; Medical and Molecular Laboratories (MML), Kampala, Uganda
| | | | | | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | | | | | - Praiscillia Kia
- BSL-3 Mycobacteriology Laboratory, Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - William Muwambi
- BSL-3 Mycobacteriology Laboratory, Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Divine Tracy Toskin
- BSL-3 Mycobacteriology Laboratory, Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- BSL-3 Mycobacteriology Laboratory, Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Natasha Walbaum
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
| | - Evelin Dombay
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
| | | | - Kizza David-Martin Ssemambo
- BSL-3 Mycobacteriology Laboratory, Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda; Medical and Molecular Laboratories (MML), Kampala, Uganda
| | - Moses Joloba
- BSL-3 Mycobacteriology Laboratory, Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda; Medical and Molecular Laboratories (MML), Kampala, Uganda
| | - Davis Kuchaka
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | | | - Laurence Huang
- Infectious Diseases Research Collaboration, Kampala, Uganda; Division of Pulmonary and Critical Care Medicine and Division of HIV, Infectious Diseases, and Global Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Stephen H Gillespie
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
| | - Wilber Sabiiti
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK.
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Abelman RA, Fitzpatrick J, Zawedde J, Sanyu I, Byanyima P, Kaswabuli S, Musisi E, Hsieh J, Gardner K, Zhang M, Byanova KL, Sessolo A, Hunt PW, Lalitha R, Davis JL, Crothers K, Worodria W, Huang L. Sex modifies the risk of HIV-associated obstructive lung disease in Ugandans postpneumonia. AIDS 2023; 37:1683-1692. [PMID: 37352494 PMCID: PMC10527596 DOI: 10.1097/qad.0000000000003626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2023]
Abstract
OBJECTIVES Spirometric abnormalities are frequent, and obstructive lung disease (OLD) is a common comorbidity among people with HIV (PWH). HIV increases the risk of many comorbidities to a greater degree in women than in men. Few studies have evaluated whether sex modifies the HIV-associated risk of OLD. DESIGN AND METHODS To evaluate the associations between sex and HIV with abnormal lung function, women and men with and without HIV underwent spirometric testing after completing therapy for pneumonia, including tuberculosis (TB), in Kampala, Uganda. OLD was defined as a postbronchodilator forced expiratory volume in the first second to forced vital capacity (FEV 1 /FVC) ratio less than 0.70. Associations between sex, HIV, and lung function were evaluated using multivariable regression models including sex-by-HIV interaction terms after adjusting for age, BMI, smoking status, and TB status. RESULTS Among 348 participants, 147 (42%) were women and 135 (39%) were HIV-positive. Sixteen (11%) women and 23 men (11%) had OLD. The HIV-sex interaction was significant for obstructive lung disease ( P = 0.04). In the adjusted stratified analysis, women with HIV had 3.44 (95% CI 1.11-12.0; P = 0.04) increased odds of having OLD compared with men with HIV. Women without HIV did not have increased odds of having OLD compared with men without HIV. CONCLUSION HIV appears to increase the risk of OLD to a greater degree in women than in men in an urban Ugandan setting. The mechanistic explanation for this interaction by sex remains unclear and warrants further study.
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Affiliation(s)
- Rebecca A Abelman
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Jessica Fitzpatrick
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | | | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | | | - Emmanuel Musisi
- Division of Infection and Global Health, School of Medicine, University of St. Andrews, St. Andrews, United Kingdom
| | - Jenny Hsieh
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine
| | - Kendall Gardner
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Michelle Zhang
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | | | - Abdul Sessolo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Peter W Hunt
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Rejani Lalitha
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - J Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Pulmonary, Critical Care, and Sleep Medicine Section, Yale School of Medicine, New Haven, Connecticut
| | - Kristina Crothers
- Division of Pulmonary, Critical Care and Sleep, Department of Medicine, Veterans Affairs (VA) Puget Sound Healthcare System and University of Washington, Seattle, Washington, USA
| | - William Worodria
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
- Division of Pulmonary Medicine, Department of Medicine, Mulago Hospital and Complex, Kampala, Uganda
| | - Laurence Huang
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine
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Sessolo A, Musisi E, Kaswabuli S, Zawedde J, Byanyima P, Sabiiti W, Walimbwa S, Ola J, Sanyu I, Lalitha R, Kamya M, Davis L, Worodria W, Huang L. Diagnostic accuracy of Xpert MTB/RIF Ultra and culture assays to detect Mycobacterium Tuberculosis using OMNIgene-sputum processed stool among adult TB presumptive patients in Uganda. PLoS One 2023; 18:e0284041. [PMID: 37083706 PMCID: PMC10121033 DOI: 10.1371/journal.pone.0284041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/22/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Stool is a potential sample for diagnosing Mycobacterium tuberculosis (Mtb) in patients with difficulty in expectorating. However, high mycobacterial culture contamination rates and Xpert MTB/RIF Ultra test error rates on stool samples have limited its use. OMNIgene SPUTUM (OM-S) is a sample transport reagent with characteristics of sputum decontamination while maintaining viable Mtb. We evaluated the impact of OM-S on Mtb diagnostic yield from stool using smear microscopy, Xpert MTB/RIF Ultra, and culture among presumptive TB patients. METHODS Paired stool and expectorated sputum samples were collected from consecutive Ugandan adults undergoing diagnostic evaluation for pulmonary TB between June 2018 and June 2019. Stool was divided into 2 portions: one was homogenized in OM-S (OM-S stool) and the other in PBS (PBS stool) as control. Both sputum and processed stool were tested for Mtb using concentrated smear fluorescence microscopy (CFM), Xpert MTB/RIF Ultra (Xpert) and Mycobacteria Growth Indicator Tube (MGIT) culture. Sensitivity, specificity, and predictive values for each test were calculated against sputum MGIT culture as the reference standard. RESULTS Of the 200 participants, 120 (60%) were male, 73 (37%) were HIV positive (median CD4 120 cells/uL (IQR 43-297)) and 128 (64%) had confirmed pulmonary TB by sputum MGIT culture. Seven (4%) OM-S stool Xpert samples reported errors while 47 (25%) and 103 (61%) were contaminated on OM-S stool MGIT and PBS stool MGIT, respectively. OM-S stool MGIT was able to accurately diagnose 56 of the contaminated PBS stool MGIT samples compared to only 5 of the contaminated OM-S stool MGIT samples diagnosed by PBS stool MGIT. Sensitivity (95% Confidence Interval, CI) 89% (83-94) for OM-S stool Xpert was higher compared to that of OM-S stool MGIT 60% (51-69) and PBS stool MGIT 42% (32-52). Specificity (95%CI) 91% (82-97) was also higher for OM-S stool Xpert compared to OM-S stool MGIT 64% (51-75) and PBS stool MGIT 26% (16-38). CONCLUSION Stool processed with OM-S showed potential to improve Mtb diagnostic yield and reduce rates of indeterminate results when tested on Xpert and MGIT culture. The method may thus be of value in Mtb detection among patients with difficulty to expectorate.
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Affiliation(s)
| | - Emmanuel Musisi
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Biochemistry and Sports Science, Makerere University, Kampala, Uganda
- Division of Infection and Global Health, School of Medicine, University of St. Andrews, Scotland, United Kingdom
| | | | | | | | - Wilber Sabiiti
- Division of Infection and Global Health, School of Medicine, University of St. Andrews, Scotland, United Kingdom
| | | | - Joseph Ola
- China Uganda Friendship Hospital Naguru, Kampala, Uganda
| | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Rejani Lalitha
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Moses Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States of America
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States of America
| | | | - Laurence Huang
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, United States of America
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA, United States of America
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Byanyima P, Kaswabuli S, Musisi E, Nabakiibi C, Zawedde J, Sanyu I, Sessolo A, Andama A, Worodria W, Huang L, Davis JL. Feasibility and Sensitivity of Saliva GeneXpert MTB/RIF Ultra for Tuberculosis Diagnosis in Adults in Uganda. Microbiol Spectr 2022; 10:e0086022. [PMID: 36154664 PMCID: PMC9603304 DOI: 10.1128/spectrum.00860-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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: 03/25/2022] [Accepted: 08/30/2022] [Indexed: 12/30/2022] Open
Abstract
The objective of this prospective observational study carried out at China-Uganda Friendship Hospital-Naguru in Kampala, Uganda, was to determine the performance of GeneXpert MTB/RIF Ultra (Xpert Ultra) molecular testing on saliva for active tuberculosis (TB) disease among consecutive adults undergoing TB diagnostic evaluation who were Xpert Ultra positive on sputum. We calculated sensitivity to determine TB diagnostic performance in comparison to a composite reference standard of Mycobacterium tuberculosis liquid and solid cultures on two spot sputum specimens. Xpert Ultra on a single saliva sample had a sensitivity of 90% (95% confidence interval [CI], 81 to 95%) relative to the composite sputum culture-based reference standard, similar to the composite sensitivity of 87% (95% CI, 77 to 94%) for fluorescence microscopy (FM) for acid-fast bacilli on two sputum smears. The sensitivity of salivary Xpert Ultra was 24% lower (95% CI for difference, 2 to 48%; P = 0.003) among persons living with HIV (71%; 95% CI, 44 to 90%) than among persons living without HIV (95%; 95% CI, 86 to 99%) and 46% higher (95% CI, 14 to 77%; P < 0.0001) among FM-positive (96%; 95% CI, 87 to 99%) than among FM-negative (50%; 95% CI, 19 to 81%) patients. The semiquantitative Xpert Ultra grade was systematically higher in sputum than in a paired saliva sample from the same patient. In conclusion, molecular testing of saliva for active TB diagnosis was feasible and almost as sensitive as molecular testing of sputum in a high TB burden setting. IMPORTANCE Tuberculosis is among the leading causes of morbidity and mortality worldwide, in large part because >3 million people go undiagnosed and untreated each year. Sputum has been the mainstay for TB diagnosis for over a century but can be difficult for patients to produce. In addition, the vigorous coughing required during sputum collection can lead to infection of nearby individuals and health workers. In this case-only study, applying the ultra-sensitive GeneXpert MTB/RIF Ultra molecular diagnostic assay to saliva detected 90% of culture-confirmed TB cases among 81 adults who were undergoing TB evaluation at the outpatient department of a general hospital in Uganda and tested sputum GeneXpert MTB/RIF Ultra positive. These results suggest that saliva may be a feasible and sensitive alternative to sputum for TB diagnosis, thereby meeting two key metrics proposed by the World Health Organization in its target performance profile for a nonsputum test for TB.
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Affiliation(s)
| | | | - Emmanuel Musisi
- Division of Infection and Global Health, School of Medicine, University of St. Andrews, United Kingdom
| | | | | | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Abdul Sessolo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Alfred Andama
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - William Worodria
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, USA
- Division of HIV, Infectious Diseases, and Global Medicine, University of California San Francisco, San Francisco, California, USA
| | - J. Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Pulmonary, Critical Care, and Sleep Medicine Section, Yale School of Medicine, New Haven, Connecticut, USA
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Kaswabuli S, Musisi E, Byanyima P, Sessolo A, Sanyu I, Zawedde J, Worodria W, Huang L, Okeng A, Bwanga F. Accuracy of GenoQuick MTB test in detection of Mycobacterium tuberculosis in sputum from TB presumptive patients in Uganda. SAGE Open Med 2022; 10:20503121221116861. [PMID: 35993094 PMCID: PMC9386833 DOI: 10.1177/20503121221116861] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022] Open
Abstract
Objective: The objective of the study was to determine the diagnostic performance of the GenoQuick MTB test on heated sputum against the conventional Lowenstein–Jensen Mycobacterium tuberculosis culture as the reference method for tuberculosis diagnosis. Introduction: Fast, reliable, and easy-to-use tests for tuberculosis diagnosis are essential to achieving the Sustainable Development Goal of diagnosing and treating 90% of tuberculosis patients by 2030. We evaluated the diagnostic performance of the GenoQuick MTB, a polymerase chain reaction–lateral flow test, in Uganda, a resource-constrained, high tuberculosis- and HIV-burden setting. Methods: Fresh sputum samples from presumptive tuberculosis patients at Mulago Hospital were tested for M. tuberculosis using smear microscopy, GenoQuick MTB test, and Lowenstein–Jensen culture. For the GenoQuick MTB test, mycobacterial DNA was extracted by heating sputum at 95°C for 30 min while DNA amplification and detection were done following the manufacturer’s protocol (Hain Lifescience, Nehren, Germany). Sensitivity, specificity, and kappa agreements were calculated against Lowenstein–Jensen M. tuberculosis culture as a reference test using STATA V12. Results: Of the 86 tested samples, 30.2% had culture-confirmed pulmonary tuberculosis. Overall, sensitivity was higher for GenoQuick MTB (81%, 95% confidence interval: 60%−93%) than for smear microscopy (69%, 95% confidence interval: 48%−86%). Among people living with HIV, sensitivity was identical for GenoQuick MTB and smear tests (75%, 95% confidence interval: 42%−95%). Contrastingly, smear had a higher overall specificity (98%, 95% confidence interval: 91%−100%) than for GenoQuick MTB (92%, 95% confidence interval: 81%−97%). A similar trend of specificity was observed among the people living with HIV for smear microscopy (100%, 95% CI: 87%−100%) and for GenoQuick MTB (96%, 95% confidence interval: 81%−100%). Conclusion: The GenoQuick MTB test could be a potential tuberculosis diagnostic test given its higher sensitivity. Evaluation of this test in larger studies is recommended.
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Affiliation(s)
| | - Emmanuel Musisi
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
| | | | - Abdul Sessolo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | | | - Laurence Huang
- Infectious Diseases Research Collaboration, Kampala, Uganda.,Division of HIV, Infectious Diseases & Global Medicine, University of California San Francisco, San Francisco, CA, USA.,Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Freddie Bwanga
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
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Spottiswoode N, Bloomstein JD, Caldera S, Sessolo A, McCauley K, Byanyima P, Zawedde J, Kalantar K, Kaswabuli S, Rutishauser RL, Lieng MK, Davis JL, Moore J, Jan A, Iwai S, Shenoy M, Sanyu I, DeRisi JL, Lynch SV, Worodria W, Huang L, Langelier CR. Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study. Lancet Microbe 2022; 3:e357-e365. [PMID: 35544096 DOI: 10.1016/s2666-5247(21)00357-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 12/01/2021] [Accepted: 12/14/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Pneumonia is a leading cause of death worldwide and is a major health-care challenge in people living with HIV. Despite this, the causes of pneumonia in this population remain poorly understood. We aimed to assess the feasibility of metatranscriptomics for epidemiological surveillance of pneumonia in patients with HIV in Uganda. METHODS We performed a retrospective observational study in patients with HIV who were admitted to Mulago Hospital, Kampala, Uganda between Oct 1, 2009, and Dec 31, 2011. Inclusion criteria were age 18 years or older, HIV-positivity, and clinically diagnosed pneumonia. Exclusion criteria were contraindication to bronchoscopy or an existing diagnosis of tuberculosis. Bronchoalveolar lavage fluid was collected within 72 h of admission and a combination of RNA sequencing and Mycobacterium tuberculosis culture plus PCR were performed. The primary outcome was detection of an established or possible respiratory pathogen in the total study population. FINDINGS We consecutively enrolled 217 patients during the study period. A potential microbial cause for pneumonia was identified in 211 (97%) patients. At least one microorganism of established respiratory pathogenicity was identified in 113 (52%) patients, and a microbe of possible pathogenicity was identified in an additional 98 (45%). M tuberculosis was the most commonly identified established pathogen (35 [16%] patients; in whom bacterial or viral co-infections were identified in 13 [37%]). Streptococcus mitis, although not previously reported as a cause of pneumonia in patients with HIV, was the most commonly identified bacterial organism (37 [17%] patients). Haemophilus influenzae was the most commonly identified established bacterial pathogen (20 [9%] patients). Pneumocystis jirovecii was only identified in patients with a CD4 count of less than 200 cells per mL. INTERPRETATION We show the feasibility of using metatranscriptomics for epidemiologic surveillance of pneumonia by describing the spectrum of respiratory pathogens in adults with HIV in Uganda. Applying these methods to a contemporary cohort could enable broad assessment of changes in pneumonia aetiology following the emergence of SARS-CoV-2. FUNDING US National Institutes of Health, Chan Zuckerberg Biohub.
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Affiliation(s)
- Natasha Spottiswoode
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua D Bloomstein
- Department of Medicine, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Saharai Caldera
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Abdul Sessolo
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Kathryn McCauley
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Patrick Byanyima
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | | | | | - Sylvia Kaswabuli
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Rachel L Rutishauser
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Monica K Lieng
- Department of Medicine, University of California Davis School of Medicine, Sacramento, CA, USA
| | - J Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health and Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Julia Moore
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amanda Jan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health and Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shoko Iwai
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Meera Shenoy
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Ingvar Sanyu
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Joseph L DeRisi
- Department of Biochemistry, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Susan V Lynch
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - William Worodria
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charles R Langelier
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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7
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Wang RJ, Moore J, Moisi D, Chang EG, Byanyima P, Kaswabuli S, Musisi E, Sanyu I, Sessolo A, Lalitha R, Worodria W, Davis JL, Crothers K, Lin J, Lederman MM, Hunt PW, Huang L. HIV infection is associated with elevated biomarkers of immune activation in Ugandan adults with pneumonia. PLoS One 2019; 14:e0216680. [PMID: 31091258 PMCID: PMC6519791 DOI: 10.1371/journal.pone.0216680] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/08/2019] [Indexed: 01/12/2023] Open
Abstract
INTRODUCTION Pneumonia is an important cause of morbidity and mortality in persons living with human immunodeficiency virus (HIV) infection. How immune activation differs among HIV-infected and HIV-uninfected adults with pneumonia is unknown. METHODS The Inflammation, Aging, Microbes, and Obstructive Lung Disease (I AM OLD) Cohort is a prospective cohort of adults with pneumonia in Uganda. In this cross-sectional analysis, plasma was collected at pneumonia presentation to measure the following 12 biomarkers: interleukin 6 (IL-6), soluble tumor necrosis factor receptors 1 and 2 (sTNFR-1 and sTNFR-2), high sensitivity C-reactive protein (hsCRP), fibrinogen, D-dimer, soluble CD27 (sCD27), interferon gamma-inducible protein 10 (IP-10), soluble CD14 (sCD14), soluble CD163 (sCD163), hyaluronan, and intestinal fatty acid binding protein. We asked whether biomarker levels differed between HIV-infected and HIV-uninfected participants, and whether higher levels of these biomarkers were associated with mortality. RESULTS One hundred seventy-three participants were enrolled. Fifty-three percent were HIV-infected. Eight plasma biomarkers-sTNFR-1, sTNFR-2, hsCRP, D-dimer, sCD27, IP-10, sCD14, and hyaluronan-were higher among participants with HIV infection, after adjustment for pneumonia severity. Higher levels of 8 biomarkers-IL-6, sTNFR-1, sTNFR-2, hsCRP, IP-10, sCD14, sCD163, and hyaluronan-were associated with increased 2-month mortality. CONCLUSIONS As in other clinical contexts, HIV infection is associated with a greater degree of immune activation among Ugandan adults with pneumonia. Some of these are also associated with short-term mortality. Further study is needed to explore whether these biomarkers might predict poor long-term outcomes-such as the development of obstructive lung disease-in patients with HIV who have recovered from pneumonia.
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Affiliation(s)
- Richard J. Wang
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (RW); (LH)
| | - Julia Moore
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Daniela Moisi
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Emily G. Chang
- Department of Statistics, University of California Davis, Davis, California, United States of America
| | - Patrick Byanyima
- Makerere University – University of California San Francisco Research Collaboration, Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Sylvia Kaswabuli
- Makerere University – University of California San Francisco Research Collaboration, Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Emmanuel Musisi
- Makerere University – University of California San Francisco Research Collaboration, Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Ingvar Sanyu
- Makerere University – University of California San Francisco Research Collaboration, Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Abdulwahab Sessolo
- Makerere University – University of California San Francisco Research Collaboration, Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Rejani Lalitha
- Department of Internal Medicine, Makerere College of Health Sciences, Kampala, Uganda
| | - William Worodria
- Department of Internal Medicine, Makerere College of Health Sciences, Kampala, Uganda
| | - J. Lucian Davis
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Kristina Crothers
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Michael M. Lederman
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Peter W. Hunt
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Laurence Huang
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (RW); (LH)
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Shenoy MK, Fadrosh DW, Lin DL, Worodria W, Byanyima P, Musisi E, Kaswabuli S, Zawedde J, Sanyu I, Chang E, Fong S, McCauley K, Davis JL, Huang L, Lynch SV. Gut microbiota in HIV-pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction. Microbiome 2019; 7:37. [PMID: 30857553 PMCID: PMC6413461 DOI: 10.1186/s40168-019-0651-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 02/22/2019] [Indexed: 05/23/2023]
Abstract
Pneumonia is common and frequently fatal in HIV-infected patients, due to rampant, systemic inflammation and failure to control microbial infection. While airway microbiota composition is related to local inflammatory response, gut microbiota has been shown to correlate with the degree of peripheral immune activation (IL6 and IP10 expression) in HIV-infected patients. We thus hypothesized that both airway and gut microbiota are perturbed in HIV-infected pneumonia patients, that the gut microbiota is related to peripheral CD4+ cell counts, and that its associated products differentially program immune cell populations necessary for controlling microbial infection in CD4-high and CD4-low patients. To assess these relationships, paired bronchoalveolar lavage and stool microbiota (bacterial and fungal) from a large cohort of Ugandan, HIV-infected patients with pneumonia were examined, and in vitro tests of the effect of gut microbiome products on macrophage effector phenotypes performed. While lower airway microbiota stratified into three compositionally distinct microbiota as previously described, these were not related to peripheral CD4 cell count. In contrast, variation in gut microbiota composition significantly related to CD4 cell count, lung microbiota composition, and patient mortality. Compared with patients with high CD4+ cell counts, those with low counts possessed more compositionally similar airway and gut microbiota, evidence of microbial translocation, and their associated gut microbiome products reduced macrophage activation and IL-10 expression and increased IL-1β expression in vitro. These findings suggest that the gut microbiome is related to CD4 status and plays a key role in modulating macrophage function, critical to microbial control in HIV-infected patients with pneumonia.
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Affiliation(s)
- Meera K Shenoy
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
- Biomedical Sciences Graduate Program, UCSF, San Francisco, CA, USA
- Current address: Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Douglas W Fadrosh
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Din L Lin
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - William Worodria
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Patrick Byanyima
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Emmanuel Musisi
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Sylvia Kaswabuli
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Josephine Zawedde
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Emily Chang
- HIV, Infectious Diseases and Global Medicine Division, Department of Medicine, San Francisco General Hospital, UCSF, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, San Francisco General Hospital, UCSF, San Francisco, CA, USA
| | - Serena Fong
- HIV, Infectious Diseases and Global Medicine Division, Department of Medicine, San Francisco General Hospital, UCSF, San Francisco, CA, USA
| | - Kathryn McCauley
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - J Lucian Davis
- Department of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Laurence Huang
- HIV, Infectious Diseases and Global Medicine Division, Department of Medicine, San Francisco General Hospital, UCSF, San Francisco, CA, USA.
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, San Francisco General Hospital, UCSF, San Francisco, CA, USA.
| | - Susan V Lynch
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA.
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Farr K, Ravindran R, Strnad L, Chang E, Chaisson LH, Yoon C, Worodria W, Andama A, Ayakaka I, Bbosa Nalwanga P, Byanyima P, Kalema N, Kaswabuli S, Katagira W, Aman KD, Musisi E, Tumwine NW, Sanyu I, Ssebunya R, Davis JL, Huang L, Khan IH, Cattamanchi A. Diagnostic performance of blood inflammatory markers for tuberculosis screening in people living with HIV. PLoS One 2018; 13:e0206119. [PMID: 30352099 PMCID: PMC6198956 DOI: 10.1371/journal.pone.0206119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 10/08/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Approaches to screening for active tuberculosis (TB) among people living with HIV are inadequate, leading to missed diagnoses and poor implementation of preventive therapy. METHODS Consecutive HIV-infected adults hospitalized at Mulago Hospital (Kampala, Uganda) between June 2011 and July 2013 with a cough ≥ 2 weeks were enrolled. Patients underwent extensive evaluation for pulmonary TB. Concentrations of 43 cytokines/chemokines were measured at the same time point as C-reactive protein (CRP) in banked plasma samples using commercially-available multiplex kits. Advanced classification algorithms were used to rank cytokines/chemokines for their ability to identify TB, and to model the specificity of the top-ranked cytokines/chemokines individually and in combination with sensitivity constrained to ≥ 90% as recommended for TB screening. RESULTS The median plasma level of 5 biomarkers (IL-6, INF-γ, MIG, CRP, IL-18) was significantly different between patients with and without TB. With sensitivity constrained to 90%, all had low specificity with IL-6 showing the highest specificity (44%; 95% CI 37.4-49.5). Biomarker panels were found to be more valuable than any biomarker alone. A panel combining IFN-γ and IL-6 had the highest specificity (50%; 95% CI 46.7-53.3). Sensitivity remained high (>85%) for all panels among sputum smear-negative TB patients. CONCLUSIONS Direct measurement of unstimulated plasma cytokines/chemokines in peripheral blood is a promising approach to TB screening. Cytokine/chemokine panels retained high sensitivity for smear-negative TB and achieved improved specificity compared to individual cytokines/chemokines. These markers should be further evaluated in outpatient settings where most TB screening occurs and where other illnesses associated with systematic inflammation are less common.
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Affiliation(s)
- Katherine Farr
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco and Zuckerberg San Francisco General Hospital, San Francisco, California, United States of America
- Curry International Tuberculosis Center, University of California San Francisco, San Francisco, California, United States of America
| | - Resmi Ravindran
- Department of Pathology and Laboratory Medicine, University of California at Davis, Sacramento, California, United States of America
| | - Luke Strnad
- Division of Infectious Diseases, Oregon Health & Science University, Portland, Oregon, United States of America
- Epidemiology Programs, Oregon Health & Science University-Portland State University School of Public Health, Portland, Oregon, United States of America
| | - Emily Chang
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco and Zuckerberg San Francisco General Hospital, San Francisco, California, United States of America
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco and Zuckerberg San Francisco General Hospital, San Francisco, California, United States of America
| | - Lelia H. Chaisson
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Christina Yoon
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco and Zuckerberg San Francisco General Hospital, San Francisco, California, United States of America
| | - William Worodria
- Department of Medicine, School of Medicine, Makerere University, Kampala, Uganda
- Division of Respiratory Medicine, Department of Medicine, Mulago Hospital, Kampala, Uganda
| | - Alfred Andama
- Department of Medicine, Mulago Hospital, Makerere University, Kampala, Uganda
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Irene Ayakaka
- Infectious Diseases Research Collaboration, Kampala, Uganda
- International Multidisciplinary Programme to Address Lung Health and TB in Africa, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | | | - Nelson Kalema
- Infectious Diseases Institute, Department of Research, Makerere College Health Sciences, Makerere University, Kampala, Uganda
| | | | | | | | - Emmanuel Musisi
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Biochemistry, College of Natural Sciences, Makerere University, Kampala, Uganda
| | | | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - J. Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco and Zuckerberg San Francisco General Hospital, San Francisco, California, United States of America
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco and Zuckerberg San Francisco General Hospital, San Francisco, California, United States of America
| | - Imran H. Khan
- Department of Pathology and Laboratory Medicine, University of California at Davis, Sacramento, California, United States of America
| | - Adithya Cattamanchi
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco and Zuckerberg San Francisco General Hospital, San Francisco, California, United States of America
- Curry International Tuberculosis Center, University of California San Francisco, San Francisco, California, United States of America
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10
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Musisi E, Matovu DK, Bukenya A, Kaswabuli S, Zawedde J, Andama A, Byanyima P, Sanyu I, Sessolo A, Seremba E, Davis JL, Worodria W, Huang L, Walter ND, Mayanja-Kizza H. Effect of anti-retroviral therapy on oxidative stress in hospitalized HIV-infected adults with and without TB. Afr Health Sci 2018; 18:512-522. [PMID: 30602982 PMCID: PMC6306996 DOI: 10.4314/ahs.v18i3.7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background HIV infection and opportunistic infections cause oxidative stress (OS), which is associated with tissue damage. Anti-retroviral therapy (ART) is used to treat HIV and decrease the risk of opportunistic infections, but it is unclear whether ART reduces OS. Association of ART with OS was investigated. Methods We stratified a convenience sample of frozen serum or plasma from HIV-infected, ART-naïve (n=21); HIV-infected, ART-treated (n=14); HIV and PTB co-infected, ART-naïve (n=21); HIV and PTB co-infected, ART-treated (n=25) patients. Controls (n=21) were HIV-negative adults without TB symptoms. Concentration of OS markers namely: transaminases (ALT and AST), gamma glutamyl transpeptidase (GGT), albumin, total protein, malondialdehyde (MDA), vitamin C, and total anti-oxidant status (TAS) were determined. Results AST (p<0.001), GGT (p<0.001), total protein (p=0.001) and MDA (p<0.001) were higher in HIV patients compared to controls. Vitamin C (P<0.0001) and albumin (p<0.01) were lower in HIV-patients relative to controls. ART was only associated with higher albumin (p=0.001), higher GGT (p=0.02) and lower vitamin C (p=0.009). HIV and PTB co-infection was only significantly associated with higher GGT (p=0.01) and AST (p=0.03). Conclusion We identified severe OS among HIV-patients. ART was associated with both increased and reduced markers of OS hence suggesting that ART may not attenuate OS.
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Affiliation(s)
- Emmanuel Musisi
- Infectious Diseases Research Collaboration, Plot 2C Nakasero Hill Road PO Box 7475, Kampala Uganda
- College of Natural Science Department of Biochemistry and Sports Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Denis Kasozi Matovu
- College of Natural Science Department of Biochemistry and Sports Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Andrew Bukenya
- College of Health Sciences, Department of Medical Biochemistry, Makerere University, PO Box 7072, Kampala, Uganda
| | - Sylvia Kaswabuli
- Infectious Diseases Research Collaboration, Plot 2C Nakasero Hill Road PO Box 7475, Kampala Uganda
| | - Josephine Zawedde
- Infectious Diseases Research Collaboration, Plot 2C Nakasero Hill Road PO Box 7475, Kampala Uganda
| | - Alfred Andama
- Infectious Diseases Research Collaboration, Plot 2C Nakasero Hill Road PO Box 7475, Kampala Uganda
| | - Patrick Byanyima
- Infectious Diseases Research Collaboration, Plot 2C Nakasero Hill Road PO Box 7475, Kampala Uganda
| | - Ingvar Sanyu
- Infectious Diseases Research Collaboration, Plot 2C Nakasero Hill Road PO Box 7475, Kampala Uganda
| | - Abdul Sessolo
- Infectious Diseases Research Collaboration, Plot 2C Nakasero Hill Road PO Box 7475, Kampala Uganda
| | - Emmanuel Seremba
- College of Health Sciences, Department of Medicine, Makerere University PO Box 7072, Kampala, Uganda
| | | | - William Worodria
- Infectious Diseases Research Collaboration, Plot 2C Nakasero Hill Road PO Box 7475, Kampala Uganda
| | - Laurence Huang
- Infectious Diseases Research Collaboration, Plot 2C Nakasero Hill Road PO Box 7475, Kampala Uganda
- HIV, Infectious Diseases, and Global Medicine Division, University of California, San Francisco, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas D Walter
- Infectious Diseases Research Collaboration, Plot 2C Nakasero Hill Road PO Box 7475, Kampala Uganda
- Pulmonary Section, Denver Veterans Affairs Medical Center, Denver, USA
| | - Harriet Mayanja-Kizza
- College of Health Sciences, Department of Medicine, Makerere University PO Box 7072, Kampala, Uganda
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11
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Kelly-Cirino CD, Musisi E, Byanyima P, Kaswabuli S, Andama A, Sessolo A, Sanyu I, Zawedde J, Curry PS, Huang L. Investigation of OMNIgene·SPUTUM performance in delayed tuberculosis testing by smear, culture, and Xpert MTB/RIF assays in Uganda. J Epidemiol Glob Health 2017; 7:103-109. [PMID: 28413105 PMCID: PMC7320428 DOI: 10.1016/j.jegh.2017.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
OMNIgene·SPUTUM (OM-S) is a sample transport reagent designed to work with all tuberculosis diagnostics while eliminating the need for cold chain. OM-S-treated sputum samples were assayed in several tests after multiday holds. Raw sputa from 100 patients underwent direct smear microscopy, were manually split and assigned to the OM-S group [OM-S added at collection (no other processing required) and tested after 0- to 5-day holds at room temperature] or standard-of-care (SOC) group (NaOH/N-acetyl l-cysteine decontamination, all tested on day of collection). Concentrated smear microscopy, Lowenstein Jensen (LJ) culture, and mycobacteria growth indicator tube (MGIT) culture were performed. For patients with negative direct smear, a second sample was split, with SOC (raw sputum) and OM-S portions (sediment) tested in the Xpert MTB/RIF (Xpert) assay. OM-S group and SOC group results were strongly concordant on all four tests [range, 89% (MGIT)–97% (Xpert)]. OM-S MGIT, LJ, and Xpert tests were in statistical agreement with SOC MGIT as reference. OM-S specimens had lower culture contamination rates (3% vs. 10% LJ; 2% vs. 5% MGIT) but required, on average, 5.6 additional days to become MGIT-positive. The findings suggest that samples held/transported in OM-S are compatible with smear microscopy, LJ or MGIT culture, and Xpert, and perform comparably to fresh sputum samples. Larger feasibility studies are warranted.
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Affiliation(s)
- C D Kelly-Cirino
- DNA Genotek, 500 Palladium Dr., Suite 3000, Ottawa, Ontario K2V 1C2, Canada.
| | - E Musisi
- Infectious Diseases Research Collaboration Kampala, 2C Nakasero Hill Road, PO Box 7475, Kampala, Uganda.
| | - P Byanyima
- Infectious Diseases Research Collaboration Kampala, 2C Nakasero Hill Road, PO Box 7475, Kampala, Uganda.
| | - S Kaswabuli
- Infectious Diseases Research Collaboration Kampala, 2C Nakasero Hill Road, PO Box 7475, Kampala, Uganda.
| | - A Andama
- Infectious Diseases Research Collaboration Kampala, 2C Nakasero Hill Road, PO Box 7475, Kampala, Uganda.
| | - A Sessolo
- Infectious Diseases Research Collaboration Kampala, 2C Nakasero Hill Road, PO Box 7475, Kampala, Uganda.
| | - I Sanyu
- Infectious Diseases Research Collaboration Kampala, 2C Nakasero Hill Road, PO Box 7475, Kampala, Uganda.
| | - J Zawedde
- Infectious Diseases Research Collaboration Kampala, 2C Nakasero Hill Road, PO Box 7475, Kampala, Uganda.
| | - P S Curry
- DNA Genotek, 500 Palladium Dr., Suite 3000, Ottawa, Ontario K2V 1C2, Canada.
| | - L Huang
- University of California San Francisco, HIV, Infectious Diseases, and Global Medicine Division and Division of Pulmonary and Critical Care Medicine - Ward 84, San Francisco General Hospital, 995 Potrero Avenue, San Francisco, CA 94110, USA.
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12
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Shenoy MK, Iwai S, Lin DL, Worodria W, Ayakaka I, Byanyima P, Kaswabuli S, Fong S, Stone S, Chang E, Davis JL, Faruqi AA, Segal MR, Huang L, Lynch SV. Immune Response and Mortality Risk Relate to Distinct Lung Microbiomes in Patients with HIV and Pneumonia. Am J Respir Crit Care Med 2017; 195:104-114. [PMID: 27447987 PMCID: PMC5214918 DOI: 10.1164/rccm.201603-0523oc] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [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: 03/11/2016] [Accepted: 07/22/2016] [Indexed: 02/01/2023] Open
Abstract
RATIONALE The potential role of the airway microbiota in dictating immune responses and infection outcomes in HIV-associated pneumonia is largely unknown. OBJECTIVES To investigate whether microbiologically and immunologically distinct subsets of patients with HIV and pneumonia exist and are related to mortality. METHODS Bronchoalveolar lavage samples from Ugandan patients with HIV and pneumonia (n = 182) were obtained at study enrollment (following antibiotic treatment); patient demographics including 8- and 70-day mortality were collected. Lower airway bacterial community composition was assessed via amplification and sequencing of the V4 region of the 16S ribosomal RNA gene. Host immune response gene expression profiles were generated by quantitative polymerase chain reaction using RNA extracted from bronchoalveolar lavage fluid. Liquid and gas chromatography mass spectrometry was used to profile serum metabolites. MEASUREMENTS AND MAIN RESULTS Based on airway microbiome composition, most patients segregated into three distinct groups, each of which were predicted to encode metagenomes capable of producing metabolites characteristically enriched in paired serum samples from these patients. These three groups also exhibited differences in mortality; those with the highest rate had increased ceftriaxone administration and culturable Aspergillus, and demonstrated significantly increased induction of airway T-helper cell type 2 responses. The group with the lowest mortality was characterized by increased expression of T-cell immunoglobulin and mucin domain 3, which down-regulates T-helper cell type 1 proinflammatory responses and is associated with chronic viral infection. CONCLUSIONS These data provide evidence that compositionally and structurally distinct lower airway microbiomes are associated with discrete local host immune responses, peripheral metabolic reprogramming, and different rates of mortality.
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Affiliation(s)
- Meera K. Shenoy
- Division of Gastroenterology, Department of Medicine
- Biomedical Sciences Graduate Program
| | - Shoko Iwai
- Division of Gastroenterology, Department of Medicine
| | - Din L. Lin
- Division of Gastroenterology, Department of Medicine
| | - William Worodria
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Irene Ayakaka
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Patrick Byanyima
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Sylvia Kaswabuli
- Infectious Diseases Research Collaboration, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Serena Fong
- HIV, Infectious Diseases and Global Medicine Division, San Francisco General Hospital
| | - Stephen Stone
- HIV, Infectious Diseases and Global Medicine Division, San Francisco General Hospital
| | - Emily Chang
- HIV, Infectious Diseases and Global Medicine Division, San Francisco General Hospital
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, and
| | - J. Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut; and
- Pulmonary, Critical Care, and Sleep Medicine Section, Yale School of Medicine, New Haven, Connecticut
| | | | - Mark R. Segal
- Division of Biostatistics, University of California San Francisco, San Francisco, California
| | - Laurence Huang
- HIV, Infectious Diseases and Global Medicine Division, San Francisco General Hospital
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, and
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13
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Kalema N, Lindan C, Glidden D, Yoo SD, Katamba A, Alfred A, Katagira W, Byanyima P, Musisi E, Kaswabuli S, Ingvar S, Zawedde J, Yoon C, Ayakaka I, Davis JL, Huang L, Worodria W, Cattamanchi A. Predictors and short-term outcomes of recurrent pulmonary tuberculosis, Uganda: a cohort study. S Afr Respir J 2017; 23:106-112. [PMID: 29368752 PMCID: PMC5777612] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
INTRODUCTION Recurrent tuberculosis (TB) occurring >2 years after completing treatment for a prior TB episode is most often due to reinfection with a new strain of M. tuberculosis. OBJECTIVES We determined the prevalence and outcome of late recurrent TB among hospitalized patients in Kampala, Uganda. METHODS We conducted a retrospective analysis of patients admitted to Mulago Hospital who had cough of >2 weeks' duration and completed TB treatment >2 years prior to admission. All patients had mycobacterial culture performed on two sputum specimens and vital status ascertained 2-months post-enrollment. We performed modeling to identify predictors of recurrent TB and of survival. RESULTS Among 234 patients, 84 (36%) had recurrent TB. Independent predictors included younger age (aOR=0.64, 95% CI=0.42-0.97, p=0.04), chest pain >2 weeks (aOR=3.32, 95% CI=1.38-8.02, p=0.007), severe weight loss ≥5 kilograms (aOR=4.88, 95% CI=1.66-14.29, p=0.004) and presence of ≥1 WHO danger sign of severe illness (aOR=3.55, 95% CI=1.36-9.29, p=0.01). Two-month mortality was 17.8% (95% CI=10.5-29.2%), and was higher among patients not initiated on TB treatment (aHR=16.67, 95% CI=1.18-200, p=0.04), not on ART if HIV-positive (aHR=16.99, 95% CI=1.17-246.47, p=0.04) and with a history of smoking (aHR=1.20, 95% CI=1.03-1.40, p=0.02). CONCLUSION The high prevalence of late recurrent TB likely reflects high levels of TB transmission in Kampala. Increased use of empiric TB treatment and early ART treatment initiation if HIV-positive should be considered in patients with a prior history of TB, particularly if young, with weight loss ≥5kgs, chest pain >2 weeks or ≥1 WHO danger sign of severe illness.
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Affiliation(s)
- Nelson Kalema
- Infectious Disease Research Collaboration, Kampala, Uganda
- Department of Medicine, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Christina Lindan
- Department of Epidemiology and Biostatistics and Global Health Sciences, University of California San Francisco, San Francisco, CA
| | - Dave Glidden
- Department of Epidemiology and Biostatistics and Global Health Sciences, University of California San Francisco, San Francisco, CA
| | - Samuel D. Yoo
- Infectious Disease Research Collaboration, Kampala, Uganda
- Department of Internal Medicine, Jimma University, Jimma, Ethiopia
| | - Achilles Katamba
- Department of Medicine, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Andama Alfred
- Infectious Disease Research Collaboration, Kampala, Uganda
| | | | | | | | | | - Sanyu Ingvar
- Infectious Disease Research Collaboration, Kampala, Uganda
| | | | - Christina Yoon
- Infectious Disease Research Collaboration, Kampala, Uganda
- Division of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital, University of California San Francisco, San Francisco, CA
| | - Irene Ayakaka
- Infectious Disease Research Collaboration, Kampala, Uganda
| | - J. Lucian Davis
- Yale School of Public Health, New Haven, CT
- Pulmonary, Critical Care, and Sleep Medicine Section, Yale School of Medicine, New Haven, CT
| | - Laurence Huang
- Infectious Disease Research Collaboration, Kampala, Uganda
- Division of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital, University of California San Francisco, San Francisco, CA
- HIV, Infectious Diseases, and Global Medicine Division, Zuckerberg San Francisco General Hospital, University of California San Francisco, San Francisco, CA
| | - William Worodria
- Infectious Disease Research Collaboration, Kampala, Uganda
- Department of Medicine, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Adithya Cattamanchi
- Infectious Disease Research Collaboration, Kampala, Uganda
- Department of Epidemiology and Biostatistics and Global Health Sciences, University of California San Francisco, San Francisco, CA
- Division of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital, University of California San Francisco, San Francisco, CA
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14
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Iwai S, Huang D, Fong S, Jarlsberg LG, Worodria W, Yoo S, Cattamanchi A, Davis JL, Kaswabuli S, Segal M, Huang L, Lynch SV. The lung microbiome of Ugandan HIV-infected pneumonia patients is compositionally and functionally distinct from that of San Franciscan patients. PLoS One 2014; 9:e95726. [PMID: 24752365 PMCID: PMC3994144 DOI: 10.1371/journal.pone.0095726] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/28/2014] [Indexed: 11/21/2022] Open
Abstract
Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome was significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population.
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Affiliation(s)
- Shoko Iwai
- Division of Gastroenterology, University of California San Francisco, San Francisco, California, United States of America
| | - Delphine Huang
- Division of Gastroenterology, University of California San Francisco, San Francisco, California, United States of America
- School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Serena Fong
- HIV/AIDS Division, University of California San Francisco, San Francisco, California, United States of America
| | - Leah G. Jarlsberg
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - William Worodria
- Department of Medicine, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Samuel Yoo
- Department of Medicine, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Adithya Cattamanchi
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - J. Lucian Davis
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Sylvia Kaswabuli
- Department of Medicine, Mulago Hospital, Makerere University, Kampala, Uganda
| | - Mark Segal
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Laurence Huang
- HIV/AIDS Division, University of California San Francisco, San Francisco, California, United States of America
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Susan V. Lynch
- Division of Gastroenterology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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15
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Taylor SM, Meshnick SR, Worodria W, Andama A, Cattamanchi A, Davis JL, Yoo SD, Byanyima P, Kaswabuli S, Goodman CD, Huang L. Low prevalence of Pneumocystis pneumonia (PCP) but high prevalence of pneumocystis dihydropteroate synthase (dhps) gene mutations in HIV-infected persons in Uganda. PLoS One 2012; 7:e49991. [PMID: 23166805 PMCID: PMC3500344 DOI: 10.1371/journal.pone.0049991] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 10/19/2012] [Indexed: 12/03/2022] Open
Abstract
Pneumocystis jirovecii pneumonia (PCP) is an important opportunistic infection in patients infected with HIV, but its burden is incompletely characterized in those areas of sub-Saharan Africa where HIV is prevalent. We explored the prevalence of both PCP in HIV-infected adults admitted with pneumonia to a tertiary-care hospital in Uganda and of putative P. jirovecii drug resistance by mutations in fungal dihydropteroate synthase (dhps) and dihydrofolate reductase (dhfr). In 129 consecutive patients with sputum smears negative for mycobacteria, 5 (3.9%) were diagnosed with PCP by microscopic examination of Giemsa-stained bronchoalveolar lavage fluid. Concordance was 100% between Giemsa stain and PCR (dhps and dhfr). PCP was more prevalent in patients newly-diagnosed with HIV (11.4%) than in patients with known HIV (1.1%; p = 0.007). Mortality at 2 months after discharge was 29% overall: 28% among PCP-negative patients, and 60% (3 of 5) among PCP-positive patients. In these 5 fungal isolates and an additional 8 from consecutive cases of PCP, all strains harbored mutant dhps haplotypes; all 13 isolates harbored the P57S mutation in dhps, and 3 (23%) also harbored the T55A mutation. No non-synonymous dhfr mutations were detected. PCP is an important cause of pneumonia in patients newly-diagnosed with HIV in Uganda, is associated with high mortality, and putative molecular evidence of drug resistance is prevalent. Given the reliability of field diagnosis in our cohort, future studies in sub-Saharan Africa can investigate the clinical impact of these genotypes.
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Affiliation(s)
- Steve M Taylor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America.
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16
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Yoon C, Cattamanchi A, Davis JL, Worodria W, den Boon S, Kalema N, Katagira W, Kaswabuli S, Miller C, Andama A, Albert H, Nabeta P, Gray C, Ayakaka I, Huang L. Impact of Xpert MTB/RIF testing on tuberculosis management and outcomes in hospitalized patients in Uganda. PLoS One 2012; 7:e48599. [PMID: 23139799 PMCID: PMC3490868 DOI: 10.1371/journal.pone.0048599] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/27/2012] [Indexed: 02/07/2023] Open
Abstract
RATIONALE The clinical impact of Xpert MTB/RIF for tuberculosis (TB) diagnosis in high HIV-prevalence settings is unknown. OBJECTIVE To determine the diagnostic accuracy and impact of Xpert MTB/RIF among high-risk TB suspects. METHODS WE PROSPECTIVELY ENROLLED CONSECUTIVE, HOSPITALIZED, UGANDAN TB SUSPECTS IN TWO PHASES: baseline phase in which Xpert MTB/RIF results were not reported to clinicians and an implementation phase in which results were reported. We determined the diagnostic accuracy of Xpert MTB/RIF in reference to culture (solid and liquid) and compared patient outcomes by study phase. RESULTS 477 patients were included (baseline phase 287, implementation phase 190). Xpert MTB/RIF had high sensitivity (187/237, 79%, 95% CI: 73-84%) and specificity (190/199, 96%, 95% CI: 92-98%) for culture-positive TB overall, but sensitivity was lower (34/81, 42%, 95% CI: 31-54%) among smear-negative TB cases. Xpert MTB/RIF reduced median days-to-TB detection for all TB cases (1 [IQR 0-26] vs. 0 [IQR 0-1], p<0.001), and for smear-negative TB (35 [IQR 22-55] vs. 22 [IQR 0-33], p=0.001). However, median days-to-TB treatment was similar for all TB cases (1 [IQR 0-5] vs. 0 [IQR 0-2], p=0.06) and for smear-negative TB (7 [IQR 3-53] vs. 6 [IQR 1-61], p=0.78). Two-month mortality was also similar between study phases among 252 TB cases (17% vs. 14%, difference +3%, 95% CI: -21% to +27%, p=0.80), and among 87 smear-negative TB cases (28% vs. 22%, difference +6%, 95% CI: -34 to +46%, p=0.77). CONCLUSIONS Xpert MTB/RIF facilitated more accurate and earlier TB diagnosis, leading to a higher proportion of TB suspects with a confirmed TB diagnosis prior to hospital discharge in a high HIV/low MDR TB prevalence setting. However, our study did not detect a decrease in two-month mortality following implementation of Xpert MTB/RIF possibly because of insufficient powering, differences in empiric TB treatment rates, and disease severity between study phases.
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Affiliation(s)
- Christina Yoon
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Adithya Cattamanchi
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
- Curry International Tuberculosis Center, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
| | - J. Lucian Davis
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
- Curry International Tuberculosis Center, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - William Worodria
- Department of Medicine, Faculty of Medicine, Makerere University, Kampala, Uganda
- Uganda Ministry of Health, Kampala, Uganda
| | - Saskia den Boon
- Makerere University-University of California San Francisco Research Collaboration, Kampala, Uganda
| | - Nelson Kalema
- Makerere University-University of California San Francisco Research Collaboration, Kampala, Uganda
| | - Winceslaus Katagira
- Makerere University-University of California San Francisco Research Collaboration, Kampala, Uganda
| | - Sylvia Kaswabuli
- Makerere University-University of California San Francisco Research Collaboration, Kampala, Uganda
| | - Cecily Miller
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Alfred Andama
- Department of Medicine, Faculty of Medicine, Makerere University, Kampala, Uganda
| | - Heidi Albert
- Foundation for Innovative New Diagnostics, Kampala, Uganda
| | - Pamela Nabeta
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Christen Gray
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Irene Ayakaka
- Makerere University-University of California San Francisco Research Collaboration, Kampala, Uganda
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
- HIV/AIDS Division, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
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17
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Kalema N, Boon SD, Cattamanchi A, Davis JL, Andama A, Katagira W, Everett C, Walter N, Byanyima P, Kaswabuli S, Worodria W, Huang L. Oral antimicrobial rinse to reduce mycobacterial culture contamination among tuberculosis suspects in Uganda: a prospective study. PLoS One 2012; 7:e38888. [PMID: 22808020 PMCID: PMC3395623 DOI: 10.1371/journal.pone.0038888] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 05/15/2012] [Indexed: 12/26/2022] Open
Abstract
RATIONALE Contamination by bacterial or fungal organisms reduces the effectiveness of mycobacterial culture for diagnosis of pulmonary tuberculosis (TB). We evaluated the effect of an anti-microbial and an anti-fungal oral rinse prior to expectoration on culture-contamination rates. METHODS We enrolled a consecutive random sample of adults with cough for ≥ 2 weeks and suspected TB admitted to Mulago Hospital (Kampala, Uganda) between October 2008 and June 2009. We randomly assigned patients to oral rinse (60 seconds with chlorhexidine followed by 60 seconds with nystatin) vs. no oral rinse prior to initial sputum collection. Uganda National Tuberculosis Reference Laboratory technicians blinded to the method of sputum collection (with or without oral rinse) processed all sputum specimens for smear microscopy (direct Ziehl-Neelsen) and mycobacterial culture (Lowenstein-Jensen media). RESULTS Of 220 patients enrolled, 177 (80%) were HIV-seropositive (median CD4-count 37 cells/uL, IQR 13-171 cells/uL). Baseline characteristics were similar between patients in the oral-rinse (N = 110) and no oral-rinse (N = 110) groups. The proportion of contaminated cultures was significantly lower in the oral-rinse group compared to the no oral-rinse group (4% vs. 15%, risk difference -11%, 95% CI -18 to -3%, p = 0.005). Oral rinse significantly reduced the proportion of contaminated cultures among HIV-infected patients (3% vs. 18%, risk difference -14%, 95% CI -23 to -6%, p = 0.002) but not HIV-uninfected (6% vs. 4%, risk difference 2%, 95% CI -12 to +15%, p = 0.81) patients. However, the proportion of smear-positive specimens (25% vs. 35%, p = 0.10) and culture-positive specimens (48% vs. 56%, p = 0.24) were lower in the oral-rinse compared to the no oral-rinse group, although the differences were not statistically significant. CONCLUSIONS Oral rinse prior to sputum expectoration is a promising strategy to reduce mycobacterial culture contamination in areas with high HIV prevalence, if strategies can be devised to reduce the adverse impact of oral rinse on smear- and culture-positivity.
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Affiliation(s)
- Nelson Kalema
- Makerere University - University of California San Francisco Research Collaboration, Kampala, Uganda.
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