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Ofori-Anyinam B, Dolganov G, Van T, Davis JL, Walter ND, Garcia BJ, Voskuil M, Fissette K, Diels M, Driesen M, Meehan CJ, Yeboah-Manu D, Coscolla M, Gagneux S, Antonio M, Schoolnik G, Gehre F, de Jong BC. Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum. Tuberculosis (Edinb) 2017; 104:58-64. [PMID: 28454650 PMCID: PMC5421582 DOI: 10.1016/j.tube.2017.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/21/2017] [Accepted: 03/02/2017] [Indexed: 11/19/2022]
Abstract
Mycobacterium africanum lineage (L) 6 is an important pathogen in West Africa, causing up to 40% of pulmonary tuberculosis (TB). The biology underlying the clinical differences between M. africanum and M. tuberculosis sensu stricto remains poorly understood. We performed ex vivo expression of 2179 genes of the most geographically dispersed cause of human TB, M. tuberculosis L4 and the geographically restricted, M. africanum L6 directly from sputa of 11 HIV-negative TB patients from The Gambia who had not started treatment. The DosR regulon was the most significantly decreased category in L6 relative to L4. Further, we identified nonsynonymous mutations in major DosR regulon genes of 44 L6 genomes of TB patients from The Gambia and Ghana. Using Lebek's test, we assessed differences in oxygen requirements for growth. L4 grew only at the aerobic surface while L6 grew throughout the medium. In the host, the DosR regulon is critical for M. tuberculosis in adaptation to oxygen limitation. However, M. africanum L6 appears to have adapted to growth under hypoxic conditions or to different biological niches. The observed under expression of DosR in L6 fits with the genomic changes in DosR genes, microaerobic growth and the association with extrapulmonary disease.
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Affiliation(s)
- Boatema Ofori-Anyinam
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium; Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, The Gambia, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, Gambia
| | - Gregory Dolganov
- Department of Microbiology and Immunology, Stanford University, 299 Campus Drive, Stanford, CA, 94305, USA
| | - Tran Van
- Department of Microbiology and Immunology, Stanford University, 299 Campus Drive, Stanford, CA, 94305, USA
| | - J Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, P.O. Box 208034, New Haven, CT, 06520-8034, USA; Department of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, P.O. Box 208057, 300 Cedar Street TAC - 441 South, New Haven, CT, 06520-8057, USA
| | - Nicholas D Walter
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Building 500 - 13001 E, 17th Place, Campus Box C290, Aurora, CO, 80045, USA; Pulmonary Section, Denver Veterans Affairs Medical Center, 1055 Clermont Street, Denver, CO, 80220, USA; Integrated Center for Genes, Environment, & Health, National Jewish Health, Smith Building; A647, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Benjamin J Garcia
- Integrated Center for Genes, Environment, & Health, National Jewish Health, Smith Building; A647, 1400 Jackson Street, Denver, CO, 80206, USA; Computational Bioscience Program, University of Colorado Denver, Building 500 - 13001 E, 17th Place, Campus Box C290, Aurora, CO, 80045, USA
| | - Marty Voskuil
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 E. 19th Ave., Mail Stop 8333, Aurora, CO, 80045, USA
| | - Kristina Fissette
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium
| | - Maren Diels
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium
| | - Michèle Driesen
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium
| | - Conor J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana
| | - Mireia Coscolla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, P.O. Box 4002, Basel, Switzerland; University of Basel, Petersplatz 1, P.O. Box 4001, Basel, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, P.O. Box 4002, Basel, Switzerland; University of Basel, Petersplatz 1, P.O. Box 4001, Basel, Switzerland
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, The Gambia, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, Gambia
| | - Gary Schoolnik
- Department of Microbiology and Immunology, Stanford University, 299 Campus Drive, Stanford, CA, 94305, USA
| | - Florian Gehre
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium; Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, The Gambia, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, Gambia
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Nationalestraat 155, 2000, Antwerp, Belgium.
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Garcia BJ, Loxton AG, Dolganov GM, Van TT, Davis JL, de Jong BC, Voskuil MI, Leach SM, Schoolnik GK, Walzl G, Strong M, Walter ND. Sputum is a surrogate for bronchoalveolar lavage for monitoring Mycobacterium tuberculosis transcriptional profiles in TB patients. Tuberculosis (Edinb) 2016; 100:89-94. [PMID: 27553415 PMCID: PMC4999252 DOI: 10.1016/j.tube.2016.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/03/2016] [Accepted: 07/09/2016] [Indexed: 12/19/2022]
Abstract
Pathogen-targeted transcriptional profiling in human sputum may elucidate the physiologic state of Mycobacterium tuberculosis (M. tuberculosis) during infection and treatment. However, whether M. tuberculosis transcription in sputum recapitulates transcription in the lung is uncertain. We therefore compared M. tuberculosis transcription in human sputum and bronchoalveolar lavage (BAL) samples from 11 HIV-negative South African patients with pulmonary tuberculosis. We additionally compared these clinical samples with in vitro log phase aerobic growth and hypoxic non-replicating persistence (NRP-2). Of 2179 M. tuberculosis transcripts assayed in sputum and BAL via multiplex RT-PCR, 194 (8.9%) had a p-value <0.05, but none were significant after correction for multiple testing. Categorical enrichment analysis indicated that expression of the hypoxia-responsive DosR regulon was higher in BAL than in sputum. M. tuberculosis transcription in BAL and sputum was distinct from both aerobic growth and NRP-2, with a range of 396-1020 transcripts significantly differentially expressed after multiple testing correction. Collectively, our results indicate that M. tuberculosis transcription in sputum approximates M. tuberculosis transcription in the lung. Minor differences between M. tuberculosis transcription in BAL and sputum suggested lower oxygen concentrations or higher nitric oxide concentrations in BAL. M. tuberculosis-targeted transcriptional profiling of sputa may be a powerful tool for understanding M. tuberculosis pathogenesis and monitoring treatment responses in vivo.
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Affiliation(s)
- Benjamin J Garcia
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA; Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.
| | - Andre G Loxton
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gregory M Dolganov
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Tran T Van
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - J Lucian Davis
- Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - Martin I Voskuil
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sonia M Leach
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA; Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Gary K Schoolnik
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Gerhard Walzl
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA; Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Nicholas D Walter
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA; Pulmonary Section, Denver Veterans Affairs Medical Center, Denver, CO, USA; Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
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Walter ND, de Jong BC, Garcia BJ, Dolganov GM, Worodria W, Byanyima P, Musisi E, Huang L, Chan ED, Van TT, Antonio M, Ayorinde A, Kato-Maeda M, Nahid P, Leung AM, Yen A, Fingerlin TE, Kechris K, Strong M, Voskuil MI, Davis JL, Schoolnik GK. Adaptation of Mycobacterium tuberculosis to Impaired Host Immunity in HIV-Infected Patients. J Infect Dis 2016; 214:1205-11. [PMID: 27534685 DOI: 10.1093/infdis/jiw364] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND It is unknown whether immunosuppression influences the physiologic state of Mycobacterium tuberculosis in vivo. We evaluated the impact of host immunity by comparing M. tuberculosis and human gene transcription in sputum between human immunodeficiency virus (HIV)-infected and uninfected patients with tuberculosis. METHODS We collected sputum specimens before treatment from Gambians and Ugandans with pulmonary tuberculosis, revealed by positive results of acid-fast bacillus smears. We quantified expression of 2179 M. tuberculosis genes and 234 human immune genes via quantitative reverse transcription-polymerase chain reaction. We summarized genes from key functional categories with significantly increased or decreased expression. RESULTS A total of 24 of 65 patients with tuberculosis were HIV infected. M. tuberculosis DosR regulon genes were less highly expressed among HIV-infected patients with tuberculosis than among HIV-uninfected patients with tuberculosis (Gambia, P < .0001; Uganda, P = .037). In profiling of human genes from the same sputa, HIV-infected patients had 3.4-fold lower expression of IFNG (P = .005), 4.9-fold higher expression of ARG1 (P = .0006), and 3.4-fold higher expression of IL10 (P = .0002) than in HIV-uninfected patients with tuberculosis. CONCLUSIONS M. tuberculosis in HIV-infected patients had lower expression of the DosR regulon, a critical metabolic and immunomodulatory switch induced by NO, carbon monoxide, and hypoxia. Our human data suggest that decreased DosR expression may result from alternative pathway activation of macrophages, with consequent decreased NO expression and/or by poor granuloma formation with consequent decreased hypoxic stress.
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Affiliation(s)
- Nicholas D Walter
- Pulmonary Section, Denver Veterans Affairs Medical Center Integrated Center for Genes, Environment, and Health Division of Pulmonary Sciences and Critical Care Medicine
| | - Bouke C de Jong
- New York University, New York Institute of Tropical Medicine, Antwerp, Belgium Medical Research Council Laboratories, Serrekunda, Gambia
| | - Benjamin J Garcia
- Integrated Center for Genes, Environment, and Health Computational Bioscience Program
| | | | - William Worodria
- Makerere University-UCSF Research Collaboration, Kampala, Uganda
| | - Patrick Byanyima
- Makerere University-UCSF Research Collaboration, Kampala, Uganda
| | - Emmanuel Musisi
- Makerere University-UCSF Research Collaboration, Kampala, Uganda
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine HIV/AIDS Division, University of California-San Francisco (UCSF)
| | - Edward D Chan
- Pulmonary Section, Denver Veterans Affairs Medical Center Department of Academic Affairs and Medicine, National Jewish Health, Denver Division of Pulmonary Sciences and Critical Care Medicine
| | - Tran T Van
- Department of Microbiology and Immunology
| | - Martin Antonio
- Medical Research Council Laboratories, Serrekunda, Gambia
| | | | | | - Payam Nahid
- Division of Pulmonary and Critical Care Medicine
| | - Ann M Leung
- Department of Radiology, Stanford University Medical Center
| | - Andrew Yen
- Department of Radiology, University of California-San Diego
| | | | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora
| | - Michael Strong
- Integrated Center for Genes, Environment, and Health Computational Bioscience Program
| | - Martin I Voskuil
- Department of Immunology and Microbiology, University of Colorado-Denver Anschutz Medical Campus
| | - J Lucian Davis
- Department of Epidemiology of Microbial Diseases Department of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
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Ofori-Anyinam B, Kanuteh F, Agbla SC, Adetifa I, Okoi C, Dolganov G, Schoolnik G, Secka O, Antonio M, de Jong BC, Gehre F. Impact of the Mycobaterium africanum West Africa 2 Lineage on TB Diagnostics in West Africa: Decreased Sensitivity of Rapid Identification Tests in The Gambia. PLoS Negl Trop Dis 2016; 10:e0004801. [PMID: 27387550 PMCID: PMC4936735 DOI: 10.1371/journal.pntd.0004801] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/02/2016] [Indexed: 01/19/2023] Open
Abstract
Background MPT64 rapid speciation tests are increasingly being used in diagnosis of tuberculosis (TB). Mycobacterium africanum West Africa 2 (Maf 2) remains an important cause of TB in West Africa and causes one third of disease in The Gambia. Since the introduction of MPT64 antigen tests, a higher than expected rate of suspected non-tuberculous mycobacteria (NTM) was seen among AFB smear positive TB suspects, which led us to prospectively assess sensitivity of the MPT64 antigen test in our setting. Methodology/Principal Findings We compared the abundance of mRNA encoded by the mpt64 gene in sputa of patients with untreated pulmonary TB caused by Maf 2 and Mycobacterium tuberculosis (Mtb). Subsequently, prospectively collected sputum samples from presumptive TB patients were inoculated in the BACTEC MGIT 960 System. One hundred and seventy-three acid fast bacilli (AFB)-positive and blood agar negative MGIT cultures were included in the study. Cultures were tested on the day of MGIT positivity with the BD MGIT TBc Identification Test. A random set of positives and all negatives were additionally tested with the SD Bioline Ag MPT64 Rapid. MPT64 negative cultures were further incubated at 37°C and retested until positive. Bacteria were spoligotyped and assigned to different lineages. Maf 2 isolates were 2.52-fold less likely to produce a positive test result and sensitivity ranged from 78.4% to 84.3% at the beginning and end of the recommended 10 day testing window, respectively. There was no significant difference between the tests. We further showed that the decreased rapid test sensitivity was attributable to variations in mycobacterial growth behavior and the smear grades of the patient. Conclusions/Significance In areas where Maf 2 is endemic MPT64 tests should be cautiously used and MPT64 negative results confirmed by a second technique, such as nucleic acid amplification tests, to avoid their misclassification as NTMs. Diagnostics for rapid confirmation of positive liquid cultures presumptive of Mycobacterium tuberculosis bacteria, based on the detection of the MPT64 antigen, are being used in many TB diagnostic laboratories worldwide. Of note, diagnostic performance of these tests in West Africa, where TB is uniquely caused by the geographically restricted Mycobacterium africanum (Maf 1 and 2) and Mycobacterium tuberculosis lineages, has not been properly assessed. Although M. tuberculosis and M. africanum are genetically related, they differ in various aspects. Amongst several differences, Maf 2 grows significantly slower than Mtb bacteria. Because secretion of the MTP64 protein is dependent on the bacterial growth rate, we found that the MPT64 rapid test performance for detecting Maf 2 was lower in our setting in The Gambia. These findings might be relevant for other West African Maf 2 endemic countries where this rapid test is commonly used, as Maf 2 infected patients might have been missed in the past. Our finding emphasizes the need to thoroughly consider the presence of bacterial variants specific to certain regions during product development and implementation of novel diagnostic tests.
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Affiliation(s)
- Boatema Ofori-Anyinam
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Fatoumatta Kanuteh
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Schadrac C. Agbla
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Ifedayo Adetifa
- Disease Control and Elimination Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
- Department of Infectious Diseases Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Catherine Okoi
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Gregory Dolganov
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Gary Schoolnik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Ousman Secka
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
- Division of Microbiology & Immunity, Warwick Medical School, Coventry, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Bouke C. de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
- Division of Infectious Diseases, New York University, New York, New York, United States of America
| | - Florian Gehre
- Mycobacteriology Unit, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Vaccines and Immunity Theme, Medical Research Council (MRC) Unit, Serrekunda, The Gambia
- * E-mail:
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Walter ND, Dolganov GM, Garcia BJ, Worodria W, Andama A, Musisi E, Ayakaka I, Van TT, Voskuil MI, de Jong BC, Davidson RM, Fingerlin TE, Kechris K, Palmer C, Nahid P, Daley CL, Geraci M, Huang L, Cattamanchi A, Strong M, Schoolnik GK, Davis JL. Transcriptional Adaptation of Drug-tolerant Mycobacterium tuberculosis During Treatment of Human Tuberculosis. J Infect Dis 2015; 212:990-8. [PMID: 25762787 DOI: 10.1093/infdis/jiv149] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 03/02/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Treatment initiation rapidly kills most drug-susceptible Mycobacterium tuberculosis, but a bacterial subpopulation tolerates prolonged drug exposure. We evaluated drug-tolerant bacilli in human sputum by comparing messenger RNA (mRNA) expression of drug-tolerant bacilli that survive the early bactericidal phase with treatment-naive bacilli. METHODS M. tuberculosis gene expression was quantified via reverse-transcription polymerase chain reaction in serial sputa from 17 Ugandans treated for drug-susceptible pulmonary tuberculosis. RESULTS Within 4 days, bacterial mRNA abundance declined >98%, indicating rapid killing. Thereafter, the rate of decline slowed >94%, indicating drug tolerance. After 14 days, 16S ribosomal RNA transcripts/genome declined 96%, indicating slow growth. Drug-tolerant bacilli displayed marked downregulation of genes associated with growth, metabolism, and lipid synthesis and upregulation in stress responses and key regulatory categories-including stress-associated sigma factors, transcription factors, and toxin-antitoxin genes. Drug efflux pumps were upregulated. The isoniazid stress signature was induced by initial drug exposure, then disappeared after 4 days. CONCLUSIONS Transcriptional patterns suggest that drug-tolerant bacilli in sputum are in a slow-growing, metabolically and synthetically downregulated state. Absence of the isoniazid stress signature in drug-tolerant bacilli indicates that physiological state influences drug responsiveness in vivo. These results identify novel drug targets that should aid in development of novel shorter tuberculosis treatment regimens.
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Affiliation(s)
- Nicholas D Walter
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora Pulmonary Division, Denver Veterans Administration Medical Center, Colorado
| | - Gregory M Dolganov
- Department of Microbiology and Immunology, Stanford University, California
| | - Benjamin J Garcia
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver Computational Bioscience Program, University of Colorado Denver, Aurora
| | - William Worodria
- Makerere University-University of California, San Francisco Research Collaboration, Kampala, Uganda
| | - Alfred Andama
- Makerere University-University of California, San Francisco Research Collaboration, Kampala, Uganda
| | - Emmanuel Musisi
- Makerere University-University of California, San Francisco Research Collaboration, Kampala, Uganda
| | - Irene Ayakaka
- Makerere University-University of California, San Francisco Research Collaboration, Kampala, Uganda
| | - Tran T Van
- Department of Microbiology and Immunology, Stanford University, California
| | - Martin I Voskuil
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora
| | | | - Rebecca M Davidson
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver
| | - Tasha E Fingerlin
- Department of Epidemiology and Biostatistics Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora
| | - Claire Palmer
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora
| | - Payam Nahid
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco
| | - Charles L Daley
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora Division of Mycobacterial and Respiratory Infections, National Jewish Health, Denver, Colorado
| | - Mark Geraci
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco HIV/AIDS Division, University of California San Francisco
| | - Adithya Cattamanchi
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco
| | - Michael Strong
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver
| | - Gary K Schoolnik
- Department of Microbiology and Immunology, Stanford University, California
| | - John Lucian Davis
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco
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