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Affiliation(s)
- Sushma K Cribbs
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, Emory University School of Medicine, Atlanta, Georgia
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Lagier JC, Raoult D. Whipple's disease and Tropheryma whipplei infections: when to suspect them and how to diagnose and treat them. Curr Opin Infect Dis 2019; 31:463-470. [PMID: 30299363 DOI: 10.1097/qco.0000000000000489] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW The delay between first clinical signs and diagnosis of Whipple's disease and Tropheryma whipplei infections is more than 6 years, and relapses are frequently observed, resulting in a need for clinicians to be aware of this infection. RECENT FINDINGS 18 FDG-PET is useful in the diagnosis and the follow-up of patients (particularly in case of neurological involvement). Histological involvement remains the goldstandard for classic Whipple's disease diagnosis. PCR performed on biopsies of fluid is the main tool for the diagnosis of localized chronic infections. PCR performed on urine samples should become an important role of noninvasive diagnostic strategies, while T. whipplei PCR performed on saliva and stool lack specificity. Because of lifetime susceptibility to T. whipplei and in-vitro susceptibility data, a 1-year course of doxycycline and hydroxychloroquine followed by a lifelong treatment by doxycycline is recommended for Whipple's disease, localized endocarditis and encephalitis. SUMMARY Clinical involvement of the different T. whipplei infections is well described, as well as the treatment of Whipple's disease, endocarditis and encephalitis. The place of PCR performed on urine remains to be clarified for diagnosis of localized T. whipplei infections and acute infections as well as the optimal treatment for arthritis and acute infections.
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53
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Cribbs SK, Crothers K, Morris A. Pathogenesis of HIV-Related Lung Disease: Immunity, Infection, and Inflammation. Physiol Rev 2019; 100:603-632. [PMID: 31600121 DOI: 10.1152/physrev.00039.2018] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Despite anti-retroviral therapy (ART), human immunodeficiency virus-1 (HIV)-related pulmonary disease continues to be a major cause of morbidity and mortality for people living with HIV (PLWH). The spectrum of lung diseases has changed from acute opportunistic infections resulting in death to chronic lung diseases for those with access to ART. Chronic immune activation and suppression can result in impairment of innate immunity and progressive loss of T cell and B cell functionality with aberrant cytokine and chemokine responses systemically as well as in the lung. HIV can be detected in the lungs of PLWH and has profound effects on cellular immune functions. In addition, HIV-related lung injury and disease can occur secondary to a number of mechanisms including altered pulmonary and systemic inflammatory pathways, viral persistence in the lung, oxidative stress with additive effects of smoke exposure, microbial translocation, and alterations in the lung and gut microbiome. Although ART has had profound effects on systemic viral suppression in HIV, the impact of ART on lung immunology still needs to be fully elucidated. Understanding of the mechanisms by which HIV-related lung diseases continue to occur is critical to the development of new preventive and therapeutic strategies to improve lung health in PLWH.
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Affiliation(s)
- Sushma K Cribbs
- Pulmonary Medicine, Department of Veterans Affairs, Atlanta, Georgia; Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep, Emory University, Atlanta, Georgia; Department of Medicine, Veterans Affairs Puget Sound Health Care System and Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington; and Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kristina Crothers
- Pulmonary Medicine, Department of Veterans Affairs, Atlanta, Georgia; Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep, Emory University, Atlanta, Georgia; Department of Medicine, Veterans Affairs Puget Sound Health Care System and Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington; and Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Alison Morris
- Pulmonary Medicine, Department of Veterans Affairs, Atlanta, Georgia; Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep, Emory University, Atlanta, Georgia; Department of Medicine, Veterans Affairs Puget Sound Health Care System and Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington; and Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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54
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Abstract
The use of next-generation sequencing and multiomic analysis reveals new insights on the identity of microbes in the lower airways blurring the lines between commensals and pathogens. Microbes are not found in isolation; rather they form complex metacommunities where microbe-host and microbe-microbe interactions play important roles on the host susceptibility to pathogens. In addition, the lower airway microbiota exert significant effects on host immune tone. Thus, this review highlights the roles that microbes in the respiratory tract play in the development of pneumonia.
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Affiliation(s)
- Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU Human Microbiome Program, New York University School of Medicine, New York, NY 10028, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU Human Microbiome Program, New York University School of Medicine, New York, NY 10028, USA.
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55
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Toward a Deeper Understanding of Chronic Obstructive Pulmonary Disease: The Role of Bronchoscopy in Therapeutic Discovery. Ann Am Thorac Soc 2019; 16:431-432. [PMID: 30932707 DOI: 10.1513/annalsats.201902-105ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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56
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Zhai J, Knox K, Twigg HL, Zhou H, Zhou JJ. Exact variance component tests for longitudinal microbiome studies. Genet Epidemiol 2019; 43:250-262. [PMID: 30623484 DOI: 10.1002/gepi.22185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/28/2018] [Accepted: 11/26/2018] [Indexed: 01/12/2023]
Abstract
In metagenomic studies, testing the association between microbiome composition and clinical outcomes translates to testing the nullity of variance components. Motivated by a lung human immunodeficiency virus (HIV) microbiome project, we study longitudinal microbiome data by using variance component models with more than two variance components. Current testing strategies only apply to models with exactly two variance components and when sample sizes are large. Therefore, they are not applicable to longitudinal microbiome studies. In this paper, we propose exact tests (score test, likelihood ratio test, and restricted likelihood ratio test) to (a) test the association of the overall microbiome composition in a longitudinal design and (b) detect the association of one specific microbiome cluster while adjusting for the effects from related clusters. Our approach combines the exact tests for null hypothesis with a single variance component with a strategy of reducing multiple variance components to a single one. Simulation studies demonstrate that our method has a correct type I error rate and superior power compared to existing methods at small sample sizes and weak signals. Finally, we apply our method to a longitudinal pulmonary microbiome study of HIV-infected patients and reveal two interesting genera Prevotella and Veillonella associated with forced vital capacity. Our findings shed light on the impact of the lung microbiome on HIV complexities. The method is implemented in the open-source, high-performance computing language Julia and is freely available at https://github.com/JingZhai63/VCmicrobiome.
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Affiliation(s)
- Jing Zhai
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, Arizona
| | - Kenneth Knox
- Division of Pulmonary, Allergy, Critical Care, Sleep Medicine, Department of Medicine, University of Arizona, Tucson, Arizona
| | - Homer L Twigg
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Indiana University Medical Center, Indianapolis, Indiana
| | - Hua Zhou
- Department of Biostatistics, University of California, Los Angeles, California
| | - Jin J Zhou
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, Arizona
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57
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Sulaiman I, Wu BG, Li Y, Scott AS, Malecha P, Scaglione B, Wang J, Basavaraj A, Chung S, Bantis K, Carpenito J, Clemente JC, Shen N, Bessich J, Rafeq S, Michaud G, Donington J, Naidoo C, Theron G, Schattner G, Garofano S, Condos R, Kamelhar D, Addrizzo-Harris D, Segal LN. Evaluation of the airway microbiome in nontuberculous mycobacteria disease. Eur Respir J 2018; 52:13993003.00810-2018. [PMID: 30093571 DOI: 10.1183/13993003.00810-2018] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/29/2018] [Indexed: 01/15/2023]
Abstract
Aspiration is associated with nontuberculous mycobacterial (NTM) pulmonary disease and airway dysbiosis is associated with increased inflammation. We examined whether NTM disease was associated with a distinct airway microbiota and immune profile.297 oral wash and induced sputum samples were collected from 106 participants with respiratory symptoms and imaging abnormalities compatible with NTM. Lower airway samples were obtained in 20 participants undergoing bronchoscopy. 16S rRNA gene and nested mycobacteriome sequencing approaches characterised microbiota composition. In addition, inflammatory profiles of lower airway samples were examined.The prevalence of NTM+ cultures was 58%. Few changes were noted in microbiota characteristics or composition in oral wash and sputum samples among groups. Among NTM+ samples, 27% of the lower airway samples were enriched with Mycobacterium A mycobacteriome approach identified Mycobacterium in a greater percentage of samples, including some nonpathogenic strains. In NTM+ lower airway samples, taxa identified as oral commensals were associated with increased inflammatory biomarkers.The 16S rRNA gene sequencing approach is not sensitive in identifying NTM among airway samples that are culture-positive. However, associations between lower airway inflammation and microbiota signatures suggest a potential role for these microbes in the inflammatory process in NTM disease.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Adrienne S Scott
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Patrick Malecha
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin Scaglione
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jing Wang
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Ashwin Basavaraj
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Samuel Chung
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Katrina Bantis
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Joseph Carpenito
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose C Clemente
- Dept of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nan Shen
- Dept of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jamie Bessich
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Samaan Rafeq
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Gaetene Michaud
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jessica Donington
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Charissa Naidoo
- Medicine and Health Sciences, Stellenbosch University, DST/NRF of Excellence for Biomedical Tuberculosis Research and SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics Tygerberg, Cape Town, South Africa
| | - Grant Theron
- Medicine and Health Sciences, Stellenbosch University, DST/NRF of Excellence for Biomedical Tuberculosis Research and SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics Tygerberg, Cape Town, South Africa
| | - Gail Schattner
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Suzette Garofano
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Rany Condos
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - David Kamelhar
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Doreen Addrizzo-Harris
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA.,Dept of Medicine, New York University School of Medicine, New York, NY, USA
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58
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Qin S, Clausen E, Nouraie SM, Kingsley L, McMahon D, Kleerup E, Huang L, Ghedin E, Greenblatt RM, Morris A. Tropheryma whipplei colonization in HIV-infected individuals is not associated with lung function or inflammation. PLoS One 2018; 13:e0205065. [PMID: 30286195 PMCID: PMC6171914 DOI: 10.1371/journal.pone.0205065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 08/24/2018] [Indexed: 11/20/2022] Open
Abstract
Studies demonstrate that Tropheryma whipplei (T. whipplei) is present in the lungs of healthy individuals without acute respiratory symptoms or acute respiratory infection and is more common in the lungs of HIV-infected individuals and in smokers. The impact of T. whipplei colonization in the lung on local inflammation and pulmonary dysfunction in HIV-infected individuals is currently unknown. In this study, we performed specific polymerase chain reaction (PCR) and sequencing for T. whipplei in bronchoalveolar lavage (BAL) and induced sputum (IS) samples in 76 HIV-infected participants from three clinical sites. Pulmonary function and proinflammatory cytokine and chemokine levels in BAL were measured. Frequency of T. whipplei in either BAL or IS was 43.4%. The sensitivity and specificity of IS compared to BAL for detection of T. whipplei was 92.3% and 84.2%, respectively, and isolates of T. whipplei in the BAL and IS in the same subject shared genetic identity. Pulmonary function measures were not associated with T. whipplei colonization, and proinflammatory cytokine and chemokine levels in BAL and plasma as well as percentages of inflammatory cells in BAL and IS were not higher in colonized individuals. Overall, these results indicate that T. whipplei colonization in the lung is common, but may not be associated with decreased pulmonary function or inflammation in HIV-infected individuals.
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Affiliation(s)
- Shulin Qin
- Departments of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Emily Clausen
- Departments of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Seyed Mehdi Nouraie
- Departments of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Lawrence Kingsley
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Deborah McMahon
- Departments of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Eric Kleerup
- Department of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Laurence Huang
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, and Global Institute of Public Health, New York University, New York, New York, United States of America
| | - Ruth M. Greenblatt
- Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, California, United States of America
| | - Alison Morris
- Departments of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Departments of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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59
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Xu S, Tsai A, Sze MA, Vucic EA, Shaipanich T, Harris M, Guillemi S, Yang J, Sinha S, Nislow C, Montaner J, Lam W, Lam S, Sin DD, Paul Man SF, Leung JM. Decreased microbiome diversity in the HIV small airway epithelium. Respir Res 2018; 19:140. [PMID: 30053882 PMCID: PMC6062954 DOI: 10.1186/s12931-018-0835-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/25/2018] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Persons living with human immunodeficiency virus (PLWH) face an increased burden of chronic obstructive pulmonary disease (COPD). Repeated pulmonary infections, antibiotic exposures, and immunosuppression may contribute to an altered small airway epithelium (SAE) microbiome. METHODS SAE cells were collected from 28 PLWH and 48 HIV- controls through bronchoscopic cytologic brushings. DNA extracted from SAE cells was subjected to 16S rRNA amplification and sequencing. Comparisons of alpha and beta diversity between HIV+ and HIV- groups were performed and key operational taxonomic units (OTUs) distinguishing the two groups were identified using the Boruta feature selection after Random Forest Analysis. RESULTS PLWH demonstrated significantly reduced Shannon diversity compared with HIV- volunteers (1.82 ± 0.10 vs. 2.20 ± 0.073, p = 0.0024). This was primarily driven by a reduction in bacterial richness (23.29 ± 2.75 for PLWH and 46.04 ± 3.716 for HIV-, p < 0.0001). Phyla distribution was significantly altered among PLWH, with an increase in relative abundance of Proteobacteria (p = 0.0003) and a decrease in Bacteroidetes (p = 0.0068) and Firmicutes (p = 0.0002). Six discriminative OTUs were found to distinguish PLWH from HIV- volunteers, aligning to Veillonellaceae, Fusobacterium, Verrucomicrobiaceae, Prevotella, Veillonella, and Campylobacter. CONCLUSIONS Compared to HIV- controls, PLWH's SAE microbiome is marked by reduced bacterial diversity and richness with significant differences in community composition.
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Affiliation(s)
- Stella Xu
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Amy Tsai
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marc A Sze
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Emily A Vucic
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Tawimas Shaipanich
- Division of Respiratory Medicine, St. Paul's Hospital, Vancouver, BC, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, Vancouver, BC, Canada
| | - Silvia Guillemi
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, Vancouver, BC, Canada
| | - Julia Yang
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Sunita Sinha
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Julio Montaner
- British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, Vancouver, BC, Canada
| | - Wan Lam
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Stephen Lam
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
- Division of Respiratory Medicine, St. Paul's Hospital, Vancouver, BC, Canada
| | - S F Paul Man
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
- Division of Respiratory Medicine, St. Paul's Hospital, Vancouver, BC, Canada
| | - Janice M Leung
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada.
- Division of Respiratory Medicine, St. Paul's Hospital, Vancouver, BC, Canada.
- Centre for Heart Lung Innovation, St. Paul's Hospital, Room 166-1081 Burrard Street, Vancouver, V6Z 1Y6, Canada.
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Abstract
PURPOSE OF REVIEW The purpose of this review is to summarize recent findings on the lung microbiome in HIV-infected patients and associated pulmonary diseases, and the relationship of airway microbial communities to metabolic and immune signatures within this patient population. RECENT FINDINGS The lung microbiome in HIV infection is a relatively new and rapidly developing field; early studies in the field produced inconclusive evidence as to whether HIV-infection changes the lower airway microbiome. More recent microbiome investigations have addressed these inconsistencies by incorporating systems biology approaches and laboratory models. Several investigations have now identified enrichment of Prevotella, Veillonella, and Streptococcus in the lower airways as consistent correlates of advanced HIV-infection and HIV-associated pulmonary diseases. These bacteria are associated with specific metabolic and immune profiles within the lung and circulation, providing the first indication that the lung microbiome may play a functional role in the pathogenesis of HIV-infection and HIV-associated pulmonary disease. SUMMARY This review summarizes knowledge to date on the lung microbiome in HIV infection, as well as challenges and accomplishments in the field within the last 2 years. Although the lung microbiome in HIV infection is still an emerging field, recent studies have formed a framework for future functional analysis of microbes in HIV pathogenesis.
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61
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Zhai J, Kim J, Knox KS, Twigg HL, Zhou H, Zhou JJ. Variance Component Selection With Applications to Microbiome Taxonomic Data. Front Microbiol 2018; 9:509. [PMID: 29643839 PMCID: PMC5883493 DOI: 10.3389/fmicb.2018.00509] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/06/2018] [Indexed: 12/21/2022] Open
Abstract
High-throughput sequencing technology has enabled population-based studies of the role of the human microbiome in disease etiology and exposure response. Microbiome data are summarized as counts or composition of the bacterial taxa at different taxonomic levels. An important problem is to identify the bacterial taxa that are associated with a response. One method is to test the association of specific taxon with phenotypes in a linear mixed effect model, which incorporates phylogenetic information among bacterial communities. Another type of approaches consider all taxa in a joint model and achieves selection via penalization method, which ignores phylogenetic information. In this paper, we consider regression analysis by treating bacterial taxa at different level as multiple random effects. For each taxon, a kernel matrix is calculated based on distance measures in the phylogenetic tree and acts as one variance component in the joint model. Then taxonomic selection is achieved by the lasso (least absolute shrinkage and selection operator) penalty on variance components. Our method integrates biological information into the variable selection problem and greatly improves selection accuracies. Simulation studies demonstrate the superiority of our methods versus existing methods, for example, group-lasso. Finally, we apply our method to a longitudinal microbiome study of Human Immunodeficiency Virus (HIV) infected patients. We implement our method using the high performance computing language Julia. Software and detailed documentation are freely available at https://github.com/JingZhai63/VCselection.
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Affiliation(s)
- Jing Zhai
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, United States
| | - Juhyun Kim
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kenneth S Knox
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, AZ, United States
| | - Homer L Twigg
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Indiana University Medical Center, Indianapolis, IN, United States
| | - Hua Zhou
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jin J Zhou
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, United States
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Pragman AA, Lyu T, Baller JA, Gould TJ, Kelly RF, Reilly CS, Isaacson RE, Wendt CH. The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease. MICROBIOME 2018; 6:7. [PMID: 29316977 PMCID: PMC5759273 DOI: 10.1186/s40168-017-0381-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/11/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Oral taxa are often found in the chronic obstructive pulmonary disease (COPD) lung microbiota, but it is not clear if this is due to a physiologic process such as aspiration or experimental contamination at the time of specimen collection. METHODS Microbiota samples were obtained from nine subjects with mild or moderate COPD by swabbing lung tissue and upper airway sites during lung lobectomy. Lung specimens were not contaminated with upper airway taxa since they were obtained surgically. The microbiota were analyzed with 16S rRNA gene qPCR and 16S rRNA gene hypervariable region 3 (V3) sequencing. Data analyses were performed using QIIME, SourceTracker, and R. RESULTS Streptococcus was the most common genus in the oral, bronchial, and lung tissue samples, and multiple other taxa were present in both the upper and lower airways. Each subject's own bronchial and lung tissue microbiota were more similar to each other than were the bronchial and lung tissue microbiota of two different subjects (permutation test, p = 0.0139), indicating more within-subject similarity than between-subject similarity at these two lung sites. Principal coordinate analysis of all subject samples revealed clustering by anatomic sampling site (PERMANOVA, p = 0.001), but not by subject. SourceTracker analysis found that the sources of the lung tissue microbiota were 21.1% (mean) oral microbiota, 8.7% nasal microbiota, and 70.1% unknown. An analysis using the neutral theory of community ecology revealed that the lung tissue microbiota closely reflects the bronchial, oral, and nasal microbiota (immigration parameter estimates 0.69, 0.62, and 0.74, respectively), with some evidence of ecologic drift occurring in the lung tissue. CONCLUSION This is the first study to evaluate the mild-moderate COPD lung tissue microbiota without potential for upper airway contamination of the lung samples. In our small study of subjects with COPD, we found oral and nasal bacteria in the lung tissue microbiota, confirming that aspiration is a source of the COPD lung microbiota.
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Affiliation(s)
- Alexa A Pragman
- Department of Medicine, University of Minnesota and Minneapolis Veterans Affairs Medical Center, Minneapolis VA Health Care System, Research Service (151), 1 Veterans Drive, Minneapolis, MN, 55417, USA.
| | - Tianmeng Lyu
- Division of Biostatistics, University of Minnesota School of Public Health, MMC 303 Mayo, 8303A, 420 Delaware St. SE, Minneapolis, MN, 55455, USA
| | - Joshua A Baller
- Minnesota Supercomputing Institute, University of Minnesota, Room 599 Walter Library, 3721A, 117 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Trevor J Gould
- Biological Science Dean's Office, University of Minnesota Informatics Institute, Room 123 SnH, 6174A, 1475 Gortner Ave., St. Paul, MN, 55108, USA
| | - Rosemary F Kelly
- Division of Cardiothoracic Surgery, University of Minnesota and Minneapolis Veterans Affairs Medical Center, 1 Veterans Dr., Minneapolis, MN, 55417, USA
| | - Cavan S Reilly
- Division of Biostatistics, University of Minnesota School of Public Health, MMC 303 Mayo, 8303A, 420 Delaware St. SE, Minneapolis, MN, 55455, USA
| | - Richard E Isaacson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Room 205G VetS, 6187A, 1971 Commonwealth Ave., St. Paul, MN, 55108, USA
| | - Chris H Wendt
- Department of Medicine, University of Minnesota and Minneapolis Veterans Affairs Medical Center, Minneapolis VA Health Care System, Research Service (151), 1 Veterans Drive, Minneapolis, MN, 55417, USA
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64
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Abstract
Pulmonary complications remain among the most frequent causes of morbidity and mortality for individuals with HIV despite the advent of antiretroviral therapy (ART) and improvement in its efficacy and availability. The prevalence of non-infectious pulmonary diseases is rising in this population, reflecting both an increase in smoking and the independent risk associated with HIV. The unique mechanisms of pulmonary disease in these patients remain poorly understood, and direct effects of HIV, genetic predisposition, inflammatory pathways, and co-infections have all been implicated. Lung cancer, chronic obstructive pulmonary disease (COPD), and pulmonary hypertension are the most prevalent non-infectious pulmonary diseases in persons with HIV, and the risk of each of these diseases is higher among HIV-infected (HIV+) persons than in the general population. This review discusses the latest advances in the literature on these important complications of HIV infection.
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Affiliation(s)
- M Triplette
- Division of Pulmonary and Critical Care, Department of Medicine, University of Washington, Seattle, WA, USA.
| | - K Crothers
- Division of Pulmonary and Critical Care, Department of Medicine, University of Washington, Seattle, WA, USA
| | - E F Attia
- Division of Pulmonary and Critical Care, Department of Medicine, University of Washington, Seattle, WA, USA
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Lu J, Xiong L, Zhang X, Liu Z, Wang S, Zhang C, Zheng J, Wang G, Zheng R, Simpson JL, Wang F. The Role of Lower Airway Dysbiosis in Asthma: Dysbiosis and Asthma. Mediators Inflamm 2017; 2017:3890601. [PMID: 29386750 PMCID: PMC5745728 DOI: 10.1155/2017/3890601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/13/2017] [Accepted: 10/04/2017] [Indexed: 12/12/2022] Open
Abstract
With the development of culture-independent techniques, numerous studies have demonstrated that the lower airway is not sterile in health and harbors diverse microbial communities. Furthermore, new evidence suggests that there is a distinct lower airway microbiome in those with chronic respiratory disease. To understand the role of lower airway dysbiosis in the pathogenesis of asthma, in this article, we review the published reports about the lung microbiome of healthy controls, provide an outlook on the contribution of lower airway dysbiosis to asthma, especially steroid-resistant asthma, and discuss the potential therapies targeted for lower airway dysbiosis.
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Affiliation(s)
- Junying Lu
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Department of Intensive Care Unit, First Hospital of Jilin University, Changchun 130021, China
| | - Lingxin Xiong
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Xiaohao Zhang
- Department of Cardiology, Second Hospital of Jilin University, Changchun 130041, China
| | - Zhongmin Liu
- Department of Intensive Care Unit, First Hospital of Jilin University, Changchun 130021, China
| | - Shiji Wang
- Department of Intensive Care Unit, First Hospital of Jilin University, Changchun 130021, China
| | - Chao Zhang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Jingtong Zheng
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Guoqiang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Ruipeng Zheng
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Department of Interventional Therapy, First Hospital of Jilin University, Changchun 130021, China
| | - Jodie L. Simpson
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Department of Respiratory and Sleep Medicine, University of Newcastle, New Lambton, NSW, Australia
| | - Fang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
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66
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Segal LN, Dickson RP. The Lung Microbiome in HIV. Getting to the HAART of the Host-Microbe Interface. Am J Respir Crit Care Med 2017; 194:136-7. [PMID: 27420358 DOI: 10.1164/rccm.201602-0280ed] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Leopoldo N Segal
- 1 Division of Pulmonary and Critical Care Medicine New York University School of Medicine New York, New York and
| | - Robert P Dickson
- 2 Division of Pulmonary and Critical Care Medicine University of Michigan Medical School Ann Arbor, Michigan
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67
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Zemanick ET, Wagner BD, Robertson CE, Ahrens RC, Chmiel JF, Clancy JP, Gibson RL, Harris WT, Kurland G, Laguna TA, McColley SA, McCoy K, Retsch-Bogart G, Sobush KT, Zeitlin PL, Stevens MJ, Accurso FJ, Sagel SD, Harris JK. Airway microbiota across age and disease spectrum in cystic fibrosis. Eur Respir J 2017; 50:50/5/1700832. [PMID: 29146601 DOI: 10.1183/13993003.00832-2017] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/10/2017] [Indexed: 01/20/2023]
Abstract
Our objectives were to characterise the microbiota in cystic fibrosis (CF) bronchoalveolar lavage fluid (BALF), and determine its relationship to inflammation and disease status.BALF from paediatric and adult CF patients and paediatric disease controls undergoing clinically indicated bronchoscopy was analysed for total bacterial load and for microbiota by 16S rDNA sequencing.We examined 191 BALF samples (146 CF and 45 disease controls) from 13 CF centres. In CF patients aged <2 years, nontraditional taxa (e.gStreptococcus, Prevotella and Veillonella) constituted ∼50% of the microbiota, whereas in CF patients aged ≥6 years, traditional CF taxa (e.gPseudomonas, Staphylococcus and Stenotrophomonas) predominated. Sequencing detected a dominant taxon not traditionally associated with CF (e.gStreptococcus or Prevotella) in 20% of CF BALF and identified bacteria in 24% of culture-negative BALF. Microbial diversity and relative abundance of Streptococcus, Prevotella and Veillonella were inversely associated with airway inflammation. Microbiota communities were distinct in CF compared with disease controls, but did not differ based on pulmonary exacerbation status in CF.The CF microbiota detected in BALF differs with age. In CF patients aged <2 years, Streptococcus predominates, whereas classic CF pathogens predominate in most older children and adults.
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Affiliation(s)
| | - Brandie D Wagner
- University of Colorado School of Medicine, Aurora, CO, USA.,Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | | | | | - James F Chmiel
- Case Western Reserve University School of Medicine, Rainbow Babies and Children's Hospital, Cleveland, OH, USA
| | - John P Clancy
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ronald L Gibson
- University of Washington, Seattle Children's Hospital, Seattle, WA, USA
| | | | | | | | - Susanna A McColley
- Ann and Robert H. Lurie Children's Hospital of Chicago and Northwestern University, Chicago, IL, USA
| | - Karen McCoy
- Nationwide Children's Hospital, Columbus, OH, USA
| | | | | | | | - Mark J Stevens
- University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Scott D Sagel
- University of Colorado School of Medicine, Aurora, CO, USA
| | - J Kirk Harris
- University of Colorado School of Medicine, Aurora, CO, USA
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68
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Clinical Manifestations, Treatment, and Diagnosis of Tropheryma whipplei Infections. Clin Microbiol Rev 2017; 30:529-555. [PMID: 28298472 DOI: 10.1128/cmr.00033-16] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Whipple's disease is a rare infectious disease that can be fatal if left untreated. The disease is caused by infection with Tropheryma whipplei, a bacterium that may be more common than was initially assumed. Most patients present with nonspecific symptoms, and as routine cultivation of the bacterium is not feasible, it is difficult to diagnose this infection. On the other hand, due to the generic symptoms, infection with this bacterium is actually quite often in the differential diagnosis. The gold standard for diagnosis used to be periodic acid-Schiff (PAS) staining of duodenal biopsy specimens, but PAS staining has a poor specificity and sensitivity. The development of molecular techniques has resulted in more convenient methods for detecting T. whipplei infections, and this has greatly improved the diagnosis of this often missed infection. In addition, the molecular detection of T. whipplei has resulted in an increase in knowledge about its pathogenicity, and this review gives an overview of the new insights in epidemiology, pathogenesis, clinical manifestations, diagnosis, and treatment of Tropheryma whipplei infections.
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69
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Abstract
INTRODUCTION The respiratory tract is constantly exposed to various environmental and endogenous microbes; however, unlike other similar mucosal surfaces, there has been limited investigation of the microbiome of the respiratory tract. AREAS COVERED In this review, we summarize the current state of knowledge of the bacterial, fungal, and viral respiratory microbiomes during HIV infection and how the microbiome might relate to HIV-associated lung disease. Expert commentary: HIV infection is associated with alterations in the respiratory microbiome. The clinical implications of lung microbial dysbiosis are however currently unknown. Mechanistic studies are needed to establish causality between shifts in the respiratory microbiome and pulmonary complications in HIV-infected individuals.
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Affiliation(s)
- M B Lawani
- a University of Pittsburgh , School of Medicine, Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine , Pittsburgh , PA , USA
| | - A Morris
- a University of Pittsburgh , School of Medicine, Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine , Pittsburgh , PA , USA
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70
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Abstract
The use of culture-independent techniques has allowed us to appreciate that the upper and lower respiratory tract contain a diverse community of microbes in health and disease. Research has only recently explored the effects of the microbiome on the host immune response. The exposure of the human body to the bacterial environment is an important factor for immunological development; thus, the interaction between the microbiome and its host is critical to understanding the pathogenesis of disease. In this article, we discuss the mechanisms that determine the composition of the airway microbiome and its effects on the host immune response. With the use of ecological principles, we have learned how the lower airways constitute a unique niche subjected to frequent microbial migration (e.g., through aspiration) and constant immunological pressure. The discussion will focus on the possible inflammatory pathways that are up- and downregulated when the immune system is challenged by dysbiosis. Identification of potential markers and microbial targets to address the modulation of inflammation in early disease, when changes may have the most effect, will be critical for future therapies.
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71
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Grønseth R, Drengenes C, Wiker HG, Tangedal S, Xue Y, Husebø GR, Svanes Ø, Lehmann S, Aardal M, Hoang T, Kalananthan T, Hjellestad Martinsen EM, Orvedal Leiten E, Aanerud M, Nordeide E, Haaland I, Jonassen I, Bakke P, Eagan T. Protected sampling is preferable in bronchoscopic studies of the airway microbiome. ERJ Open Res 2017; 3:00019-2017. [PMID: 28875147 PMCID: PMC5576223 DOI: 10.1183/23120541.00019-2017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/21/2017] [Indexed: 01/03/2023] Open
Abstract
The aim was to evaluate susceptibility of oropharyngeal contamination with various bronchoscopic sampling techniques. 67 patients with obstructive lung disease and 58 control subjects underwent bronchoscopy with small-volume lavage (SVL) through the working channel, protected bronchoalveolar lavage (PBAL) and bilateral protected specimen brush (PSB) sampling. Subjects also provided an oral wash (OW) sample, and negative control samples were gathered for each bronchoscopy procedure. DNA encoding bacterial 16S ribosomal RNA was sequenced and bioinformatically processed to cluster into operational taxonomic units (OTU), assign taxonomy and obtain measures of diversity. The proportion of Proteobacteria increased, whereas Firmicutes diminished in the order OW, SVL, PBAL, PSB (p<0.01). The alpha-diversity decreased in the same order (p<0.01). Also, beta-diversity varied by sampling method (p<0.01), and visualisation of principal coordinates analyses indicated that differences in diversity were smaller between OW and SVL and OW and PBAL samples than for OW and the PSB samples. The order of sampling (left versus right first) did not influence alpha- or beta-diversity for PSB samples. Studies of the airway microbiota need to address the potential for oropharyngeal contamination, and protected sampling might represent an acceptable measure to minimise this problem. Protected bronchoscopic sampling is most suitable for identification of a distinct airway microbiomehttp://ow.ly/qIIy30eqB9M
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Affiliation(s)
- Rune Grønseth
- Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Christine Drengenes
- Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway.,Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Harald G Wiker
- Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway.,Dept of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Solveig Tangedal
- Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway.,Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Yaxin Xue
- Computational Biology Unit, Dept of Informatics, University of Bergen, Bergen, Norway
| | - Gunnar Reksten Husebø
- Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway.,Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Øistein Svanes
- Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway.,Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Sverre Lehmann
- Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway.,Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Marit Aardal
- Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Tuyen Hoang
- Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | | | | | - Elise Orvedal Leiten
- Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Marianne Aanerud
- Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Eli Nordeide
- Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway.,Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Ingvild Haaland
- Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway.,Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Inge Jonassen
- Computational Biology Unit, Dept of Informatics, University of Bergen, Bergen, Norway
| | - Per Bakke
- Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Tomas Eagan
- Dept of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway.,Dept of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
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72
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Head BM, Trajtman A, Rueda ZV, Vélez L, Keynan Y. Atypical bacterial pneumonia in the HIV-infected population. Pneumonia (Nathan) 2017; 9:12. [PMID: 28856082 PMCID: PMC5571654 DOI: 10.1186/s41479-017-0036-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/13/2017] [Indexed: 01/02/2023] Open
Abstract
Human immunodeficiency virus (HIV)-infected individuals are more susceptible to respiratory tract infections by other infectious agents (viruses, bacteria, parasites, and fungi) as their disease progresses to acquired immunodeficiency syndrome. Despite effective antiretroviral therapy, bacterial pneumonia (the most frequently occurring HIV-associated pulmonary illness) remains a common cause of morbidity and mortality in the HIV-infected population. Over the last few decades, studies have looked at the role of atypical bacterial pneumonia (i.e. pneumonia that causes an atypical clinical presentation or responds differently to typical therapeutics) in association with HIV infection. Due to the lack of available diagnostic strategies, the lack of consideration, and the declining immunity of the patient, HIV co-infections with atypical bacteria are currently believed to be underreported. Thus, following an extensive database search, this review aimed to highlight the current knowledge and gaps regarding atypical bacterial pneumonia in HIV. The authors discuss the prevalence of Chlamydophila pneumoniae, Mycoplasma pneumoniae, Coxiella burnetii, Legionella species and others in the HIV-infected population as well as their clinical presentation, methods of detection, and treatment. Further studies looking at the role of these microbes in association with HIV are required. Increased knowledge of these atypical bacteria will lead to a more rapid diagnosis of these infections, resulting in an improved quality of life for the HIV-infected population.
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Affiliation(s)
- Breanne M. Head
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Adriana Trajtman
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Zulma V. Rueda
- Facultad de Medicina, Universidad Pontificia Bolivariana, Medellin, Colombia
| | - Lázaro Vélez
- Grupo Investigador de Problemas en Enfermedades Infecciosas, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Yoav Keynan
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Canada
- Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
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73
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Twigg HL, Knox KS, Zhou J, Crothers KA, Nelson DE, Toh E, Day RB, Lin H, Gao X, Dong Q, Mi D, Katz BP, Sodergren E, Weinstock GM. Effect of Advanced HIV Infection on the Respiratory Microbiome. Am J Respir Crit Care Med 2017; 194:226-35. [PMID: 26835554 DOI: 10.1164/rccm.201509-1875oc] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
RATIONALE Previous work found the lung microbiome in healthy subjects infected with HIV was similar to that in uninfected subjects. We hypothesized the lung microbiome from subjects infected with HIV with more advanced disease would differ from that of an uninfected control population. OBJECTIVES To measure the lung microbiome in an HIV-infected population with advanced disease. METHODS 16s RNA gene sequencing was performed on acellular bronchoalveolar lavage (BAL) fluid from 30 subjects infected with HIV with advanced disease (baseline mean CD4 count, 262 cells/mm(3)) before and up to 3 years after starting highly active antiretroviral therapy (HAART) and compared with 22 uninfected control subjects. MEASUREMENTS AND MAIN RESULTS The lung microbiome in subjects infected with HIV with advanced disease demonstrated decreased alpha diversity (richness and diversity) and greater beta diversity compared with uninfected BAL. Differences improved with HAART, but still persisted up to 3 years after starting therapy. Population dispersion in the group infected with HIV was significantly greater than in the uninfected cohort and declined after treatment. There were differences in the relative abundance of some bacteria between the two groups at baseline and after 1 year of therapy. After 1 year on HAART, HIV BAL contained an increased abundance of Prevotella and Veillonella, bacteria previously associated with lung inflammation. CONCLUSIONS The lung microbiome in subjects infected with HIV with advanced disease is altered compared with an uninfected population both in diversity and bacterial composition. Differences remain up to 3 years after starting HAART. We speculate an altered lung microbiome in HIV infection may contribute to chronic inflammation and lung complications seen in the HAART era.
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Affiliation(s)
| | - Kenneth S Knox
- 2 Department of Medicine, University of Arizona, Tucson, Arizona
| | - Jin Zhou
- 2 Department of Medicine, University of Arizona, Tucson, Arizona
| | | | | | - Evelyn Toh
- 4 Department of Microbiology and Immunology, and
| | | | - Huaiying Lin
- 5 Center for Biomedical Informatics, Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois; and
| | - Xiang Gao
- 5 Center for Biomedical Informatics, Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois; and
| | - Qunfeng Dong
- 5 Center for Biomedical Informatics, Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois; and
| | - Deming Mi
- 6 Department of Biostatistics, Indiana University, Indianapolis, Indiana
| | - Barry P Katz
- 6 Department of Biostatistics, Indiana University, Indianapolis, Indiana
| | - Erica Sodergren
- 7 Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
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74
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Presti RM, Flores SC, Palmer BE, Atkinson JJ, Lesko CR, Lau B, Fontenot AP, Roman J, McDyer JF, Twigg HL. Mechanisms Underlying HIV-Associated Noninfectious Lung Disease. Chest 2017; 152:1053-1060. [PMID: 28427967 DOI: 10.1016/j.chest.2017.04.154] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 02/28/2017] [Accepted: 04/05/2017] [Indexed: 01/15/2023] Open
Abstract
Pulmonary disease remains a primary source of morbidity and mortality in persons living with HIV (PLWH), although the advent of potent combination antiretroviral therapy has resulted in a shift from predominantly infectious to noninfectious pulmonary complications. PLWH are at high risk for COPD, pulmonary hypertension, and lung cancer even in the era of combination antiretroviral therapy. The underlying mechanisms of this are incompletely understood, but recent research in both human and animal models suggests that oxidative stress, expression of matrix metalloproteinases, and genetic instability may result in lung damage, which predisposes PLWH to these conditions. Some of the factors that drive these processes include tobacco and other substance use, direct HIV infection and expression of specific HIV proteins, inflammation, and shifts in the microbiome toward pathogenic and opportunistic organisms. Further studies are needed to understand the relative importance of these factors to the development of lung disease in PLWH.
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Affiliation(s)
- Rachel M Presti
- Department of Medicine, Washington University School of Medicine, St. Louis, MO.
| | - Sonia C Flores
- Department of Medicine, University of Colorado Denver, Aurora, CO
| | - Brent E Palmer
- Department of Medicine, University of Colorado Denver, Aurora, CO
| | - Jeffrey J Atkinson
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Catherine R Lesko
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Bryan Lau
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, School of Medicine, Johns Hopkins University, Baltimore, MD
| | | | - Jesse Roman
- Department of Medicine, University of Louisville, Health Sciences Center and Robley Rex VA Medical Center, Louisville, KY
| | - John F McDyer
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Homer L Twigg
- Department of Medicine, Indiana University, Indianapolis, IN
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75
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Segal LN, Clemente JC, Li Y, Ruan C, Cao J, Danckers M, Morris A, Tapyrik S, Wu BG, Diaz P, Calligaro G, Dawson R, van Zyl-Smit RN, Dheda K, Rom WN, Weiden MD. Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV Patients. Cell Host Microbe 2017; 21:530-537.e4. [PMID: 28366509 DOI: 10.1016/j.chom.2017.03.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/01/2017] [Accepted: 03/02/2017] [Indexed: 02/06/2023]
Abstract
Despite the immune-reconstitution with antiretroviral therapy (ART), HIV-infected individuals remain highly susceptible to tuberculosis (TB) and have an enrichment of oral anaerobes in the lung. Products of bacterial anaerobic metabolism, like butyrate and other short-chain fatty acids (SCFAs), induce regulatory T cells (Tregs). We tested whether SCFAs contribute to poor TB control in a longitudinal cohort of ART-treated HIV-infected South Africans. Increase in serum SCFAs was associated with increased TB susceptibility. SCFAs inhibited IFN-γ and IL-17A production in peripheral blood mononuclear cells from HIV-infected ART-treated individuals in response to M. tuberculosis antigen stimulation. Pulmonary SCFAs correlated with increased oral anaerobes, such as Prevotella in the lung, and with M. tuberculosis antigen-induced Tregs. Metabolites from anaerobic bacterial fermentation may, therefore, increase TB susceptibility by suppressing IFN-γ and IL-17A production during the cellular immune response to M. tuberculosis.
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Affiliation(s)
- Leopoldo N Segal
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, New York University, New York, NY 10016, USA
| | - Jose C Clemente
- Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, New York University, New York, NY 10016, USA
| | - Chunhai Ruan
- Metabolomics Core, University of Michigan School of Medicine, Ann Arbor, MI 48105, USA
| | - Jane Cao
- Metabolomics Core, University of Michigan School of Medicine, Ann Arbor, MI 48105, USA
| | - Mauricio Danckers
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, New York University, New York, NY 10016, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, and Critical Care Medicine, Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Sarah Tapyrik
- Division of Pulmonary, Critical Care & Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, New York University, New York, NY 10016, USA
| | - Philip Diaz
- Division of Pulmonary, Critical Care & Sleep Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Gregory Calligaro
- Division of Pulmonology, Department of Medicine & UCT Lung Institute, University of Cape Town, Cape Town 7925, South Africa
| | - Rodney Dawson
- Division of Pulmonology, Department of Medicine & UCT Lung Institute, University of Cape Town, Cape Town 7925, South Africa
| | - Richard N van Zyl-Smit
- Division of Pulmonology, Department of Medicine & UCT Lung Institute, University of Cape Town, Cape Town 7925, South Africa
| | - Keertan Dheda
- Division of Pulmonology, Department of Medicine & UCT Lung Institute, University of Cape Town, Cape Town 7925, South Africa
| | - William N Rom
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, New York University, New York, NY 10016, USA
| | - Michael D Weiden
- Division of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, New York University, New York, NY 10016, USA.
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76
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Lagier JC, Fenollar F, Raoult D. Acute infections caused by Tropheryma whipplei. Future Microbiol 2017; 12:247-254. [DOI: 10.2217/fmb-2017-0178] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Tropheryma whipplei is the causative bacterium of Whipple's disease. Its first culture has led to an enlargement of the field of the caused infections. Here, we comprehensively review acute T. whipplei infections. In a cohort study featuring 4000 children, T. whipplei was significantly more common in patients with diarrhea (4%) than in those without (1.7%). A case–controlled study highlighted 58 patients suffering from pneumonia with the detection of T. whipplei in their bronchoalveolar fluids. Finally, a recent study detected T. whipplei in the blood of 36 febrile patients experiencing pulmonary symptoms in a rural area of Senegal. T. whipplei is definitively an agent of acute gastroenteritis, a cause of nonmalarial fever in Africa, and probably a cause of pulmonary infections.
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Affiliation(s)
- Jean-Christophe Lagier
- Aix Marseille Université, URMITE, IHU Méditerranée-Infection, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Florence Fenollar
- Aix Marseille Université, URMITE, IHU Méditerranée-Infection, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Didier Raoult
- Aix Marseille Université, URMITE, IHU Méditerranée-Infection, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
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77
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Presti R, Pantaleo G. The Immunopathogenesis of HIV-1 Infection. Infect Dis (Lond) 2017. [DOI: 10.1016/b978-0-7020-6285-8.00092-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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78
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Twigg HL, Weinstock GM, Knox KS. Lung microbiome in human immunodeficiency virus infection. Transl Res 2017; 179:97-107. [PMID: 27496318 PMCID: PMC5164960 DOI: 10.1016/j.trsl.2016.07.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/06/2016] [Accepted: 07/07/2016] [Indexed: 12/28/2022]
Abstract
The lung microbiome plays a significant role in normal lung function and disease. Because microbial colonization is likely influenced by immunodeficiency, one would speculate that infection with human immunodeficiency virus (HIV) alters the lung microbiome. Furthermore, how this alteration might impact pulmonary complications now seen in HIV-infected patients on antiretroviral therapy (ART), which has shifted from opportunistic infections to diseases associated with chronic inflammation, is not known. There have been limited publications on the lung microbiome in HIV infection, many of them emanating from the Lung HIV Microbiome Project. Current evidence suggests that the lung microbiome in healthy HIV-infected individuals with preserved CD4 counts is similar to uninfected individuals. However, in individuals with more advanced disease, there is an altered alveolar microbiome characterized by a loss of richness and evenness (alpha diversity) within individuals. Furthermore, as a group the taxa making up the HIV-infected and uninfected lung microbiome are different (differences in beta diversity), and the HIV-infected population is more spread out (greater dispersion) than the uninfected population. These differences decline with ART, but even after effective therapy the alveolar microbiome in HIV-infected individuals contains increased amounts of signature bacteria, some of which have previously been associated with chronic lung inflammation. Furthermore, more recent investigations into the lung virome in HIV infection suggest that perturbations in lung viral communities also exist in HIV infection, and that these too are associated with evidence of lung inflammation. Thus, it is likely both microbiome and virome alterations in HIV infection contribute to lung inflammation in these individuals, which has important implications on the changing spectrum of pulmonary complications in patients living with HIV.
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Affiliation(s)
- Homer L Twigg
- Department of Medicine, Indiana University, Indianapolis, Ind.
| | - George M Weinstock
- Microbial Genomics, The Jackson Laboratory for Genomic Medicine, Farmington, Conn
| | - Kenneth S Knox
- Department of Medicine, University of Arizona, Tucson, Ariz
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79
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Morris A, Flores SC. Study of the Lung Microbiome. Have We Reached the End of the Beginning? Am J Respir Crit Care Med 2017; 195:15-16. [PMID: 28035854 DOI: 10.1164/rccm.201608-1635ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Alison Morris
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania and
| | - Sonia C Flores
- 2 University of Colorado Anschutz Medical Campus Aurora, Colorado
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80
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Williams B, Landay A, Presti RM. Microbiome alterations in HIV infection a review. Cell Microbiol 2016; 18:645-51. [PMID: 26945815 DOI: 10.1111/cmi.12588] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 02/28/2016] [Accepted: 03/03/2016] [Indexed: 12/25/2022]
Abstract
Recent developments in molecular techniques have allowed researchers to identify previously uncultured organisms, which has propelled a vast expansion of our knowledge regarding our commensal microbiota. Interest in the microbiome specific to HIV grew from earlier findings suggesting that bacterial translocation from the intestines is the cause of persistent immune activation despite effective viral suppression with antiretroviral therapy (ART). Studies of SIV infected primates have demonstrated that Proteobacteria preferentially translocate and that mucosal immunity can be restored with probiotics. Pathogenic SIV infection results in a massive expansion of the virome, whereas non-pathogenic SIV infection does not. Human HIV infected cohorts have been shown to have microbiota distinctive from that of HIV negative controls and efforts to restore the intestinal microbiome via probiotics have often had positive results on host markers. The microbiota of the genital tract may play a significant role in acquisition and transmission of HIV. Modification of commensal microbial communities likely represents an important therapeutic adjunct to treatment of HIV. Here we review the literature regarding human microbiome in HIV infection.
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Affiliation(s)
- Brett Williams
- Division of Infectious Diseases, Rush University Medical Center, USA
| | - Alan Landay
- Department of Immunology/microbiology, Rush University Medical Center, USA
| | - Rachel M Presti
- Division of Infectious Disease, Washington University School of Medicine, USA
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81
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Abstract
In recent years, it has become apparent that Tropheryma whipplei not only causes a chronic multisystemic infection which is often preceded by arthropathies for many years, well known as 'classical' Whipple's disease, but also clinically becomes manifest with localized organ affections and acute (transient) infections in children. T. whipplei is found ubiquitously in the environment and colonizes in some healthy carriers. In this review, we highlight new aspects of this enigmatic infectious disorder.
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82
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Branton WG, Lu JQ, Surette MG, Holt RA, Lind J, Laman JD, Power C. Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis. Sci Rep 2016; 6:37344. [PMID: 27892518 PMCID: PMC5125007 DOI: 10.1038/srep37344] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/26/2016] [Indexed: 12/14/2022] Open
Abstract
Microbial communities reside in healthy tissues but are often disrupted during disease. Bacterial genomes and proteins are detected in brains from humans, nonhuman primates, rodents and other species in the absence of neurological disease. We investigated the composition and abundance of microbiota in frozen and fixed autopsied brain samples from patients with multiple sclerosis (MS) and age- and sex-matched nonMS patients as controls, using neuropathological, molecular and bioinformatics tools. 16s rRNA sequencing revealed Proteobacteria to be the dominant phylum with restricted diversity in cerebral white matter (WM) from MS compared to nonMS patients. Both clinical groups displayed 1,200–1,400 bacterial genomes/cm3 and low bacterial rRNA:rDNA ratios in WM. RNAseq analyses showed a predominance of Proteobacteria in progressive MS patients’ WM, associated with increased inflammatory gene expression, relative to a broader range of bacterial phyla in relapsing-remitting MS patients’ WM. Although bacterial peptidoglycan (PGN) and RNA polymerase beta subunit immunoreactivities were observed in all patients, PGN immunodetection was correlated with demyelination and neuroinflammation in MS brains. Principal component analysis revealed that demyelination, PGN and inflammatory gene expression accounted for 86% of the observed variance. Thus, inflammatory demyelination is linked to an organ-specific dysbiosis in MS that could contribute to underlying disease mechanisms.
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Affiliation(s)
- W G Branton
- Department of Medicine, University of Alberta, Edmonton AB Canada.,Department of Laboratory Medicine &Pathology, University of Alberta, Edmonton AB Canada
| | - J Q Lu
- Department of Laboratory Medicine &Pathology, University of Alberta, Edmonton AB Canada.,Department of Psychiatry, University of Alberta, Edmonton AB Canada
| | - M G Surette
- Department of Medicine, McMaster University, Hamilton ON Canada
| | - R A Holt
- Genome Sciences Centre, Vancouver BC, Canada
| | - J Lind
- Department of Neurosciences, Section of Medical Physiology, Faculty of Medical Sciences, University Medical Center Groningen, University of Groningen, Groningen Netherlands
| | - J D Laman
- Multiple Sclerosis Centre, University of Alberta, Edmonton AB Canada
| | - C Power
- Department of Medicine, University of Alberta, Edmonton AB Canada.,Department of Laboratory Medicine &Pathology, University of Alberta, Edmonton AB Canada.,Department of Neurosciences, Section of Medical Physiology, Faculty of Medical Sciences, University Medical Center Groningen, University of Groningen, Groningen Netherlands
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83
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Scher JU, Joshua V, Artacho A, Abdollahi-Roodsaz S, Öckinger J, Kullberg S, Sköld M, Eklund A, Grunewald J, Clemente JC, Ubeda C, Segal LN, Catrina AI. The lung microbiota in early rheumatoid arthritis and autoimmunity. MICROBIOME 2016; 4:60. [PMID: 27855721 PMCID: PMC5114783 DOI: 10.1186/s40168-016-0206-x] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/02/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Airway abnormalities and lung tissue citrullination are found in both rheumatoid arthritis (RA) patients and individuals at-risk for disease development. This suggests the possibility that the lung could be a site of autoimmunity generation in RA, perhaps in response to microbiota changes. We therefore sought to test whether the RA lung microbiome contains distinct taxonomic features associated with local and/or systemic autoimmunity. METHODS 16S rRNA gene high-throughput sequencing was utilized to compare the bacterial community composition of bronchoalveolar lavage fluid (BAL) in patients with early, disease-modifying anti-rheumatic drugs (DMARD)-naïve RA, patients with lung sarcoidosis, and healthy control subjects. Samples were further assessed for the presence and levels of anti-citrullinated peptide antibodies (including fine specificities) in both BAL and serum. RESULTS The BAL microbiota of RA patients was significantly less diverse and abundant when compared to healthy controls, but similar to sarcoidosis patients. This distal airway dysbiosis was attributed to the reduced presence of several genus (i.e., Actynomyces and Burkhordelia) as well as reported periodontopathic taxa, including Treponema, Prevotella, and Porphyromonas. While multiple clades correlated with local and systemic levels of autoantibodies, the genus Pseudonocardia and various related OTUs were the only taxa overrepresented in RA BAL and correlated with higher disease activity and erosions. CONCLUSIONS Distal airway dysbiosis is present in untreated early RA and similar to that detected in sarcoidosis lung inflammation. This community perturbation, which correlates with local and systemic autoimmune/inflammatory changes, may potentially drive initiation of RA in a proportion of cases.
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Affiliation(s)
- Jose U. Scher
- Division of Rheumatology, NYU School of Medicine, New York, NY USA
| | - Vijay Joshua
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Johan Öckinger
- Respiratory Medicine Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Susanna Kullberg
- Respiratory Medicine Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Sköld
- Respiratory Medicine Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anders Eklund
- Respiratory Medicine Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Johan Grunewald
- Respiratory Medicine Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Carles Ubeda
- Institute for Research in Public Health, Valencia, Spain
| | - Leopoldo N. Segal
- Division of Pulmonary and Critical Care Medicine, NYU School of Medicine, New York, NY USA
| | - Anca I. Catrina
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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84
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Sze MA, Xu S, Leung JM, Vucic EA, Shaipanich T, Moghadam A, Harris M, Guillemi S, Sinha S, Nislow C, Murphy D, Hague C, Leipsic J, Lam S, Lam W, Montaner JS, Sin DD, Man SFP. The bronchial epithelial cell bacterial microbiome and host response in patients infected with human immunodeficiency virus. BMC Pulm Med 2016; 16:142. [PMID: 27829448 PMCID: PMC5103452 DOI: 10.1186/s12890-016-0303-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chronic Obstructive Pulmonary Disease (COPD) is an important comorbidity in patients living with human immunodeficiency virus (HIV). Previous bacterial microbiome studies have shown increased abundance of specific bacterium, like Tropheryma whipplei, and no overall community differences. However, the host response to the lung microbiome is unknown in patients infected with HIV. METHODS Two bronchial brush samples were obtained from 21 HIV-infected patients. One brush was used for bacterial microbiome analysis using the Illumina MiSeqTM platform, while the other was used to evaluate gene expression patterns of the host using the Affymetrix Human Gene ST 2.0 array. Weighted gene co-expression network analysis was used to determine the relationship between the bacterial microbiome and host gene expression response. RESULTS The Shannon Diversity was inversely related to only one gene expression module (p = 0.02); whereas evenness correlated with five different modules (p ≤ 0.05). After FDR correction only the Firmicutes phylum was significantly correlated with any modules (FDR < 0.05). These modules were enriched for cilia, transcription regulation, and immune response. Specific operational taxonomic units (OTUs), such as OTU4 (Pasteurellaceae), were able to distinguish HIV patients with and without COPD and severe emphysema. CONCLUSION These data support the hypothesis that the bacterial microbiome in HIV lungs is associated with specific host immune responses. Whether or not these responses are also seen in non-HIV infected individuals needs to be addressed in future studies.
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Affiliation(s)
- Marc A Sze
- Centre for Heart Lung Innovation, St. Paul's Hospital & Department of Medicine, University of British Columbia, Rm 166 - 1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada.
| | - Stella Xu
- Centre for Heart Lung Innovation, St. Paul's Hospital & Department of Medicine, University of British Columbia, Rm 166 - 1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada
| | - Janice M Leung
- Centre for Heart Lung Innovation, St. Paul's Hospital & Department of Medicine, University of British Columbia, Rm 166 - 1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada
| | - Emily A Vucic
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Tawimas Shaipanich
- Division of Respiratory Medicine, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Aida Moghadam
- AIDS Research Program, St. Paul's Hospital, Vancouver, BC, Canada
| | - Marianne Harris
- AIDS Research Program, St. Paul's Hospital, Vancouver, BC, Canada.,Department of Family Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Division of HIV/AIDS, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Silvia Guillemi
- AIDS Research Program, St. Paul's Hospital, Vancouver, BC, Canada.,Department of Family Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Division of HIV/AIDS, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sunita Sinha
- Faculty of Pharmaceutical Sciences, Pharmaceutical Sciences Building, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, Pharmaceutical Sciences Building, University of British Columbia, Vancouver, BC, Canada
| | - Darra Murphy
- Department of Radiology and Diagnostic Imaging, St. Paul's Hospital, Vancouver, BC, Canada
| | - Cameron Hague
- Department of Radiology and Diagnostic Imaging, St. Paul's Hospital, Vancouver, BC, Canada
| | - Jonathon Leipsic
- Department of Radiology and Diagnostic Imaging, St. Paul's Hospital, Vancouver, BC, Canada
| | - Stephen Lam
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Wan Lam
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Julio S Montaner
- Division of HIV/AIDS, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, Vancouver, BC, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital & Department of Medicine, University of British Columbia, Rm 166 - 1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada.,Division of Respiratory Medicine, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - S F Paul Man
- Centre for Heart Lung Innovation, St. Paul's Hospital & Department of Medicine, University of British Columbia, Rm 166 - 1081 Burrard St., Vancouver, BC, V6Z 1Y6, Canada.,Division of Respiratory Medicine, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
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85
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Hauptmann M, Schaible UE. Linking microbiota and respiratory disease. FEBS Lett 2016; 590:3721-3738. [PMID: 27637588 DOI: 10.1002/1873-3468.12421] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/30/2016] [Accepted: 09/07/2016] [Indexed: 12/13/2022]
Abstract
An increasing body of evidence indicates the relevance of microbiota for pulmonary health and disease. Independent investigations recently demonstrated that the lung harbors a resident microbiota. Therefore, it is intriguing that a lung microbiota can shape pulmonary immunity and epithelial barrier functions. Here, we discuss the ways how the composition of the microbial community in the lung may influence pulmonary health and vice versa, factors that determine community composition. Prominent microbiota at other body sites such as the intestinal one may also contribute to pulmonary health and disease. However, it is difficult to discriminate between influences of lung vs. gut microbiota due to systemic mutuality between both communities. With focuses on asthma and respiratory infections, we discuss how microbiota of lung and gut can determine pulmonary immunity and barrier functions.
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Affiliation(s)
- Matthias Hauptmann
- Priority Program Infections, Cellular Microbiology, Research Center Borstel, Germany
| | - Ulrich E Schaible
- Priority Program Infections, Cellular Microbiology, Research Center Borstel, Germany.,German Centre for Infection Research, TTU-TB, Borstel, Germany
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86
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Lagier JC, Papazian L, Fenollar F, Edouard S, Melenotte C, Laroumagne S, Michel G, Martin C, Gainnier M, Lions C, Carrieri P, Stein A, Brouqui P, Raoult D. Tropheryma whipplei DNA in bronchoalveolar lavage samples: a case control study. Clin Microbiol Infect 2016; 22:875-879. [DOI: 10.1016/j.cmi.2016.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 07/04/2016] [Accepted: 07/07/2016] [Indexed: 11/15/2022]
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87
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Abstract
PURPOSE OF REVIEW Human immunodeficiency virus (HIV) is now managed as a chronic disease. Non-infectious pulmonary conditions have replaced infection as the biggest threat to lung health, particularly as HIV cohorts age, but there is no consensus on how best to maintain long-term lung health. We review the epidemiology and pathogenesis of chronic obstructive pulmonary disease (COPD), pulmonary arterial hypertension (PAH), and lung cancer in HIV-seropositive individuals. RECENT FINDINGS Diagnoses of COPD are now up to 50% more prevalent in HIV-seropositive individuals than HIV-uninfected controls, and prospective pulmonary function studies find significant impairment in 7% to more than 50% of HIV-seropositive individuals. The prevalence of HIV-PAH is 0.2-0.5%, and lung cancer is two to three times more prevalent in HIV-seropositive individuals. Although host factors such as age and smoking have a role, HIV is an independent contributor to the pathogenesis of COPD, PAH, and lung cancer. Chronic inflammation, immune senescence, oxidative stress, and direct effects of viral proteins are all potential pathogenetic mechanisms. Despite their prevalence, non-infectious lung diseases remain underrecognized and evidence for effective screening strategies in HIV-seropositive individuals is limited. SUMMARY COPD, PAH, and lung cancer are a growing threat to lung health in the highly active antiretroviral therapy era necessitating early recognition.
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Affiliation(s)
- Paul Collini
- aDepartment of Infection, Immunity & Cardiovascular Disease, University of Sheffield Medical School, Sheffield, UK bDepartment of Medicine, University of Pittsburgh, 628 NW Montefiore University Hospital, Pittsburgh, Pennsylvania, USA
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88
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Tsarfati EM, Sutherland R. Whipple's disease. Br J Hosp Med (Lond) 2016; 77:C82-5. [PMID: 27269764 DOI: 10.12968/hmed.2016.77.6.c82] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- E M Tsarfati
- Medical Microbiology Registrar in the Department of Clinical Microbiology, Royal Infirmary of Edinburgh, Edinburgh
| | - R Sutherland
- Consultant Infectious Diseases in the Regional Infectious Diseases Unit, Western General Hospital, Edinburgh EH4 2XU
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89
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Rylance J, Kankwatira A, Nelson DE, Toh E, Day RB, Lin H, Gao X, Dong Q, Sodergren E, Weinstock GM, Heyderman RS, Twigg HL, Gordon SB. Household air pollution and the lung microbiome of healthy adults in Malawi: a cross-sectional study. BMC Microbiol 2016; 16:182. [PMID: 27514621 PMCID: PMC4982214 DOI: 10.1186/s12866-016-0803-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 08/04/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Domestic combustion of biomass fuels, such as wood, charcoal, crop residue and dung causes Household Air Pollution (HAP). These inhaled particulates affect more than half of the world's population, causing respiratory problems such as infection and inflammatory lung disease. We examined whether the presence of black carbon in alveolar macrophages was associated with alterations in the lung microbiome in a Malawi population. METHODS Bronchoalveolar lavage samples from 44 healthy adults were sequenced using 16S rDNA amplification to assess microbial diversity, richness and relative taxa abundance. Individuals were classified as high or low particulate exposure as determined by questionnaire and the percentage of black carbon within their alveolar macrophages. RESULTS Subjects in the low and high particulate groups did not differ in terms of source of fuels used for cooking or lighting. There was no difference in alpha or beta diversity by particulate group. Neisseria and Streptococcus were significantly more abundant in samples from high particulate exposed individuals, and Tropheryma was found less abundant. Petrobacter abundance was higher in people using biomass fuel for household cooking and lighting, compared with exclusive use of electricity. CONCLUSIONS Healthy adults in Malawi exposed to higher levels of particulates have higher abundances of potentially pathogenic bacteria (Streptococcus, Neisseria) within their lung microbiome. Domestic biomass fuel use was associated with an uncommon environmental bacterium (Petrobacter) associated with oil-rich niches.
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Affiliation(s)
- Jamie Rylance
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK. .,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.
| | - Anstead Kankwatira
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - David E Nelson
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Evelyn Toh
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Richard B Day
- Department of Medicine, Indiana University, Indianapolis, IN, USA
| | - Huaiying Lin
- Center for Biomedical Informatics, Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Xiang Gao
- Center for Biomedical Informatics, Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Qunfeng Dong
- Center for Biomedical Informatics, Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, 06032, USA
| | - George M Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, 06032, USA
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Homer L Twigg
- Department of Medicine, Indiana University, Indianapolis, IN, USA
| | - Stephen B Gordon
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
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90
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Segal LN, Clemente JC, Wu BG, Wikoff WR, Gao Z, Li Y, Ko JP, Rom WN, Blaser MJ, Weiden MD. Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung. Thorax 2016; 72:13-22. [PMID: 27486204 PMCID: PMC5329050 DOI: 10.1136/thoraxjnl-2016-208599] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/22/2016] [Accepted: 07/06/2016] [Indexed: 12/16/2022]
Abstract
Introduction Azithromycin (AZM) reduces pulmonary inflammation and exacerbations in patients with COPD having emphysema. The antimicrobial effects of AZM on the lower airway microbiome are not known and may contribute to its beneficial effects. Here we tested whether AZM treatment affects the lung microbiome and bacterial metabolites that might contribute to changes in levels of inflammatory cytokines in the airways. Methods 20 smokers (current or ex-smokers) with emphysema were randomised to receive AZM 250 mg or placebo daily for 8 weeks. Bronchoalveolar lavage (BAL) was performed at baseline and after treatment. Measurements performed in acellular BAL fluid included 16S rRNA gene sequences and quantity; 39 cytokines, chemokines and growth factors and 119 identified metabolites. The response to lipopolysaccharide (LPS) by alveolar macrophages after ex-vivo treatment with AZM or bacterial metabolites was assessed. Results Compared with placebo, AZM did not alter bacterial burden but reduced α-diversity, decreasing 11 low abundance taxa, none of which are classical pulmonary pathogens. Compared with placebo, AZM treatment led to reduced in-vivo levels of chemokine (C-X-C) ligand 1 (CXCL1), tumour necrosis factor (TNF)-α, interleukin (IL)-13 and IL-12p40 in BAL, but increased bacterial metabolites including glycolic acid, indol-3-acetate and linoleic acid. Glycolic acid and indol-3-acetate, but not AZM, blunted ex-vivo LPS-induced alveolar macrophage generation of CXCL1, TNF-α, IL-13 and IL-12p40. Conclusion AZM treatment altered both lung microbiota and metabolome, affecting anti-inflammatory bacterial metabolites that may contribute to its therapeutic effects. Trial registration number NCT02557958.
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Affiliation(s)
- Leopoldo N Segal
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York, USA.,Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin G Wu
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York, USA
| | - William R Wikoff
- Department of Molecular and Cellular Biology & Genome Center, University of California, Davis, California, USA
| | - Zhan Gao
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York, USA
| | - Jane P Ko
- Department of Radiology, New York University School of Medicine, New York, New York, USA
| | - William N Rom
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York, USA.,Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Martin J Blaser
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Michael D Weiden
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York, USA.,Department of Medicine, New York University School of Medicine, New York, New York, USA
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91
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Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis Study. Alpha-1 Protocol. Ann Am Thorac Soc 2016; 12:1551-60. [PMID: 26153726 DOI: 10.1513/annalsats.201503-143oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Severe deficiency of alpha-1 antitrypsin has a highly variable clinical presentation. The Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis α1 Study is a prospective, multicenter, cross-sectional study of adults older than age 35 years with PiZZ or PiMZ alpha-1 antitrypsin genotypes. It is designed to better understand if microbial factors influence this heterogeneity. Clinical symptoms, pulmonary function testing, computed chest tomography, exercise capacity, and bronchoalveolar lavage (BAL) will be used to define chronic obstructive pulmonary disease (COPD) phenotypes that can be studied with an integrated systems biology approach that includes plasma proteomics; mouth, BAL, and stool microbiome and virome analysis; and blood microRNA and blood mononuclear cell RNA and DNA profiling. We will rely on global genome, transcriptome, proteome, and metabolome datasets. Matched cohorts of PiZZ participants on or off alpha-1 antitrypsin augmentation therapy, PiMZ participants not on augmentation therapy, and control participants from the Subpopulations and Intermediate Outcome Measures in COPD Study who match on FEV1 and age will be compared. In the primary analysis, we will determine if the PiZZ individuals on augmentation therapy have a difference in lower respiratory tract microbes identified compared with matched PiZZ individuals who are not on augmentation therapy. By characterizing the microbiome in alpha-1 antitrypsin deficiency (AATD), we hope to define new phenotypes of COPD that explain some of the diversity of clinical presentations. As a unique genetic cause of COPD, AATD may inform typical COPD pathogenesis, and better understanding of it may illuminate the complex interplay between environment and genetics. Although the biologic approaches are hypothesis generating, the results may lead to development of novel biomarkers, better understanding of COPD phenotypes, and development of novel diagnostic and therapeutic trials in AATD and COPD. Clinical trial registered with www.clinicaltrials.gov (NCT01832220).
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92
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Qin S, Clausen E, Lucht L, Michael H, Beck JM, Curtis JL, Freeman CM, Morris A. Presence of Tropheryma whipplei in Different Body Sites in a Cohort of Healthy Subjects. Am J Respir Crit Care Med 2016; 194:243-5. [PMID: 27420361 PMCID: PMC5003220 DOI: 10.1164/rccm.201601-0162le] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Shulin Qin
- 1 University of Pittsburgh Pittsburgh, Pennsylvania
| | | | - Lorrie Lucht
- 1 University of Pittsburgh Pittsburgh, Pennsylvania
| | | | - James M Beck
- 2 University of Colorado School of Medicine Aurora, Colorado
- 3 Veterans Affairs Eastern Colorado Health Care System Denver, Colorado
| | - Jeffrey L Curtis
- 4 University of Michigan Ann Arbor, Michigan and
- 5 VA Healthcare System Ann Arbor, Michigan
| | - Christine M Freeman
- 4 University of Michigan Ann Arbor, Michigan and
- 5 VA Healthcare System Ann Arbor, Michigan
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93
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Morris A, Paulson JN, Talukder H, Tipton L, Kling H, Cui L, Fitch A, Pop M, Norris KA, Ghedin E. Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection. MICROBIOME 2016; 4:38. [PMID: 27391224 PMCID: PMC4939015 DOI: 10.1186/s40168-016-0183-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/27/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND Longitudinal studies of the lung microbiome are challenging due to the invasive nature of sample collection. In addition, studies of the lung microbiome in human disease are usually performed after disease onset, limiting the ability to determine early events in the lung. We used a non-human primate model to assess lung microbiome alterations over time in response to an HIV-like immunosuppression and determined impact of the lung microbiome on development of obstructive lung disease. Cynomolgous macaques were infected with the SIV-HIV chimeric virus SHIV89.6P. Bronchoalveolar lavage fluid samples were collected pre-infection and every 4 weeks for 53 weeks post-infection. The microbiota was characterized at each time point by 16S ribosomal RNA (rRNA) sequencing. RESULTS We observed individual variation in the composition of the lung microbiota with a proportion of the macaques having Tropheryma whipplei as the dominant organism in their lungs. Bacterial communities varied over time both within and between animals, but there did not appear to be a systematic alteration due to SHIV infection. Development of obstructive lung disease in the SHIV-infected animals was characterized by a relative increase in abundance of oral anaerobes. Network analysis further identified a difference in community composition that accompanied the development of obstructive disease with negative correlations between members of the obstructed and non-obstructed groups. This emphasizes how species shifts can impact multiple other species, potentially resulting in disease. CONCLUSIONS This study is the first to investigate the dynamics of the lung microbiota over time and in response to immunosuppression in a non-human primate model. The persistence of oral bacteria in the lung and their association with obstruction suggest a potential role in pathogenesis. The lung microbiome in the non-human primate is a valuable tool for examining the impact of the lung microbiome in human health and disease.
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Affiliation(s)
- Alison Morris
- />Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
- />Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Joseph N. Paulson
- />Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
- />Present address: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- />Present address: Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Hisham Talukder
- />Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
| | - Laura Tipton
- />Department of Biology, Center for Genomics & Systems Biology and College of Global Public Health, New York University, 12 Waverly Place, New York, NY 10003 USA
- />Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Heather Kling
- />Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Lijia Cui
- />Tsinghua University School of Medicine, Beijing, China
| | - Adam Fitch
- />Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Mihai Pop
- />Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
| | - Karen A. Norris
- />Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Elodie Ghedin
- />Department of Biology, Center for Genomics & Systems Biology and College of Global Public Health, New York University, 12 Waverly Place, New York, NY 10003 USA
- />Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
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94
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Mwalukomo T, Rylance SJ, Webb EL, Anderson S, O'Hare B, van Oosterhout JJ, Ferrand RA, Corbett EL, Rylance J. Clinical Characteristics and Lung Function in Older Children Vertically Infected With Human Immunodeficiency Virus in Malawi. J Pediatric Infect Dis Soc 2016; 5:161-9. [PMID: 26407277 PMCID: PMC5407134 DOI: 10.1093/jpids/piv045] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/03/2015] [Indexed: 11/13/2022]
Abstract
BACKGROUND Antiretroviral therapy (ART) has led to increased survival of children with vertically acquired human immunodeficiency virus infection. Significant morbidity arises from respiratory symptoms, but aetiology and pulmonary function abnormalities have not been systematically studied. METHODS Human immunodeficiency virus-positive children aged 8-16 years were systematically recruited within clinics in Blantyre, Malawi. Clinical review, quality of life assessment, spirometry, and chest radiography were performed. RESULTS One hundred sixty participants had a mean of age 11.1 (range, 8-16) years and 50.0% were female. Cough was present in 60 (37.5%) participants, and 55 (34.4%) had moderate or severe dyspnoea. Thirty-four (22.1%) participants had digital clubbing. Thirty-three (20.6%) participants were hypoxic at rest. One hundred eighteen (73.8%) of the children were receiving ART; median CD4 count was 698 cells/µL in these compared with 406 cells/µL in ART-naive individuals (P < .001). From 145 spirometry traces (90.6%), mean forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) were 1.06 and 0.89 standard deviations below predicted mean, respectively. Twenty-one (14.5%) traces demonstrated obstructive defects and 26 (17.9%) reduced FVC. Lung function abnormality was not associated with any clinical findings. Of the 51 individuals with abnormal lung function, the mean increase in FEV1 after salbutamol was 3.8% (95% confidence interval, 0.02-7.53). "Tramlines" and ring shadows were seen on chest radiographs in over half of cases. CONCLUSIONS Symptoms of chronic lung disease were highly prevalent with 2 main clinical phenotypes: "cough" and "hypoxia". Lung function abnormalities are common, poorly responsive to bronchodilators, and apparent throughout the age range of our cohort. Pathological causes remain to be elucidated. Cough and hypoxic phenotypes could be a useful part of diagnostic algorithms if further validated.
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Affiliation(s)
- Thandie Mwalukomo
- College of Medicine, University of Malawi,London School of Hygiene & Tropical Medicine, United Kingdom
| | | | - Emily L. Webb
- London School of Hygiene & Tropical Medicine, United Kingdom
| | | | - Bernadette O'Hare
- College of Medicine, University of Malawi,University of St Andrews, United Kingdom
| | | | | | - Elizabeth L. Corbett
- College of Medicine, University of Malawi,London School of Hygiene & Tropical Medicine, United Kingdom
| | - Jamie Rylance
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre,Liverpool School of Tropical Medicine, United Kingdom
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95
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Beck JM, Schloss PD, Venkataraman A, Twigg H, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, Frank I, Ghedin E, Huang L, Lynch SV, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB. Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. Am J Respir Crit Care Med 2016; 192:1335-44. [PMID: 26247840 DOI: 10.1164/rccm.201501-0128oc] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RATIONALE Improved understanding of the lung microbiome in HIV-infected individuals could lead to better strategies for diagnosis, therapy, and prophylaxis of HIV-associated pneumonias. Differences in the oral and lung microbiomes in HIV-infected and HIV-uninfected individuals are not well defined. Whether highly active antiretroviral therapy influences these microbiomes is unclear. OBJECTIVES We determined whether oral and lung microbiomes differed in clinically healthy groups of HIV-infected and HIV-uninfected subjects. METHODS Participating sites in the Lung HIV Microbiome Project contributed bacterial 16S rRNA sequencing data from oral washes and bronchoalveolar lavages (BALs) obtained from HIV-uninfected individuals (n = 86), HIV-infected individuals who were treatment naive (n = 18), and HIV-infected individuals receiving antiretroviral therapy (n = 38). MEASUREMENTS AND MAIN RESULTS Microbial populations differed in the oral washes among the subject groups (Streptococcus, Actinomyces, Rothia, and Atopobium), but there were no individual taxa that differed among the BALs. Comparison of oral washes and BALs demonstrated similar patterns from HIV-uninfected individuals and HIV-infected individuals receiving antiretroviral therapy, with multiple taxa differing in abundance. The pattern observed from HIV-infected individuals who were treatment naive differed from the other two groups, with differences limited to Veillonella, Rothia, and Granulicatella. CD4 cell counts did not influence the oral or BAL microbiome in these relatively healthy, HIV-infected subjects. CONCLUSIONS The overall similarity of the microbiomes in participants with and without HIV infection was unexpected, because HIV-infected individuals with relatively preserved CD4 cell counts are at higher risk for lower respiratory tract infections, indicating impaired local immune function.
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Affiliation(s)
- James M Beck
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado.,2 Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado
| | - Patrick D Schloss
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Arvind Venkataraman
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Homer Twigg
- 4 Department of Medicine, Indiana University, Indianapolis, Indiana
| | - Kathleen A Jablonski
- 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | | | - Thomas B Campbell
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Emily S Charlson
- 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronald G Collman
- 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kristina Crothers
- 8 Department of Medicine, University of Washington, Seattle, Washington
| | - Jeffrey L Curtis
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,9 Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Kimberly L Drews
- 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | - Sonia C Flores
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Andrew P Fontenot
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Mary A Foulkes
- 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | - Ian Frank
- 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elodie Ghedin
- 10 Department of Computational and Systems Biology and
| | - Laurence Huang
- 11 Department of Medicine, University of California San Francisco, San Francisco, California; and
| | - Susan V Lynch
- 11 Department of Medicine, University of California San Francisco, San Francisco, California; and
| | - Alison Morris
- 12 Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brent E Palmer
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Thomas M Schmidt
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Erica Sodergren
- 13 The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | | | - Vincent B Young
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
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96
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Segal LN, Clemente JC, Tsay JCJ, Koralov SB, Keller BC, Wu BG, Li Y, Shen N, Ghedin E, Morris A, Diaz P, Huang L, Wikoff WR, Ubeda C, Artacho A, Rom WN, Sterman DH, Collman RG, Blaser MJ, Weiden MD. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nat Microbiol 2016; 1:16031. [PMID: 27572644 PMCID: PMC5010013 DOI: 10.1038/nmicrobiol.2016.31] [Citation(s) in RCA: 393] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/19/2016] [Indexed: 12/19/2022]
Abstract
Microaspiration is a common phenomenon in healthy subjects, but its frequency is increased in chronic inflammatory airway diseases, and its role in inflammatory and immune phenotypes is unclear. We have previously demonstrated that acellular bronchoalveolar lavage samples from half of the healthy people examined are enriched with oral taxa (here called pneumotypeSPT) and this finding is associated with increased numbers of lymphocytes and neutrophils in bronchoalveolar lavage. Here, we have characterized the inflammatory phenotype using a multi-omic approach. By evaluating both upper airway and acellular bronchoalveolar lavage samples from 49 subjects from three cohorts without known pulmonary disease, we observed that pneumotypeSPT was associated with a distinct metabolic profile, enhanced expression of inflammatory cytokines, a pro-inflammatory phenotype characterized by elevated Th-17 lymphocytes and, conversely, a blunted alveolar macrophage TLR4 response. The cellular immune responses observed in the lower airways of humans with pneumotypeSPT indicate a role for the aspiration-derived microbiota in regulating the basal inflammatory status at the pulmonary mucosal surface.
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Affiliation(s)
- Leopoldo N. Segal
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, USA
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jun-Chieh J. Tsay
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, USA
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Sergei B. Koralov
- Department of Pathology, New York University School of Medicine, New York, New York, USA
| | - Brian C. Keller
- Division of Pulmonary and Critical Care Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Benjamin G. Wu
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, USA
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, USA
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Nan Shen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Elodie Ghedin
- Department of Biology, Center for Genomics & Systems Biology, College of Global Public Health, New York University, New York, New York, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pennsylvania, USA
| | - Phillip Diaz
- Division of Pulmonary and Critical Care Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Laurence Huang
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - William R. Wikoff
- Department of Molecular and Cellular Biology & Genome Center, University of California, Davis, California, USA
| | - Carles Ubeda
- Center for Public Health Research, FISABIO, Valencia, Spain
| | | | - William N. Rom
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, USA
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Daniel H. Sterman
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, USA
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Ronald G. Collman
- Department of Medicine and Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Martin J. Blaser
- Department of Medicine, New York University School of Medicine, New York, New York, USA
| | - Michael D. Weiden
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, USA
- Department of Medicine, New York University School of Medicine, New York, New York, USA
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97
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Spatial Variation in the Healthy Human Lung Microbiome and the Adapted Island Model of Lung Biogeography. Ann Am Thorac Soc 2016; 12:821-30. [PMID: 25803243 PMCID: PMC4590020 DOI: 10.1513/annalsats.201501-029oc] [Citation(s) in RCA: 320] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
RATIONALE The lung microbiome is spatially heterogeneous in advanced airway diseases, but whether it varies spatially in health is unknown. We postulated that the primary determinant of lung microbiome constitution in health is the balance of immigration and elimination of communities from the upper respiratory tract (URT; "adapted island model of lung biogeography"), rather than differences in regional bacterial growth conditions. OBJECTIVES To determine if the lung microbiome is spatially varied in healthy adults. METHODS Bronchoscopy was performed on 15 healthy subjects. Specimens were sequentially collected in the lingula and right middle lobe (by bronchoalveolar lavage [BAL]), then in the right upper lobe, left upper lobe, and supraglottic space (by protected-specimen brush). Bacterial 16S ribosmal RNA-encoding genes were sequenced using MiSeq (Illumina, San Diego, CA). MEASUREMENTS AND MAIN RESULTS There were no significant differences between specimens collected by BAL and protected-specimen brush. Spatially separated intrapulmonary sites, when compared with each other, did not contain consistently distinct microbiota. On average, intrasubject variation was significantly less than intersubject variation (P = 0.00003). By multiple ecologic parameters (community richness, community composition, intersubject variability, and similarity to source community), right upper lobe microbiota more closely resembled those of the URT than did microbiota from more distal sites. As predicted by the adapted island model, community richness decreased with increasing distance from the source community of the URT (P < 0.05). CONCLUSIONS In healthy lungs, spatial variation in microbiota within an individual is significantly less than variation across individuals. The lung microbiome in health is more influenced by microbial immigration and elimination (the adapted island model) than by the effects of local growth conditions on bacterial reproduction rates, which are more determinant in advanced lung diseases. BAL of a single lung segment is an acceptable method of sampling the healthy lung microbiome. Clinical trial registered with www.clinicaltrials.gov (NCT02392182).
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98
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Drummond MB, Kunisaki KM, Huang L. Obstructive Lung Diseases in HIV: A Clinical Review and Identification of Key Future Research Needs. Semin Respir Crit Care Med 2016; 37:277-88. [PMID: 26974304 DOI: 10.1055/s-0036-1578801] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
HIV infection has shifted from what was once a disease directly impacting short-term mortality to what is now a chronic illness controllable in the era of effective combination antiretroviral therapy (ART). In this setting, life expectancy for HIV-infected individual is nearly comparable to that of individuals without HIV. Subsequent to this increase in life expectancy, there has been recognition of increased multimorbidity among HIV-infected persons, with prevalence of comorbid chronic illnesses now approaching 65%. Obstructive lung diseases, including chronic obstructive pulmonary disease (COPD) and asthma, are prevalent conditions associated with substantial morbidity and mortality in the United States. There is overlap in risk factors for HIV acquisition and chronic lung diseases, including lower socioeconomic status and the use of tobacco and illicit drugs. Objectives of this review are to (1) summarize the current state of knowledge regarding COPD and asthma among HIV-infected persons, (2) highlight implications for clinicians caring for patients with these combined comorbidities, and (3) identify key research initiatives to reduce the burden of obstructive lung diseases among HIV-infected persons.
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Affiliation(s)
- M Bradley Drummond
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ken M Kunisaki
- Section of Pulmonary, Critical Care, and Sleep Medicine, Minneapolis VA Health Care System, Minneapolis, Minnesota
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California
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99
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Charles TP, Shellito JE. Human Immunodeficiency Virus Infection and Host Defense in the Lungs. Semin Respir Crit Care Med 2016; 37:147-56. [PMID: 26974294 DOI: 10.1055/s-0036-1572553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Immunosuppression associated with human immunodeficiency virus (HIV) infection impacts all components of host defense against pulmonary infection. Cells within the lung have altered immune function and are important reservoirs for HIV infection. The host immune response to infected lung cells further compromises responses to a secondary pathogenic insult. In the upper respiratory tract, mucociliary function is impaired and there are decreased levels of salivary immunoglobulin A. Host defenses in the lower respiratory tract are controlled by alveolar macrophages, lymphocytes, and polymorphonuclear leukocytes. As HIV infection progresses, lung CD4 T cells are reduced in number causing a lack of activation signals from CD4 T cells and impaired defense by macrophages. CD8 T cells, on the other hand, are increased in number and cause lymphocytic alveolitis. Specific antibody responses by B-lymphocytes are decreased and opsonization of microorganisms is impaired. These observed defects in host defense of the respiratory tract explain the susceptibility of HIV-infected persons for oropharyngeal candidiasis, bacterial pneumonia, Pneumocystis pneumonia, and other opportunistic infections.
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Affiliation(s)
- Tysheena P Charles
- Section of Pulmonary/Critical Care & Allergy/Immunology, Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Judd E Shellito
- Section of Pulmonary/Critical Care & Allergy/Immunology, Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana
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100
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Boyton RJ, Altmann DM. Bronchiectasis: Current Concepts in Pathogenesis, Immunology, and Microbiology. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2016; 11:523-54. [PMID: 26980162 DOI: 10.1146/annurev-pathol-012615-044344] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bronchiectasis is a disorder of persistent lung inflammation and recurrent infection, defined by a common pathological end point: irreversible bronchial dilatation arrived at through diverse etiologies. This suggests an interplay between immunogenetic susceptibility, immune dysregulation, bacterial infection, and lung damage. The damaged epithelium impairs mucus removal and facilitates bacterial infection with increased cough, sputum production, and airflow obstruction. Lung infection is caused by respiratory bacterial and fungal pathogens, including Pseudomonas aeruginosa, Haemophilus, Aspergillus fumigatus, and nontuberculous mycobacteria. Recent studies have highlighted the relationship between the lung microbiota and microbial-pathogen niches. Disease may result from environments favoring interleukin-17-driven neutrophilia. Bronchiectasis may present in autoimmune disease, as well as conditions of immune dysregulation, such as combined variable immune deficiency, transporter associated with antigen processing-deficiency syndrome, and hyperimmunoglobulin E syndrome. Differences in prevalence across geography and ethnicity implicate an etiological mix of genetics and environment underpinning susceptibility.
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Affiliation(s)
- Rosemary J Boyton
- Lung Immunology Group, Department of Medicine, Imperial College London, London W12 0NN, United Kingdom; .,Department of Respiratory Medicine, Royal Brompton & Harefield NHS Foundation Trust, London SW3 6NP, United Kingdom
| | - Daniel M Altmann
- Division of Immunology and Inflammation, Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
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