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Fillion-Bertrand G, Dickson RP, Boivin R, Lavoie JP, Huffnagle GB, Leclere M. Lung Microbiome Is Influenced by the Environment and Asthmatic Status in an Equine Model of Asthma. Am J Respir Cell Mol Biol 2019; 60:189-197. [PMID: 30183323 DOI: 10.1165/rcmb.2017-0228oc] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
There is evidence that the lung microbiome differs between patients with asthma and healthy humans, but the effect of environmental conditions and medication is unknown and difficult to study. Equine asthma is a naturally occurring chronic airway disease characterized by reversible airway inflammation and bronchoconstriction upon exposure to inhaled antigens. In the present study, we evaluated the effect that environmental conditions and disease status have on pulmonary, nasal, and oral microbiomes. Six asthmatic and six healthy horses were studied while at pasture ("low antigen exposure"), as well as when being housed indoors and fed good-quality hay ("moderate exposure") and poor-quality hay ("high exposure"). At each time point, lung function was recorded; BAL, oral, and nasal rinses were collected; and 16S rRNA gene sequencing was performed. Asthmatic horses developed airway obstruction and inflammation under moderate and high antigen exposure conditions, whereas nonasthmatic horses showed mild inflammation under high antigen exposure, without bronchoconstriction. Lung, oral, and nasal communities clustered by environmental condition, but only lung communities were different between healthy and asthmatic horses. The association between asthma and lung microbiome was strongest in horses under moderate antigen exposure. Pulmonary, oral, and nasal microbiomes are influenced by environmental conditions, but only the pulmonary microbiome differs between horses with and without asthma. This difference, seen mainly when airway inflammation was present in horses with asthma but not in control animals, suggests that the altered lung microbiome in asthma might not be inherent but coincident with inflammation.
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Affiliation(s)
- Gabrielle Fillion-Bertrand
- 1 Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Montreal, St. Hyacinthe, Quebec, Canada; and
| | - Robert P Dickson
- 2 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Roxane Boivin
- 1 Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Montreal, St. Hyacinthe, Quebec, Canada; and
| | - Jean-Pierre Lavoie
- 1 Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Montreal, St. Hyacinthe, Quebec, Canada; and
| | - Gary B Huffnagle
- 2 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Mathilde Leclere
- 1 Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Montreal, St. Hyacinthe, Quebec, Canada; and
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Fastrès A, Taminiau B, Vangrinsven E, Tutunaru AC, Moyse E, Farnir F, Daube G, Clercx C. Effect of an antimicrobial drug on lung microbiota in healthy dogs. Heliyon 2019; 5:e02802. [PMID: 31844730 PMCID: PMC6895694 DOI: 10.1016/j.heliyon.2019.e02802] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/20/2019] [Accepted: 10/31/2019] [Indexed: 12/21/2022] Open
Abstract
Alterations of the lung microbiota (LM) are associated with clinical features in chronic lung diseases (CLDs) with growing evidence that an altered LM contributes to the pathogenesis of such disorders. The common use of antimicrobial drugs in the management of CLDs likely represents a confounding factor in the study of the LM. The aim of the present study was to assess the effect of oral administration of amoxicillin/clavulanic acid (AC) on the LM in healthy dogs (n = 6) at short (immediately after stopping AC [D10]) and medium-term (16 days after stopping AC [D26]). Metagenetic analyses were performed on the V1–V3 hypervariable region of 16S rDNA after extraction of total bacterial DNA from samples of bronchoalveolar lavage fluid (BALF). AC did not induce significant changes in BALF cellular counts or in the bacterial load or microbial richness, evenness and α-diversity, while the β-diversity was clearly modified at D10 compared with D0 (before AC administration) and D26 (P < 0.01). The relative abundance of Bacteroidetes and Proteobacteria increased at D10 (P < 0.01) in comparison with D0 and D26 (P < 0.01). The relative abundance of Firmicutes decreased from D0 to D10 (P < 0.01) and increased from D10 to D26 (P < 0.01), but was still lower than at D0 (P < 0.01). The proportion of Actinobacteria increased at D26 compared with D0 and D10 (P < 0.01). Significant differences between timepoints at the level of family, genus or species were not found. In conclusion, in healthy dogs, oral administration of AC induces significant changes in LM at the phyla level and in the β-diversity. Most changes normalize within 2 weeks after discontinuation of AC.
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Affiliation(s)
- Aline Fastrès
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, 4000, Liège, Belgium
| | - Bernard Taminiau
- Department of Food Sciences - Microbiology, FARAH, Faculty of Veterinary Medicine, University of Liège, 4000, Liège, Belgium
| | - Emilie Vangrinsven
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, 4000, Liège, Belgium
| | - Alexandru-Cosmin Tutunaru
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, 4000, Liège, Belgium
| | - Evelyne Moyse
- Department of Veterinary Management of Animal Resources, FARAH, Faculty of Veterinary Medicine, University of Liège, 4000, Liège, Belgium
| | - Frederic Farnir
- Department of Veterinary Management of Animal Resources, FARAH, Faculty of Veterinary Medicine, University of Liège, 4000, Liège, Belgium
| | - Georges Daube
- Department of Food Sciences - Microbiology, FARAH, Faculty of Veterinary Medicine, University of Liège, 4000, Liège, Belgium
| | - Cécile Clercx
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, 4000, Liège, Belgium
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53
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Bai F, Cai Z, Yang L. Recent progress in experimental and human disease-associated multi-species biofilms. Comput Struct Biotechnol J 2019; 17:1234-1244. [PMID: 31921390 PMCID: PMC6944735 DOI: 10.1016/j.csbj.2019.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/18/2019] [Accepted: 09/21/2019] [Indexed: 12/16/2022] Open
Abstract
Human bodies are colonized by trillions of microorganisms, which are often referred to as human microbiota and play important roles in human health. Next generation sequencing studies have established links between the genetic content of human microbiota and various human diseases. However, it remains largely unknown about the spatial organizations and interspecies interactions of individual species within the human microbiota. Bacterial cells tend to form surface-attached biofilms in many natural environments, which enable intercellular communications and interactions in a microbial ecosystem. In this review, we summarize the recent progresses on the experimental and human disease-associated multi-species biofilm studies. We hypothesize that engineering biofilm structures and interspecies interactions might provide a tool for manipulating the composition and function of human microbiota.
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Affiliation(s)
- Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhao Cai
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technology University, Singapore
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, China
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54
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Rodriguez AE, Restrepo MI. New perspectives in aspiration community acquired Pneumonia. Expert Rev Clin Pharmacol 2019; 12:991-1002. [PMID: 31516051 DOI: 10.1080/17512433.2019.1663730] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Introduction: Aspiration pneumonia is a subclass of community-acquired pneumonia that is expected to have an increasing contribution in mortality and morbidity, particularly in the elderly population over the next coming decades. While studies have revealed significant progress in identifying risk factors for aspiration pneumonia, the clinical presentation and diagnosis remain challenging to healthcare providers. Areas covered: We conducted a broad literature review using the MeSH heading in PubMed/MEDLINE of 'aspiration pneumonia' from January 1970 to July 2019. The understanding of the microbiology of aspiration pneumonia has evolved from a possible shift in the causative organisms away from anaerobes to traditional community-acquired pneumonia organisms. The importance of this shift is not yet known, but it has questioned the pathogenic role of anaerobes, appropriate anaerobic testing and the role of these pathogens in the pulmonary microbiome in patients with pneumonia. The identification of risk factors led to strategies to prevent or minimize the risk of aspiration pneumonia with moderate success. Expert opinion: Our expert opinion is that further research is needed to determine the role of the microbiome with aspiration pneumonia and patient risk factors. There is also a great need to develop clinical tools to help providers diagnose, treat, and prevent aspiration pneumonia.
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Affiliation(s)
- Abraham E Rodriguez
- Division of Pulmonary Diseases & Critical Care Medicine, University of Texas Health , San Antonio , TX , USA.,Division of Pulmonary Diseases & Critical Care Medicine, South Texas Veterans Health Care System , San Antonio , TX , USA
| | - Marcos I Restrepo
- Division of Pulmonary Diseases & Critical Care Medicine, University of Texas Health , San Antonio , TX , USA.,Division of Pulmonary Diseases & Critical Care Medicine, South Texas Veterans Health Care System , San Antonio , TX , USA
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Interactions between microbiome and lungs: Paving new paths for microbiome based bio-engineered drug delivery systems in chronic respiratory diseases. Chem Biol Interact 2019; 310:108732. [DOI: 10.1016/j.cbi.2019.108732] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/18/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022]
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Jin J, Gan Y, Liu H, Wang Z, Yuan J, Deng T, Zhou Y, Zhu Y, Zhu H, Yang S, Shen W, Xie D, Wu H, Liu D, Li W. Diminishing microbiome richness and distinction in the lower respiratory tract of lung cancer patients: A multiple comparative study design with independent validation. Lung Cancer 2019; 136:129-135. [PMID: 31494531 DOI: 10.1016/j.lungcan.2019.08.022] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 08/18/2019] [Accepted: 08/20/2019] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Current evidence suggests that microorganisms are associated with neoplastic diseases; however, the role of the airway microbiome in lung cancer remains unknown. To investigate the taxonomic profiles of the lower respiratory tract (LRT) microbiome in patients with lung cancer. MATERIALS AND METHODS BALF samples were collected in a discovery set comprising 150 individuals, including 91 patients with lung cancer, 29 patients with nonmalignant pulmonary diseases and 30 healthy subjects, and an independent validation set including 85 participants. The samples were assessed by metagenomics analysis. Random forest regression analysis was performed to select a diagnostic panel. RESULTS In the discovery set, richness was reduced in lung cancer patients compared with that in healthy subjects, and the microbiome of patients with nonmalignant diseases resembled that of patients with lung cancer. Interestingly, Bradyrhizobium japonicum was only found in patients with lung cancer, whereas Acidovorax was found in patients with cancer and nonmalignant pulmonary diseases. A microbiota-related diagnostic model consisting of age, pack year of smoking and eleven types of bacteria was built, and the area under the curve (AUC) for discriminating the patients with cancer was 0.882 (95%CI: 0.807-0.957) in the training set and 0.796 (95%CI: 0.673-0.920) in the independent validation set. CONCLUSION Our study demonstrates that the LRT microbiome richness is diminished in lung cancer patients compared with that in healthy subjects and that microbiota-specific biomarkers may be useful for diagnosing patients for whom lung biopsy is not feasible.
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Affiliation(s)
- Jing Jin
- Department of Respiratory & Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China
| | - Yuncui Gan
- Department of Respiratory & Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China
| | - Huayong Liu
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Zirong Wang
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Jianying Yuan
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Taibing Deng
- Department of Respiratory Medicine. West China-Guangan Hospital, Sichuan University, Guangan, 638500, Sichuan Province, China
| | - Yongzhao Zhou
- Department of Respiratory & Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China
| | - Yingying Zhu
- Department of Respiratory & Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China
| | - Hui Zhu
- Department of Respiratory & Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China
| | - Sai Yang
- Department of Respiratory & Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China
| | - Wei Shen
- Hangzhou YITU Healthcare Technology Co, Ltd, Zhejiang, Hangzhou, 310000, China
| | - Dan Xie
- Center of Precision Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and National Collaborative Innovation Center, Chengdu, Sichuan Province, 610041, China
| | - Honglong Wu
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
| | - Dan Liu
- Department of Respiratory & Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China.
| | - Weimin Li
- Department of Respiratory & Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, 610041, China.
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57
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The Human Lung Mycobiome in Chronic Respiratory Disease: Limitations of Methods and Our Current Understanding. CURRENT FUNGAL INFECTION REPORTS 2019. [DOI: 10.1007/s12281-019-00347-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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58
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Response of Beef Cattle Fecal Microbiota to Grazing on Toxic Tall Fescue. Appl Environ Microbiol 2019; 85:AEM.00032-19. [PMID: 31126949 DOI: 10.1128/aem.00032-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022] Open
Abstract
Tall fescue, the predominant southeastern United States cool-season forage grass, frequently becomes infected with an ergot alkaloid-producing toxic endophyte, Epichloë coenophialum Consumption of endophyte-infected fescue results in fescue toxicosis (FT), a condition that lowers beef cow productivity. Limited data on the influence of ergot alkaloids on rumen fermentation profiles or ruminal bacteria that could degrade the ergot alkaloids are available, but how FT influences the grazing bovine fecal microbiota or what role fecal microbiota might play in FT etiology and associated production losses has yet to be investigated. Here, we used 16S rRNA gene sequencing of fecal samples from weaned Angus steers grazing toxic endophyte-infected (E+; n = 6) or nontoxic (Max-Q; n = 6) tall fescue before and 1, 2, 14, and 28 days after pasture assignment. Bacteria in the Firmicutes and Bacteroidetes phyla comprised 90% of the Max-Q and E+ steer fecal microbiota throughout the trial. Early decreases in the Erysipelotrichaceae family and delayed increases of the Ruminococcaceae and Lachnospiraceae families were among the major effects of E+ grazing. E+ also increased abundances within the Planctomycetes, Chloroflexi, and Proteobacteria phyla and the Clostridiaceae family. Multiple operational taxonomic units classified as Ruminococcaceae and Lachnospiraceae were correlated negatively with weight gains (lower in E+) and positively with respiration rates (increased by E+). These data provide insights into how E+ grazing alters the Angus steer microbiota and the relationship of fecal microbiota dynamics with FT.IMPORTANCE Consumption of E+ tall fescue has an estimated annual $1 billion negative impact on the U.S. beef industry, with one driver of these costs being lowered weight gains. As global agricultural demand continues to grow, mitigating production losses resulting from grazing the predominant southeastern United States forage grass is of great value. Our investigation of the effects of E+ grazing on the fecal microbiota furthers our understanding of bovine fescue toxicosis in a real-world grazing production setting and provides a starting point for identifying easy-to-access fecal bacteria that could serve as potential biomarkers of animal productivity and/or FT severity for tall fescue-grazing livestock.
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Kim HJ, Jo A, Jeon YJ, An S, Lee KM, Yoon SS, Choi JY. Nasal commensal Staphylococcus epidermidis enhances interferon-λ-dependent immunity against influenza virus. MICROBIOME 2019; 7:80. [PMID: 31146794 PMCID: PMC6542144 DOI: 10.1186/s40168-019-0691-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 05/08/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Staphylococcus epidermidis is one of the most abundant colonizers of healthy human mucosa including that in the respiratory tract. As the respiratory microbiome has been linked to host immune responses, this study sought to determine the role of nasal mucosa-associated S. epidermidis in innate immune responses against the influenza A virus (IAV). S. epidermidis strains were isolated from nasal mucus samples of healthy individuals. The effects of these mucosa-derived commensal strains on interferon (IFN)-dependent innate immunity and IAV infection dynamics were tested in vitro using normal human nasal epithelial (NHNE) cells and human turbinate mucosa. The effects of S. epidermidis on antiviral immunity were also tested in vivo using an acute IAV infection mouse model. RESULTS Exposure of NHNE cells to nasal mucosa-derived S. epidermidis increased IFN-λ mRNA and secreted protein levels in the absence of viral stimulation. In the context of IAV infection, NHNE exposure to S. epidermidis prevented an increase in the viral burden, as revealed by IAV PA mRNA abundance, IAV nucleoprotein levels, and viral titers. S. epidermidis also enhanced transcription of IFN-stimulated genes independently of Toll-like receptor 2 and further induced IFN-λ production in IAV-infected cells by promoting phosphorylation of interferon regulatory factor 7. In a murine infection model, S. epidermidis prevented the spread of IAV to the lungs by stimulating IFN-λ innate immunity and suppressing IAV replication in the nasal mucosa. CONCLUSION The human nasal commensal S. epidermidis mediates front-line antiviral protection against IAV infection through modulation of IFN-λ-dependent innate immune mechanisms in the nasal mucosa, thereby demonstrating the role of host-bacterial commensalism in shaping human antiviral responses.
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Affiliation(s)
- Hyun Jik Kim
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Hospital, Seoul, Republic of Korea
| | - Ara Jo
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yung Jin Jeon
- Department of Otorhinolaryngology, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Sujin An
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kang-Mu Lee
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Sciences, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Sciences, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Jae Young Choi
- Department of Otorhinolaryngology, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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Leitao Filho FS, Alotaibi NM, Ngan D, Tam S, Yang J, Hollander Z, Chen V, FitzGerald JM, Nislow C, Leung JM, Man SFP, Sin DD. Sputum Microbiome Is Associated with 1-Year Mortality after Chronic Obstructive Pulmonary Disease Hospitalizations. Am J Respir Crit Care Med 2019; 199:1205-1213. [DOI: 10.1164/rccm.201806-1135oc] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
| | - Nawaf M. Alotaibi
- Centre for Heart Lung Innovation, St. Paul’s Hospital
- Division of Pulmonary Medicine, Department of Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - David Ngan
- Centre for Heart Lung Innovation, St. Paul’s Hospital
| | - Sheena Tam
- Centre for Heart Lung Innovation, St. Paul’s Hospital
| | - Julia Yang
- Centre for Heart Lung Innovation, St. Paul’s Hospital
| | - Zsuzsanna Hollander
- Centre for Heart Lung Innovation, St. Paul’s Hospital
- Centre of Excellence for the Prevention of Organ Failure
| | - Virginia Chen
- Centre for Heart Lung Innovation, St. Paul’s Hospital
- Centre of Excellence for the Prevention of Organ Failure
| | | | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada; and
| | - Janice M. Leung
- Centre for Heart Lung Innovation, St. Paul’s Hospital
- Division of Respiratory Medicine, Department of Medicine, and
| | - S. F. Paul Man
- Centre for Heart Lung Innovation, St. Paul’s Hospital
- Division of Respiratory Medicine, Department of Medicine, and
| | - Don D. Sin
- Centre for Heart Lung Innovation, St. Paul’s Hospital
- Division of Respiratory Medicine, Department of Medicine, and
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Abstract
Although chronic obstructive pulmonary disease (COPD) is regarded as a chronic inflammatory lung disease, the disease mechanism is still not known. Intriguingly, aging lungs are quite similar to COPD-affected lungs in many ways, and COPD has been viewed as a disease of accelerated premature aging of the lungs. In this paper, based on a literature review, we would like to propose immunosenescence, age-associated decline in immunity, as a critical mechanism for the development of COPD. Immunosenescence can cause a low-grade, systemic inflammation described as inflammaging. This inflammaging may be directly involved in the COPD pathogenesis. The potential contributors to the development of inflammaging in the lungs possibly leading to COPD are discussed in the review paper. A notable fact about COPD is that only 15% to 20% of smokers develop clinically significant COPD. Given that there is a substantial inter-individual variation in inflammaging susceptibility, which is genetically determined and significantly affected by the history of the individual's exposure to pathogens, immunosenescence and inflammaging may also provide the answer for this unexpectedly low susceptibility of smokers to clinically significant COPD.
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Affiliation(s)
- Won Kyung Cho
- Department of Pulmonary and Critical Care Medicine, International Healthcare Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| | - Chun Geun Lee
- Department of Molecular Microbiology and Immunology, Division of Biology and Medical Sciences, Brown University, Providence, RI, USA
| | - Lark Kyun Kim
- Severance Biomedical Science Institute and BK21 PLUS Project for Medical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea.
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62
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Li H, Wang Y, Jiang J, Zhao H, Feng X, Zhao B, Wang L. A Novel Human Microbe-Disease Association Prediction Method Based on the Bidirectional Weighted Network. Front Microbiol 2019; 10:676. [PMID: 31024478 PMCID: PMC6465552 DOI: 10.3389/fmicb.2019.00676] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/18/2019] [Indexed: 12/12/2022] Open
Abstract
The survival of human beings is inseparable from microbes. More and more studies have proved that microbes can affect human physiological processes in various aspects and are closely related to some human diseases. In this paper, based on known microbe-disease associations, a bidirectional weighted network was constructed by integrating the schemes of normalized Gaussian interactions and bidirectional recommendations firstly. And then, based on the newly constructed bidirectional network, a computational model called BWNMHMDA was developed to predict potential relationships between microbes and diseases. Finally, in order to evaluate the superiority of the new prediction model BWNMHMDA, the framework of LOOCV and 5-fold cross validation were implemented, and simulation results indicated that BWNMHMDA could achieve reliable AUCs of 0.9127 and 0.8967 ± 0.0027 in these two different frameworks respectively, which is outperformed some state-of-the-art methods. Moreover, case studies of asthma, colorectal carcinoma, and chronic obstructive pulmonary disease were implemented to further estimate the performance of BWNMHMDA. Experimental results showed that there are 10, 9, and 8 out of the top 10 predicted microbes having been confirmed by related literature in these three kinds of case studies separately, which also demonstrated that our new model BWNMHMDA could achieve satisfying prediction performance.
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Affiliation(s)
- Hao Li
- Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, China
| | - Yuqi Wang
- Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, China
| | - Jingwu Jiang
- Clinical Lab, Yongcheng People's Hospital, Shangqiu, China
| | - Haochen Zhao
- Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, China
| | - Xiang Feng
- College of Computer Engineering & Applied Mathematics, Changsha University, Changsha, China
| | - Bihai Zhao
- College of Computer Engineering & Applied Mathematics, Changsha University, Changsha, China
| | - Lei Wang
- Key Laboratory of Hunan Province for Internet of Things and Information Security, Xiangtan University, Xiangtan, China
- College of Computer Engineering & Applied Mathematics, Changsha University, Changsha, China
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63
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Yu YY, Xie XH, Ren L, Deng Y, Gao Y, Zhang Y, Li H, Luo J, Luo ZX, Liu EM. Epidemiological characteristics of nasopharyngeal Streptococcus pneumoniae strains among children with pneumonia in Chongqing, China. Sci Rep 2019; 9:3324. [PMID: 30824811 PMCID: PMC6397308 DOI: 10.1038/s41598-019-40088-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 01/29/2019] [Indexed: 12/22/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is the most common respiratory pathogen worldwide. Nasopharyngeal carriage with S. pneumoniae is the major source of lower respiratory tract infection and horizontal spread among children. Investigating nasopharyngeal S. pneumoniae is crucial for clinicians to control pneumococcus disease. Here, we retrospectively analyzed clinical information of 5,960 hospitalized children, focusing on pneumonia children less than five years with positive nasopharyngeal pneumococcal cultures. Nasopharyngeal aspirates (NPAs) were collected between June 2009 and December 2016, which were outside the pneumococcal conjugate vaccine(PCV) period. NPAs were subjected to common bacterial culture and antibiotic susceptibility tests, and serotypes were identified by both multiplex PCR and DNA sequencing. Results clearly revealed that clinical manifestations of the children whose NPAs were S. pneumoniae culture positive were serious, especially in those less than twelve months old. Fifteen different serotypes of nasopharyngeal S. pneumoniae were detected, the most common ones being 19F (35.2%), 6A/B (23.8%), 19A (11.4%), 15B/C (9.3%) and 23F (7.8%). Eight serotypes, accounting for 85.5% of the isolates, corresponded to the PCV13 serotypes. Approximately one-third of all S. pneumoniae strains were susceptible to penicillin. Overall, we consider nasopharyngeal S. pneumoniae culture is beneficial in assessing the situations of pneumonia children. Moreover, PCV13 could be useful in preventing pneumococcal disease in Chongqing, China.
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Affiliation(s)
- Yi-Yi Yu
- Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China.,Department of Pediatrics, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Xiao-Hong Xie
- Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China.,Department of Respiratory Medicine, Children´s Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Luo Ren
- Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Yu Deng
- Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China.,Department of Respiratory Medicine, Children´s Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Yu Gao
- Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Yao Zhang
- Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Hui Li
- Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Jian Luo
- Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China.,Department of Respiratory Medicine, Children´s Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Zheng-Xiu Luo
- Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China.,Department of Respiratory Medicine, Children´s Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - En-Mei Liu
- Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China. .,Department of Respiratory Medicine, Children´s Hospital of Chongqing Medical University, Chongqing, 400014, China.
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64
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Affiliation(s)
- Lionel A Mandell
- From McMaster University, Hamilton, ON, Canada (L.A.M.); and Weill Cornell Medical College, New York (M.S.N.)
| | - Michael S Niederman
- From McMaster University, Hamilton, ON, Canada (L.A.M.); and Weill Cornell Medical College, New York (M.S.N.)
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Whittle E, Leonard MO, Harrison R, Gant TW, Tonge DP. Multi-Method Characterization of the Human Circulating Microbiome. Front Microbiol 2019; 9:3266. [PMID: 30705670 PMCID: PMC6345098 DOI: 10.3389/fmicb.2018.03266] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/17/2018] [Indexed: 01/14/2023] Open
Abstract
The term microbiome describes the genetic material encoding the various microbial populations that inhabit our body. Whilst colonization of various body niches (e.g., the gut) by dynamic communities of microorganisms is now universally accepted, the existence of microbial populations in other "classically sterile" locations, including the blood, is a relatively new concept. The presence of bacteria-specific DNA in the blood has been reported in the literature for some time, yet the true origin of this is still the subject of much deliberation. The aim of this study was to investigate the phenomenon of a "blood microbiome" by providing a comprehensive description of bacterially derived nucleic acids using a range of complementary molecular and classical microbiological techniques. For this purpose we utilized a set of plasma samples from healthy subjects (n = 5) and asthmatic subjects (n = 5). DNA-level analyses involved the amplification and sequencing of the 16S rRNA gene. RNA-level analyses were based upon the de novo assembly of unmapped mRNA reads and subsequent taxonomic identification. Molecular studies were complemented by viability data from classical aerobic and anaerobic microbial culture experiments. At the phylum level, the blood microbiome was predominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key phyla detected were consistent irrespective of molecular method (DNA vs. RNA), and consistent with the results of other published studies. In silico comparison of our data with that of the Human Microbiome Project revealed that members of the blood microbiome were most likely to have originated from the oral or skin communities. To our surprise, aerobic and anaerobic cultures were positive in eight of out the ten donor samples investigated, and we reflect upon their source. Our data provide further evidence of a core blood microbiome, and provide insight into the potential source of the bacterial DNA/RNA detected in the blood. Further, data reveal the importance of robust experimental procedures, and identify areas for future consideration.
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Affiliation(s)
- Emma Whittle
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, United Kingdom
| | - Martin O. Leonard
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, United Kingdom
| | - Rebecca Harrison
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, United Kingdom
| | - Timothy W. Gant
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, United Kingdom
| | - Daniel Paul Tonge
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, United Kingdom
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66
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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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Mathieu E, Escribano-Vazquez U, Descamps D, Cherbuy C, Langella P, Riffault S, Remot A, Thomas M. Paradigms of Lung Microbiota Functions in Health and Disease, Particularly, in Asthma. Front Physiol 2018; 9:1168. [PMID: 30246806 PMCID: PMC6110890 DOI: 10.3389/fphys.2018.01168] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/03/2018] [Indexed: 12/22/2022] Open
Abstract
Improvements in our knowledge of the gut microbiota have broadened our vision of the microbes associated with the intestine. These microbes are essential actors and protectors of digestive and extra-digestive health and, by extension, crucial for human physiology. Similar reconsiderations are currently underway concerning the endogenous microbes of the lungs, with a shift in focus away from their involvement in infections toward a role in physiology. The discovery of the lung microbiota was delayed by the long-held view that the lungs of healthy individuals were sterile and by sampling difficulties. The lung microbiota has a low density, and the maintenance of small numbers of bacteria seems to be a critical determinant of good health. This review aims to highlight how knowledge about the lung microbiota can change our conception of lung physiology and respiratory health. We provide support for this point of view with knowledge acquired about the gut microbiota and intestinal physiology. We describe the main characteristics of the lung microbiota and its functional impact on lung physiology, particularly in healthy individuals, after birth, but also in asthma. We describe some of the physiological features of the respiratory tract potentially favoring the installation of a dysbiotic microbiota. The gut microbiota feeds and matures the intestinal epithelium and is involved in immunity, when the principal role of the lung microbiota seems to be the orientation and balance of aspects of immune and epithelial responsiveness. This implies that the local and remote effects of bacterial communities are likely to be determinant in many respiratory diseases caused by viruses, allergens or genetic deficiency. Finally, we discuss the reciprocal connections between the gut and lungs that render these two compartments inseparable.
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Affiliation(s)
- Elliot Mathieu
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Unai Escribano-Vazquez
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Delphyne Descamps
- Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Claire Cherbuy
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Sabine Riffault
- Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Aude Remot
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Muriel Thomas
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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68
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Lu D, Yao X, Abulimiti A, Cai L, Zhou L, Hong J, Li N. Profiling of lung microbiota in the patients with obstructive sleep apnea. Medicine (Baltimore) 2018; 97:e11175. [PMID: 29952967 PMCID: PMC6039595 DOI: 10.1097/md.0000000000011175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Lung microbiota may affect innate immunity and treatment consequence in the obstructive sleep apnea (OSA) patients. Bronchoalveolar lavage fluid (BALF) was obtained from 11 OSA patients and 8 patients with other lung diseases as control, and used for lung microbiota profiling by PCR amplification and sequencing of the microbial samples. It was demonstrated that phyla of Firmicutes, Fusobacteria, and Bacteriodetes were relatively abundant in the lung microbiota. Alpha-diversity comparison between OSA and control group revealed that Proteobacteria and Fusobacteria were significantly higher in OSA patients (0.3863 ± 0.0631 and 0.0682 ± 0.0159, respectively) than that in control group (0.119 ± 0.074 and 0.0006 ± 0.0187, respectively, P < .05 for both phyla). In contrast, Firmicutes was significantly less in OSA patients (0.1371 ± 0.0394) compared with that in the control group (0.384 ± 0.046, P < .05). Comparison within a group (ß-diversity) indicated that the top 5 phyla in the OSA lung were Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Acidobacteria, while the top 5 phyla in the control group were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Acidobacteria. These findings indicated that lung microbiota in OSA is distinct from that of non-OSA patients. Manipulation of the microbiota may be an alternative strategy to augment airway immunity and to reduce susceptibility to airway infection.
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Affiliation(s)
- Dongmei Lu
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
- Pulmonary and Critical Care Medicine Department, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Xiaoguang Yao
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
| | - Ayinigeer Abulimiti
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
| | - Li Cai
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
| | - Ling Zhou
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
| | - Jing Hong
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
| | - Nanfang Li
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
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69
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Masekela R, Vosloo S, Venter SN, de Beer WZ, Green RJ. The lung microbiome in children with HIV-bronchiectasis: a cross-sectional pilot study. BMC Pulm Med 2018; 18:87. [PMID: 29788934 PMCID: PMC5964725 DOI: 10.1186/s12890-018-0632-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 04/25/2018] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Data on the lung microbiome in HIV-infected children is limited. The current study sought to determine the lung microbiome in HIV-associated bronchiectasis and to assess its association with pulmonary exacerbations. METHODS A cross-sectional pilot study of 22 children (68% male; mean age 10.8 years) with HIV-associated bronchiectasis and a control group of 5 children with cystic fibrosis (CF). Thirty-one samples were collected, with 11 during exacerbations. Sputum samples were processed with 16S rRNA pyrosequencing. RESULTS The average number of operational taxonomy units (OTUs) was 298 ± 67 vs. 434 ± 90, for HIV-bronchiectasis and CF, respectively. The relative abundance of Proteobacteria was higher in HIV-bronchiectasis (72.3%), with only 22.2% Firmicutes. There was no correlation between lung functions (FEV1% and FEF25/75%) and bacterial community (r = 0.154; p = 0.470 and r = 0.178; p = 0.403), respectively. Bacterial assemblage of exacerbation and non-exacerbation samples in HIV-bronchiectasis was not significantly different (ANOSIM, RHIV-bronchiectasis = 0.08; p = 0.14 and RCF = 0.08, p = 0.50). Higher within-community heterogeneity and lower evenness was associated with CF (Shannon-Weiner (H') = 5.39 ± 0.38 and Pielou's evenness (J) 0.79 ± 0.10 vs. HIV-bronchiectasis (Shannon-Weiner (H') = 4.45 ± 0.49 and Pielou's (J) 0.89 ± 0.03. CONCLUSION The microbiome in children with HIV-associated bronchiectasis seems to be less rich, diverse and heterogeneous with predominance of Proteobacteria when compared to cystic fibrosis.
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Affiliation(s)
- Refiloe Masekela
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- Department of Maternal and Child Health, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Congella, Durban, 4013 South Africa
| | - Solize Vosloo
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
| | - Stephanus N. Venter
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
| | - Wilhelm Z. de Beer
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa
| | - Robin J. Green
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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70
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Ballard ZS, Brown C, Ozcan A. Mobile Technologies for the Discovery, Analysis, and Engineering of the Global Microbiome. ACS NANO 2018; 12:3065-3082. [PMID: 29553706 DOI: 10.1021/acsnano.7b08660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The microbiome has been heralded as a gauge of and contributor to both human health and environmental conditions. Current challenges in probing, engineering, and harnessing the microbiome stem from its microscopic and nanoscopic nature, diversity and complexity of interactions among its members and hosts, as well as the spatiotemporal sampling and in situ measurement limitations induced by the restricted capabilities and norm of existing technologies, leaving some of the constituents of the microbiome unknown. To facilitate significant progress in the microbiome field, deeper understanding of the constituents' individual behavior, interactions with others, and biodiversity are needed. Also crucial is the generation of multimodal data from a variety of subjects and environments over time. Mobile imaging and sensing technologies, particularly through smartphone-based platforms, can potentially meet some of these needs in field-portable, cost-effective, and massively scalable manners by circumventing the need for bulky, expensive instrumentation. In this Perspective, we outline how mobile sensing and imaging technologies could lead the way to unprecedented insight into the microbiome, potentially shedding light on various microbiome-related mysteries of today, including the composition and function of human, animal, plant, and environmental microbiomes. Finally, we conclude with a look at the future, propose a computational microbiome engineering and optimization framework, and discuss its potential impact and applications.
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71
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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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72
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Paska C, Barta I, Drozdovszky O, Antus B. Improving Gene-Expression Studies from Sputum: A Multistep Optimization of RNA Isolation and qPCR Protocols. Am J Respir Cell Mol Biol 2018; 57:626-628. [PMID: 29090961 DOI: 10.1165/rcmb.2017-0198le] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Csilla Paska
- 1 National Koranyi Institute for Pulmonology Budapest, Hungary
| | - Imre Barta
- 1 National Koranyi Institute for Pulmonology Budapest, Hungary
| | | | - Balazs Antus
- 1 National Koranyi Institute for Pulmonology Budapest, Hungary
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73
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Nicola I, Cerutti F, Grego E, Bertone I, Gianella P, D'Angelo A, Peletto S, Bellino C. Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves. MICROBIOME 2017; 5:152. [PMID: 29157308 PMCID: PMC5697440 DOI: 10.1186/s40168-017-0372-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 11/09/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND The microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchopneumonia, the most common respiratory syndrome affecting cattle. With this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community composition of the upper and lower respiratory tracts in calves. RESULTS The microbiota of the upper (nasal swab [NS]) and the lower (trans-tracheal aspiration [TTA]) respiratory tracts of 19 post-weaned Piedmontese calves with (8/19) and without (11/19) clinical signs of respiratory disease, coming from six different farms, was characterized by 16S rRNA gene metabarcoding. A total of 29 phyla (29 in NS, 21 in TTA) and 305 genera (289 in NS, 182 in TTA) were identified. Mycoplasma (60.8%) was the most abundant genus identified in both the NS (27.3%) and TTA (76.7%) samples, followed by Moraxella (16.6%) in the NS and Pasteurella (7.3%) in the TTA samples. Pasteurella multocida (7.3% of total operational taxonomic units [OTUs]) was the most abundant species in the TTA and Psychrobacter sanguinis (1.1% of total OTUs) in the NS samples. Statistically significant differences between the NS and the TTA samples were found for both alpha (Shannon index, observed species, Chao1 index, and Simpson index; P = 0.001) and beta (Adonis; P = 0.001) diversity. Comparison of the NS and TTA samples by farm origin and clinical signs revealed no statistical difference (P > 0.05), except for farm origin for the NS samples when compared by the unweighted UniFrac metric (P = 0.05). CONCLUSIONS Using 16S rRNA gene sequencing, we characterized the microbiota of the upper and lower respiratory tracts of calves, both healthy individuals and those with clinical signs of respiratory disease. Our results suggest that environmental factors may influence the composition of the upper airway microbiota in cattle. While the two microbial communities (upper and lower airways) differed in microbial composition, they shared several OTUs, suggesting that the lung microbiota may be a self-sustaining, more homogeneous ecosystem, influenced by the upper respiratory tract microbiota.
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Affiliation(s)
- Isabella Nicola
- Department of Veterinary Sciences, Clinical section, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Francesco Cerutti
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154, Turin, TO, Italy
| | - Elena Grego
- Department of Veterinary Sciences, Clinical section, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Iride Bertone
- Department of Veterinary Sciences, Clinical section, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Paola Gianella
- Department of Veterinary Sciences, Clinical section, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Antonio D'Angelo
- Department of Veterinary Sciences, Clinical section, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
| | - Simone Peletto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154, Turin, TO, Italy
| | - Claudio Bellino
- Department of Veterinary Sciences, Clinical section, University of Turin, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy.
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74
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Roux D, van Oort PM, Ricard JD, Bos LDJ. Airway microbiome research: a modern perspective on surveillance cultures? ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:445. [PMID: 29264362 DOI: 10.21037/atm.2017.08.05] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The incidence of ventilator-associated pneumonia (VAP) is estimated to be around 10% in a high-risk population. Over the last decade, major improvements have been made in the prevention of VAP, with great cost-effectiveness. However, we still do not understand the exact pathogenesis of VAP. A better understanding might explain why some patients develop ventilator-associated tracheobronchitis, while others develop VAP even though they are infected with the same types of pathogens. Microbiome research has been a hot topic in translational medicine over the past decade. Slowly, microbiome research has also been introduced to the intensive care setting. One of the areas where it may influence our pathophysiological considerations is in VAP. The adapted island has been proposed for the colonization and infection of the respiratory tract. In this model, not only the immigration of bacteria into the lung is important, but elimination and regional growth factors are of equal significance. The importance of these factors can be supported by epidemiological studies. Several small observational studies on the development of the pulmonary microbiome during mechanical ventilation also support this theory. We speculate on the consequences of the newest insights in microbiome research on the prevention and targeted treatment of VAP. We conclude that there is still a strong need for more in-depth analyses of the changes in the microbial composition of the pulmonary microbiome during mechanical ventilation and with the development of VAP.
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Affiliation(s)
- Damien Roux
- Inserm, IAME, UMR 1137, Paris Diderot University, Paris, France
| | - Pouline M van Oort
- Department of Intensive Care, Academic Medical Center, Amsterdam, the Netherlands
| | | | - Lieuwe D J Bos
- Department of Intensive Care, Academic Medical Center, Amsterdam, the Netherlands
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75
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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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76
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Wang J, Lesko M, Badri MH, Kapoor BC, Wu BG, Li Y, Smaldone GC, Bonneau R, Kurtz ZD, Condos R, Segal LN. Lung microbiome and host immune tone in subjects with idiopathic pulmonary fibrosis treated with inhaled interferon-γ. ERJ Open Res 2017; 3:00008-2017. [PMID: 28717640 PMCID: PMC5507144 DOI: 10.1183/23120541.00008-2017] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/14/2017] [Indexed: 01/27/2023] Open
Abstract
Therapies targeting inflammation reveal inconsistent results in idiopathic pulmonary fibrosis (IPF). Aerosolised interferon (IFN)-γ has been proposed as a novel therapy. Changes in the host airway microbiome are associated with the inflammatory milieu and may be associated with disease progression. Here, we evaluate whether treatment with aerosolised IFN-γ in IPF impacts either the lower airway microbiome or the host immune phenotype. Patients with IPF who enrolled in an aerosolised IFN-γ trial underwent bronchoscopy at baseline and after 6 months. 16S rRNA sequencing of bronchoalveolar lavage fluid (BALF) was used to evaluate the lung microbiome. Biomarkers were measured by Luminex assay in plasma, BALF and BAL cell supernatant. The compPLS framework was used to evaluate associations between taxa and biomarkers. IFN-γ treatment did not change α or β diversity of the lung microbiome and few taxonomic changes occurred. While none of the biomarkers changed in plasma, there was an increase in IFN-γ and a decrease in Fit-3 ligand, IFN-α2 and interleukin-5 in BAL cell supernatant, and a decrease in tumour necrosis factor-β in BALF. Multiple correlations between microbial taxa common to the oral mucosa and host inflammatory biomarkers were found. These data suggest that the lung microbiome is independently associated with the host immune tone and may have a potential mechanistic role in IPF. Lower airway microbiome and immunological tone are associated in IPF, an effect independent of IFN-γ treatmenthttp://ow.ly/cTDo30bsJiN
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Affiliation(s)
- Jing Wang
- Division of Pulmonary and Critical Care Medicine, Beijing Chaoyang Hospital, The Capital University of Medicine, Beijing, China.,Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Melissa Lesko
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Michelle H Badri
- Dept of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Bianca C Kapoor
- 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
| | - Gerald C Smaldone
- Division of Pulmonary, Critical Care and Sleep Medicine, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Richard Bonneau
- Dept of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.,Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.,Simons Center for Data Analysis, Simons Foundation, New York, NY, USA
| | - Zachary D Kurtz
- Dept of Microbiology, 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
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
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77
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Feikin DR, Hammitt LL, Murdoch DR, O'Brien KL, Scott JAG. The Enduring Challenge of Determining Pneumonia Etiology in Children: Considerations for Future Research Priorities. Clin Infect Dis 2017; 64:S188-S196. [PMID: 28575369 PMCID: PMC5447852 DOI: 10.1093/cid/cix143] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Pneumonia kills more children each year worldwide than any other disease. Nonetheless, accurately determining the causes of childhood pneumonia has remained elusive. Over the past century, the focus of pneumonia etiology research has shifted from studies of lung aspirates and postmortem specimens intent on identifying pneumococcal disease to studies of multiple specimen types distant from the lung that are tested for multiple pathogens. Some major challenges facing modern pneumonia etiology studies include the use of nonspecific and variable case definitions, poor access to pathologic lung tissue and to specimens from fatal cases, poor diagnostic accuracy of assays (especially when testing nonpulmonary specimens), and the interpretation of results when multiple pathogens are detected in a given individual. The future of childhood pneumonia etiology research will likely require integrating data from complementary approaches, including applications of advanced molecular diagnostics and vaccine probe studies, as well as a renewed emphasis on lung aspirates from radiologically confirmed pneumonia and postmortem examinations.
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Affiliation(s)
- Daniel R Feikin
- International Vaccine Access Center, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Laura L Hammitt
- International Vaccine Access Center, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - David R Murdoch
- Department of Pathology, University of Otago, and
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Katherine L O'Brien
- International Vaccine Access Center, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom
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78
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Sriram KB, Cox AJ, Clancy RL, Slack MPE, Cripps AW. Nontypeable Haemophilus influenzae and chronic obstructive pulmonary disease: a review for clinicians. Crit Rev Microbiol 2017; 44:125-142. [PMID: 28539074 DOI: 10.1080/1040841x.2017.1329274] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Chronic Obstructive Pulmonary Disease (COPD) is a leading cause of morbidity and mortality worldwide. In the lower airways of COPD patients, bacterial infection is a common phenomenon and Haemophilus influenzae is the most commonly identified bacteria. Haemophilus influenzae is divided into typeable and nontypeable (NTHi) strains based on the presence or absence of a polysaccharide capsule. While NTHi is a common commensal in the human nasopharynx, it is associated with considerable inflammation when it is present in the lower airways of COPD patients, resulting in morbidity due to worsening symptoms and increased frequency of COPD exacerbations. Treatment of lower airway NTHi infection with antibiotics, though successful in the short term, does not offer long-term protection against reinfection, nor does it change the course of the disease. Hence, there has been much interest in the development of an effective NTHi vaccine. This review will summarize the current literature concerning the role of NTHi infections in COPD patients and the consequences of using prophylactic antibiotics in patients with COPD. There is particular focus on the rationale, findings of clinical studies and possible future directions of NTHi vaccines in patients with COPD.
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Affiliation(s)
- Krishna Bajee Sriram
- a Department of Respiratory Medicine , Gold Coast University Hospital, Gold Coast Health , Southport , Australia.,b Griffith University School of Medicine , Southport , Australia
| | - Amanda J Cox
- c Menzies Health Institute , Griffith University School of Medical Science , Gold Coast , Australia
| | - Robert L Clancy
- d Faculty of Health and Medicine , University of Newcastle , Callaghan , Australia
| | - Mary P E Slack
- b Griffith University School of Medicine , Southport , Australia
| | - Allan W Cripps
- b Griffith University School of Medicine , Southport , Australia
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79
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Wilkinson TMA, Aris E, Bourne S, Clarke SC, Peeters M, Pascal TG, Schoonbroodt S, Tuck AC, Kim V, Ostridge K, Staples KJ, Williams N, Williams A, Wootton S, Devaster JM. A prospective, observational cohort study of the seasonal dynamics of airway pathogens in the aetiology of exacerbations in COPD. Thorax 2017; 72:919-927. [PMID: 28432209 PMCID: PMC5738531 DOI: 10.1136/thoraxjnl-2016-209023] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 02/14/2017] [Accepted: 03/09/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND The aetiology of acute exacerbations of COPD (AECOPD) is incompletely understood. Understanding the relationship between chronic bacterial airway infection and viral exposure may explain the incidence and seasonality of these events. METHODS In this prospective, observational cohort study (NCT01360398), patients with COPD aged 40-85 years underwent sputum sampling monthly and at exacerbation for detection of bacteria and viruses. Results are presented for subjects in the full cohort, followed for 1 year. Interactions between exacerbation occurrence and pathogens were investigated by generalised estimating equation and stratified conditional logistic regression analyses. FINDINGS The mean exacerbation rate per patient-year was 3.04 (95% CI 2.63 to 3.50). At AECOPD, the most common bacterial species were non-typeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis, and the most common virus was rhinovirus. Logistic regression analyses (culture bacterial detection) showed significant OR for AECOPD occurrence when M. catarrhalis was detected regardless of season (5.09 (95% CI 2.76 to 9.41)). When NTHi was detected, the increased risk of exacerbation was greater in high season (October-March, OR 3.04 (1.80 to 5.13)) than low season (OR 1.22 (0.68 to 2.22)). Bacterial and viral coinfection was more frequent at exacerbation (24.9%) than stable state (8.6%). A significant interaction was detected between NTHi and rhinovirus presence and AECOPD risk (OR 5.18 (1.92 to 13.99); p=0.031). CONCLUSIONS AECOPD aetiology varies with season. Rises in incidence in winter may be driven by increased pathogen presence as well as an interaction between NTHi airway infection and effects of viral infection. TRIAL REGISTRATION NUMBER Results, NCT01360398.
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Affiliation(s)
- Tom M A Wilkinson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK.,Southampton NIHR Respiratory Biomedical Research Unit, Southampton General Hospital, Southampton, UK.,Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK
| | | | - Simon Bourne
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK.,Portsmouth Hospitals NHS Trust, Queen Alexandra Hospital, Portsmouth, UK
| | - Stuart C Clarke
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK.,Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK
| | | | | | | | - Andrew C Tuck
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Viktoriya Kim
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK.,Southampton NIHR Respiratory Biomedical Research Unit, Southampton General Hospital, Southampton, UK
| | - Kristoffer Ostridge
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK.,Southampton NIHR Respiratory Biomedical Research Unit, Southampton General Hospital, Southampton, UK
| | - Karl J Staples
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK.,Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK
| | - Nicholas Williams
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK.,Southampton NIHR Respiratory Biomedical Research Unit, Southampton General Hospital, Southampton, UK
| | - Anthony Williams
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK
| | - Stephen Wootton
- Southampton NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
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80
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Kitsios GD, Morowitz MJ, Dickson RP, Huffnagle GB, McVerry BJ, Morris A. Dysbiosis in the intensive care unit: Microbiome science coming to the bedside. J Crit Care 2017; 38:84-91. [PMID: 27866110 PMCID: PMC5328797 DOI: 10.1016/j.jcrc.2016.09.029] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/20/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022]
Abstract
Complex microbial communities within the human body, constituting the microbiome, have a broad impact on human health and disease. A growing body of research now examines the role of the microbiome in patients with critical illness, such as sepsis and acute respiratory failure. In this article, we provide an introduction to microbiome concepts and terminology and we systematically review the current evidence base of the critical-illness microbiome, including 51 studies in animal models and pediatric and adult critically ill patients. We further examine how this emerging scientific discipline may transform the way we manage infectious and inflammatory diseases in intensive care units. The evolving molecular, culture-independent techniques offer the ability to study microbial communities in unprecedented depth and detail, and in the short-term, may enable us to diagnose and treat infections in critical care more precisely and effectively. Longer term, these tools may also give us insights in the underlying pathophysiology of critical illness and reveal previously unsuspected targets for innovative, microbiome-targeted therapeutics. We finally propose a roadmap for future studies in the field for transforming critical care from its current isolated focus on the host to a more personalized paradigm addressing both human and microbial contributions to critical illness.
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Affiliation(s)
- Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Center for Medicine and the Microbiome, University of Pittsburgh Department of Medicine, Pittsburgh, PA, USA.
| | - Michael J Morowitz
- Center for Medicine and the Microbiome, University of Pittsburgh Department of Medicine, Pittsburgh, PA, USA; Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Division of Pediatric Surgery, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Gary B Huffnagle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Center for Medicine and the Microbiome, University of Pittsburgh Department of Medicine, Pittsburgh, PA, USA.
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Center for Medicine and the Microbiome, University of Pittsburgh Department of Medicine, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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81
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Foo JL, Ling H, Lee YS, Chang MW. Microbiome engineering: Current applications and its future. Biotechnol J 2017; 12. [PMID: 28133942 DOI: 10.1002/biot.201600099] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 12/12/2016] [Accepted: 12/19/2016] [Indexed: 01/07/2023]
Abstract
Microbiomes exist in all ecosystems and are composed of diverse microbial communities. Perturbation to microbiomes brings about undesirable phenotypes in the hosts, resulting in diseases and disorders, and disturbs the balance of the associated ecosystems. Engineering of microbiomes can be used to modify structures of the microbiota and restore ecological balance. Consequently, microbiome engineering has been employed for improving human health and agricultural productivity. The importance and current applications of microbiome engineering, particularly in humans, animals, plants and soil is reviewed. Furthermore, we explore the challenges in engineering microbiome and the future of this field, thus providing perspectives and outlook of microbiome engineering.
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Affiliation(s)
- Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
| | - Yung Seng Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore
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82
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Sullivan A, Hunt E, MacSharry J, Murphy DM. 'The Microbiome and the Pathophysiology of Asthma'. Respir Res 2016; 17:163. [PMID: 27919249 PMCID: PMC5139145 DOI: 10.1186/s12931-016-0479-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/26/2016] [Indexed: 02/06/2023] Open
Abstract
Asthma is a chronic respiratory disease whose prevalence is increasing in the western world. Recently research has begun to focus on the role the microbiome plays in asthma pathogenesis in the hope of further understanding this respiratory disorder. Considered sterile until recently, the lungs have revealed themselves to contain a unique microbiota. A shift towards molecular methods for the quantification and sequencing of microbial DNA has revealed that the airways harbour a unique microbiota with apparent, reproducible differences present between healthy and diseased lungs. There is a hope that in classifying the microbial load of the asthmatic airway an insight may be afforded as to the possible role pulmonary microbes may have in propagating an asthmatic airway response. This could potentially pave the way for new therapeutic strategies for the treatment of chronic lung conditions such as asthma.
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Affiliation(s)
- Ashley Sullivan
- APC Microbiome Institute, School of Medicine, University College Cork, Cork, Ireland
| | - Eoin Hunt
- The Department of Respiratory Medicine, Cork University Hospital, Wilton, Cork, Ireland.,Health Research Board Clinical Research Facility, University College Cork, Cork, Ireland
| | - John MacSharry
- APC Microbiome Institute, School of Medicine, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Desmond M Murphy
- The Department of Respiratory Medicine, Cork University Hospital, Wilton, Cork, Ireland. .,Health Research Board Clinical Research Facility, University College Cork, Cork, Ireland.
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83
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He Y, Wen Q, Yao F, Xu D, Huang Y, Wang J. Gut-lung axis: The microbial contributions and clinical implications. Crit Rev Microbiol 2016; 43:81-95. [PMID: 27781554 DOI: 10.1080/1040841x.2016.1176988] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gut microbiota interacts with host immune system in ways that influence the development of disease. Advances in respiratory immune system also broaden our knowledge of the interaction between host and microbiome in the lung. Increasing evidence indicated the intimate relationship between the gastrointestinal tract and respiratory tract. Exacerbations of chronic gut and lung disease have been shown to share key conceptual features with the disorder and dysregulation of the microbial ecosystem. In this review, we discuss the impact of gut and lung microbiota on disease exacerbation and progression, and the recent understanding of the immunological link between the gut and the lung, the gut-lung axis.
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Affiliation(s)
- Yang He
- a Department of Cancer Center, Union Hospital , Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Qu Wen
- a Department of Cancer Center, Union Hospital , Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Fangfang Yao
- a Department of Cancer Center, Union Hospital , Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Dong Xu
- b Department of Infectious Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Yuancheng Huang
- b Department of Infectious Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Junshuai Wang
- c Department of Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
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84
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Li J, Hao C, Ren L, Xiao Y, Wang J, Qin X. Data Mining of Lung Microbiota in Cystic Fibrosis Patients. PLoS One 2016; 11:e0164510. [PMID: 27741283 PMCID: PMC5065158 DOI: 10.1371/journal.pone.0164510] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/26/2016] [Indexed: 12/18/2022] Open
Abstract
The major therapeutic strategy used to treat exacerbated cystic fibrosis (CF) is antibiotic treatment. As this approach easily generates antibiotic-resistant strains of opportunistic bacteria, optimized antibiotic therapies are required to effectively control chronic and recurrent bacterial infections in CF patients. A promising future for the proper use of antibiotics is the management of lung microbiota. However, the impact of antibiotic treatments on CF microbiota and vice versa is not fully understood. This study analyzed 718 sputum samples from 18 previous studies to identify differences between CF and uninfected lung microbiota and to evaluate the effects of antibiotic treatments on exacerbated CF microbiota. A reference-based OTU (operational taxonomic unit) picking method was used to combine analyses of data generated using different protocols and platforms. Findings show that CF microbiota had greater richness and lower diversity in the community structure than uninfected control (NIC) microbiota. Specifically, CF microbiota showed higher levels of opportunistic bacteria and dramatically lower levels of commensal bacteria. Antibiotic treatment affected exacerbated CF microbiota notably but only transiently during the treatment period. Limited decrease of the dominant opportunistic bacteria and a dramatic decrease of commensal bacteria were observed during the antibiotic treatment for CF exacerbation. Simultaneously, low abundance opportunistic bacteria were thriving after the antibiotic treatment. The inefficiency of the current antibiotic treatment against major opportunistic bacteria and the detrimental effects on commensal bacteria indicate that the current empiric antibiotic treatment on CF exacerbation should be reevaluated and optimized.
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Affiliation(s)
- Jianguo Li
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China
| | - Chunyan Hao
- College of Chemical & Biological Engineering, Taiyuan University of Science & Technology, Taiyuan 030021, China
| | - Lili Ren
- MOH Key Laboratory of System Pathogen Biology and Christophe Mérieux Laboratory, IPB, CAMS-Foundation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Yan Xiao
- MOH Key Laboratory of System Pathogen Biology and Christophe Mérieux Laboratory, IPB, CAMS-Foundation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Jianwei Wang
- MOH Key Laboratory of System Pathogen Biology and Christophe Mérieux Laboratory, IPB, CAMS-Foundation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China
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85
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Kosikowska U, Rybojad P, Stępień-Pyśniak D, Żbikowska A, Malm A. Changes in the prevalence and biofilm formation of Haemophilus influenzae and Haemophilus parainfluenzae from the respiratory microbiota of patients with sarcoidosis. BMC Infect Dis 2016; 16:449. [PMID: 27562460 PMCID: PMC5000413 DOI: 10.1186/s12879-016-1793-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 08/21/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Healthy condition and chronic diseases may be associated with microbiota composition and its properties. The prevalence of respiratory haemophili with respect to their phenotypes including the ability to biofilm formation in patients with sarcoidosis was assayed. METHODS Nasopharynx and sputum specimens were taken in 31 patients with sarcoidosis (average age 42.6 ± 13), and nasopharynx specimens were taken in 37 healthy people (average age 44.6 ± 11.6). Haemophili were identified by API-NH microtest and by the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system. Biofilm was visualised by crystal violet staining and confocal scanning laser microscopy (CSLM). The statistical analysis was performed with Statgraphics Plus for Windows. RESULTS In total, 30/31 patients with sarcoidosis and 31/37 healthy people were colonized by Haemophilus influenzae (6/30 vs. 1/31) and Haemophilus parainfluenzae (28/30 vs. 31/31) in the nasopharynx. The overall number of nasopharyngeal haemophili isolates was 59 in patients with sarcoidosis and 67 in healthy volunteers (H. influenzae 6/59 vs. 1/67, P = 0.05; H. parainfluenzae 47/59 vs. 65/67, P = 0.0032). Moreover, the decreased number of H. parainfluenzae biofilm-producing isolates was shown in nasopharyngeal samples in patients with sarcoidosis as compared to healthy people (19/31 vs. 57/65, P = 0.006), especially with respect to isolates classified as strong and very strong biofilm-producers (8/31 vs. 39/65, P = 0.002). CONCLUSIONS The obtained data suggest that the qualitative and quantitative changes within the respiratory microbiota concerning the overall prevalence of H. influenzae together with the decreased number of H. parainfluenzae strains and the decreased rate of H. parainfluenzae biofilm-producing isolates as compared to healthy people may be associated with sarcoidosis.
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Affiliation(s)
- Urszula Kosikowska
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki Str. 1, 20-093, Lublin, Poland.
| | - Paweł Rybojad
- Department of Thoracic Surgery, Medical University of Lublin, Lublin, Poland
| | - Dagmara Stępień-Pyśniak
- Sub-Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
| | - Anna Żbikowska
- Department of Food Technology, Faculty of Food Sciences, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland
| | - Anna Malm
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki Str. 1, 20-093, Lublin, Poland
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86
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Stehling F, Pieper N, Bouikidis A, Steinmann J, Rath PM, Mellies U. Upper airway microbial colonization in patients with neuromuscular disorders. Respirology 2016; 21:1285-91. [DOI: 10.1111/resp.12814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 02/03/2016] [Accepted: 02/27/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Florian Stehling
- Pediatric Pulmonology and Sleep Medicine; University of Duisburg-Essen Children's Hospital; Essen Germany
| | - Nadine Pieper
- Pediatric Pulmonology and Sleep Medicine; University of Duisburg-Essen Children's Hospital; Essen Germany
| | - Anastasios Bouikidis
- Pediatric Pulmonology and Sleep Medicine; University of Duisburg-Essen Children's Hospital; Essen Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology; University Hospital Essen, University of Duisburg-Essen; Essen Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology; University Hospital Essen, University of Duisburg-Essen; Essen Germany
| | - Uwe Mellies
- Pediatric Pulmonology and Sleep Medicine; University of Duisburg-Essen Children's Hospital; Essen Germany
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87
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Jo BS, Lee J, Cho Y, Byun J, Kim HR, Koo JW, Myong JP. Risk factors associated with mortality from pneumonia among patients with pneumoconiosis. Ann Occup Environ Med 2016; 28:19. [PMID: 27057317 PMCID: PMC4823892 DOI: 10.1186/s40557-016-0103-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 03/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aim of this study was to evaluate factors associated with increased risk of mortality from pneumonia among patients with pneumoconiosis. METHODS Medical records of 103 pneumoconiosis patients hospitalized for pneumonia were investigated. Seven patients who had lung cancer or other malignancy and 13 patients with insufficient medical record were excluded. Two female patients were excluded due to small number to analyze. The subjects were divided into two groups by clinical outcome of pneumonia, the deceased group and the survival group. The two groups were compared in terms of age, smoking history, episode of recent pneumonia, concomitancy of interstitial fibrosis or fungal ball infection, extent of small opacities, grade of large opacities and results of spirometry. Multiple logistic regression was applied to determine the association between these variables and mortality from pneumonia. RESULTS The deceased group showed more frequent history of recent pneumonia (p = 0.006), higher prevalence of interstitial fibrosis (p = 0.007) and longer hospitalization period (p = 0.044). The proportion of subjects who had decreased FVC, less than 70 % of predicted value, was higher in the deceased group (p < 0.001). In multiple logistic regression, after adjusting age, smoking history, recent pneumonia, fungal ball, large opacity, profusion and FVC (or FEV1) less than 70 % of predicted value, history of recent pneumonia, concomitancy of interstitial fibrosis, type of pneumoconiosis and fungal ball presented statistically significant association with mortality from pneumonia. CONCLUSIONS The concomitancy of fungal ball or interstitial fibrosis, history of recent pneumonia within last 90 days, type of pneumoconiosis, FVC less than 70 % of predicted value, FEV1 less than 70 % of predicted value presented statistically significant association with mortality from pneumonia. More attention should be given to patients who have such factors when treating pneumonia with pneumoconiosis.
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Affiliation(s)
- Bum Seak Jo
- Department of Occupational and Environmental Medicine, College of Medicine, The Catholic University of Korea, Banpo-daero 222, Seoul, Seocho-gu 137-701 Republic of Korea
| | - Jongin Lee
- Department of Occupational and Environmental Medicine, College of Medicine, The Catholic University of Korea, Banpo-daero 222, Seoul, Seocho-gu 137-701 Republic of Korea
| | - YounMo Cho
- Department of Occupational and Environmental Medicine, College of Medicine, The Catholic University of Korea, Banpo-daero 222, Seoul, Seocho-gu 137-701 Republic of Korea
| | - Junsu Byun
- Department of Occupational and Environmental Medicine, College of Medicine, The Catholic University of Korea, Banpo-daero 222, Seoul, Seocho-gu 137-701 Republic of Korea
| | - Hyoung Ryoul Kim
- Department of Occupational and Environmental Medicine, College of Medicine, The Catholic University of Korea, Banpo-daero 222, Seoul, Seocho-gu 137-701 Republic of Korea
| | - Jung Wan Koo
- Department of Occupational and Environmental Medicine, College of Medicine, The Catholic University of Korea, Banpo-daero 222, Seoul, Seocho-gu 137-701 Republic of Korea
| | - Jun Pyo Myong
- Department of Occupational and Environmental Medicine, College of Medicine, The Catholic University of Korea, Banpo-daero 222, Seoul, Seocho-gu 137-701 Republic of Korea
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88
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D’Anna SE, Balbi B, Cappello F, Carone M, Di Stefano A. Bacterial-viral load and the immune response in stable and exacerbated COPD: significance and therapeutic prospects. Int J Chron Obstruct Pulmon Dis 2016; 11:445-53. [PMID: 27042037 PMCID: PMC4780195 DOI: 10.2147/copd.s93398] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by persistent airflow limitation and an abnormal inflammatory response of the lung. Bacteria and viruses are a major cause of COPD exacerbations and may contribute to COPD progression by perpetuating the inflammatory response in the airways. Bacterial variety diminishes with increasing COPD severity. Respiratory viruses can colonize the lower respiratory tract in stable COPD, altering the respiratory microbiome and facilitating secondary bacterial infections. In this review, we present the most updated information about the role of bacteria and viruses in stable and exacerbated COPD. In our opinion, to optimize therapeutic strategies, the dynamic events involving bacterial-viral infections and related immune response in COPD phenotypes need to be better clarified. Our paper would address these points that we consider of great importance for the clinical management of COPD.
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Affiliation(s)
- Silvestro Ennio D’Anna
- Department of Rehabilitation, Cardiorespiratory Unit, Fondazione Istituto G. Giglio di Cefalù, University of Palermo, Palermo, Italy
| | - Bruno Balbi
- Pneumology Unit and Laboratory of Cytoimmunopathology of Heart and Lung, Fondazione Salvatore Maugeri, IRCCS, Veruno (NO) and Cassano delle Murge (BA), University of Palermo, Palermo, Italy
| | - Francesco Cappello
- Human Anatomy Section, Department of Experimental Biomedicine and Clinical Neuroscience, University of Palermo, Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology, Palermo, Italy
| | - Mauro Carone
- Pneumology Unit and Laboratory of Cytoimmunopathology of Heart and Lung, Fondazione Salvatore Maugeri, IRCCS, Veruno (NO) and Cassano delle Murge (BA), University of Palermo, Palermo, Italy
| | - Antonino Di Stefano
- Pneumology Unit and Laboratory of Cytoimmunopathology of Heart and Lung, Fondazione Salvatore Maugeri, IRCCS, Veruno (NO) and Cassano delle Murge (BA), University of Palermo, Palermo, Italy
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89
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Grunig G, Baghdassarian A, Park SH, Pylawka S, Bleck B, Reibman J, Berman-Rosenzweig E, Durmus N. Challenges and Current Efforts in the Development of Biomarkers for Chronic Inflammatory and Remodeling Conditions of the Lungs. Biomark Insights 2016; 10:59-72. [PMID: 26917944 PMCID: PMC4756863 DOI: 10.4137/bmi.s29514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/14/2015] [Accepted: 10/18/2015] [Indexed: 02/06/2023] Open
Abstract
This review discusses biomarkers that are being researched for their usefulness to phenotype chronic inflammatory lung diseases that cause remodeling of the lung's architecture. The review focuses on asthma, chronic obstructive pulmonary disease (COPD), and pulmonary hypertension. Bio-markers of environmental exposure and specific classes of biomarkers (noncoding RNA, metabolism, vitamin, coagulation, and microbiome related) are also discussed. Examples of biomarkers that are in clinical use, biomarkers that are under development, and biomarkers that are still in the research phase are discussed. We chose to present examples of the research in biomarker development by diseases, because asthma, COPD, and pulmonary hypertension are distinct entities, although they clearly share processes of inflammation and remodeling.
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Affiliation(s)
- Gabriele Grunig
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA.; Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Aram Baghdassarian
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Sung-Hyun Park
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Serhiy Pylawka
- College of Dental Medicine, Columbia University, New York, NY, USA
| | - Bertram Bleck
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Joan Reibman
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | | | - Nedim Durmus
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
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90
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Xu Z, Takizawa F, Parra D, Gómez D, von Gersdorff Jørgensen L, LaPatra SE, Sunyer JO. Mucosal immunoglobulins at respiratory surfaces mark an ancient association that predates the emergence of tetrapods. Nat Commun 2016; 7:10728. [PMID: 26869478 PMCID: PMC4754351 DOI: 10.1038/ncomms10728] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 01/14/2016] [Indexed: 12/24/2022] Open
Abstract
Gas-exchange structures are critical for acquiring oxygen, but they also represent portals for pathogen entry. Local mucosal immunoglobulin responses against pathogens in specialized respiratory organs have only been described in tetrapods. Since fish gills are considered a mucosal surface, we hypothesized that a dedicated mucosal immunoglobulin response would be generated within its mucosa on microbial exposure. Supporting this hypothesis, here we demonstrate that following pathogen exposure, IgT+ B cells proliferate and generate pathogen-specific IgT within the gills of fish, thus providing the first example of locally induced immunoglobulin in the mucosa of a cold-blooded species. Moreover, we demonstrate that gill microbiota is predominantly coated with IgT, thus providing previously unappreciated evidence that the microbiota present at a respiratory surface of a vertebrate is recognized by a mucosal immunoglobulin. Our findings indicate that respiratory surfaces and mucosal immunoglobulins are part of an ancient association that predates the emergence of tetrapods. In teleost fish the gills perform—in addition to respiration—functions such as immune defence. Here the authors show that IgT, a teleost specific Ig previously shown to be involved in gut and skin mucosal immunity, is locally induced in the gill, where it plays a key role in immunity in rainbow trout.
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Affiliation(s)
- Zhen Xu
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 413 Rosenthal building, 3800 Spruce Street, Philadelphia, Pennsylvania 19104, USA.,Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Fumio Takizawa
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 413 Rosenthal building, 3800 Spruce Street, Philadelphia, Pennsylvania 19104, USA
| | - David Parra
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Daniela Gómez
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 413 Rosenthal building, 3800 Spruce Street, Philadelphia, Pennsylvania 19104, USA
| | - Louise von Gersdorff Jørgensen
- Laboratory of Aquatic Pathobiology, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiskberg DK-1870, Denmark
| | - Scott E LaPatra
- Research Division, Clear Springs Foods Inc., P O Box 712, Buhl, Idaho 83316, USA
| | - J Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 413 Rosenthal building, 3800 Spruce Street, Philadelphia, Pennsylvania 19104, USA
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91
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Gates K, Martinez F. The Human Microbiome in the Lung: Are Infections Contributing to Lung Health and Disease? CHRONIC OBSTRUCTIVE PULMONARY DISEASES-JOURNAL OF THE COPD FOUNDATION 2016; 3:466-472. [PMID: 28848868 DOI: 10.15326/jcopdf.3.1.2015.0174] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This article serves as a CME-available, enduring material summary of the following COPD9USA presentations: "The Human Microbiome in the Lung: The Way Forward" Presenter: Gary B. Huffnagle, PhD "COPD: Is it Just Bacteria?" Presenter: Alison Morris, MD, MS "What We Have Learned From Other Disease States and How It Applies to COPD" Presenter: Fernando Martinez, MD, MS.
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Affiliation(s)
- Khalilah Gates
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Fernando Martinez
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
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92
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ElMaraachli W, Conrad DJ, Wang ACC. Using Cystic Fibrosis Therapies for Non-Cystic Fibrosis Bronchiectasis. Clin Chest Med 2015; 37:139-46. [PMID: 26857775 DOI: 10.1016/j.ccm.2015.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Non-cystic fibrosis bronchiectasis (NCFB) is an increasingly prevalent disease that places a significant burden on patients and health systems globally. Although many of the therapies used to treat NCFB were originally developed as cystic fibrosis (CF) therapies, not all of them have been demonstrated to be efficacious in NCFB and some may even be harmful. This article explores the evidence for which therapeutic strategies used to treat CF have been translated into the care of NCFB. The conclusion is that therapies for adult NCFB cannot be simply extrapolated from CF clinical trials, and in some instances, doing so may actually result in harm.
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Affiliation(s)
- Wael ElMaraachli
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, San Diego, 200 West Arbor Drive, MC 8372, San Diego, CA 92013, USA
| | - Douglas J Conrad
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, San Diego, 200 West Arbor Drive, MC 8372, San Diego, CA 92013, USA.
| | - Angela C C Wang
- Division of Chest and Critical Care Medicine, Scripps Clinic, 10666 North Torrey Pines Road, W203, San Diego, CA 92037, USA
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Rogers GB, Shaw D, Marsh RL, Carroll MP, Serisier DJ, Bruce KD. Republished: Respiratory microbiota: addressing clinical questions, informing clinical practice. Postgrad Med J 2015; 91:463-70. [PMID: 26304986 PMCID: PMC4552901 DOI: 10.1136/postgradmedj-2014-205826rep] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/23/2014] [Indexed: 12/30/2022]
Abstract
Over the last decade, technological advances have revolutionised efforts to understand the role played by microbes in airways disease. With the application of ever more sophisticated techniques, the literature has become increasingly inaccessible to the non-specialist reader, potentially hampering the translation of these gains into improvements in patient care. In this article, we set out the key principles underpinning microbiota research in respiratory contexts and provide practical guidance on how best such studies can be designed, executed and interpreted. We examine how an understanding of the respiratory microbiota both challenges fundamental assumptions and provides novel clinical insights into lung disease, and we set out a number of important targets for ongoing research.
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Affiliation(s)
- Geraint B Rogers
- SAHMRI Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia
| | - Dominick Shaw
- Nottingham Respiratory Research Unit, University of Nottingham, Nottingham City Hospital, Nottingham, Notts, UK
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mary P Carroll
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
| | - David J Serisier
- Immunity, Infection, and Inflammation Program, Mater Research Institute, University of Queensland, and Translational Research Institute, Woolloongabba, Queensland, Australia
- Department of Respiratory Medicine, Mater Adult Hospital, South Brisbane, Australia
| | - Kenneth D Bruce
- King's College London, Institute of Pharmaceutical Science, London, UK
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94
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Murray MA, Chotirmall SH. The Impact of Immunosenescence on Pulmonary Disease. Mediators Inflamm 2015; 2015:692546. [PMID: 26199462 PMCID: PMC4495178 DOI: 10.1155/2015/692546] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 06/09/2015] [Indexed: 01/09/2023] Open
Abstract
The global population is aging with significant gains in life expectancy particularly in the developed world. Consequently, greater focus on understanding the processes that underlie physiological aging has occurred. Key facets of advancing age include genomic instability, telomere shortening, epigenetic changes, and declines in immune function termed immunosenescence. Immunosenescence and its associated chronic low grade systemic "inflamm-aging" contribute to the development and progression of pulmonary disease in older individuals. These physiological processes predispose to pulmonary infection and confer specific and unique clinical phenotypes observed in chronic respiratory disease including late-onset asthma, chronic obstructive pulmonary disease, and pulmonary fibrosis. Emerging concepts of the gut and airway microbiome further complicate the interrelationship between host and microorganism particularly from an immunological perspective and especially so in the setting of immunosenescence. This review focuses on our current understanding of the aging process, immunosenescence, and how it can potentially impact on various pulmonary diseases and the human microbiome.
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Affiliation(s)
- Michelle A. Murray
- Department of Respiratory Medicine, Mater Misericordiae Hospital, Eccles Street, Dublin 7, Ireland
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232
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95
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Abstract
Microbes are ubiquitous on the human body and comprise approximately 90% of the cells and 99% of the genes of the human supraorganism. High-throughput sequencing technology has permitted the development of culture-independent means to identify the microbiota that are unique to the various microenvironments of the body and probably contribute some function. Although the respiratory tract interfaces with the environment, the lungs were always thought to be a sterile environment - until recently, when these techniques were applied to healthy and disease states. Further, there appears to be a complex interplay between the development of the gastrointestinal and respiratory microbiota and the regulation of immune function. The contribution of this dynamic metabolic mass to respiratory disease in the newborn is unknown. This article will review emerging data from recent human and murine studies that suggest there is a microbial influence on the development of respiratory disease, but it will also highlight many of the gaps that remain in understanding the function of the respiratory microbiome.
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Affiliation(s)
- Barbara B. Warner
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO USA
| | - Aaron Hamvas
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO USA
- Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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96
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97
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Whiley RA, Fleming EV, Makhija R, Waite RD. Environment and colonisation sequence are key parameters driving cooperation and competition between Pseudomonas aeruginosa cystic fibrosis strains and oral commensal streptococci. PLoS One 2015; 10:e0115513. [PMID: 25710466 PMCID: PMC4339374 DOI: 10.1371/journal.pone.0115513] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 11/25/2014] [Indexed: 11/18/2022] Open
Abstract
Cystic fibrosis (CF) patient airways harbour diverse microbial consortia that, in addition to the recognized principal pathogen Pseudomonas aeruginosa, include other bacteria commonly regarded as commensals. The latter include the oral (viridans) streptococci, which recent evidence indicates play an active role during infection of this environmentally diverse niche. As the interactions between inhabitants of the CF airway can potentially alter disease progression, it is important to identify key cooperators/competitors and environmental influences if therapeutic intervention is to be improved and pulmonary decline arrested. Importantly, we recently showed that virulence of the P. aeruginosa Liverpool Epidemic Strain (LES) could be potentiated by the Anginosus-group of streptococci (AGS). In the present study we explored the relationships between other viridans streptococci (Streptococcus oralis, Streptococcus mitis, Streptococcus gordonii and Streptococcus sanguinis) and the LES and observed that co-culture outcome was dependent upon inoculation sequence and environment. All four streptococcal species were shown to potentiate LES virulence factor production in co-culture biofilms. However, in the case of S. oralis interactions were environmentally determined; in air cooperation within a high cell density co-culture biofilm occurred together with stimulation of LES virulence factor production, while in an atmosphere containing added CO2 this species became a competitor antagonising LES growth through hydrogen peroxide (H2O2) production, significantly altering biofilm population dynamics and appearance. Streptococcus mitis, S. gordonii and S. sanguinis were also capable of H2O2 mediated inhibition of P. aeruginosa growth, but this was only visible when inoculated as a primary coloniser prior to introduction of the LES. Therefore, these observations, which are made in conditions relevant to the biology of CF disease pathogenesis, show that the pathogenic and colonisation potential of P. aeruginosa isolates can be modulated positively and negatively by the presence of oral commensal streptococci.
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Affiliation(s)
- Robert A. Whiley
- Department of Clinical & Diagnostic Oral Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, United Kingdom, E1 2AT
| | - Emily V. Fleming
- Centre for Immunology and Infectious Disease, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, United Kingdom, E1 2AT
| | - Ridhima Makhija
- Department of Clinical & Diagnostic Oral Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, United Kingdom, E1 2AT
| | - Richard D. Waite
- Centre for Immunology and Infectious Disease, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, United Kingdom, E1 2AT
- * E-mail:
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98
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Rogers GB, Shaw D, Marsh RL, Carroll MP, Serisier DJ, Bruce KD. Respiratory microbiota: addressing clinical questions, informing clinical practice. Thorax 2015; 70:74-81. [PMID: 25035125 PMCID: PMC4283665 DOI: 10.1136/thoraxjnl-2014-205826] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/23/2014] [Indexed: 12/23/2022]
Abstract
Over the last decade, technological advances have revolutionised efforts to understand the role played by microbes in airways disease. With the application of ever more sophisticated techniques, the literature has become increasingly inaccessible to the non-specialist reader, potentially hampering the translation of these gains into improvements in patient care. In this article, we set out the key principles underpinning microbiota research in respiratory contexts and provide practical guidance on how best such studies can be designed, executed and interpreted. We examine how an understanding of the respiratory microbiota both challenges fundamental assumptions and provides novel clinical insights into lung disease, and we set out a number of important targets for ongoing research.
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Affiliation(s)
- Geraint B Rogers
- SAHMRI Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia
| | - Dominick Shaw
- Nottingham Respiratory Research Unit, University of Nottingham, Nottingham City Hospital, Nottingham, Notts, UK
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mary P Carroll
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
| | - David J Serisier
- Immunity, Infection, and Inflammation Program, Mater Research Institute, University of Queensland, and Translational Research Institute, Woolloongabba, Queensland, Australia
- Department of Respiratory Medicine, Mater Adult Hospital, South Brisbane, Australia
| | - Kenneth D Bruce
- King's College London, Institute of Pharmaceutical Science, London, UK
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99
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Baldwin DA, Feldman M, Alwine JC, Robertson ES. Metagenomic assay for identification of microbial pathogens in tumor tissues. mBio 2014; 5:e01714-14. [PMID: 25227467 PMCID: PMC4172075 DOI: 10.1128/mbio.01714-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Screening for thousands of viruses and other pathogenic microorganisms, including bacteria, fungi, and parasites, in human tumor tissues will provide a better understanding of the contributory role of the microbiome in the predisposition for, causes of, and therapeutic responses to the associated cancer. Metagenomic assays designed to perform these tasks will have to include rapid and economical processing of large numbers of samples, supported by straightforward data analysis pipeline and flexible sample preparation options for multiple input tissue types from individual patients, mammals, or environmental samples. To meet these requirements, the PathoChip platform was developed by targeting viral, prokaryotic, and eukaryotic genomes with multiple DNA probes in a microarray format that can be combined with a variety of upstream sample preparation protocols and downstream data analysis. PathoChip screening of DNA plus RNA from formalin-fixed, paraffin-embedded tumor tissues demonstrated the utility of this platform, and the detection of oncogenic viruses was validated using independent PCR and deep sequencing methods. These studies demonstrate the use of the PathoChip technology combined with PCR and deep sequencing as a valuable strategy for detecting the presence of pathogens in human cancers and other diseases. IMPORTANCE This work describes the design and testing of a PathoChip array containing probes with the ability to detect all known publicly available virus sequences as well as hundreds of pathogenic bacteria, fungi, parasites, and helminths. PathoChip provides wide coverage of microbial pathogens in an economical format. PathoChip screening of DNA plus RNA from formalin-fixed, paraffin-embedded tumor tissues demonstrated the utility of this platform, and the detection of oncogenic viruses was validated using independent PCR and sequencing methods. These studies demonstrate that the PathoChip technology is a valuable strategy for detecting the presence of pathogens in human cancers and other diseases.
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Affiliation(s)
- Don A Baldwin
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Wong EHC, Porter JD, Edwards MR, Johnston SL. The role of macrolides in asthma: current evidence and future directions. THE LANCET RESPIRATORY MEDICINE 2014; 2:657-70. [PMID: 24948430 DOI: 10.1016/s2213-2600(14)70107-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Macrolides, such as clarithromycin and azithromycin, possess antimicrobial, immunomodulatory, and potential antiviral properties. They represent a potential therapeutic option for asthma, a chronic inflammatory disorder characterised by airway hyper-responsiveness that leads to recurrent episodes of wheezing, breathlessness, chest tightness, and coughing. Results from clinical trials, however, have been contentious. The findings could be confounded by many factors, including the heterogeneity of asthma, treatment duration, dose, and differing outcome measures. Recent evidence suggests improved effectiveness of macrolides in patients with sub-optimally controlled severe neutrophilic asthma and in asthma exacerbations. We examine the evidence from clinical trials and discuss macrolide properties and their relevance to the pathophysiology of asthma. At present, the use of macrolides in chronic asthma or acute exacerbations is not justified. Further work, including proteomic, genomic, and microbiome studies, will advance our knowledge of asthma phenotypes, and help to identify a macrolide-responsive subgroup. Future clinical trials should target this subgroup and place emphasis on clinically relevant outcomes such as asthma exacerbations.
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Affiliation(s)
- Ernie H C Wong
- Airway Disease Infection Section, National Heart and Lung Institute, Imperial College London, London, UK; MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK; Centre for Respiratory Infection, London, UK; Imperial College Healthcare NHS Trust, London, UK
| | - James D Porter
- Airway Disease Infection Section, National Heart and Lung Institute, Imperial College London, London, UK; MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK; Centre for Respiratory Infection, London, UK
| | - Michael R Edwards
- Airway Disease Infection Section, National Heart and Lung Institute, Imperial College London, London, UK; MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK; Centre for Respiratory Infection, London, UK
| | - Sebastian L Johnston
- Airway Disease Infection Section, National Heart and Lung Institute, Imperial College London, London, UK; MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK; Centre for Respiratory Infection, London, UK; Imperial College Healthcare NHS Trust, London, UK.
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