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Wang B, Tan M, Li W, Xu Q, Jin L, Xie S, Wang C. Exploring the microbiota difference of bronchoalveolar lavage fluid between community-acquired pneumonia with or without COPD based on metagenomic sequencing: a retrospective study. BMC Pulm Med 2024; 24:278. [PMID: 38867204 PMCID: PMC11167785 DOI: 10.1186/s12890-024-03087-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Community-acquired pneumonia (CAP) patients with chronic obstructive pulmonary disease (COPD) have higher disease severity and mortality compared to those without COPD. However, deep investigation into microbiome distribution of lower respiratory tract of CAP with or without COPD was unknown. METHODS So we used metagenomic next generation sequencing (mNGS) to explore the microbiome differences between the two groups. RESULTS Thirty-six CAP without COPD and 11 CAP with COPD cases were retrieved. Bronchoalveolar lavage fluid (BALF) was collected and analyzed using untargeted mNGS and bioinformatic analysis. mNGS revealed that CAP with COPD group was abundant with Streptococcus, Prevotella, Bordetella at genus level and Cutibacterium acnes, Rothia mucilaginosa, Bordetella genomosp. 6 at species level. While CAP without COPD group was abundant with Ralstonia, Prevotella, Streptococcus at genus level and Ralstonia pickettii, Rothia mucilaginosa, Prevotella melaninogenica at species level. Meanwhile, both alpha and beta microbiome diversity was similar between groups. Linear discriminant analysis found that pa-raburkholderia, corynebacterium tuberculostearicum and staphylococcus hominis were more enriched in CAP without COPD group while the abundance of streptococcus intermedius, streptococcus constellatus, streptococcus milleri, fusarium was higher in CAP with COPD group. CONCLUSIONS These findings revealed that concomitant COPD have an mild impact on lower airway microbiome of CAP patients.
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Affiliation(s)
- Bingbing Wang
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Min Tan
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Wei Li
- Department of Geriatrics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Qinghua Xu
- Vision Medicals Center for Infectious Disease, Guangzhou, Guangdong, China
| | - Lianfeng Jin
- Vision Medicals Center for Infectious Disease, Guangzhou, Guangdong, China
| | - Shuanshuan Xie
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.
| | - Changhui Wang
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.
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2
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Campaña-Duel E, Ceccato A, Morales-Quinteros L, Camprubí-Rimblas M, Artigas A. Hypercapnia and its relationship with respiratory infections. Expert Rev Respir Med 2024; 18:41-47. [PMID: 38489161 DOI: 10.1080/17476348.2024.2331767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
INTRODUCTION Hypercapnia is developed in patients with acute and/or chronic respiratory conditions. Clinical data concerning hypercapnia and respiratory infections interaction is limited. AREAS COVERED Currently, the relationship between hypercapnia and respiratory infections remains unclear. In this review, we summarize studies on the effects of hypercapnia on models of pulmonary infections to clarify the role of elevated CO2 in these pulmonary pathologies. Hypercapnia affects different cell types in the alveoli, leading to changes in the immune response. In vitro studies show that hypercapnia downregulates the NF-κβ pathway, reduces inflammation and impairs epithelial wound healing. While in vivo models show a dual role between short- and long-term effects of hypercapnia on lung infection. However, it is still controversial whether the effects observed under hypercapnia are pH dependent or not. EXPERT OPINION The role of hypercapnia is still a controversial debate. Hypercapnia could play a beneficial role in mechanically ventilated models, by lowering the inflammation produced by the stretch condition. But it could be detrimental in infectious scenarios, causing phagocyte dysfunction and lack of infection control. Further data concerning hypercapnia on respiratory infections is needed to elucidate this interaction.
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Affiliation(s)
- Elena Campaña-Duel
- Critical care center, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA). Universitat Autònoma de Barcelona, Sabadell, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Adrian Ceccato
- Critical care center, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA). Universitat Autònoma de Barcelona, Sabadell, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Intensive care unit, Hospital Universitari Sagrat Cor, Grupo Quironsalud, Barcelona, Spain
| | - Luis Morales-Quinteros
- Critical care center, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA). Universitat Autònoma de Barcelona, Sabadell, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Servei de Medicina Intensiva, Hospital de la Santa Creu y Sant Pau, Barcelona, Spain
| | - Marta Camprubí-Rimblas
- Critical care center, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA). Universitat Autònoma de Barcelona, Sabadell, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Antonio Artigas
- Critical care center, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí (I3PT-CERCA). Universitat Autònoma de Barcelona, Sabadell, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
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3
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Xue-Meng C, Gao-Wang L, Xiao-Mei L, Fan-Fang Z, Jin-Fang X. Effect of mechanical ventilation under intubation on respiratory tract change of bacterial count and alteration of bacterial flora. Exp Lung Res 2023; 49:165-177. [PMID: 37789686 DOI: 10.1080/01902148.2023.2264947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/24/2023] [Indexed: 10/05/2023]
Abstract
Background: The most common 'second strike' in mechanically ventilated patients is a pulmonary infection caused by the ease with which bacteria can invade and colonize the lungs due to mechanical ventilation. At the same time, metastasis of lower airway microbiota may have significant implications in developing intubation mechanical ventilation lung inflammation. Thus, we establish a rat model of tracheal intubation with mechanical ventilation and explore the effects of mechanical ventilation on lung injury and microbiological changes in rats. To provide a reference for preventing and treating bacterial flora imbalance and pulmonary infection injury caused by mechanical ventilation of tracheal intubation. Methods: Sprague-Dawley rats were randomly divided into Control, Mechanical ventilation under intubation (1, 3, 6 h) groups, and Spontaneously breathing under intubation (1, 3, 6 h). Lung histopathological injury scores were evaluated. 16SrDNA sequencing was performed to explore respiratory microbiota changes, especially, changes of bacterial count and alteration of bacterial flora. Results: Compared to groups C and SV, critical pathological changes in pulmonary lesions occurred in the MV group after 6 h (p < 0.05). The Alpha diversity and Beta diversity of lower respiratory tract microbiota in MV6, SV6, and C groups were statistically significant (p < 0.05). The main dominant bacterial phyla in the respiratory tract of rats were Proteobacteria, Firmicutes, Bacteroidetes, and Cyanobacteria. Acinetobacter radioresistens in group C was significant, Megaonas in group MV6 was significantly increased, and Parvibacter in group SV6 was significantly increased. Anaerobic, biofilm formation, and Gram-negative bacteria-related functional genes were altered during mechanical ventilation with endotracheal intubation. Conclusion: Mechanical ventilation under intubation may cause dysregulation of lower respiratory microbiota in rats.
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Affiliation(s)
- Chen Xue-Meng
- Department of Anesthesiology, Deyang People's Hospital, Deyang, Sichuan, China
- Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Liu Gao-Wang
- Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ling Xiao-Mei
- Department of Anesthesiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zeng Fan-Fang
- Department of Anesthesiology, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiao Jin-Fang
- Department of Anesthesiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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4
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Losol P, Ji MH, Kim JH, Choi JP, Yun JE, Seo JH, Kim BK, Chang YS, Kim SH. Bronchial epithelial cells release inflammatory markers linked to airway inflammation and remodeling in response to TLR5 ligand flagellin. World Allergy Organ J 2023; 16:100786. [PMID: 37332524 PMCID: PMC10276272 DOI: 10.1016/j.waojou.2023.100786] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/25/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023] Open
Abstract
Background/Aims Flagellin, which is abundant in gram-negative bacteria, including Pseudomonas, is reported to influence on inflammatory responses in various lung diseases. However, its effect on airway epithelial cells in contribution to asthma pathogenesis is not elucidated yet. We aimed to investigate the effect of TLR5 ligand flagellin on the transcriptomic profile of primary human epithelial cells and to determine the markers of airway inflammation. Methods Normal human bronchial epithelial (NHBE) cells were grown and differentiated in air-liquid interface (ALI) culture for 14-16 days. The cells were treated with flagellin in vitro at 10 and 100 ng/ml for 3 and 24 h. The conditioned media and cells were harvested to validate inflammatory markers involved in airway inflammation using ELISA, Western blot, and quantitative PCR methods. RNA-sequencing was performed to investigate the transcriptional response to flagellin in ALI-NHBE cells. Results Altered transcriptional responses to flagellin in differentiated bronchial epithelial cells were determined, including genes encoding chemokines, matrix metalloproteinases, and antimicrobial biomolecules. Pathway analysis of the transcriptionally responsive genes revealed enrichment of signaling pathways. Flagellin induced the mRNA expressions of proinflammatory cytokines and chemokines, and secretion of GM-CSF, CXCL5, CCL5 and CXCL10. Flagellin enhanced the protein expression of MMP-13 in TGF-β1 and TGF-β2 pretreated cell lysates and Wnt/β-catenin signaling. Conclusions These findings suggest that flagellin could be a potent inducer of inflammatory markers that may contribute to airway inflammation and remodeling.
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Affiliation(s)
- Purevsuren Losol
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Medical Research Center, Seoul National University, Seoul, South Korea
| | - Mi-Hong Ji
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jin Hee Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jun-Pyo Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jeong-Eun Yun
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Jang-Ho Seo
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Byung-Keun Kim
- Department of Internal Medicine, Korea University Medical Center Anam Hospital, Seoul, South Korea
| | - Yoon-Seok Chang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Medical Research Center, Seoul National University, Seoul, South Korea
| | - Sae-Hoon Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
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5
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Abstract
This narrative review seeks to examine the relationships between bacterial microbiomes and infectious disease. This is achieved by detailing how different human host microbiomes develop and function, from the earliest infant acquisitions of maternal and environmental species through to the full development of microbiomes by adulthood. Communication between bacterial species or communities of species within and outside of the microbiome is a factor in both maintenance of homeostasis and management of threats from the external environment. Dysbiosis of this homeostasis is key to understanding the development of disease states. Several microbiomes and the microbiota within are used as prime examples of how changes in species composition, particularly at the phylum level, leads to such diverse conditions as inflammatory bowel disease (IBD), type 2 diabetes, psoriasis, Parkinson's disease, reflux oesophagitis and others. The review examines spatial relationships between microbiomes to understand how dysbiosis in the gut microbiome in particular can influence diseases in distant host sites via routes such as the gut-lung, gut-skin and gut-brain axes. Microbiome interaction with host processes such as adaptive immunity is increasingly identified as critical to developing the capacity of the immune system to react to pathogens. Dysbiosis of essential bacteria involved in modification of host substrates such as bile acid components can result in development of Crohn's disease, small intestine bacterial overgrowth, hepatic cancer and obesity. Interactions between microbiomes in distantly located sites are being increasingly being identified, resulting in a 'whole of body' effect by the combined host microbiome.
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Affiliation(s)
- Jim Manos
- Infection, Immunity and InflammationSchool of Medical SciencesFaculty of Medicine and HealthThe Charles Perkins CentreThe University of SydneySydneyNSWAustralia
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6
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Alorfi NM, Algarni AS. Clinical Impact of Semaglutide, a Glucagon-Like Peptide-1 Receptor Agonist, on Obesity Management: A Review. Clin Pharmacol 2022; 14:61-67. [PMID: 35958046 PMCID: PMC9357557 DOI: 10.2147/cpaa.s374741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/15/2022] [Indexed: 12/11/2022] Open
Affiliation(s)
- Nasser M Alorfi
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
- Correspondence: Nasser M Alorfi, Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia, Tel +966500644261, Email
| | - Alanood S Algarni
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
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7
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Kotlyarov S. High-Density Lipoproteins: A Role in Inflammation in COPD. Int J Mol Sci 2022; 23:8128. [PMID: 35897703 PMCID: PMC9331387 DOI: 10.3390/ijms23158128] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 02/04/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a widespread disease associated with high rates of disability and mortality. COPD is characterized by chronic inflammation in the bronchi as well as systemic inflammation, which contributes significantly to the clinically heterogeneous course of the disease. Lipid metabolism disorders are common in COPD, being a part of its pathogenesis. High-density lipoproteins (HDLs) are not only involved in lipid metabolism, but are also part of the organism's immune and antioxidant defense. In addition, HDL is a versatile transport system for endogenous regulatory agents and is also involved in the removal of exogenous substances such as lipopolysaccharide. These functions, as well as information about lipoprotein metabolism disorders in COPD, allow a broader assessment of their role in the pathogenesis of heterogeneous and comorbid course of the disease.
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Affiliation(s)
- Stanislav Kotlyarov
- Department of Nursing, Ryazan State Medical University, 390026 Ryazan, Russia
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8
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Jiang X, Wang C, Guo J, Hou J, Guo X, Zhang H, Tan J, Li M, Li X, Zhu H. Global Meta-analysis of Airborne Bacterial Communities and Associations with Anthropogenic Activities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9891-9902. [PMID: 35785964 PMCID: PMC9301914 DOI: 10.1021/acs.est.1c07923] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Airborne microbiome alterations, an emerging global health concern, have been linked to anthropogenic activities in numerous studies. However, these studies have not reached a consensus. To reveal general trends, we conducted a meta-analysis using 3226 air samples from 42 studies, including 29 samples of our own. We found that samples in anthropogenic activity-related categories showed increased microbial diversity, increased relative abundance of pathogens, increased co-occurrence network complexity, and decreased positive edge proportions in the network compared with the natural environment category. Most of the above conclusions were confirmed using the samples we collected in a particular period with restricted anthropogenic activities. Additionally, unlike most previous studies, we used 15 human-production process factors to quantitatively describe anthropogenic activities. We found that microbial richness was positively correlated with fine particulate matter concentration, NH3 emissions, and agricultural land proportion and negatively correlated with the gross domestic product per capita. Airborne pathogens showed preferences for different factors, indicating potential health implications. SourceTracker analysis showed that the human body surface was a more likely source of airborne pathogens than other environments. Our results advance the understanding of relationships between anthropogenic activities and airborne bacteria and highlight the role of airborne pathogens in public health.
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Affiliation(s)
- Xiaoqing Jiang
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
| | - Chunhui Wang
- School
of Life Sciences, Peking University, Beijing 100871, China
| | - Jinyuan Guo
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Jiaheng Hou
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
| | - Xiao Guo
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
| | - Haoyu Zhang
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
| | - Jie Tan
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
| | - Mo Li
- School
of Life Sciences, Peking University, Beijing 100871, China
| | - Xin Li
- School
of Life Sciences, Peking University, Beijing 100871, China
- Beijing
National Day School, Beijing 100039, China
| | - Huaiqiu Zhu
- State
Key Laboratory for Turbulence and Complex Systems, Department of Biomedical
Engineering, College of Future Technology, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Peking University, Beijing 100871, China
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30332, United States
- . Phone: 8610-6276-7261
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9
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Wang G, Cai Y. APPLICATION OF EXERCISE COMBINED WITH LUNG REHABILITATION IN RESPIRATORY DISEASE. REV BRAS MED ESPORTE 2022. [DOI: 10.1590/1517-8692202228012021_0451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
ABSTRACT Introduction: Chronic obstructive pulmonary disease (COPD) is a respiratory disease characterized by incomplete reversibility of airflow obstruction and persistent respiratory symptoms. Objective: To explore the therapeutic effect of physical exercise on patients with chronic obstructive pulmonary disease in pulmonary rehabilitation. Methods: Forty-eight experimental subjects were divided into control group, experimental group 1, and experimental group 2 for research. The control group received normal medical-related treatment without any other means of intervention. In addition to normal medical-related treatment, experimental group 1 received breathing training and educational interventions and experimental group 2 received exercise, breathing training and educational interventions. Results: The vital capacity of female subjects before and during the experiment ranged from 2.23±0.01 to 2.26±0.04, the FVC ranged from 2.00±0.02 to 2.01±0.03, the FEV1 ranged from 1.03±0.01 to 1.03±0.01,the FEV1% ranged from 55.50±1.29 to 55.25±1.71,the FEV1/FVC ranged from 51.44±0.24 to 50.84±1.00, andthe heart rate ranges from 65.00±0.82 to 65.50±1.29. Conclusions: Exercise training can increase the exercise tolerance of patients with COPD, relieve dyspnea, and improve the quality of life. Level of evidence II; Therapeutic studies - investigation of treatment results.
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Affiliation(s)
| | - Yuqi Cai
- Qingyang People’s Hospital, China
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10
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Su L, Qiao Y, Luo J, Huang R, Li Z, Zhang H, Zhao H, Wang J, Xiao Y. Characteristics of the sputum microbiome in COPD exacerbations and correlations between clinical indices. J Transl Med 2022; 20:76. [PMID: 35123490 PMCID: PMC8818176 DOI: 10.1186/s12967-022-03278-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/24/2022] [Indexed: 12/18/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a prevalent, progressive respiratory disease, and acute exacerbations of COPD (AECOPD) can accelerate the deterioration of the disease. Increasing evidence suggests that airway bacterial dysbiosis is associated with AECOPD. However, the exact relationship between changes in the sputum microbiome during AECOPD and clinical indices remains unclear. Methods In this study, a total of 76 sputum samples were collected from patients with AECOPD (n = 28), stable COPD (n = 23), recovery (n = 15) and healthy controls (HCs; n = 10). The sputum microbiome profile was analysed by sequencing the V3‑V4 amplicon of the 16S rRNA (ribosomal RNA) gene. Results The bacterial diversity (Shannon and Simpson’s index) was found to be significantly decreased in the AECOPD and recovery groups when compared to that in the stable COPD and HC groups. The most dominant phylum identified in the sputum samples of AECOPD patients was Proteobacteria, accounting for 30% of the microbiome. Compared to the stable COPD groups, the relative abundances of Firmicutes and Bacteroidetes were decreased, whereas those of Proteobacteria and Actinobacteria were increased in AECOPD patients. Furthermore, discriminative bacteria, such as Haemophilus, were identified as being specific taxa in AECOPD patients. Functional analysis showed that genes involved in membrane transport and signal transduction metabolism were enriched in the AECOPD group. Importantly, the proportions of Veillonella were positively correlated with lung function, and Staphylococcus was positively correlated with inflammatory indices. Conclusion Our study revealed variations in the sputum microbiome of AECOPD (based on composition and function) in a Chinese cohort and highlighted its correlation to clinical indices. These results indicated that microbial dysbiosis may contribute to disease progression and provide microbial biomarkers for the diagnosis of AECOPD. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03278-x.
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11
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Cheng YN, Huang WC, Wang CY, Fu PK. Compared the Microbiota Profiles between Samples from Bronchoalveolar Lavage and Endotracheal Aspirates in Severe Pneumonia: A Real-World Experience. J Clin Med 2022; 11:jcm11020327. [PMID: 35054022 PMCID: PMC8778781 DOI: 10.3390/jcm11020327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/26/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
Lower respiratory tract sampling from endotracheal aspirate (EA) and bronchoalveolar lavage (BAL) are both common methods to identify pathogens in severe pneumonia. However, the difference between these two methods in microbiota profiles remains unclear. We compared the microbiota profiles of pairwise EA and BAL samples in ICU patients with respiratory failure due to severe pneumonia. We prospectively enrolled 50 ICU patients with new onset of pneumonia requiring mechanical ventilation. EA and BAL were performed on the first ICU day, and samples were analyzed for microbial community composition via 16S rRNA metagenomic sequencing. Pathogens were identified in culture medium from BAL samples in 21 (42%) out of 50 patients. No difference was observed in the antibiotic prescription pattern, ICU mortality, or hospital mortality between BAL-positive and BAL-negative patients. The microbiota profiles in the EA and BAL samples are similar with respect to diversity, microbial composition, and microbial community correlations. The antibiotic treatment regimen was rarely changed based on the BAL findings. The samples from BAL did not provide more information than EA in the microbiota profiles. We suggest that EA is more useful than BAL for microbiome identification in mechanically ventilated patients.
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Affiliation(s)
- Yeong-Nan Cheng
- Institute of Bioinformatics and Systems Biology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan; (Y.-N.C.); (W.-C.H.)
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Wei-Chih Huang
- Institute of Bioinformatics and Systems Biology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan; (Y.-N.C.); (W.-C.H.)
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Chen-Yu Wang
- Department of Nursing, Hungkuang University, Taichung 43302, Taiwan;
- Department of Critical Care Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Pin-Kuei Fu
- Department of Critical Care Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
- College of Human Science and Social Innovation, Hungkuang University, Taichung 433304, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 402010, Taiwan
- Correspondence: ; Tel.: +886-937-701-592
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12
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Cho HJ, Ha JG, Lee SN, Kim CH, Wang DY, Yoon JH. Differences and similarities between the upper and lower airway: focusing on innate immunity. Rhinology 2021; 59:441-450. [PMID: 34339483 DOI: 10.4193/rhin21.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The nose is the first respiratory barrier to external pathogens, allergens, pollutants, or cigarette smoke, and vigorous immune responses are triggered when external pathogens come in contact with the nasal epithelium. The mucosal epithelial cells of the nose are essential to the innate immune response against external pathogens and transmit signals that modulate the adaptive immune response. The upper and lower airways share many physiological and immunological features, but there are also numerous differences. It is crucial to understand these differences and their contribution to pathophysiology in order to optimize treatments for inflammatory diseases of the respiratory tract. This review summarizes important differences in the embryological development, histological features, microbiota, immune responses, and cellular subtypes of mucosal epithelial cells of the nose and lungs.
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Affiliation(s)
- H-J Cho
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.,Global Research Laboratory for Allergic Airway Disease, Yonsei University College of Medicine, Seoul, Korea.,The Airway Mucus Institute, Yonsei University College of Medicine, Seoul, Korea
| | - J G Ha
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - S N Lee
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea 2 Global Research Laboratory for Allergic Airway Disease, Yonsei University College of Medicine, Seoul, Korea
| | - C-H Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.,The Airway Mucus Institute, Yonsei University College of Medicine, Seoul, Korea
| | - D-Y Wang
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - J-H Yoon
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.,Global Research Laboratory for Allergic Airway Disease, Yonsei University College of Medicine, Seoul, Korea.,The Airway Mucus Institute, Yonsei University College of Medicine, Seoul, Korea
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13
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Schroeder T, Kruse JM, Marcy F, Piper SK, Storm C, Nee J. Is the routine use of antipseudomonal antibiotics in acutely exacerbated COPD patients indicated: A retrospective analysis in 437 ICU patients. J Crit Care 2021; 65:49-55. [PMID: 34082255 DOI: 10.1016/j.jcrc.2021.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 10/21/2022]
Abstract
PURPOSE Chronic obstructive pulmonary disease (COPD) is a risk factor for acquiring multiple drug resistant bacteria. The main objective of this analysis was to question a beneficial outcome in the routine use of antipseudomonal antibiotics in the empiric treatment of severe AECOPD in Intensive Care Unit patients. MATERIAL AND METHODS We report a retrospective, observational cohort study in adult patients with severe AECOPD admitted to ICU at a tertiary care university hospital. Antibiotic treatment on admission as well as microbiology samples were analyzed. The influence of SOFA score at admission, age, sex and antibiotic choice upon survival was investigated by multivariable analysis. RESULTS 437 patients were included. Mean age was 68 years (±10), 46.5% were female. 271/437 patients (62%) were initially treated with antibiotics covering Pseudomonas aeruginosa. Overall, positive microbiology samples were found in 107 patients (24.5%). P. aeruginosa was only found in 3.7%. There was no significant difference in 30-day ICU mortality after adjusting for age, sex and severity of illness (20.4% ± 11.6 in patients with Pseudomonas inactive antibiotics versus 29.3% ± 10.8 in patients with PAA, p=0.113). CONCLUSIONS Empiric use of antipseudomonal antibiotics did not result in improved ICU survival in this retrospective analysis.
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Affiliation(s)
- Tim Schroeder
- Charité - Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care Medicine, Berlin, Germany.
| | - Jan Matthias Kruse
- Charité - Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care Medicine, Berlin, Germany
| | - Florian Marcy
- Charité - Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care Medicine, Berlin, Germany
| | - Sophie K Piper
- Charité - Universitätsmedizin Berlin, Institute of Biometry and Clinical Epidemiology, Berlin, Germany; Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Christian Storm
- Charité - Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care Medicine, Berlin, Germany
| | - Jens Nee
- Charité - Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care Medicine, Berlin, Germany
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14
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Consensus document on the diagnosis and treatment of chronic bronchial infection in chronic obstructive pulmonary disease. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.arbr.2020.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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15
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de la Rosa Carrillo D, López-Campos JL, Alcázar Navarrete B, Calle Rubio M, Cantón Moreno R, García-Rivero JL, Máiz Carro L, Olveira Fuster C, Martínez-García MÁ. Consensus Document on the Diagnosis and Treatment of Chronic Bronchial Infection in Chronic Obstructive Pulmonary Disease. Arch Bronconeumol 2020; 56:651-664. [PMID: 32540279 DOI: 10.1016/j.arbres.2020.04.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/22/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023]
Abstract
Although the chronic presence of microorganisms in the airways of patients with stable chronic obstructive pulmonary disease (COPD) confers a poor outcome, no recommendations have been established in disease management guidelines on how to diagnose and treat these cases. In order to guide professionals, the Spanish Society of Pulmonology and Thoracic Surgery (SEPAR) has prepared a document which aims to answer questions on the clinical management of COPD patients in whom microorganisms are occasionally or habitually isolated. Since the available scientific evidence is too heterogeneous to use in the creation of a clinical practice guideline, we have drawn up a document based on existing scientific literature and clinical experience, addressing the definition of different clinical situations and their diagnosis and management. The text was drawn up by consensus and approved by a large group of respiratory medicine experts with extensive clinical and scientific experience in the field, and has been endorsed by the SEPAR Scientific Committee.
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Affiliation(s)
| | - José Luís López-Campos
- Servicio de Neumología, Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Sevilla, España; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, España
| | - Bernardino Alcázar Navarrete
- Servicio de Neumología, Hospital Regional Universitario de Málaga. Instituto de Investigación Biomédica de Málaga (IBIMA), Universidad de Málaga, Málaga, España
| | - Myriam Calle Rubio
- Servicio de Neumología, Hospital de Alta Resolución de Loja, Loja, Granada, España
| | - Rafael Cantón Moreno
- Servicio de Neumología, Unidad de Infección Bronquial Crónica, Fibrosis Quística y Bronquiectasias, Hospital Universitario Ramón y Cajal, Madrid, España
| | - Juan Luis García-Rivero
- Servicio de Neumología, Hospital Clínico San Carlos. Departamento de Medicina, Facultad de Medicina, UCM, Madrid, España
| | - Luís Máiz Carro
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal. Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, España
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16
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Menéndez R, Cantón R, García-Caballero A, Barberán J. [Three keys to the appropriate choice of oral antibiotic treatment in the respiratory tract infections]. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2019; 32:497-515. [PMID: 31795630 PMCID: PMC6913073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 11/25/2019] [Indexed: 11/18/2022]
Abstract
Exacerbation of chronic obstructive pulmonary disease and community-acquired pneumonia are the most frequent infections of the lower respiratory tract in daily clinical practice. Antibiotic selection is a crucial component in its treatment and, in most cases, it is performed empirically. Scientific societies make therapeutic recommendations based on scientific evidence and / or expert recommendations that are of great help to clinicians. Beta-lactams, fluoroquinolones and macrolides are the most commonly used drugs for oral administration. From a practical point of view, there are three keys to the appropriate choice of oral antibiotic treatment, which are the effectiveness, safety and the ecological impact on the patient's microbiota, including the development of resistance, which will be assessed in depth in this review.
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Affiliation(s)
| | | | | | - J Barberán
- José Barberán, Servicio de Medicina Interna y Enfermedades infecciosas, Hospital Universitario HM Montepríncipe, Universidad San Pablo CEU. Madrid, Spain.
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17
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O'Farrell HE, Shaw JG, Goh F, Bowman RV, Fong KM, Krause L, Yang IA. Potential clinical utility of multiple target quantitative polymerase chain reaction (qPCR) array to detect microbial pathogens in patients with chronic obstructive pulmonary disease (COPD). J Thorac Dis 2019; 11:S2254-S2265. [PMID: 31737352 DOI: 10.21037/jtd.2019.10.39] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Culture-independent methods such as quantitative polymerase chain reaction (qPCR) are more sensitive for detecting pathogens than conventional culture. This study aimed to test the clinical potential of a multiple target qPCR array in identifying sputum pathogens, compared to traditional culture. Methods Forty chronic obstructive pulmonary disease (COPD) patients provided spontaneous sputum and blood samples during an exacerbation event (n=25 patients) and in stable state (n=15 patients). Sputum was processed and analysed by microscopy, culture and sensitivity testing (MCS) to identify living microbial isolates, and multiple target qPCR (44 targets for bacterial and fungal pathogens and antibiotic resistance genes), and 16S rRNA gene sequencing. Results Six microbial isolates (5 bacterial, 1 fungal) were cultured from 20 exacerbation and 10 stable patient sputum samples. Four of these microbial isolates had their presence in patient sputum confirmed by qPCR. All bacterial targets detected by qPCR were further confirmed by 16S rRNA gene sequencing at a genus level. qPCR identified significantly more bacterial pathogens than culture (P<0.001). The most prevalent bacterial species identified by qPCR were Streptococcus pneumoniae (72% of patients), Pseudomonas aeruginosa (40%), Prevotella oris (32%) and Haemophilus influenzae (17%). Microbial species diversity and richness were not significantly different between samples obtained from exacerbating and clinically stable cases. 16S rRNA gene sequencing identified Pseudomonas 4408227 (P=0.022, FDR =0.043 AUC =0.72) as a significantly different bacterial OTU (operational taxonomic units) in exacerbation sputum samples compared to stable state samples. Conclusions Multiple target qPCR was more sensitive for detection of sputum pathogens in COPD patients than conventional culture. 16S rRNA gene sequencing confirmed the identity at a genus level of all bacterial targets detected by qPCR, as well as identifying bacterial OTUs that could potentially be used to distinguish between exacerbation and stable COPD disease states. Multiple target qPCR pathogen detection in the sputum of COPD patients warrants further investigation to determine how it may influence COPD clinical management.
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Affiliation(s)
- Hannah E O'Farrell
- The University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Janet G Shaw
- The University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Felicia Goh
- The University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Rayleen V Bowman
- The University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Kwun M Fong
- The University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, QLD, Australia
| | | | - Ian A Yang
- The University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, QLD, Australia
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18
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Parris BA, O'Farrell HE, Fong KM, Yang IA. Chronic obstructive pulmonary disease (COPD) and lung cancer: common pathways for pathogenesis. J Thorac Dis 2019; 11:S2155-S2172. [PMID: 31737343 DOI: 10.21037/jtd.2019.10.54] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) and lung cancer comprise the leading causes of lung disease-related mortality worldwide. Exposure to tobacco smoke is a mutual aetiology underlying the two diseases, accounting for almost 90% of cases. There is accumulating evidence supporting the role of immune dysfunction, the lung microbiome, extracellular vesicles and underlying genetic susceptibility in the development of COPD and lung cancer. Further, epigenetic factors, involving DNA methylation and microRNA expression, have been implicated in both diseases. Chronic inflammation is a key feature of COPD and could be a potential driver of lung cancer development. Using next generation technologies, further studies investigating the genomics, epigenetics and gene-environment interaction in key molecular pathways will continue to elucidate the pathogenic mechanisms underlying the development of COPD and lung cancer, and contribute to the development of novel diagnostic and prognostic tools for early intervention and personalised therapeutic strategies.
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Affiliation(s)
- Brielle A Parris
- UQ Thoracic Research Centre, The Prince Charles Hospital, University of Queensland, Brisbane, Australia
| | - Hannah E O'Farrell
- UQ Thoracic Research Centre, The Prince Charles Hospital, University of Queensland, Brisbane, Australia
| | - Kwun M Fong
- UQ Thoracic Research Centre, The Prince Charles Hospital, University of Queensland, Brisbane, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Metro North Hospital and Health Service, Brisbane, Australia
| | - Ian A Yang
- UQ Thoracic Research Centre, The Prince Charles Hospital, University of Queensland, Brisbane, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Metro North Hospital and Health Service, Brisbane, Australia
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19
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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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20
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Shi X, Shao C, Luo C, Chu Y, Wang J, Meng Q, Yu J, Gao Z, Kang Y. Microfluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway Metagenomics. mSystems 2019; 4:e00198-19. [PMID: 31117025 PMCID: PMC6589435 DOI: 10.1128/msystems.00198-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/04/2019] [Indexed: 01/13/2023] Open
Abstract
Dysbiosis of airway microbiomes has been found in various respiratory diseases, but its molecular details in terms of taxonomic profile, metabolic characteristics, defensive function, and inhabit adaption are far from clear. Shotgun metagenome sequencing provides detailed information for microbes, whereas its application is rather limited in airways due to host DNA contaminants that overwhelm a minute amount of microbial content. Here, we describe a microfluidics-based enrichment device and an emulsion-based whole-genome amplification procedure (MEEA) for the preparation of DNA from sputa for shotgun sequencing in a metagenomics study. The two protocols coupled in MEEA are first separately assayed with mock samples and are both promising in efficiency and bias. The efficiency and consistency of MEEA are further evaluated in six clinical sputum samples against direct sequencing without enrichment, and MEEA enables 2 to 14 times enrichment for microbial reads, which take 14.68% to 33.52% of total reads. The dominant pathogens detected in MEEA are in excellent agreement with those from clinical etiological tests. Meanwhile, MEEA presents much more microbiome complexity and genome information at a strain level than direct sequencing, exhibiting high sensitivity for identifying prophages and DNA viruses. MEEA provides better microbiome profiling than direct sequencing without a preference for specific microorganisms. The more detailed functional and taxonomic characterization of their species constituents, including both bacterium and virus, facilitates metagenomics studies on the pathogenesis of respiratory microbiomes.IMPORTANCE The airway microbial community, which takes important pathogenic roles for respiratory diseases, is far from clear in terms of taxonomy and gene functions. One of the critical reasons is the heavy contamination of host cell/DNA in airway samples, which hinders the subsequent sequencing of the whole genomic contents of the microbial community-the metagenome. Here, we describe a protocol for airway sample preparation which couples a microbe enrichment microfluidic device and a DNA amplification method performed in numerous droplets. When evaluated with mock and clinical sputum samples, the microfluidics-based enrichment device and emulsion-based whole-genome amplification (MEEA) procedure efficiently removes host cells, amplifies the microbial genome, and shows no obvious bias among microbes. The efficiency of MEEA makes it a promising method in research of respiratory microbial communities and their roles in diseases.
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Affiliation(s)
- Xing Shi
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, People's Republic of China
| | - Changjun Shao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, People's Republic of China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Yanan Chu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Qingren Meng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, People's Republic of China
| | - Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
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21
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Zakrzewski M, Simms LA, Brown A, Appleyard M, Irwin J, Waddell N, Radford-Smith GL. IL23R-Protective Coding Variant Promotes Beneficial Bacteria and Diversity in the Ileal Microbiome in Healthy Individuals Without Inflammatory Bowel Disease. J Crohns Colitis 2019; 13:451-461. [PMID: 30445599 DOI: 10.1093/ecco-jcc/jjy188] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND AIMS This study aimed to characterize the mucosa-associated microbiota in ileal Crohn's disease [CD] patients and in healthy controls in terms of host genotype and inflammation status. METHODS The mucosa-associated microbiotas of intestinal pinch biopsies from 15 ileal CD patients with mild and moderate disease and from 58 healthy controls were analysed based on 16S ribosomal sequencing to determine microbial profile differences between [1] IL23R, NOD2 and ATG16L1 genotypes in healthy subjects, [2] ileal CD patients and control subjects, and [3] inflamed and non-inflamed mucosal tissue in CD patients. RESULTS The protective variant of the IL23R gene [rs11209026] significantly impacted the microbial composition in the ileum of healthy subjects and was associated with an increased abundance of phylotypes within the family Christensenellaceae as well as increases in diversity and richness. Comparative analysis of healthy and non-inflamed CD microbiome samples indicated a notable decrease in the abundance of Faecalibacterium prausnitzii as well as Shannon diversity and richness. Inflamed and non-inflamed ileal samples of CD subjects had high intra-individual stability and inter-individual variability, but no significant alterations in diversity, richness or taxa were identified. Calprotectin correlated positively with the abundance of Proteobacteria and negatively with diversity in the samples from healthy subjects. CONCLUSIONS The observation of low diversity and low abundance of beneficial bacteria in healthy control subjects carrying the IL23R [rs11209026] wild-type GG genotype indicates that the gut microbiome is influenced by host genetics and is altered prior to disease diagnosis. Faecal calprotectin may be a potential non-invasive screening tool for dysbiosis in subjects without disorders of intestinal inflammation.
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Affiliation(s)
- Martha Zakrzewski
- Medical Genomics, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia
| | - Lisa A Simms
- Gut Health, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia
| | - Allison Brown
- Gut Health, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia.,Department of Gastroenterology and Hepatology, Royal Brisbane and Women's Hospital, Herston, Brisbane 4029, Australia
| | - Mark Appleyard
- Department of Gastroenterology and Hepatology, Royal Brisbane and Women's Hospital, Herston, Brisbane 4029, Australia
| | - James Irwin
- Gut Health, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia.,Department of Gastroenterology, Palmerston North Hospital, Palmerston North, New Zealand
| | - Nicola Waddell
- Medical Genomics, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia
| | - Graham L Radford-Smith
- Gut Health, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia.,Department of Gastroenterology and Hepatology, Royal Brisbane and Women's Hospital, Herston, Brisbane 4029, Australia.,University of Queensland School of Medicine, Herston, Brisbane 4029, Australia
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22
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Zhang R, Chen L, Cao L, Li KJ, Huang Y, Luan XQ, Li G. Effects of smoking on the lower respiratory tract microbiome in mice. Respir Res 2018; 19:253. [PMID: 30547792 PMCID: PMC6295055 DOI: 10.1186/s12931-018-0959-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 11/30/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Recent studies break with traditional opinion that the lower respiratory tract is sterile, and increasingly focus on the lung microbiome and disease. Smoking, as an important etiology of inflammatory lung disease, was considered as a factor influencing lung microbiome variations in our study, and we aimed to study the effect of smoking on inflammation and microbial diversity and community. METHODS Forty male mice were selected and randomly divided into a smoking and a non-smoking group. Mice in the smoking group were exposed to smoke smog for 2 h/day for 90 days. Blood and lung tissues were obtained after the experiment, and ELISA was used to measure interleukin-6 and C reactive protein concentrations. 16S rRNA gene quantification and sequencing technology were used to compare microbial diversity and community between the two groups. SAS 9.1 and R software were used to analyze the data. RESULTS Thirty-six mice survived, and the weight of the smoking group increased more slowly than that of the non-smoking group. Denser inflammation and congestion were observed in the lungs of the smoking mice compared with the non-smoking group Higher microbial diversity was observed in the smoking group, and Enterobacter, Acidimicrobiales_norank, and Caulobacteraceae_Unclassified genus were significantly more abundant in the non-smoking group (P < 0.001). CONCLUSIONS Smoking altered microbial diversities and communities in the lower respiratory tract of mice. Microbial variation should be considered in future studies focusing on smoking-induced inflammatory disease.
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Affiliation(s)
- Rui Zhang
- Research Center for Medicine and Social Development, Collaborative Innovation Center of Social Risks Governance in Health, School of Public Health and Management, Chongqing Medical University, Chongqing, 400016 China
| | - Ling Chen
- The Center of Experimental Teaching Management, Chongqing Medical University, Chongqing, 401331 China
| | - Lei Cao
- Research Center for Medicine and Social Development, Collaborative Innovation Center of Social Risks Governance in Health, School of Public Health and Management, Chongqing Medical University, Chongqing, 400016 China
| | - Kang-jie Li
- Research Center for Medicine and Social Development, Collaborative Innovation Center of Social Risks Governance in Health, School of Public Health and Management, Chongqing Medical University, Chongqing, 400016 China
| | - Yao Huang
- First Clinical College, Chongqing Medical University, Chongqing, 400016 China
| | - Xiao-qian Luan
- Research Center for Medicine and Social Development, Collaborative Innovation Center of Social Risks Governance in Health, School of Public Health and Management, Chongqing Medical University, Chongqing, 400016 China
| | - Ge Li
- The Center of Experimental Teaching Management, Chongqing Medical University, Chongqing, 401331 China
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23
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Su YC, Jalalvand F, Thegerström J, Riesbeck K. The Interplay Between Immune Response and Bacterial Infection in COPD: Focus Upon Non-typeable Haemophilus influenzae. Front Immunol 2018; 9:2530. [PMID: 30455693 PMCID: PMC6230626 DOI: 10.3389/fimmu.2018.02530] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/15/2018] [Indexed: 12/12/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a debilitating respiratory disease and one of the leading causes of morbidity and mortality worldwide. It is characterized by persistent respiratory symptoms and airflow limitation due to abnormalities in the lower airway following consistent exposure to noxious particles or gases. Acute exacerbations of COPD (AECOPD) are characterized by increased cough, purulent sputum production, and dyspnea. The AECOPD is mostly associated with infection caused by common cold viruses or bacteria, or co-infections. Chronic and persistent infection by non-typeable Haemophilus influenzae (NTHi), a Gram-negative coccobacillus, contributes to almost half of the infective exacerbations caused by bacteria. This is supported by reports that NTHi is commonly isolated in the sputum from COPD patients during exacerbations. Persistent colonization of NTHi in the lower airway requires a plethora of phenotypic adaptation and virulent mechanisms that are developed over time to cope with changing environmental pressures in the airway such as host immuno-inflammatory response. Chronic inhalation of noxious irritants in COPD causes a changed balance in the lung microbiome, abnormal inflammatory response, and an impaired airway immune system. These conditions significantly provide an opportunistic platform for NTHi colonization and infection resulting in a "vicious circle." Episodes of large inflammation as the consequences of multiple interactions between airway immune cells and NTHi, accumulatively contribute to COPD exacerbations and may result in worsening of the clinical status. In this review, we discuss in detail the interplay and crosstalk between airway immune residents and NTHi, and their effect in AECOPD for better understanding of NTHi pathogenesis in COPD patients.
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Affiliation(s)
- Yu-Ching Su
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Farshid Jalalvand
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark
| | - John Thegerström
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
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24
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Yatera K, Noguchi S, Mukae H. The microbiome in the lower respiratory tract. Respir Investig 2018; 56:432-439. [PMID: 30392534 DOI: 10.1016/j.resinv.2018.08.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 12/31/2022]
Abstract
With the advent of new technologies evaluating the microbiome in the sample such as next-generation sequencer (NGS), current increase of an interest in understanding of the lung microbiome and its roles in lung diseases are marked. Gathering the data of bacterial flora in the lung and their changes during disease courses is unraveling the pathogenesis and the mechanism of disease progression particularly in patients with bronchial asthma, chronic obstructive pulmonary disease and infectious lung diseases. To clarify the relationship between the lung microbiome and pulmonary diseases, new information may help us to create new treatment and prevention strategies of some pulmonary diseases by controlling the lung microbiome. Using bacterial 16S ribosomal RNA gene sequence, NGS can rapidly estimate large amount of bacterial sequences in the phylum and genus levels, and some of them in species levels in a very short period of time. In addition to new information of the microbiome using NGS in the respiratory tract, other techniques using basically Sanger method in combination with the clone library construction can also be useful to identify pathogenic bacterial species with their ratio in the respiratory samples such as bacterial pneumonia, lung abscess and nontuberculous mycobacteriosis. These modalities to identify and semi-quantify bacterial burden in the respiratory tract have revealed new bacterial information in each infectious lung disease. This review describes current understanding of the lung microbiome in several representative lung diseases.
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Affiliation(s)
- Kazuhiro Yatera
- Department of Respiratory Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishiku, Kitakyushu City, Fukuoka, 807-8555, Japan.
| | - Shingo Noguchi
- Department of Respiratory Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishiku, Kitakyushu City, Fukuoka, 807-8555, Japan.
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Unit of Translational Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki City, Nagasaki, Japan.
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25
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González Del Castillo J, Candel FJ, de la Fuente J, Gordo F, Martín-Sánchez FJ, Menéndez R, Mujal A, Barberán J. [Integral approach to the acute exacerbation of chronic obstructive pulmonary disease]. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2018; 31:461-484. [PMID: 30284414 PMCID: PMC6194861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/04/2018] [Indexed: 11/12/2022]
Abstract
Chronic obstructive pulmonary disease is a set of clinical processes that have in common a chronic and progressive obstruction to airflow, with episodes of exacerbation. These exacerbations are more frequent and severe over time, deteriorating the lung function. The main cause of exacerbations is bacterial infection. There are multiple guidelines and documents that statement the management of this pathology. However, they focus primarily on the treatment during the stable phase. This document addresses the problem of acute exacerbation due to an infection from a multidisciplinary perspective, focusing on the integral approach to the process, and including etiology, microbiological studies, resistance to antimicrobials, risk stratification and initial empirical therapeutic management (antibiotic and concomitant). In addition, it includes an approach to more complex aspects such as the management of special populations (elderly and immunosuppressed) or therapeutic failure. Finally, more controversial topics such as prophylaxis of infection or palliative treatment are specifically discussed.
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Affiliation(s)
- J González Del Castillo
- Juan González del Castillo, Servicio de Urgencias. Hospital Clínico San Carlos. Calle Profesor Martín-Lagos s/n, 28040 Madrid. Spain.
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Aghapour M, Raee P, Moghaddam SJ, Hiemstra PS, Heijink IH. Airway Epithelial Barrier Dysfunction in Chronic Obstructive Pulmonary Disease: Role of Cigarette Smoke Exposure. Am J Respir Cell Mol Biol 2018; 58:157-169. [DOI: 10.1165/rcmb.2017-0200tr] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
| | - Pourya Raee
- Department of Basic Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Seyed Javad Moghaddam
- Department of Pulmonary Medicine, Division of Internal Medicine, the University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Pieter S. Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands; and
| | - Irene H. Heijink
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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Rohde GGU, Welte T. Pseudomonas-aeruginosa-Infektion bei chronisch obstruktiver Lungenerkrankung. Internist (Berl) 2017; 58:1142-1149. [DOI: 10.1007/s00108-017-0332-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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