Perspective on the clone library method for infectious diseases

Recently, culture-independent molecular methods, such as DNA sequencing techniques targeting the 16S-ribosomal RNA (rRNA) gene and/or other housekeeping genes with Sanger method-based technologies, next generation sequencing (NGS), and metagenomic analysis, have been developed for detecting microorganisms in the human body; these can provide information on microbiomes of samples from individuals with or without infectious diseases. Determining the bacterial species is crucial in identifying causative bacteria of upper and lower respiratory tract infections, especially for Streptococcus species, but NGS analysis is often not precise enough to identify bacteria at the species level. This review briefly introduces previous observations of the microbiome of samples from various respiratory and other infections assessed using the clone library method with Sanger sequencing of the 16S-rRNA gene. On analysis of 16S-rRNA gene-sequence data of bronchoalveolar lavage fluid obtained from pneumonia lesions in patients with bacterial pneumonia and lung abscess, anaerobes are often detected in non-elderly patients with pneumonia, and the detection rate of Staphylococcus aureus in patients with hospital-acquired pneumonia is lower than that previously reported. Analysis of pleural effusion samples from patients with pleurisy indicated a more important role of anaerobes than previous believed. The other topics reviewed include microbiomes of nontuberculous mycobacteriosis and lower respiratory tract infections in children with permanent tracheostomy due to neuromuscular disorders, in nasal discharge, in bacterial vaginosis, in the intracystic fluid of postoperative maxillary cyst, and in bacterial conjunctivitis; urine microbiota in urethritis; fecal microbiota; and newly detected infectious organisms in the human respiratory tract.     

慢性气道炎症性疾病的下呼吸道细菌负荷

近年来,由于慢性气道和肺部疾病患者生存率的提高、痰监测频率增加以及新的分子技术应用于微生物的鉴定,人们发现既往认为无菌的下呼吸道竟然寄居着大量微生物.这些微生物不仅出现在慢性气道和肺部疾病的急性加重期或急性发作期,稳定期甚至正常健康人群也可检测到.微生态多样性和构成的改变与某些慢性气道和肺部疾病密切相关.本文着重介绍COPD、支气管哮喘、支气管扩张症及特发性肺纤维化的菌群多样性及构成变化.     

下呼吸道微生态在支气管哮喘中的研究进展

随着二代测序的不断发展,过去人们认为无菌的下呼吸道现已被证实有多种不同的微生物群落定植.同时,越来越多的研究也证明,微生态在宿主免疫系统的发生发展中起着重要的作用.呼吸道微生态紊乱可能与多种呼吸道疾病密切相关,包括肺结核、COPD及支气管哮喘(简称哮喘)等.该研究主要回顾了近年来对哮喘患者及健康人群呼吸道微生态的研究,探讨在哮喘患者中呼吸道菌群定植的改变趋势,以及呼吸道微生态的改变与哮喘发病机制之间的关系,并且对呼吸道微生态在哮喘治疗中的研究进展进行讨论.     

COPD and the microbiome

Traditional culture techniques confirm that bacteria have an important role in Chronic Obstructive Pulmonary Disease (COPD). In individuals with COPD, acquisition of novel bacterial strains is associated with onset of acute exacerbation of COPD, which leads to further lung dysfunction and enormous health‐care costs. Recent study of the human microbiome, the total composite of the bacteria on the human body, posited the microbiome as the last human organ studied, as the microbiome performs a multitude of metabolic functions absent in the human genome. The largest project to study the human microbiome was the National Institutes of Health (NIH) human microbiome project (HMP) started in 2007 to understand the ‘normal’ microbiome. However due to the presumption that the healthy human lung was sterile, the respiratory tract was not included in that study. The advent of next‐generation sequencing technologies has allowed the investigation of the human respiratory microbiome, which revealed that the healthy lung does have a robust microbiome. Subsequent studies in individuals with COPD revealed that the microbiome composition fluctuates with severity of COPD, composition of the individual aero‐digestive tract microbiomes, age, during an acute exacerbation of COPD and with the use of steroids and/or antibiotics. Understanding the impact of the microbiome on COPD progression and risk of exacerbation will lead to directed therapies for prevention of COPD progression and exacerbation.     

Clinical role of bronchoalveolar lavage in adults with pulmonary disease

BAL remains a powerful investigative tool. In a short span of 20 yr, it has helped tremendously in understanding some of the aspects of the pathogenesis of diseases involving the lower respiratory tract. To realize its full potential in the diagnosis and management of diseases involving the lower respiratory tract, there is a great need for standardization of the technical aspects of BAL as well as processing and analysis of the BAL cellular- and fluid-phase components. Despite these hurdles, BAL has been found to be diagnostic in several infectious and noninfectious diseases involving the lower respiratory tract, and it provides valuable information that may be helpful in characterizing the prognosis and response to therapy in certain interstitial diseases of the lung. It is expected that with future research, in particular long-term prospective epidemiologic and clinical studies in pneumoconioses and in other interstitial lung disease, BAL will prove more valuable in the diagnosis and management of such disease.     

维生素D在肺部疾病中的作用

除了维持钙盐代谢和骨骼的稳态以外，研究发现维生素D还可调控包括机体防御，炎症，免疫，损伤修复等在内的多种生理和病理生理过程。流行病学资料表明，血清低水平的维生素D与肺功能受损、炎症反应和感染性疾病相关。因此，支气管哮喘、慢性阻塞性肺疾病和肺部感染性疾病都可能与维生素D水平有关，但具体的机制尚不明确。因此，本文通过文献回顾，概述维生素D在肺部疾病，包括支气管哮喘、慢性阻塞性肺疾病、肺结核和呼吸道感染中的作用。     

Microbiomes in respiratory health and disease: An Asia‐Pacific perspective

There is currently enormous interest in studying the role of the microbiome in health and disease. Microbiome's role is increasingly being applied to respiratory diseases, in particular COPD, asthma, cystic fibrosis and bronchiectasis. The changes in respiratory microbiomes that occur in these diseases and how they are modified by environmental challenges such as cigarette smoke, air pollution and infection are being elucidated. There is also emerging evidence that gut microbiomes play a role in lung diseases through the modulation of systemic immune responses and can be modified by diet and antibiotic treatment. There are issues that are particular to the Asia‐Pacific region involving diet and prevalence of specific respiratory diseases. Each of these issues is further complicated by the effects of ageing. The challenges now are to elucidate the cause and effect relationships between changes in microbiomes and respiratory diseases and how to translate these into new treatments and clinical care. Here we review the current understanding and progression in these areas.     

Microbiome in the primary prevention of allergic diseases and bronchial asthma

Tremendous progress in the ability to identify and test the function of microorganisms in recent years has led to a much better understanding of the role of environmental and host microbiome in the development of immune function, allergic sensitization and asthma. In this review, the most recent findings on the relationships between environmental microbiota, respiratory, intestinal microbiome, the consequences of early-life microbial exposure type and gut–lung microbial axis and the development of asthma and atopy are summarized. The current perspective on gut and airway microbiome manipulation for the primary prevention of allergic diseases and asthma is also discussed.     

The effect of common pharmacologic agents on pulmonary antibacterial defenses: implications for the geriatric patient

Clinical and laboratory observations have raised the possibility that common pharmacologic agents disrupt lung host defense and predispose to bacterial infection of the lower respiratory tract. Epidemiologic data suggest that the potential for an impairment in pulmonary antibacterial mechanisms is greatest among individuals of advanced age. However, lung antimicrobial systems are extremely complex, and patients with pulmonary infections characteristically have a variety of predisposing conditions. Thus, it remains very difficult to assess the relative impact of drug-related derangements on lung antimicrobial systems. Indeed, it is likely that multiple intrinsic and extrinsic factors contribute to the evolution of most bacterial pneumonias. Thus, while medications may not represent major risk factors, they may act in an additive or synergistic manner with other predisposing conditions, such as age-associated changes in immunologic activity and underlying disease, to enhance susceptibility to infectious illnesses of the lung. Clearly, substantial clinical and laboratory study will be required in order to define the role that common pharmacologic agents play in predisposing to bacterial infection of the lower respiratory tract.     

Advancing respiratory research

Respiratory diseases remain a major public health problem in the United States and worldwide, with increasing morbidity and mortality. Substantial progress has been made to advance understanding of the basic mechanisms of lung disease and to optimize clinical management of patients with a range of respiratory diseases. Despite this progress, our knowledge of how to predict disease prior to symptoms, improve disease definition and subclassification, and target novel and new treatments in a more personalized manner still remains inadequate. This article highlights several future opportunities and challenges related to genomics and molecular characterization of lung disease, lung injury and repair, translational lung research, the microbiome, and sleep and circadian biology as potential frontiers to advance progress in respiratory biology in health and disease.     

Clin-STAR corner: Recent practice-changing studies at the interface of pulmonary and critical care medicine and geriatrics

Older adults suffering from chronic pulmonary diseases, such as chronic obstructive pulmonary disease and interstitial lung disease, and critical illnesses, such as sepsis and acute respiratory failure, are more vulnerable to adverse outcomes like disability and greater side effects from treatments. In this update, we discuss recent practice-changing clinical trials and observational studies in Pulmonary & Critical Care Medicine that have advanced our understanding of the diagnosis or management of older adults with chronic lung diseases or critical illnesses.     

Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children

Diarrheal diseases remain the second most common cause of mortality in young children in developing countries. Efforts have been made to explore the impact of diarrhea on bacterial communities in the human gut, but a thorough understanding has been impeded by inadequate resolution in bacterial identification and the examination of only few etiological agents. Here, by profiling an extended region of the 16S rRNA gene in the fecal microbiome, we aimed to elucidate the nature of gut microbiome perturbations during the early phase of infectious diarrhea caused by various etiological agents in Vietnamese children. Fecal samples from 145 diarrheal cases with a confirmed infectious etiology before antimicrobial therapy and 54 control subjects were analyzed. We found that the diarrheal fecal microbiota could be robustly categorized into 4 microbial configurations that either generally resembled or were highly divergent from a healthy state. Factors such as age, nutritional status, breastfeeding, and the etiology of the infection were significantly associated with these microbial community structures. We observed a consistent elevation of Fusobacterium mortiferum, Escherichia, and oral microorganisms in all diarrheal fecal microbiome configurations, proposing similar mechanistic interactions, even in the absence of global dysbiosis. We additionally found that Bifidobacterium pseudocatenulatum was significantly depleted during dysenteric diarrhea regardless of the etiological agent, suggesting that further investigations into the use of this species as a dysentery-orientated probiotic therapy are warranted. Our findings contribute to the understanding of the complex influence of infectious diarrhea on gut microbiome and identify new opportunities for therapeutic interventions.     

Viral and Bacterial Co-Infections in the Lungs: Dangerous Liaisons

Respiratory tract infections constitute a significant public health problem, with a therapeutic arsenal that remains relatively limited and that is threatened by the emergence of antiviral and/or antibiotic resistance. Viral–bacterial co-infections are very often associated with the severity of these respiratory infections and have been explored mainly in the context of bacterial superinfections following primary influenza infection. This review summarizes our current knowledge of the mechanisms underlying these co-infections between respiratory viruses (influenza viruses, RSV, and SARS-CoV-2) and bacteria, at both the physiological and immunological levels. This review also explores the importance of the microbiome and the pathological context in the evolution of these respiratory tract co-infections and presents the different in vitro and in vivo experimental models available. A better understanding of the complex functional interactions between viruses/bacteria and host cells will allow the development of new, specific, and more effective diagnostic and therapeutic approaches.     

The biology of a chronic obstructive pulmonary disease exacerbation

Much of the morbidity and mortality in chronic obstructive pulmonary disease relates to symptomatic deteriorations in respiratory health termed exacerbations. Exacerbations also are associated with changes in lung function and both airway and systemic inflammation. The most common causes of exacerbation are micro-organisms: respiratory viruses such as rhinovirus, and various bacterial species. This article reviews and discusses current understanding of the biology of exacerbations, considering the definition, epidemiology, etiology, and the nature and evolution of the changes in symptoms, lung function, and inflammation that characterize these important events.     

The contribution of respiratory microbiome analysis to a treatable traits model of care

The composition of the airway microbiome in patients with chronic airway diseases, such as severe asthma, chronic obstructive pulmonary disease (COPD), bronchiectasis and cystic fibrosis (CF), has the potential to inform a precision model of clinical care. Patients with these conditions share overlapping disease characteristics, including airway inflammation and airflow limitation. The clinical management of chronic respiratory conditions is increasingly moving away from a one‐size‐fits‐all model based on primary diagnosis, towards care targeting individual disease traits, and is particularly useful for subgroups of patients who respond poorly to conventional therapies. Respiratory microbiome analysis is an important potential contributor to such a ‘treatable traits’ approach, providing insight into both microbial drivers of airways disease, and the selective characteristics of the changing lower airway environment. We explore the potential to integrate respiratory microbiome analysis into a treatable traits model of clinical care and provide a practical guide to the application and clinical interpretation of respiratory microbiome analysis.     

非结核分枝杆菌肺病需要更多关注

非结核分枝杆菌肺病(NTM-PD)是最常见的非结核分枝杆菌感染性疾病,但误诊率高.近年来的研究报道显示,NTM-PD发病率和患病率都呈现逐渐上升趋势.NTM-PD症状和体征无特异性.CT检查主要表现肺部支气管扩张、结节、空洞和实变,常常多种CT表现形式同时存在.由于非结核分枝杆菌在自然界中普遍存在,易污染标本和定植在人...     

介入呼吸病学年度进展（2015-2016）

介入呼吸病学是现代呼吸病学的一个分支,在呼吸系统疾病的诊断和治疗方面发挥着越来越重要的作用。随着科学技术的发展,新的介入诊疗方法已经逐渐应用于一些传统疾病,如COPD、支气管哮喘、恶性肿瘤等。介入呼吸病学逐渐发展为一个成熟的亚专科,其对呼吸系统疾病的诊断范围和治疗有效性也跃上一个新的台阶。本文就2015-2016年介入呼吸病学在呼吸系统疾病临床诊疗方面的新进展和最新研究成果作一综述。     

Acute exacerbation of COPD

The literature of acute exacerbation of chronic obstructive pulmonary disease (COPD) is fast expanding. This review focuses on several aspects of acute exacerbation of COPD (AECOPD) including epidemiology, diagnosis and management. COPD poses a major health and economic burden in the Asia‐Pacific region, as it does worldwide. Triggering factors of AECOPD include infectious (bacteria and viruses) and environmental (air pollution and meteorological effect) factors. Disruption in the dynamic balance between the ‘pathogens’ (viral and bacterial) and the normal bacterial communities that constitute the lung microbiome likely contributes to the risk of exacerbations. The diagnostic approach to AECOPD varies based on the clinical setting and severity of the exacerbation. After history and examination, a number of investigations may be useful, including oximetry, sputum culture, chest X‐ray and blood tests for inflammatory markers. Arterial blood gases should be considered in severe exacerbations, to characterize respiratory failure. Depending on the severity, the acute management of AECOPD involves use of bronchodilators, steroids, antibiotics, oxygen and noninvasive ventilation. Hospitalization may be required, for severe exacerbations. Nonpharmacological interventions including disease‐specific self‐management, pulmonary rehabilitation, early medical follow‐up, home visits by respiratory health workers, integrated programmes and telehealth‐assisted hospital at home have been studied during hospitalization and shortly after discharge in patients who have had a recent AECOPD. Pharmacological approaches to reducing risk of future exacerbations include long‐acting bronchodilators, inhaled steroids, mucolytics, vaccinations and long‐term macrolides. Further studies are needed to assess the cost‐effectiveness of these interventions in preventing COPD exacerbations.     

Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance

Epidemic respiratory infections are responsible for extensive morbidity and mortality within both military and civilian populations. We describe a high-throughput method to simultaneously identify and genotype species of bacteria from complex mixtures in respiratory samples. The process uses electrospray ionization mass spectrometry and base composition analysis of PCR amplification products from highly conserved genomic regions to identify and determine the relative quantity of pathogenic bacteria present in the sample. High-resolution genotyping of specific species is achieved by using additional primers targeted to highly variable regions of specific bacterial genomes. This method was used to examine samples taken from military recruits during respiratory disease outbreaks and for follow up surveillance at several military training facilities. Analysis of respiratory samples revealed high concentrations of pathogenic respiratory species, including Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pyogenes. When S. pyogenes was identified in samples from the epidemic site, the identical genotype was found in almost all recruits. This analysis method will provide information fundamental to understanding the polymicrobial nature of explosive epidemics of respiratory disease.     

Bronchoalveolar lavage in patients with connective tissue disease.

Bronchoalveolar lavage (BAL) allows the recovery of cellular and fluid constituents that are derived from the epithelial surface of the lower respiratory tract. BAL fluid and cell analysis has become an important tool for understanding human pulmonary disease. Changes in the quantities and patterns of BAL cells and secretions have been described in a number of chronic lung disorders, especially the diffuse interstitial lung diseases. Specific BAL alterations have correlated with patient outcome and response to therapy. The connective tissue diseases have been associated with serious pleural and/or pulmonary pathology and may be a major cause of morbidity and mortality. BAL appears to be a useful semi-invasive tool in the evaluation and management of lung disease in patients with connective tissue diseases. The article describes the BAL findings in various connective tissue diseases and assesses the usefulness of BAL in the clinical management of patients with pulmonary complications.