key: cord-0728229-qq58cvjo
authors: Leung, Janice M.; Tiew, Pei Yee; Mac Aogáin, Micheál; Budden, Kurtis F.; Yong, Valerie Fei Lee; Thomas, Sangeeta S.; Pethe, Kevin; Hansbro, Philip M.; Chotirmall, Sanjay H.
title: The role of acute and chronic respiratory colonization and infections in the pathogenesis of COPD
date: 2017-03-25
journal: Respirology
DOI: 10.1111/resp.13032
sha: a353e7728d1b05982990fd47bab435332c515b07
doc_id: 728229
cord_uid: qq58cvjo

COPD is a major global concern, increasingly so in the context of ageing populations. The role of infections in disease pathogenesis and progression is known to be important, yet the mechanisms involved remain to be fully elucidated. While COPD pathogens such as Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pneumoniae are strongly associated with acute exacerbations of COPD (AECOPD), the clinical relevance of these pathogens in stable COPD patients remains unclear. Immune responses in stable and colonized COPD patients are comparable to those detected in AECOPD, supporting a role for chronic colonization in COPD pathogenesis through perpetuation of deleterious immune responses. Advances in molecular diagnostics and metagenomics now allow the assessment of microbe–COPD interactions with unprecedented personalization and precision, revealing changes in microbiota associated with the COPD disease state. As microbial changes associated with AECOPD, disease severity and therapeutic intervention become apparent, a renewed focus has been placed on the microbiology of COPD and the characterization of the lung microbiome in both its acute and chronic states. Characterization of bacterial, viral and fungal microbiota as part of the lung microbiome has the potential to reveal previously unrecognized prognostic markers of COPD that predict disease outcome or infection susceptibility. Addressing such knowledge gaps will ultimately lead to a more complete understanding of the microbe–host interplay in COPD. This will permit clearer distinctions between acute and chronic infections and more granular patient stratification that will enable better management of these features and of COPD.

The role of microbes and infection in obstructive lung disease was first proposed in the 1950s by the British hypothesis. This states that recurrent infection and mucus hypersecretion were the primary causes of progressive airways obstruction in smokers. However, subsequent studies failed to detect significant associations between infection and lung function decline and consequently exposure to noxious particles and gases was advanced as the principal cause of COPD. 1 A wealth of evidence shows that the isolation of bacteria, viruses and fungi in the airways of stable COPD patients is in fact significant and has implications for disease pathogenesis, progression and treatment. This places a renewed emphasis on microorganisms isolated from the COPD lung, driving us to revisit the original British hypothesis. 2 Advances in diagnostic technologies now permit a more accurate detection of specific pathogens in COPD while molecular studies shed light on the immune response elicited by COPD-associated microorganisms. Metagenomic studies have revealed microbial consortia in both healthy and diseased individuals, helping to define pathogenic and beneficial microbes associated with various disease states. This has major implications for our understanding of COPD and its therapy, particularly in the face of antibiotic-mediated lung dysbiosis during therapy. Therefore, both acute and chronic infections are linked to COPD progression and exist as components of overarching lung microbiome architecture, which is modulated during therapeutic intervention. Characterizing this dynamic interaction between microbes, therapy and disease states is now a central focus in COPD research. Furthermore, the emergence of antibiotic resistance in COPD-associated pathogens is also a growing international concern and greater emphasis on antimicrobial stewardship and rational therapies is of increasing importance. Ultimately, the role of microbes and infection in COPD may reveal novel prognostic markers of disease which in turn provide scope for more focused interventions and novel therapeutic approaches.

Periodic worsening of respiratory symptoms in patients with COPD is known as acute exacerbations (AECOPD). They can have marked effects on lung function, quality of life and health socio-economic burden. The exact nature and cause of these events can often be difficult to establish clinically, but in general infections are largely blamed, with up to 80% of AECOPD linked to either bacterial or viral pathogens. 3, 4 Because a certain subset of COPD patients have frequent exacerbations, the concept of inherent susceptibility to acute infection in COPD subsequently triggering AECOPD events has been developed. Several studies have now demonstrated that COPD patients feature impaired innate immunity, the first line of defence against infection. Alveolar macrophages resident in the airways provide the key initial response to bacteria by both recognizing and removing harmful pathogens through phagocytosis, but in COPD, these functions may be impaired. Recently, Berenson et al. investigated Toll-like receptor (TLR) expression and responses in alveolar macrophages collected from exacerbationprone and exacerbation-free COPD patients. 5 In response to exposure to common COPD-related pathogens including Moraxella catarrhalis, Streptococcus pneumoniae and Haemophilus influenzae, alveolar macrophages from exacerbation-prone patients had diminished TLR2 expression and cytokine responses. Similarly, alveolar macrophages from COPD patients appear to phagocytose H. influenzae and S. pneumonia poorly compared with those of control patients yet they still release reactive oxygen species (ROS). 6, 7 Together, these studies suggest that COPD patients have impaired responses to bacterial colonization and infection which in turn increases susceptibility to AECOPD and promotes an oxidative stress response (Fig. 1) .

Defects in innate immunity may also play a role in increased susceptibility to viruses. Recognition of viral infection by the innate immune system is essential for coordinating an effective antiviral response in the airways, yet in patients and mice with COPD, the cascade from recognition to response falters. This involves increases in phosphatidylinositol 3-kinase responses and impaired antiviral stress granule formation including type I interferon (IFN) signalling. 8 In the healthy host, pathogen recognition by TLR3 triggers IFN pathways that then can hinder viral replication and mediate adaptive immune responses. In epithelial cells, constitutive type 1 IFNs are critical for protection. 9, 10 In these cells and lung fibroblasts exposed to cigarette smoke, responses are reduced and even stimulation with IFN-β yields a diminished antiviral response. 11 Furthermore, mucociliary clearance, which is key for the removal of virus from the airways, appears to be perturbed in COPD. Cigarette smoke exposure reduces both the number and length of cilia, 12 while goblet cell hyperplasia in COPD leads to more viscous mucus in the airways, further impeding proper ciliary motion. 13 In mouse models, respiratory viruses themselves can induce mucus hypersecretion, contributing to the inability to clear the virus from the airway. 14 Of the 80% of exacerbations with an infectious cause, approximately half are bacterial in origin while approximately 30% are viral. 4, 15 Numerous studies have been performed to classify the most common pathogens implicated in AECOPD using sputum samples to identify bacteria and nasopharyngeal swabs to identify viruses. In a landmark 2002 study, Sethi et al. traced longitudinal sputum cultures in 81 moderate-to-severe COPD patients during both times of clinical stability and exacerbation. 16 Interestingly, the acquisition of a new strain of bacteria (discovered through molecular typing) was highly associated with the development of an AECOPD. The relative risk of an exacerbation varied with each new species: 1.69 for H. influenzae, 1.77 for S. pneumoniae and 2.96 for M. catarrhalis. Since then, more sensitive quantitative PCR methods of identifying bacteria relative to standard culture methods have enabled better quantification and typing of bacterial strains during exacerbations. In one study, while species such as H. influenzae and S. pneumonia were identified in stable states, their relative loads, determined by PCR, were considerably higher during exacerbations (10 8 cfu/mL vs 10 7 cfu/mL for both species). 17 The most prevalent species identified during exacerbation was S. pneumoniae, followed by H. influenzae, M. catarrhalis and Legionella pneumophila. In more severe COPD patients (forced expiratory volume in 1 s (FEV 1 ) < 50% predicted), Pseudomonas aeruginosa was also frequently encountered as a cause of exacerbations (Table 1) . 24 Pseudomonas aeruginosa infections appear to portend a worse prognosis with higher 30-and 90day mortality rates compared with exacerbations not associated with this bacterium. 25 Viruses implicated in the development of AECOPD include respiratory syncytial virus (RSV), rhinovirus, human metapneumovirus, influenza, parainfluenza, adenovirus and coronavirus. [33] [34] [35] A meta-analysis of 19 studies (totalling 1728 patients) evaluated the pooled prevalence of respiratory viruses in AECOPD and found that rhinoviruses/enteroviruses were the most commonly encountered virus (16%), followed by RSV (10%) and influenza (8%). Of lesser prevalence were coronaviruses (4%), parainfluenza (3%), human metapneumovirus (3%) and adenovirus (2%). 28 Coinfection with two or more viruses has also been reported, 36 with one study noting that in their cohort, only the patients with viral co-infections were severe enough to be admitted to the hospital for their exacerbations. 34 While simultaneous bacterial and viral pathogens have been detected during acute exacerbations, it remains unclear whether these co-infections carry any greater risk for poor outcomes in comparison to single infections. 37 They indeed may simply represent more severe disease as other studies have detected. 38, 39 More compelling is the notion of 'superinfection', where an acute viral infection in COPD may set up the necessary microenvironment in the lung for a subsequent bacterial infection or vice versa. In an experimental rhinovirus infection, where COPD and control patients were nasally inoculated with low doses of rhinovirus, only COPD patients developed significant increases in sputum bacterial load post-viral infection. 40 While sputum viral loads peaked between days 5 and 9 post-inoculation, bacterial loads peaked later around day 15, confirming that in these studies viral infection can promote bacterial superinfection. Subjects who ultimately developed secondary bacterial infections had lower baseline FEV 1 compared with those who remained free from secondary infections. A plausible mechanism was suggested whereby rhinovirus infection induces neutrophil elastase (NE) production, which then degrades the antimicrobial peptides elafin and secretory leukoprotease inhibitor, both of which may be important in protecting subjects from bacterial infections. 40 These data suggest that AECOPD events thought to be bacterially induced may in fact have been preceded by an initial viral infection. Moreover, greater vigilance for superinfections in patients with more severe lung function may be warranted.

Microorganisms are commonly detected in the airways in stable COPD and are considered 'colonizers' in the absence of acute infective symptoms (Table 1) . However, the term colonization in this context may be debated, as the microorganisms identified in stable COPD are not necessarily benign. Collective evidence favours the vicious cycle hypothesis whereby an inciting event (e.g. smoking) leads to an impaired innate immune response and results in bacterial colonization. 41 This in turn promotes airway and systemic inflammation leading to COPD progression. As airway inflammation persists despite smoking cessation, the presence of a persistent stimulus-independent of cigarette smoke-is consistent with a role for colonizing bacteria in the pathogenesis of COPD. 42, 43 Recognition of pathogen-associated molecular patterns (PAMPs), by pattern recognition receptors (PRRs) expressed on epithelial and innate immune cells, activates signal transduction pathways including nuclear factor kappa-B (NF-κB), p38 mitogen-activated protein kinases, phosphoinositide-3-kinase and IFN regulatory factors. 44 This results in the production of proinflammatory mediators such as cytokines and chemokines. In turn, the recruitment of neutrophils to the airways ensues, a feature characteristic of bacterially colonized COPD patients. 45 Neutrophils are antiinfective and have recently been found to have modulatory functions. 46 In COPD, neutrophils are intrinsically altered with abnormal host defence functions and have unusual chemotactic behaviour and migratory structure. 47 Activated neutrophils cause lung destruction and emphysematous change through the release of oxygen radicals and proteolytic enzymes, including NE that reduces ciliary function, induces epithelial damage and is a potent stimulator of mucin production. 47 The resulting mucus production and impaired mucociliary clearance leads to further bacterial colonization and airway obstruction. Additionally, increased levels of airway inflammatory markers such as IL-6, IL-8, IL-1β, TNF-α, leukotriene B4 (LTB4), matrix metalloproteinase (MMP), myeloperoxidase (MPO) and NE are found in stable COPD patients with bacterial colonization compared with those without bacterial colonization, strongly implicating the colonized state with a deleterious immune response. 45, 47 Such persistent inflammation is associated with increased daily symptoms, exacerbations and mortality. 48, 49 Defective phagocytosis is also characteristic of COPD particularly that of alveolar-and monocyte-derived macrophages, which in turn likely contributes to chronic bacterial colonization and infective exacerbations. 6 This is clearly evidenced by the observed impaired phagocytosis of H. influenzae and M. catarrhalis with increasing COPD severity. 50 In addition, alveolar macrophage surface receptors (TLR2, TLR4 and scavenger receptor (MARCO)) that respond to intracellular signalling and phagocytosis are seen to be diminished in both COPD and smokers. [51] [52] [53] Chronic bacterial colonization also activates adaptive immune responses, with the development of B-cell lymphoid follicles and production of mucosal IgA and serum IgG antibody including strainspecific IgG antibody against bacterial colonizers, a phenomenon characteristic of the COPD airway. 54 Increases in lymphoid follicles have been noted in the small airways of patients with severe COPD, possibly secondary to chronic airway infection. 55 Thus, impaired innate immune responses likely contribute to microbial airway colonization while the activation of adaptive immunity suggests a state of heightened immune surveillance associated with lung function decline in established COPD.

Potentially pathogenic microorganisms (PPMs) have been isolated in up to 74% of stable COPD patients. 56 The commonest PPMs identified include H. influenzae, M. catarrhalis, S. pneumonia, P. aeruginosa and Chlamydophila pneumoniae similar to the culprit repertoire in AECOPD and severe asthma. 57 Bacterial colonization is, however, a dynamic process with alterations in pathogen type, load and strain over time. Increases in bacterial load and changes in species are associated with greater lung function decline and airway inflammation. 18, 19 Non-typeable H. influenzae (NTHi) is the most common bacteria isolated in both the stable state and during AECOPD. It alone accounts for up to half of all bacteria isolated in the lower airways of stable COPD patients. 17, 18, 20 The differing cell surface proteins facilitate bacterial adhesion to the respiratory mucosa including outer membrane proteins P2 and P5 that bind to mucin, and adhesin (HMW1 and HMW2) which adhere to the epithelial and extracellular matrix. [58] [59] [60] Lipooligosaccharide, a key component of the NTHi cell wall, and the outer membrane protein P6 are potent immunomodulators for macrophages leading to increased phagocytosis and cytokine secretion, including IL-8 and TNF-α which drive neutrophil recruitment. [60] [61] [62] [63] Given the defective phagocytic ability of the COPD alveolar macrophage, a failure of bacterial clearance potentially leads to the state of persistent infection. 6,63 Furthermore, NTHi is uniquely able to survive intracellularly within the alveolar macrophages. 64 Through its secreted proteases, it cleaves IgA and in turn protects against IgA-mediated cytotoxicity. 65 Where persistent, COPD NTHi infection of the lower airway results in increased inflammation with elevated levels of IL-8, IL-1β, MPO, TNF-α and MMP-9 detectable in patient samples. 19, 66 Critically, the organisms' immunoevasive ability causes chronic airway inflammation which in turn correlates with poorer health status and lung function. 67, 68 Moraxella catarrhalis, the second most prevalent colonizing organism in stable COPD (seen in 2-22.5%), has been shown in previous studies to be linked to a heightened airway inflammation (IL-8, TNF-α and NE). 18, 22, 69 In contrast to NTHi, 70 this bacterium is cleared after a relatively short colonization period and the development of immune responses that are protective against the homologous strain. 54 Streptococcus pneumoniae is another important bacterial organism (7.5-17%) in stable COPD. 22 Its polysaccharide capsule reduces the effectiveness of host defence mechanisms, which normally cause its clearance, leading to its airway persistence and colonization. In turn, this is associated with increased exacerbations, emphysema, lower diffusion capacity and pneumonia. 71 The role of P. aeruginosa in COPD pathogenesis is underscored by its frequent isolation in patients with more severe disease. 67, 72 Two types of Pseudomonasrelated infection are described in the COPD setting: short-term colonization followed by clearance and long-term persistent colonization. 73 Risk factors for Pseudomonas isolation in COPD include bronchiectasis, antibiotic exposure, previous hospitalization, steroid use and worse BODE index. 72 The mucoid phenotype is most likely to cause persistent colonization and, amongst P. aeruginosa-positive COPD patients, there is a significant association between colonization and disease severity. 73 Despite this, a nested case-control study comparing mortality showed no difference in relation to Pseudomonas status in stable COPD; however, in AECOPD, recent work has reaffirmed this organism's association with higher COPD mortality rates. 25, 74 Finally, chronic C. pneumoniae infection in COPD has been brought to light by a number of observational studies. Through its induction of a cytokine response (TNF-α, IL-1β, IL-6 and IFN-α), airway inflammation and critical airway remodelling ensue. Prevalence varies widely (0-65%) likely attributable to the lack of samples collected, standardization in applied microbiological methodology and lack of diagnostic testing in routine use. 26, 75 Despite this, serum C. pneumoniae-specific IgG and IgA antibody levels are found in higher titres in COPD when compared with a control group. Furthermore, a statistically significant association between chronic C. pneumoniae infection and COPD has been established. 76 Employing combinations of both PCR and serological testing reveal that chronic C. pneumoniae infection is associated with more severe COPD, faster lung function declines and, importantly, exacerbations. 26 These relationships however are not clear cut as a separate study of 110 COPD patients showed no association between Chlamydia and either COPD exacerbation frequency or FEV 1 . 77 In this latter study, IgG titres were used to define chronic C. pneumoniae infection which may explain the observed disparity. Furthermore, it is likely that Chlamydia resides in the lower respiratory tract and sampling needs to occur from this site. Standardization and validation of reproducible and robust diagnostic tests to clearly define C. pneumoniae infection in COPD are necessary and will likely clarify existing differences observed in our current evidence base.

Mycobacterial diseases, both non-tuberculous mycobacteria (NTM) and tuberculosis (TB), have long been associated with COPD, whether thought to be related to an inability to clear these chronic pathogens in the setting of structurally damaged lung or potentially the concurrent burden of bronchiectasis increasingly appreciated in COPD. 78 Studies of NTM in COPD cohorts have revealed that roughly one-fifth of COPD patients culture NTM in their sputum. 27, 79 Moreover, in 126 COPD patients undergoing lung volume reduction surgery, histological evidence of mycobacterial disease (necrotizing granulomas) occurred in 14 (11%) patients, 8 of whom had acid-fast bacilli (AFB)-positive stains. 80 Conversely, COPD appears to be a major co-morbidity in patients with NTM, with estimates of prevalence ranging from 24% to 79%. 81, 82 Not merely an innocent bystander, NTM infections in COPD portend a worse prognosis with more frequent exacerbations and a more rapid decline in FEV 1 . 79 However, long-term, prospective studies on the impact of NTM on COPD mortality and antimycobacterial treatment outcomes in COPD have yet to be performed.

The relationship between TB and COPD dates back to 1955 when Anno and Tomashefski first described airflow obstruction and air trapping in patients with TB. 83 Since then, the link between TB and COPD has largely focused on COPD as a sequela of TB infection, a risk that consistently appears to be independent of smoking histories. The proportion of COPD patients found to harbour a history of TB are listed in Table 2 , while worldwide estimates of the prevalence of airflow obstruction in cohorts of TB patients are listed in Table 3 . Patients with a history of TB carry anywhere from a 1.8 (worldwide estimate) to 8.9 (South Africa) times overall risk of developing COPD. 89, 93, 97, 100, 113 In particular, TB remains an important risk factor for COPD in non-smokers, with TB patients carrying an estimated 1.3-5.8 times the risk of developing COPD compared with those without TB. 94, 96, 101, 102 Likewise, COPD patients are at higher risk of developing TB. In Pakistan, for instance, 7.5% of COPD patients were found to have TB-positive sputum cultures. 114 Even in non-endemic regions, for example in Sweden, COPD patients carry a three times higher likelihood of developing active TB, conferring a twofold higher risk of death compared with COPD patients without TB. 115 Why TB may predispose individuals to COPD, and vice versa, is a matter of some speculation, as outlined in Figure 2 . Both conditions share a number of common risk factors, including cigarette smoking and biomass fuel exposure. In addition, the spread of HIV has 

The clinical significance of fungal infections in COPD is poorly understood and likely underestimated. Fungal colonization is observed in severe COPD patients. Whether such colonization is a marker of advanced COPD or contributes to disease progression remains to be studied. Aspergillus spp. are frequently isolated from the airways of COPD patients during exacerbations (16.6%) and even during follow-up (14.1%). 29, 116 In an observational study, positive Aspergillus cultures in COPD patients were associated with increased sputum cell counts. 117 The incidence of AECOPD in the preceding year and concomitant bacterial pathogen isolation were associated with increased Aspergillus detection. Positive Aspergillus cultures in COPD patients are associated with increased sputum neutrophils suggesting the presence of host immune response in relation to the organism. 117 Up to 8-15% of COPD patients have hypersensitivity to Aspergillus, with associated reduced lung function. 118, 119 Whether the use of antifungals may mitigate such declines in pulmonary function remains to be studied. Isolation of Aspergillus in the airway may represent temporary passage, benign carriage or be an early sign of invasive pulmonary aspergillosis (IPA), especially with high steroid use for recurrent exacerbations conferring host immunosuppression. Increasing evidence suggests that COPD patients are at risk of IPA with resulting high mortality rates; up to 22% of COPD patients with detection of Aspergillus in airway culture had IPA. 120 Innate immune responses play an important role in Aspergillus clearance mechanisms. Inhaled Aspergillus conidia bind to surface receptors within terminal airways via galactomannan, which enhance uptake by alveolar macrophages and dendritic cells leading to a cascade of immune responses. Recruitment of neutrophils and alveolar macrophages leads to ingestion, phagolysosomal degradation and killing of the fungal conidia. TLR2-and TLR4-dependent signals further contribute to host recognition and the inflammatory response to both Aspergillus conidia and hyphae. 121 Steroids therefore interfere with alveolar macrophage function, thereby increasing the risk of IPA through this and other defective innate immune responses in COPD including functionally abnormal neutrophils and TLRs. 122 Pneumocystis jirovecii is another opportunistic fungal pathogen of the COPD lung (8-85% of patients). [30] [31] [32] 123 Pneumocystis colonization is described in 36.7% of severe COPD patients (GOLD stage IV) compared with 5.3% of those with milder disease (GOLD stages 0-III). Colonization is associated with severe airflow obstruction independent of smoking. 30, 124 Increased systemic inflammation (IL-8, TNF-α and IL-6) 31,124 and proteases (MMP-12) responsible for parenchymal destruction and emphysema in COPD have been found in higher concentrations in COPD patients colonized with Pneumocystis. This suggests that the organism is unlikely an innocent bystander and may contribute to disease pathogenesis and progression. An upregulation of chemokine ligands (CXCL9, CXCL10 and CXCL11) of the CXCR3 receptor predominantly expressed on activated T-helper (Th) 1 lymphocytes is also observed and may prime Th1 inflammatory pathways contributing to the progression of COPD in these cases. 32

Although respiratory viruses are associated with asthma and COPD and cause acute cell damage, release of ROS and activation of NF-κB, their significance in stable COPD is less well understood (Table 1) . Adenovirus DNA is detectable in lung tissue of stable COPD patients and when compared with healthy smokers, a 5-40-fold increase in adenovirus early region 1A (E1A) expression is observed in patients with emphysema. 125, 126 In animal models, even latent adenovirus infection amplified the inflammatory responses (increased cluster of differentiation (CD) 8 cells, macrophages and neutrophils) and emphysematous destruction, 127 and increased IL-8 and intercellular adhesion molecule 1 (ICAM-1) expressions are also described in human epithelial cell transfection with adenovirus E1A genes. 128, 129 RSV is also common in stable COPD with prevalence rates of up to 33%. [130] [131] [132] An RNA virus of the Pararmyxoviridae family and a common cause of acute respiratory tract infections, its presence in stable COPD is unsurprisingly linked to higher levels of both airway and systemic inflammation. 130, 131 

There is an emerging role for the microbiome in both stable and during exacerbations of COPD that has been recently reviewed elsewhere. [133] [134] [135] [136] [137] [138] [139] [140] [141] While most research has focused on the bacteriome, viruses (virome) and fungi (mycobiome) are also important constituents of the microbiome. The respiratory tract contains genetic material from eukaryotic viruses such as anelloviruses, herpesviruses and papillomaviruses, as well as retroviruses that may establish persistent asymptomatic infections and bacteriophages, which dominate the virome. [142] [143] [144] [145] In the lung, the virome is highly variable between individuals and is strongly influenced by environmental conditions such as oxygen availability. 144 Unfortunately, in many studies, a large proportion of sequencing reads are not matched to a reference genome and it is unclear whether the identified viruses are commensal or a latent infection. Given these difficulties, it is challenging to directly compare the entire virome in COPD patients and healthy subjects. Nevertheless, COPD patients have increased total viral load, as well as an increased prevalence or abundance of influenza, cytomegalovirus and Epstein-Barr virus. [146] [147] [148] Ultimately, the role of acute viral infection including rhinovirus, RSV and influenza, which clearly contribute to inflammation, pathology and exacerbations of COPD, 28, 149, 150 remains to be fully elucidated. As previously described, latent adenoviral infection is associated with increased inflammation and alveolar destruction 126 while total and influenza-specific viral loads of COPD patients without symptoms of infection correlated with inflammatory cell numbers in the airways. 148 Moreover, human rhinovirus-encoded proteinase 2a has been proposed to elicit a duel Th1/Th2 response in COPD patients through its impact on dendritic cell maturation, thereby driving inflammation, allergy and airway obstruction. 149 Although fungi are only detectable at low abundance in healthy individuals, several members of the mycobiome are consistently identified in the lower respiratory tract, including Cladosporium and Aspergillus spp. 120, 151 Moreover, the outgrowth of Aspergillus can lead to IPA, with COPD as the most common predisposing condition. Colonization with Pneumocystis was associated with COPD development and GOLD stage classification. 30, 152 Pneumocystis spp. are capable of inducing COPD-like disease in animal models both with and without cigarette smoke exposure. 153, 154 In the oral cavity, smoking is associated with increased prevalence of Candida spp. as a consequence of the ability of cigarette smoke to increase the growth, adherence and immunostimulatory activity of Candida albicans. 155, 156 Cigarette smoke also increased the content of chitin in the cell wall of C. albicans. While it is not clear whether cigarette smoke causes similar changes in fungi that colonize the lung or if fungi in the oral cavity affect the lung through microaspiration, notably, the activity of chitotriosidase and the chitin-binding protein YKL-40 are increased in the BAL and alveolar macrophages of COPD patients. 157, 158 Even serum levels of YKL-40 and chitotriosidase are elevated in COPD patients and inversely correlate with lung function, indicating that host responses to fungal colonization may contribute to COPD progression. 159 The bacterial microbiome, virome and mycobiome are not isolated and act in concert. Indeed, bacteria and phage populations are strongly correlated, 142,144 while eukaryotic viruses and fungi can affect bacterial growth. 150, 151 Furthermore, the gastrointestinal microbiome interacts with the respiratory microbiota and plays a critical role in the development of several chronic respiratory diseases, and likely COPD (Fig. 3) . 133 

The prominent role of bacteria in inciting acute COPD exacerbations has placed antibiotics at the forefront of COPD therapy. In 1987, Anthonisen et al. reported a 13% increase in treatment success rate with antibiotic therapy compared with placebo, particularly in patients with increased dyspnoea and sputum production and purulence. 160 Since then, antibiotics covering pathogens such as H. influenzae, S. pneumoniae and M. catarrhalis have become mainstays of therapy and numerous trials have confirmed their beneficial effects. [161] [162] [163] Nonetheless, the notion that all acute exacerbations must be treated with antibiotics has been called into question, given that not every exacerbation is the result of a bacterial infection. Efforts to better identify the subset of exacerbating COPD patients who may benefit from antibiotics have explored biomarkers such as procalcitonin, 164,165 C-reactive protein 166 and neutrophil CD64 expression, 167 but few of these have yet made it into mainstream clinical decision algorithms.

The pleiotropic effects of antibiotics, particularly those of the macrolide class that also have antiinflammatory properties, led to their use in the prevention of exacerbations. Azithromycin, for instance, has not only antimicrobial activity against both Grampositive and -negative pathogens, but also antiinflammatory and immunomodulatory effects. 168, 169 Treatment in stable COPD patients reduced severe exacerbations, and in a population of patients with frequent COPD exacerbations, chronic use of azithromycin resulted in a significantly longer time to first exacerbation and a reduced yearly exacerbation rate. 170, 171 Azithromycin was particularly effective in reducing exacerbations requiring both antibiotics and systemic corticosteroids and appeared to be more effective in older patients with milder disease. 172 The long-term effects of chronic azithromycin therapy on the lung microbial community, however, are yet to be determined although initial reports suggest that while the overall bacterial burden remains stable, the alpha diversity of the lung decreases significantly. 173 The implications of these changes are yet to be established.

While these therapies have proven beneficial for COPD patients, it is important to remember that other COPD treatments can have untoward microbial effects. ICSs, for instance, have been shown to increase the risk Figure 3 Role of the microbiome in COPD pathogenesis and progression. Bacteria, viruses and fungi enter the lung through breathing and microaspiration of oral microbes. In the healthy lung, homeostasis is achieved through an appropriate immune response and pathogen clearance. In COPD, an increased abundance of pathogenic organisms and oral taxa is seen in association with reduced overall bacterial diversity. Consequently, perpetuation of a deleterious immune response occurs with associated COPD progression. Host-microbe dialogue may also proceed via the gut-lung axis further exacerbating disease symptoms as demonstrated in other chronic respiratory disease states. IPA, invasive pulmonary aspergillosis; Th, T-helper.

of both pneumonia and TB. In initial randomized controlled trials studying ICS and ICS-long-acting β2agonist (LABA) combination drugs, a higher rate of pneumonia was noted in the ICS-containing treatment groups. 174 Subsequent analyses, however, have specifically implicated fluticasone as the ICS most likely to increase the risk of pneumonia, as budesonide does not appear to confer a significant risk. [175] [176] [177] [178] Similarly, the risk for developing TB while on ICS therapy is significant in moderately to highly TB endemic areas. Research in Taiwan and South Korea has demonstrated up to 25 times greater risk of developing TB while on ICS treatment, with a dose-dependent effect. 179 Thus, in endemic areas, clinicians should be vigilant for the development of TB in COPD patients on ICS therapy. In addition to geographical distinctions, infection is not uniform in COPD, with changes in pathogen, strain and load over time. 16, 18 Different species trigger distinct inflammatory responses. 67 Furthermore, host factors play an essential role in infection manifestation and outcome. This results in variable response to antibiotic treatments in COPD. Therapy such as long-term macrolides can be beneficial with reductions in exacerbation rates in a selected group of patients with COPD. 180 This effect has been linked to antiinflammatory properties of macrolides likely explained by their impact on the microbiome, which, in turn, modulates immune tone. Culture-independent molecular techniques have constructed a comprehensive analysis of the microbial community in the lower airway and yet how the complexities in interactions between the host, pathogen and the environment contribute to disease manifestation and progression in COPD is far from understood. Future studies are required to better define the contribution of infection in COPD pathogenesis and intervention studies incorporating antimicrobial and anti-inflammatory approaches in the treatment of COPD. The application of whole-genome metagenomics in this context may uncover mechanisms beyond the scope of culturebased and amplicon sequencing approaches revealing precise genetic and metabolic pathways that intersect key immune responses contributing to disease progression.

The differences in risk factor exposure, ethnogeography and genetic background in Asia result in distinct characteristics of Asian COPD, which is currently overlooked by existing COPD treatment guidelines. Many of the COPD risk factors, including indoor and outdoor air pollution, occupational exposure to dust and fumes, a history of repeated childhood respiratory tract infections, intrauterine growth retardation, pulmonary TB and poor socio-economic status, are observed at higher prevalence in the Asia-Pacific region. Of particular note is the higher prevalence of pulmonary TB among Asian COPD patients. 181 Concomitant NTM, TB and bronchiectasis in COPD have been associated with higher risk of exacerbations, greater declines in pulmonary function and increased risk of mortality. 78, 79 Furthermore, Asia is an epicentre of antimicrobial resistance with high prevalence of multidrug resistance (MDR) organisms, which include respiratory pathogens. 182 Consequently, there may be differing responses to antibiotic therapy during bacterial exacerbation of COPD and an array of variable organisms identified during AECOPD in the Asia-Pacific region. Gram-negative bacteria including P. aeruginosa, Klebsiella pneumoniae and Acinetobacter spp. were more common in AECOPD in Asia-Pacific region. 183 The distinction in risk factor exposure as compared with western cohorts, underutilization of spirometry, higher prevalence of TB, bronchiectasis and antibiotic resistance all pose unique challenges for better diagnosis and treatment of COPD particular to the Asia-Pacific region.

The excessive mucus production in COPD patients is a fertile ground for the stimulation of chronic bacterial infection. Pulsed therapies of antibiotics are frequently used to control bacterial multiplication, which consequently promotes the development of antimicrobial resistance. Prolonged use of macrolides for the prophylaxis and treatment of COPD exacerbations has been shown to increase antimicrobial drug resistance in H. influenzae. 184 The commonly used drug azithromycin has a long half-life of around 66 h, which can lead to drug concentrations below the minimum inhibitory concentration for an extended period of time. 185 This prolonged exposure to subinhibitory concentrations of the drug may be one of the reasons behind the increased resistance to macrolides. Indeed, a study by Desai et al. on COPD patients with S. pneumoniae infection showed a correlation between exposure to macrolides and development of resistance. 186 They advised for the use of alternative antibiotics in patients who have been taking macrolides in the previous 6 months. 186 A 15-year longitudinal study conducted by Pettigrew et al. concluded that fluoroquinolones represent the best choice for eradicating H. influenzae in COPD patients. 184 In their study, none of the bacterial isolates developed resistance to fluoroquinolones. 184 Even though P. aeruginosa is a relatively uncommon cause of COPD exacerbations, its incidence is on the rise and the rapid emergence and spread of MDR (defined by resistance to at least three antibiotic classes) is a serious cause for concern. A comparative study conducted in Spain has demonstrated that the carriage of MDR P. aeruginosa in COPD patients was associated with increased mortality rates and more recent work in AECOPD reveals a high burden of antibiotic resistance. 25, 187 The lung environment found in COPD patients is also favourable to the formation of biofilms, a mechanism by which bacteria, particularly P. aeruginosa and H. influenza, evade antibiotic killing. In addition to limiting antimicrobial penetration, the biofilm triggers the emergence of relatively quiescent bacteria that become phenotypically drug resistant to most antibiotics, therefore increasing their persistence for prolonged periods of time. 188 Currently, the most effective way of curbing antimicrobial resistance is to reduce the use of antibiotics by prescribing them only to patients with demonstrated pathological bacterial infection. In this respect, the use of sensitive markers of bacterial infection such as procalcitonin to guide the start of antibiotic therapy was shown to significantly reduce the use of antibiotics in COPD patients. 189 There is also the potential that the new therapies developed for steroid-resistant asthma may also be beneficial in COPD and possibly avoid the infection-inducing effects of ICS. 190

The majority of studies described above are of the associations between infections and microbiomes with COPD in humans. These studies are limited by the type of samples that can be collected and typically the cross-sectional nature of study design. Mouse models of cigarette smoke-induced experimental COPD that accurately recapitulate the hallmark features of the human disease have been generated. 191, 192 Chronic models that use only inhalational exposures drive the development of airway inflammation and remodelling, mucus hypersecretion, emphysema and changes in lung function similar to those in humans. 191, 192 This can be achieved in a relative short time frame of 8 weeks with exposures similar to those of a pack-a-day human smoker. 191 Importantly, these and other models have increased susceptibility to respiratory bacterial and viral infections that are relevant to those in humans described above. 8, 9, 46 They are being used to assess the mechanisms of the associations between infections, microbiomes and COPD and have recently implicated roles for immune defects, microRNAs, mast cell proteases and many other factors. In combination with parallel ex vivo human sample and primary cell culture analysis, they provide powerful tools for exploring these associations and are valuable for testing new drugs. [7] [8] [9] 53, 57, 170 Translatability into humans can be addressed by applying treatments specifically to those patients with alterations in drug targets. Through similar analysis of comparable tissues from mice and humans, using similar techniques such as the interrogation of precision-cut lung slices, important therapeutic questions can be examined in future COPD studies. [193] [194] [195] 

Although the role of pathogenic microbes in AECOPD has been extensively investigated, their clinical significance in stable but colonized COPD patients remains less clear. The question of whether colonizing microbes actively contribute to COPD pathogenesis and more importantly progression may be difficult to address with the current evidence base, given technical challenges in detecting these organisms and the subtlety of their association with disease over long periods of time. Nevertheless, immune responses observed in stable and colonized COPD patients reflect the corollary of those seen in AECOPD supporting a role for microbial colonization in COPD pathogenesis most likely through a perpetuation of negative immune responses over time. Initial work has started to uncover changes in the lung microbiome associated with the COPD state and may reveal further variables to be considered in the investigation of microbe-COPD interactions. The parallel use of mouse models and interrogation of human samples ex vivo and in primary cell culture will likely progress mechanistic insights and drug development. Importantly, however, other variables of microbiome composition may confound pathogen-centric investigations of disease-microbe interactions and it is likely that large-scale studies will be required to address the current gaps in our knowledge of bacterial, viral and fungal microbiota and their association with COPD. Precipitous drops in the costs of DNA sequencing, coupled with the technological innovations in metagenomics, may soon bring such technology into the realm of routine diagnostics in COPD. This could allow for refined patient phenotyping and stratification that in turn will allow more focused and personalized therapy based on microbiology. Finally, the impact of antimicrobial therapy and the use of antibiotic prophylaxis on the respiratory microbiome provide further challenges. The extensive remodelling of the microbiome that occurs in response to COPD antibiotic treatment while recognized has unclear long-term consequences for patients. 

The natural history of chronic airflow obstruction

The British hypothesis revisited

Infections and airway inflammation in chronic obstructive pulmonary disease severe exacerbations

Acute exacerbations of chronic obstructive pulmonary disease: identification of biologic clusters and their biomarkers

Impaired innate immune alveolar macrophage response and the predilection for COPD exacerbations

Defective macrophage phagocytosis of bacteria in COPD

Nontypeable Haemophilus influenzae induces sustained lung oxidative stress and protease expression

Targeting PI3K-p110alpha suppresses influenza virus infection in chronic obstructive pulmonary disease

Critical role of constitutive type I interferon response in bronchial epithelial cell to influenza infection

Impaired antiviral stress granule and IFN-beta enhanceosome formation enhances susceptibility to influenza infection in chronic obstructive pulmonary disease epithelium

Cigarette smoke suppresses type I interferon-mediated antiviral immunity in lung fibroblast and epithelial cells

Long-term cigarette smoke exposure in a mouse model of ciliated epithelial cell function

Mucociliary dysfunction in COPD: effect of current pharmacotherapeutic options

Elastase-and LPS-exposed mice display altered responses to rhinovirus infection

Importance of viral and bacterial infections in chronic obstructive pulmonary disease exacerbations

New strains of bacteria and exacerbations of chronic obstructive pulmonary disease

Changes in prevalence and load of airway bacteria using quantitative PCR in stable and exacerbated COPD

Airway bacterial load and FEV1 decline in patients with chronic obstructive pulmonary disease

Variability and effects of bronchial colonisation in patients with moderate COPD

Microbiologic determinants of exacerbation in chronic obstructive pulmonary disease

Relationship between bacterial colonisation and the frequency, character, and severity of COPD exacerbations

Bacterial infection in chronic obstructive pulmonary disease. A study of stable and exacerbated outpatients using the protected specimen brush

Host-pathogen interaction during pneumococcal infection in patients with chronic obstructive pulmonary disease

Infectious etiology of acute exacerbations in severe COPD patients

Pseudomonas aeruginosa resistance patterns and clinical outcomes in hospitalized exacerbations of COPD

The Chlamydia InterAction with COPD (CIAC) Study Group. Chlamydia pneumoniae and chronic bronchitis: association with severity and bacterial clearance following treatment

Prevalence of nontuberculous mycobacteria in COPD patients with exacerbations

The relevance of respiratory viral infections in the exacerbations of chronic obstructive pulmonary disease-a systematic review

Importance of Aspergillus spp. isolation in acute exacerbations of severe COPD: prevalence, factors and follow-up: the FUNGI-COPD study

Association of chronic obstructive pulmonary disease severity and Pneumocystis colonization

Horra Cde L. Systemic inflammation in patients with chronic obstructive pulmonary disease who are colonized with Pneumocystis jirovecii

Pneumocystis jirovecii colonization is associated with enhanced Th1 inflammatory gene expression in lungs of humans with chronic obstructive pulmonary disease

Viral pathogens in acute exacerbations of chronic obstructive pulmonary disease

Respiratory viral infection in exacerbations of COPD

Van Der Eerden MM. Occurrence of virus-induced COPD exacerbations during four seasons

Association between respiratory viruses and exacerbation of COPD: a case-control study

Detection of multiple viral and bacterial infections in acute exacerbation of chronic obstructive pulmonary disease: a pilot prospective study

Viral and bacterial infection in acute asthma and chronic obstructive pulmonary disease increases the risk of readmission

Respiratory infectious phenotypes in acute exacerbation of COPD: an aid to length of stay and COPD Assessment Test

Experimental rhinovirus infection as a human model of chronic obstructive pulmonary disease exacerbation

Infection in the pathogenesis and course of chronic obstructive pulmonary disease

Relation between duration of smoking cessation and bronchial inflammation in COPD

Airway mucosal inflammation in COPD is similar in smokers and ex-smokers: a pooled analysis

Airway epithelial regulation of pulmonary immune homeostasis and inflammation

Airway inflammation and bronchial bacterial colonization in chronic obstructive pulmonary disease

A novel immunomodulatory function of neutrophils on rhinovirusactivated monocytes in vitro

The neutrophil in chronic obstructive pulmonary disease

Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE) Investigators. Persistent systemic inflammation is associated with poor clinical outcomes in COPD: a novel phenotype

Bacterial colonization increases daily symptoms in patients with chronic obstructive pulmonary disease

Phagocytic dysfunction of human alveolar macrophages and severity of chronic obstructive pulmonary disease

Toll-like receptor 2 expression is decreased on alveolar macrophages in cigarette smokers and COPD patients

Targeting Nrf2 signaling improves bacterial clearance by alveolar macrophages in patients with COPD and in a mouse model

Influence of age, past smoking, and disease severity on TLR2, neutrophilic inflammation, and MMP-9 levels in COPD

Moraxella catarrhalis in chronic obstructive pulmonary disease: burden of disease and immune response

The nature of small-airway obstruction in chronic obstructive pulmonary disease

Chronic bronchial infection in COPD. Is there an infective phenotype?

COPD is characterized by increased detection of Haemophilus influenzae, Streptococcus pneumoniae and a deficiency of Bacillus species

High-molecular-weight proteins of nontypeable Haemophilus influenzae mediate attachment to human epithelial cells

Binding between outer membrane proteins of nontypeable Haemophilus influenzae and human nasopharyngeal mucin

Bacterial infection in chronic obstructive pulmonary disease in 2000: a state-of-the-art review

Outer membrane protein P6 of nontypeable Haemophilus influenzae is a potent and selective inducer of human macrophage proinflammatory cytokines

Combined Haemophilus influenzae respiratory infection and allergic airways disease drives chronic infection and features of neutrophilic asthma

Impaired alveolar macrophage response to Haemophilus antigens in chronic obstructive lung disease

Nontypeable Haemophilus influenzae in the lower respiratory tract of patients with chronic bronchitis

A clonal group of nontypeable Haemophilus influenzae with two IgA proteases is adapted to infection in chronic obstructive pulmonary disease

PAC-COPD Study Group. Effect of bronchial colonisation on airway and systemic inflammation in stable COPD

Relationship between bacterial flora in sputum and functional impairment in patients with acute exacerbations of COPD

Patients with chronic obstructive pulmonary disease and chronically colonized with Haemophilus influenzae during stable disease phase have increased airway inflammation

Moraxella catarrhalis acquisition, airway inflammation and proteaseantiprotease balance in chronic obstructive pulmonary disease

Persistent colonization by Haemophilus influenzae in chronic obstructive pulmonary disease

Virulence factors in the colonization and persistence of bacteria in the airways

Pseudomonas aeruginosa in patients hospitalised for COPD exacerbation: a prospective study

Pseudomonas aeruginosa in chronic obstructive pulmonary disease

Does a single Pseudomonas aeruginosa isolation predict COPD mortality?

The role of atypical respiratory pathogens in exacerbations of chronic obstructive pulmonary disease

Chronic Chlamydia pneumoniae infection is a risk factor for the development of COPD

Chlamydia pneumoniae and COPD exacerbation

Prognostic value of bronchiectasis in patients with moderate-to-severe chronic obstructive pulmonary disease

Impact of non-tuberculous mycobacteria on pulmonary function decline in chronic obstructive pulmonary disease

Evidence of mycobacterial disease in COPD patients with lung volume reduction surgery; the importance of histological assessment of specimens: a cohort study

Prevalence of nontuberculous mycobacterial pulmonary disease

Nontuberculous mycobacterial disease mortality in the United States, 1999-2010: a population-based comparative study

Studies on the impairment of respiratory function in pulmonary tuberculosis

Determinants of chronic obstructive pulmonary disease in Chinese patients in Hong Kong

Tuberculosis and airflow obstruction: evidence from the PLATINO study in Latin America

Prevalence of COPD in five Colombian cities situated at low, medium, and high altitude (PREPOCOL study)

Prior TB, smoking, and airflow obstruction: a cross-sectional analysis of the Guangzhou Biobank Cohort Study

COPD in never smokers: results from the population-based Burden of Obstructive Lung Disease study

Burden of obstructive lung disease in a rural setting in the Philippines

The prevalence of chronic obstructive pulmonary disease in Uppsala, Sweden -the Burden of Obstructive Lung Disease (BOLD) study: cross-sectional population-based study

Occupational exposures and chronic obstructive pulmonary disease: a hospital based casecontrol study

The risk of obstructive lung disease by previous pulmonary tuberculosis in a country with intermediate burden of tuberculosis

Risk factors for COPD spirometrically defined from the lower limit of normal in the BOLD project

Baptista Menezes AM. Airflow obstruction in never smokers in five Latin American cities: the PLATINO study

The association between airflow obstruction and radiologic change by tuberculosis

Prevalence and correlates of airflow obstruction in approximately 317,000 never-smokers in China

Tuberculosis associates with both airflow obstruction and low lung function: BOLD results

Spatial clustering and local risk factors of chronic obstructive pulmonary disease (COPD)

Prevalence of chronic obstructive pulmonary disease and variation in risk factors across four geographically diverse resource-limited settings in Peru

The relationship between chronic obstructive pulmonary disease and comorbidities: a cross-sectional study using data from KNHANES 2010-2012

Risk factors for chronic obstructive pulmonary disease among never-smokers in Korea

The risk factors and characteristics of COPD among nonsmokers in Korea: an analysis of KNHANES IV and V

Obstructive airway disease in patients with treated pulmonary tuberculosis

Chronic obstructive airways disease following treated pulmonary tuberculosis

Influence of antimicrobial chemotherapy on spirometric parameters and pro-inflammatory indices in severe pulmonary tuberculosis

Functional profile of patients with tuberculosis sequelae in a university hospital

Pulmonary impairment after tuberculosis

The burden of silicosis, pulmonary tuberculosis and COPD among former Basotho goldminers

Post-tuberculous chronic obstructive pulmonary disease

Clinical characteristics of patients with tuberculosis-destroyed lung

Chronic airway obstruction after successful treatment of tuberculosis and its impact on quality of life

Lung functions among patients with pulmonary tuberculosis in Dar es Salaam -a cross-sectional study

Chronic airflow obstruction and respiratory symptoms following tuberculosis: a review of South African studies

Concomitant presence of culture-proven active pulmonary tuberculosis in patients with chronic obstructive pulmonary disease -a hospital based study. Pak

COPD and the risk of tuberculosis -a population-based cohort study

Aspergillus-associated airway disease, inflammation, and the innate immune response

Aspergillus fumigatus during stable state and exacerbations of COPD

Aspergillus hypersensitivity in patients with chronic obstructive pulmonary disease: COPD as a risk factor for ABPA?

The prevalence of increased serum IgE and Aspergillus sensitization in patients with COPD and their association with symptoms and lung function

Pulmonary aspergillosis in patients with chronic obstructive pulmonary disease: incidence, risk factors, and outcome

Aspergillus fumigatus: principles of pathogenesis and host defense

Invasive pulmonary aspergillosis in patients with chronic obstructive pulmonary disease

Pneumocystis carinii carriage in immunocompetent patients with primary pulmonary disorders as detected by single or nested PCR

Airway obstruction is increased in Pneumocystis-colonized human immunodeficiency virusinfected outpatients

Latent adenoviral infection in the pathogenesis of chronic airways obstruction

Amplification of inflammation in emphysema and its association with latent adenoviral infection

Emphysematous lung destruction by cigarette smoke the effects of latent adenoviral infection on the lung inflammatory response

Adenovirus E1A upregulates interleukin-8 expression induced by endotoxin in pulmonary epithelial cells

Adenovirus E1A gene dysregulates ICAM-1 expression in transformed pulmonary epithelial cells

Respiratory viruses, symptoms, and inflammatory markers in acute exacerbations and stable chronic obstructive pulmonary disease

Respiratory syncytial virus, airway inflammation, and FEV1 decline in patients with chronic obstructive pulmonary disease

Detection of respiratory syncytial virus in adults with chronic obstructive pulmonary disease

Emerging pathogenic links between microbiota and the gut-lung axis

Microbiomes in respiratory health and disease: an Asia-Pacific perspective

The lung tissue microbiome in chronic obstructive pulmonary disease

The lung microbiome in moderate and severe chronic obstructive pulmonary disease

Comparison of the respiratory microbiome in healthy nonsmokers and smokers

Severityrelated changes of bronchial microbiome in chronic obstructive pulmonary disease

Host response to the lung microbiome in chronic obstructive pulmonary disease

Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease

Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients

Evaluation of unbiased next-generation sequencing of RNA (RNA-seq) as a diagnostic method in influenza virus-positive respiratory samples

Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals

Translational aspects of the human respiratory virome

High levels of Epstein-Barr virus in COPD

Levels of CMV-reactive antibodies correlate with the induction of CD28 (null) T cells and systemic inflammation in chronic obstructive pulmonary disease (COPD)

Respiratory viral detection and small airway inflammation in lung tissue of patients with stable, mild COPD

Human rhinovirus proteinase 2A induces TH1 and TH2 immunity in patients with chronic obstructive pulmonary disease

Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease

The lung mycobiome: an emerging field of the human respiratory microbiome

Topographic diversity of the respiratory tract mycobiome and alteration in HIV and lung disease

Pneumocystis murina infection and cigarette smoke exposure interact to cause increased organism burden, development of airspace enlargement, and pulmonary inflammation in mice

Persistent Pneumocystis colonization leads to the development of chronic obstructive pulmonary disease in a nonhuman primate model of AIDS

The relationship between cigarette smoking and oral colonization with Candida species in healthy adult subjects

Cigarette smoke-exposed Candida albicans increased chitin production and modulated human fibroblast cell responses

YKL-40 is elevated in patients with chronic obstructive pulmonary disease and activates alveolar macrophages

Chitotriosidase is the primary active chitinase in the human lung and is modulated by genotype and smoking habit

BIOAIR (Longitudinal Assessment of Clinical Course and Biomarkers in Severe Chronic Airway Disease) Consortium. Increased YKL-40 and chitotriosidase in asthma and chronic obstructive pulmonary disease

Antibiotic therapy in exacerbations of chronic obstructive pulmonary disease

Antibiotics in addition to systemic corticosteroids for acute exacerbations of chronic obstructive pulmonary disease

Efficacy of antibiotic therapy for acute exacerbations of mild to moderate chronic obstructive pulmonary disease

Association between antibiotic treatment and outcomes in patients hospitalized with acute exacerbation of COPD treated with systemic steroids

Antibiotic treatment of severe exacerbations of chronic obstructive pulmonary disease with procalcitonin: a randomized noninferiority trial

Acute exacerbations of chronic obstructive pulmonary disease with low serum procalcitonin values do not benefit from antibiotic treatment: a prospective randomized controlled trial

Evaluation of new laboratory tests to discriminate bacterial from nonbacterial chronic obstructive pulmonary disease exacerbations

Neutrophil CD64 as a marker of bacterial infection in acute exacerbations of chronic obstructive pulmonary disease

Erakovic Haber V. Macrolide antibiotics broadly and distinctively inhibit cytokine and chemokine production by COPD sputum cells in vitro

Azithromycin induces anti-viral effects in cultured bronchial epithelial cells from COPD patients

The effect of azithromycin in adults with stable neutrophilic COPD: a double blind randomised, placebo controlled trial

Azithromycin for prevention of exacerbations of COPD

Predictors of chronic obstructive pulmonary disease exacerbation reduction in response to daily azithromycin therapy

Randomised, double-blind, placebo-controlled trial with azithromycin selects for antiinflammatory microbial metabolites in the emphysematous lung

Salmeterol and fluticasone propionate and survival in chronic obstructive pulmonary disease

Budesonide and the risk of pneumonia: a meta-analysis of individual patient data

Pneumonia and pneumonia related mortality in patients with COPD treated with fixed combinations of inhaled corticosteroid and long acting beta2 agonist: observational matched cohort study (PATHOS)

Inhaled corticosteroids in COPD and the risk of serious pneumonia

Once-daily inhaled fluticasone furoate and vilanterol versus vilanterol only for prevention of exacerbations of COPD: two replicate double-blind, parallel-group, randomised controlled trials

TB meets COPD: an emerging global co-morbidity in human lung disease

Macrolide effects on the prevention of COPD exacerbations

Association between chronic obstructive pulmonary disease and systemic inflammation: a systematic review and a meta-analysis

Antimicrobial resistance in Asia: current epidemiology and clinical implications

A multicentre surveillance study on the characteristics, bacterial aetiologies and in vitro antibiotic susceptibilities in patients with acute exacerbations of chronic bronchitis

Effect of fluoroquinolones and macrolides on eradication and resistance of Haemophilus influenzae in chronic obstructive pulmonary disease

Pharmacokinetics and pharmacodynamics of newer macrolides

Antibiotic resistance in sputum isolates of Streptococcus pneumoniae in chronic obstructive pulmonary disease is related to antibiotic exposure

Mortality of COPD patients infected with multi-resistant Pseudomonas aeruginosa: a case and control study

Mechanisms of bacterial resistance to antibiotics in infections of COPD patients

Antibiotic treatment of exacerbations of COPD: a randomized, controlled trial comparing procalcitonin-guidance with standard therapy

Potential therapeutic targets for steroid-resistant asthma

Animal models of chronic obstructive pulmonary disease

Animal models of COPD: what do they tell us

Novel small airway bronchodilator responses to rosiglitazone in mouse lung slices

Alteration of airway reactivity and reduction of ryanodine receptor expression by cigarette smoke in mice

Pharmacological characterization of indacaterol, a novel once daily inhaled 2 adrenoceptor agonist, on small airways in human and rat precisioncut lung slices