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PURPOSE OF REVIEW: Lung transplantation presents a rescue therapy for those with end-stage lung disease. Survival in lung transplant patients remains limited due to chronic lung allograft dysfunction (CLAD), a range of pathologic manifestations leading to graft loss. The mechanisms underlying CLAD remain poorly understood, and the lung microbiome has been suggested as a potential contributor to this condition. This review aims to explore how the pulmonary microbiome is impacted by lung transplantation, and how alterations in this microbiome may contribute to the pathogenesis of CLAD. RECENT FINDINGS: The pulmonary microbiome is made up of a range of microorganisms, and it varies considerably in lung transplant patients when compared with healthy controls. The lung microbiome changes over the early transplant period, and the composition of species appears to have an impact on inflammatory responses within the lungs. A number of studies have shown that an increase in bacterial biomass in the allograft, and enrichment with the genera Proteobacteria, or more specifically, Pseudomonas species, is associated with CLAD. SUMMARY: This area of research is still in its infancy; however, the suggestion that changes in the composition of the microbiome and enrichment with certain species may predispose to the pathologic changes that underlie CLAD indicate that modulation of the microbiome may be of use in potential future therapeutics.
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Doença Enxerto-Hospedeiro , Transplante de Pulmão , Microbiota , Aloenxertos , Humanos , Pulmão , Transplante de Pulmão/efeitos adversos , Transplante HomólogoRESUMO
Pseudomonas and Burkholderia are gram-negative organisms that achieve colonization within the lungs of patients with cystic fibrosis, and are associated with accelerated pulmonary function decline. Multidrug resistance is a hallmark of these organisms, which makes eradication efforts difficult. Furthermore, the literature has outlined increased morbidity and mortality for lung transplant (LTx) recipients infected with these bacterial genera. Indeed, many treatment centers have considered Burkholderia cepacia infection an absolute contraindication to LTx. Ongoing research has delineated different species within the B. cepacia complex (BCC), with significantly varied morbidity and survival profiles. This review considers the current evidence for LTx outcomes between the different subspecies encompassed within these genera as well as prophylactic and management options. The availability of meta-genomic tools will make differentiation between species within these groups easier in the future, and will allow more evidence-based decisions to be made regarding suitability of candidates colonized with these resistant bacteria for LTx. This review suggests that based on the current evidence, not all species of BCC should be considered contraindications to LTx, going forward.
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Infecções por Burkholderia , Complexo Burkholderia cepacia , Burkholderia , Transplante de Pulmão , Infecções por Burkholderia/tratamento farmacológico , Humanos , Pseudomonas aeruginosaRESUMO
PURPOSE OF REVIEW: Lung transplantation survival is still limited compared with other solid organ transplant modalities, due to a range of factors that are continuing to be elucidated. However, new research is emerging which indicates that the microbiome of the lungs, and of other organs, may have important implications for immune response and mediating transplant outcomes. Pathogenic bacterial and viral species are known to have deleterious effects on the allograft, but taking a more global view, and considering the overall composition of the community of microbial species may undercover a greater understanding of the complex interplay involved in allograft dysfunction. RECENT FINDINGS: The microbiome appears to have an important modulatory role on immune response in both normal development, and after transplantation. A range of microbial species contributes to the resident microscopic community, with the gut and blood microbiomes having a significant impact on the function of the lungs and resistance to infection. Movement of species from within and outside the respiratory tract occurs in the early transplant period, leading to a modified donor microbiome in the recipient. There is evidence to suggest that chronic lung allograft dysfunction may be facilitated by the respiratory microbiome and interactions with immune cells within the allograft. SUMMARY: Further investigation of the respiratory microbiome, interactions with the microbiome of other organs and impact on immune and allograft function posttransplantation is needed. Promising insights are being gained regarding certain microbial profiles which may be associated with negative outcomes, and the mechanisms through which this occurs. As our understanding expands, the ability to modify the microbiome offers novel treatment strategies for combating allograft dysfunction.
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Transplante de Pulmão/métodos , Microbiota/fisiologia , HumanosRESUMO
Once considered a sterile site below the larynx, the tracheobronchial tree and parenchyma of the lungs are now known to harbor a rich diversity of microbial species including bacteria, viruses, fungi, and archaea. Many of these organisms, particularly the viruses which comprise the human respiratory virome, have not been identified, so their true role is unknown. It seems logical to conclude that a "healthy" respiratory microbiome exists which may be modified in disease states and perhaps by therapies such as antibiotics, antifungals, and antiviral treatments. It is likely that there is a critical relationship or equilibrium between components of the microbiome until such time as perturbations occur which lead to a state of dysbiosis or an "unhealthy" microbiome. The act of lung transplantation provides an extreme change to an individual's respiratory microbiome as, in effect, the donor respiratory microbiome is transplanted into the recipient. The mandatory ex-vivo period of the donor lungs appears to be associated with blooms of resident viral species in particular. Subsequently, allograft injury, rejection, and immune suppressive therapy all combine to create periods of dysbiosis which when combined with transient infections such as community acquired respiratory viruses may facilitate the development of chronic allograft dysfunction in predisposed individuals. As our understanding of the respiratory microbiome is rapidly expanding, based on the use of new-generation sequencing tools in particular, it is to be hoped that insights gained into the subtle relationship between the microbiome and the lung allograft will facilitate improved outcomes by directing novel therapeutic endeavors.
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Pneumopatias/microbiologia , Pulmão/imunologia , Pulmão/microbiologia , Microbiota , Doença Crônica , Progressão da Doença , Disbiose/imunologia , Interações Hospedeiro-Patógeno , Humanos , Pneumopatias/imunologia , Transplante de Pulmão/efeitos adversosRESUMO
BACKGROUND: Bronchiectasis is a chronic respiratory condition. Persistent bacterial colonisation in the stable state with increased and sometimes altered bacterial burden during exacerbations are accepted as key features in the pathophysiology. The extent to which respiratory viruses are present during stable periods and in exacerbations is less well understood. METHODS: This study aimed to determine the incidence of respiratory viruses within a cohort of bronchiectasis patients with acute exacerbations at a teaching hospital and, separately, in a group of patients with stable bronchiectasis. In the group of stable patients, a panel of respiratory viruses were assayed for using real time quantitative PCR in respiratory secretions and exhaled breath. The Impact of virus detection on exacerbation rates and development of symptomatic infection was evaluated. RESULTS: Routine hospital-based viral PCR testing was only requested in 28% of admissions for an exacerbation. In our cohort of stable bronchiectasis patients, viruses were detected in 92% of patients during the winter season, and 33% of patients during the summer season. In the 2-month follow up period, 2 of 27 patients presented with an exacerbation. CONCLUSIONS: This pilot study demonstrated that respiratory viruses are commonly detected in patients with stable bronchiectasis. They are frequently detected during asymptomatic viral periods, and multiple viruses are often present concurrently.
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Bronquiectasia/fisiopatologia , Bronquiectasia/virologia , Pulmão/fisiopatologia , Pulmão/virologia , Viroses/epidemiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Austrália/epidemiologia , Infecções Comunitárias Adquiridas/epidemiologia , Infecções Comunitárias Adquiridas/virologia , Progressão da Doença , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Projetos Piloto , Estudos Retrospectivos , Estações do Ano , Espirometria , Viroses/complicações , Viroses/diagnóstico , Vírus/genética , Adulto JovemRESUMO
Despite the dominant role of community-acquired respiratory viruses as etiological agents of disease, there has been little focus to date on the translation of rapidly developing diagnostic modalities, such as next-generation sequencing techniques in the examination of lower respiratory tract samples. When applied, these techniques should inform strategies to both understand the nexus between health and disease states of the respiratory virome, and drive a paradigm shift in how the practicing pulmonologist views the conceptual framework of respiratory infections. The lower respiratory tract was once thought to be a sanctuary site from microbiological colonization owing to the efficacy of upper airway-protective mechanisms and the host mucosal barrier function of the lower airways, combined with both innate and adaptive immune responses. As a small number of recent studies confirm, this is a naive vision of the lung, the viral component of which parallels recent revelations from respiratory microbiome studies. Hence, it is now timely to revise our thinking regarding the constituents, diversity, and changing nature of the respiratory virome in health and disease. One area worthy of focus is the interface between community-acquired respiratory viruses and the respiratory virome to better understand the dynamics in acute infection, as well as the factors that may lead to viral persistence and chronic disease. Given recent advances in metagenomics, the tools are now at hand to accomplish these goals.
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Microbiota/fisiologia , Sistema Respiratório/virologia , Infecções Respiratórias/virologia , Pesquisa Translacional Biomédica/métodos , HumanosRESUMO
BACKGROUND: Lung transplantation provides a unique opportunity to investigate the constituents and temporal dynamics of the human pulmonary microbiome after lung transplantation. For methodological reasons, prior studies using metagenomics have detected DNA viruses but not demonstrated the presence of RNA viruses, including those that are common community acquired. In this proof-of-concept study, we aimed to further characterize the pulmonary microbiome after lung transplantation by using metagenomic next-generation sequencing (mNGS), with a particular focus on the RNA virome. METHODS: We performed a single-center longitudinal study of lower respiratory tract RNA viruses and bacteria using bronchoalveolar lavage at postoperative day 1 and week 6 analyzed with total RNA sequencing (metatranscriptomics). Five primary and 5 repeat transplant recipients were recruited. RESULTS: mNGS identified 5 RNA viruses (nil in the normal saline control), including 4 species of human rhinovirus not previously reported in Australia: A7 (HRV-A7), C22 (HRV-C22), B52 (HRV-B52), and B72 (HRV-B72). Overall, 12/20 specimens were virus positive in 7/10 cases. Human parainfluenza virus 3 was the most frequent virus in 7/20 specimens in 5/10 cases. In this small study, we did not detect a significant difference in abundance and diversity of RNA viruses and bacteria at postoperative day 1 and 6 wk, nor differences between retransplant recipients and primary lung transplant recipients. CONCLUSIONS: Our study demonstrates how mNGS can also identify RNA viruses within the human pulmonary virome, including novel RNA viruses, and paves the way for a greater understanding of the complex relationships among the constituents of the pulmonary infectome.
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Transplante de Pulmão , RNA , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Estudos Longitudinais , Pulmão , Transplante de Pulmão/efeitos adversos , Viroma/genéticaRESUMO
One of the great challenges of lung transplantation is to bridge the dichotomy between supply and demand of donor organs so that the maximum number of potential recipients achieve a meaningful benefit in improvements in survival and quality of life. To achieve this laudable goal is predicated on choosing candidates who are sufficiently unwell, in fact possessing a terminal respiratory illness, but otherwise fit and able to undergo major surgery and a prolonged recuperation and rehabilitation stage combined with ongoing adherence to complex medical therapies. The choice of potential candidate and the timing of that referral is at times perhaps more art than science, but there are a number of solid guidelines for specific illnesses to assist the interested clinician. In this regard, the relationship between the referring clinician and the lung transplant unit is a critical one. It is an ongoing and dynamic process of education and two way communication, which is a marker of the professionalism of a highly performing unit. Lung transplantation is ultimately a team effort where the recipient is the key player. That principle has been enshrined in the three consensus position statements regarding selection criteria for lung and heart-lung transplantation promulgated by the International Society for Heart and Lung Transplantation over the last two decades. During this period, the number of indications for lung transplantation have broadened and the number of contraindications reduced. Risk management is paramount in the pre- and perioperative period to effect early successful outcomes. While it is not the province of this review to reiterate the detailed listing of those factors, an overview position will be developed that describes the rationale and evidence for selected criteria where that exists. Importantly, the authors will attempt to provide an historical and experiential basis for making these important and life-determining decisions. The reviews of this paper are available via the supplementary material section.
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Tomada de Decisão Clínica , Pneumopatias/cirurgia , Transplante de Pulmão/métodos , Seleção de Pacientes , Encaminhamento e Consulta , Seleção do Doador , Humanos , Pneumopatias/diagnóstico , Pneumopatias/fisiopatologia , Transplante de Pulmão/efeitos adversos , Recuperação de Função Fisiológica , Medição de Risco , Fatores de Risco , Doadores de Tecidos/provisão & distribuição , Resultado do Tratamento , Listas de EsperaRESUMO
There have been great advances in the methodologies available for the detection of respiratory viruses. Accompanying this, our knowledge surrounding the impact of these viruses has also made a great leap forward. We have come a long way from the once commonly accepted belief that the lower respiratory tract was sterile and that the detection of any microbial species must represent a breach in host defence and likely be associated with symptomatic infection. With the advent of molecular detection techniques and improvements in sequencing-based methodologies to make these tools more accessible and cost effective, we now know that there is an abundant and diverse ecosystem within the lower-respiratory tract. This chapter will outline the clinical impact of the human respiratory virome, techniques for sampling the lower respiratory tract, the evolution of the diagnostic tools available, and the current limitations in our instruments and knowledge in this area. The human respiratory virome is an exciting new area of research that will continue to grow with the aid of the methodologies outlined in the following chapters and the advent of even more efficient tools in the future.
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Metagenoma , Metagenômica , Microbiota , Infecções Respiratórias/virologia , Vírus/genética , Animais , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Reação em Cadeia da Polimerase , Análise de Sequência de DNARESUMO
BACKGROUND: Respiratory viruses circulate constantly in the ambient air. The risk of opportunistic infection from these viruses can be increased in mechanically ventilated patients. The present study evaluates the feasibility of detecting airborne respiratory viruses in mechanically ventilated patients using a novel sample collection method involving ventilator filters. METHODS: We collected inspiratory and expiratory filters from the ventilator circuits of mechanically ventilated patients in an intensive care unit over a 14-month period. To evaluate whether we could detect respiratory viruses collected in these filters, we performed a reverse transcription polymerase chain reaction on the extracted filter membrane with primers specific for rhinovirus, respiratory syncytial virus, influenza virus A and B, parainfluenza virus (type 1, 2 and 3) and human metapneumovirus. For each patient, we also performed a full virology screen (virus particles, antibody titres and virus-induced biomarkers) on respiratory samples (nasopharyngeal swab, tracheal aspirate or bronchoalveolar fluid) and blood samples. RESULTS: Respiratory viruses were detected in the ventilator filters of nearly half the patients in the study cohort (n = 33/70). The most common virus detected was influenza A virus (n = 29). There were more viruses detected in the inspiratory filters (n = 18) than in the expiratory filters (n = 15). A third of the patients with a positive virus detection in the ventilator filters had a hospital laboratory confirmed viral infection. In the remaining cases, the detected viruses were different from viruses already identified in the same patient, suggesting that these additional viruses come from the ambient air or from cross-contamination (staff or visitors). In patients in whom new viruses were detected in the ventilator filters, there was no evidence of clinical signs of an active viral infection. Additionally, the levels of virus-induced biomarker in these patients were not statistically different from those of non-infected patients (p = 0.33). CONCLUSIONS: Respiratory viruses were present within the ventilator circuits of patients receiving mechanical ventilation. Although no adverse clinical effect was evident in these patients, further studies are warranted, given the small sample size of the study and the recognition that ventilated patients are potentially susceptible to opportunistic infection from airborne respiratory viruses.
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BACKGROUND: Lung transplantation provides a unique opportunity to investigate the dynamics of the human pulmonary virome that is transplanted within the donor lungs. The pulmonary virome comprises both "resident" and "transient" viruses. In this study we aimed to analyze the dynamics of the "transient" members. METHODS: We conducted a single-center, prospective, longitudinal investigation of community-acquired respiratory viruses detected in nasopharyngeal swabs, swabs of explanted and donor lungs, and serial bronchoalveolar lavages post-transplant. RESULTS: Fifty-two consecutive lung transplant recipients were recruited (bilateral:heartâlung:bilateral lung-liverâ¯=â¯48:2:2) (age [mean ± SD] 48 ± 15 years, range 20 to 63 years; 27 males and 25 females). Follow-up was 344 ± 120 (range 186 to 534) days. Seventeen of 45 explanted lungs were positive for influenza A and/or B (Aâ¯=â¯14, Bâ¯=â¯2, A+Bâ¯=â¯1), despite recipient vaccination and negative nasal swabs, and 4 of 45 had human rhinovirus and 2 of 45 parainfluenza. Donor swabs showed influenza (Aâ¯=â¯1, Bâ¯=â¯1) and rhinovirus (nâ¯=â¯3). Day 1 lavage showed influenza A (nâ¯=â¯28), rhinovirus (nâ¯=â¯9), and parainfluenza (nâ¯=â¯1). Forty-seven of 52 recipients had a positive lavage for virus (38 of 47 on multiple lavages). Influenza persisted for 59 ± 38 (range 4 to 147) days in 27 of 52, and 14 had a single isolate. Rhinovirus persisted for 95 ± 84 (range 22 to 174) days in 13 of 52, and 13 had a single isolate. Analysis of 118 paired transbronchial biopsies and lavage demonstrated no association between viruses and acute cellular rejection (Fisher's exact test, 2 tailed, pâ¯=â¯1.00). CONCLUSIONS: Using a sensitive uniplex polymerase chain reaction we found that the transplanted pulmonary virome often includes community-acquired respiratory viruses, including influenza, which are variably persistent but not associated with acute rejection.
Assuntos
Transplante de Pulmão , Pulmão/virologia , Pneumonia Viral/cirurgia , Pneumonia Viral/virologia , Adulto , Líquido da Lavagem Broncoalveolar/virologia , Feminino , Seguimentos , Transplante de Coração-Pulmão , Humanos , Influenza Humana/cirurgia , Influenza Humana/virologia , Transplante de Fígado , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Doadores de Tecidos , Transplantados , Adulto JovemRESUMO
Respiratory viruses are very common in the community and contribute to the burden of illness for patients with chronic respiratory diseases, including acute exacerbations. Traditional sampling methods are invasive and problematic to repeat. Accordingly, we explored whether respiratory viruses could be isolated from disposable spirometry filters and whether detection of viruses in this context represented presence in the upper or lower respiratory tract. Discovery (n = 53) and validation (n = 49) cohorts were recruited from a hospital outpatient department during two different time periods. Spirometry mouthpiece filters were collected from all participants. Respiratory secretions were sampled from the upper and lower respiratory tract by nasal washing (NW), sputum, and bronchoalveolar lavage (BAL). All samples were examined using RT-PCR to identify a panel of respiratory viruses (rhinovirus, respiratory syncytial virus, influenza A, influenza B, parainfluenza virus 1, 2 & 3, and human metapneumovirus). Rhinovirus was quantified using qPCR. Paired filter-NW samples (n = 29), filter-sputum samples (n = 24), filter-BAL samples (n = 39) and filter-NW-BAL samples (n = 10) provided a range of comparisons. At least one virus was detected in any sample in 85% of participants in the discovery cohort versus 45% in the validation cohort. Overall, 72% of viruses identified in the paired comparator method matched those detected in spirometry filters. There was a high correlation between viruses identified in spirometry filters compared with viruses identified in both the upper and lower respiratory tract using traditional sampling methods. Our results suggest that examination of spirometry filters may be a novel and inexpensive sampling method for the presence of respiratory viruses in exhaled breath.