Method for detection of respiratory viruses in the sputa of patients with cystic fibrosis

Respiratory Viruses and Cystic Fibrosis

The threat of respiratory virus infection to human health and well-being has been clearly highlighted by the coronavirus disease 2019 (COVID-19) pandemic. For people with cystic fibrosis (CF), the clinical significance of viral infections long predated the emergence of severe acute respiratory syndrome coronavirus 2. This article reviews the epidemiology, diagnosis, and treatment of respiratory virus infection in the context of CF as well as the current understanding of interactions between viruses and other microorganisms in the CF lung. The incidence of respiratory virus infection in CF varies by age with young children typically experiencing more frequent episodes than adolescents and adults. At all ages, respiratory viruses are very common in CF and are associated with pulmonary exacerbations. Respiratory viruses are identified at up to 69% of exacerbations, while viruses are also frequently detected during clinical stability. The full impact of COVID-19 in CF is yet to be established. Early studies found that rates of COVID-19 were lower in CF cohorts than in the general population. The reasons for this are unclear but may be related to the effects of shielding, infection control practices, maintenance CF therapies, or the inflammatory milieu in the CF lung. Observational studies have consistently identified that prior solid organ transplantation is a key risk factor for poor outcomes from COVID-19 in CF. Several key priorities for future research are highlighted. First, the impact of highly effective CFTR modulator therapy on the epidemiology and pathophysiology of viral infections in CF requires investigation. Second, the impact of respiratory viruses on the development and dynamics of the CF lung microbiota is poorly understood and viral infection may have important interactions with bacteria and fungi in the airway. Finally, bacteriophages represent a key focus of future investigation both for their role in transmission of antimicrobial resistance and as a promising treatment modality for multiresistant pathogens.

Acute Pulmonary Exacerbation Phenotypes in Patients with Cystic Fibrosis

Rationale: The etiology of cystic fibrosis (CF) pulmonary exacerbations (PEx) is likely multifactorial with viral, bacterial, and non-infectious pathways contributing. Objectives: To determine whether viral infection status and CRP (C-reactive protein) can classify subphenotypes of PEx that differ in outcomes and biomarker profiles. Methods: Patients were recruited at time of admission for a PEx. Nasal swabs and sputum samples were collected and processed using the respiratory panel of the FilmArray multiplex polymerase chain reaction (PCR). Serum and plasma biomarkers were measured. PEx were classified using serum CRP and viral PCR: "pauci-inflammatory" if CRP < 5 mg/L, "non-viral with systemic inflammation" if CRP ⩾ 5 mg/L and no viral infection detected by PCR and "viral with systemic inflammation" if CRP ⩾ 5 mg/L and viral infection detected by PCR. Results: Discovery cohort (n = 59) subphenotype frequencies were 1) pauci-inflammatory (37%); 2) non-viral with systemic inflammation (41%); and 3) viral with systemic inflammation (22%). Immunoglobulin G, immunoglobulin M, interleukin-10, interleukin-13, serum calprotectin, and CRP levels differed across phenotypes. Reduction from baseline in forced expiratory volume in 1 second as percent predicted (FEV₁pp) at onset of exacerbation differed between non-viral with systemic inflammation and viral with systemic inflammation (-6.73 ± 1.78 vs. -13.5 ± 2.32%; P = 0.025). Non-viral with systemic inflammation PEx had a trend toward longer duration of intravenous antibiotics versus pauci-inflammation (18.1 ± 1.17 vs. 14.8 ± 1.19 days, P = 0.057). There were no differences in percent with lung function recovery to <10% of baseline FEV₁pp. Similar results were seen in local and external validation cohorts comparing a pauci-inflammatory to viral/non-viral inflammatory exacerbation phenotypes. Conclusions: Subphenotypes of CF PEx exist with differences in biomarker profile, clinical presentation, and outcomes.

Viruses in cystic fibrosis patients' airways

Although bacteria have historically been considered to play a major role in cystic fibrosis (CF) airway damage, a strong impact of respiratory viral infections (RVI) is also now recognized. Emerging evidence confirms that respiratory viruses are associated with deterioration of pulmonary function and exacerbation and facilitation of bacterial colonization in CF patients. The aim of this review is to provide an overview of the current knowledge on respiratory viruses in CF airways, to discuss the resulting inflammation and RVI response, to determine how to detect the viruses, and to assess their clinical consequences, prevalence, and interactions with bacteria. The most predominant are Rhinoviruses (RVs), significantly associated with CF exacerbation. Molecular techniques, and especially multiplex PCR, help to diagnose viral infections, and the coming rise of metagenomics will extend knowledge of viral populations in the complex ecosystem of CF airways. Prophylaxis and vaccination are currently available only for Respiratory syncytial and Influenza virus (IV), but antiviral molecules are being tested to improve CF patients' care. All the points raised in this review highlight the importance of taking account of RVIs and their potential impact on the CF airway ecosystem.

The diagnosis and management of respiratory viral infections in cystic fibrosis

INTRODUCTION

Respiratory viruses, such as those that cause influenza and the common cold, are a regular feature of life for the entire human population. Among people with CF, these viruses are associated with prolonged respiratory illness and show a clear association with pulmonary exacerbations which in turn are associated with lung function decline and risk of death. Human rhinovirus is the most commonly encountered respiratory viral pathogen in CF although adenovirus, bocavirus, coronavirus, influenza, parainfluenza, metapneumovirus and respiratory syncytial virus are all also responsible for infections in this population. Areas covered: This article reviews the epidemiology, clinical impact and therapeutic options for respiratory virus infection in both children and adults with CF. Expert commentary: The management of CF to date has largely focused on airway clearance strategies, nutritional support and aggressive antibacterial therapy. We highlight the significant role that respiratory viruses play in CF lung disease and argue that these pathogens represent an under-exploited target in the battle to control patients' symptoms and disease progression.

Bronchiectasis exacerbations: The role of atypical bacteria, respiratory syncytial virus and pulmonary function tests

BACKGROUND

Aside from the known role of common bacteria, there is a paucity of data regarding the possible role of atypical bacteria and viruses in exacerbations of non-cystic fibrosis bronchiectasis.

OBJECTIVE

To explore the possible role of atypical bacteria (namely, Mycoplasma pneumoniae and Chlamydophila pneumoniae) and respiratory syncytial virus (RSV) as causative agents of bronchiectasis exacerbations.

METHODS

A cohort of 33 patients was studied over a two-year period (one year follow-up for each patient). Polymerase chain reaction for the detection of M pneumoniae, C pneumoniae and RSV in bronchoalveolar lavage samples were performed during all visits. Antibody titres (immunoglobulin [Ig]M and IgG) against the aforementioned pathogens were also measured. In addition, cultures for common bacteria and mycobacteria were performed from the bronchoalveolar lavage samples.

RESULTS

Fifteen patients experienced a total of 19 exacerbations during the study period. Although RSV was detected by polymerase chain reaction during stable visits in four patients, it was never detected during an exacerbation. M pneumoniae and C pneumoniae were never detected at stable visits or during exacerbations. IgM antibody titres for these three pathogens were negative in all patient visits.

CONCLUSIONS

Atypical pathogens and RSV did not appear to be causative agents of bronchiectasis exacerbations.

Microbiome in cystic fibrosis: Shaping polymicrobial interactions for advances in antibiotic therapy

Recent molecular methodologies have demonstrated a complex microbial ecosystem in cystic fibrosis (CF) airways, with a wide array of uncommon microorganisms co-existing with the traditional pathogens. Although there are lines of evidence supporting the contribution of some of those emergent species for lung disease chronicity, clinical significance remains uncertain for most cases. A possible contribution for disease is likely to be related with the dynamic interactions established between microorganisms within the microbial community and with the host. If this is the case, management of CF will only be successful upon suitable and exhaustive modulation of such mixed ecological processes, which will also be useful to predict the effects of new therapeutic interventions.

Influenza vaccination in children with cystic fibrosis

Cystic fibrosis (CF) is an inherited autosomal recessive disease characterized by progressive pulmonary damage and respiratory failure. It is known that bacterial infections play a critical role in the development of significant lung damage, whereas the role of respiratory viruses in CF pulmonary exacerbations and the relationship between viral infections and the progression of lung damage are uncertain. Health authorities throughout the world recommend influenza vaccination for CF patients. The aim of this review is to analyze the impact of seasonal and pandemic influenza on CF patients and data concerning influenza vaccination in order to assess the current situation and identify areas for future study. As data are limited, further well-constructed clinical studies of the effectiveness of influenza vaccination on the main clinical outcome measures of pulmonary function and nutritional status in patients with CF are required.

Influenza vaccination in children at high risk of respiratory disease

Chronic respiratory diseases (CRDs) are a heterogeneous group of diseases that can affect the pediatric population and health authorities throughout the world recommend influenza vaccination because of the significant risk of influenza-related complications. However, despite this recommendation, vaccine coverage is generally unsatisfactory. The aim of this review is to analyze the impact of influenza on children at high risk of respiratory disease, and the immunogenicity, safety and efficacy of influenza vaccination in such children. The results show that there is a significant risk of influenza-related complications in preterm neonates and infants, in whom influenza vaccines are immunogenic and safe (although their efficacy has not been specifically studied). There are conflicting data concerning the effect of influenza infection on asthma morbidity in children, and whether or not influenza vaccination helps to prevent asthma exacerbations. Recent data provide no evidence that influenza is more frequent in patients with cystic fibrosis than in healthy subjects, or that it is responsible for increased lower respiratory tract morbidity. The lack of any clear correlate of protection suggests that future studies should also consider the efficacy of the different influenza vaccines and not only evaluate them in terms of immunogenicity. Furthermore, there is a need for clinical studies to assess the effectiveness of the available vaccines in patients with other rare CRDs and other chronic underlying diseases with possibly severe respiratory involvement. It is also important to determine whether children with recurrent respiratory tract infections should be included in the list of those for whom influenza vaccination is recommended. In the meantime, given the increasing evidence of the burden of influenza on the population as a whole and the benefits associated with vaccination, annual influenza vaccinations should be recommended for all children at high risk of respiratory disease and the members of their households.

Spectrum of viral infections in patients with cystic fibrosis

This review explores the extensive influence of viral infections leading to chronic deterioration of lung function in patients with cystic fibrosis (CF). The mechanisms how viral agents affect the pathogenesis as well as the inflammatory and immune response of CF are discussed. Viral infections of the upper and lower respiratory tract due to viruses in CF patients and methods for diagnosis of respiratory viruses are described in detail. The importance of respiratory and non-respiratory viral agents for the pathogenesis, especially for the exacerbation of bacterial lower respiratory tract infections and course of CF, is stressed, especially emphasizing respiratory syncytial virus, influenza virus, rhinovirus, and human herpes viruses. Possible harmful effects of further viruses like adenovirus, bocavirus, coronavirus, metapneumovirus, parainfluenzavirus on the lung function of CF patients are discussed. The potential use of adenovirus-based vectors for somatic gene therapy is mentioned.

Respiratory viruses in children with cystic fibrosis: viral detection and clinical findings

BACKGROUND

Viral detection from different respiratory sample types in children with cystic fibrosis (CF) is facilitated by available molecular methods, but optimum sampling strategies have not been identified. In addition, associations between viral detection and respiratory symptoms are not well described.

OBJECTIVES

Study goals were to compare molecular detection of viruses from concurrent upper airway and sputum samples in children with CF and to describe relative frequency of respiratory viral infections and identify potential clinical associations.

METHODS

We conducted a 2-year prospective surveillance study in 44 children with CF aged 6-18 years. Upper airway and sputum samples were collected quarterly and during pulmonary exacerbations and tested for respiratory syncytial virus (RSV), influenza viruses, parainfluenza viruses types 1-4, human metapneumovirus, coronaviruses, rhinoviruses, and adenoviruses. Physical exams and symptom surveys were used to identify respiratory signs and symptoms.

RESULTS

Upper airway samples were collected at 359 visits; concordance of PCR-based viral detection was examined in a subset of paired upper airway and sputum samples from 21 participants at 92 visits. Rhinovirus was the most commonly detected virus (23·1% overall), and rhinovirus detection was the same for both sample types (21·7% each). Sensitivity and specificity for the detection of rhinovirus in sputum relative to upper airway sampling were 70% and 91·7%, respectively. Respiratory symptoms associated with rhinovirus detection included increased cough, increased nasal congestion, increased sputum production, and wheezing.

CONCLUSIONS

A relatively high frequency of rhinovirus detection was observed by either upper airway or sputum samples, and clinical findings suggest a significant-associated symptom burden.

Lung infections in cystic fibrosis: deriving clinical insight from microbial complexity

Lower respiratory tract bacterial infections, such as those associated with cystic fibrosis lung disease, represent a major healthcare burden. Treatment strategies are currently informed by culture-based routine diagnostics whose limitations, including an inability to isolate all potentially clinically significant bacterial species present in a sample, are well documented. Some advances have resulted from the introduction of culture-independent molecular assays for the detection of specific pathogens. However, the application of bacterial community profiling techniques to the characterization of these infections has revealed much higher levels of microbial diversity than previously recognized. These findings are leading to a fundamental shift in the way such infections are considered. Increasingly, polymicrobial infections are being viewed as complex communities of interacting organisms, with dynamic processes key to their pathogenicity. Such a model requires an analytical strategy that provides insight into the interactions of all members of the infective community. The rapid advance in sequencing technology, along with protocols that limit analysis to viable bacterial cells, are for the first time providing an opportunity to gain such insight.

The changing microbial epidemiology in cystic fibrosis

Infection of the airways remains the primary cause of morbidity and mortality in persons with cystic fibrosis (CF). This review describes salient features of the epidemiologies of microbial species that are involved in respiratory tract infection in CF. The apparently expanding spectrum of species causing infection in CF and recent changes in the incidences and prevalences of infection due to specific bacterial, fungal, and viral species are described. The challenges inherent in tracking and interpreting rates of infection in this patient population are discussed.

The role of respiratory viruses in cystic fibrosis

Background

Previous studies have suggested a role played by respiratory viruses in the exacerbation of cystic fibrosis (CF). However, the impact of respiratory viruses could have been underestimated because of the low detection rate by conventional laboratory methods.

Methods

Children with CF had nasal swabs and sputum samples obtained on a routine basis and when they developed respiratory exacerbations. Nucleic Acid Sequence Based Amplification (NASBA) was used to detect respiratory viruses from nasal swabs. The definition of a respiratory exacerbation was when the symptom score totalled to 4 or more, or if the peak expiratory flow fell by more than 50 l/min from the child's usual best value, or if the parent subjectively felt that the child was developing a cold.

Results

71 patients had 165 reported episodes of respiratory exacerbations. 138 exacerbation samples were obtained of which 63 (46%) were positive for respiratory viruses. In contrast, 23 of 136 asymptomatic nasal swabs (16.9%) were positive for respiratory viruses. There was significantly more viruses being detected during respiratory exacerbations, in particular influenza A, influenza B and rhinovirus (p < 0.05).

Upper respiratory symptoms significantly correlated with positive respiratory viral detection (p < 0.05). This study also showed that viral respiratory exacerbations in CF could be independent from bacterial infections.

Conclusions

Respiratory viruses are associated with exacerbations in CF and upper respiratory symptoms are strong predictors for their presence. ‘Real-time’ NASBA has a rapid turn-around time and has the potential to aid clinical decision making, such as the use of anti-virals and administration of antibiotics.

Cystic Fibrosis: The Mechanisms of Pathogenesis of an Inherited Lung Disorder

Cystic fibrosis patients exhibit lung disease consistent with a failure of innate airway defense mechanisms. The link between abnormal ion transport and disease initiation and progression is not fully understood, but airway mucus dehydration seems paramount in the initiation of CF lung disease. New therapies are currently in development that target the ion transport defects in CF with the intention of rehydrating airway surfaces.

Airway surface dehydration in cystic fibrosis: pathogenesis and therapy

Cystic fibrosis (CF) lung disease reflects the failure of airways defense against chronic bacterial infection. Studies of CF cultures, transgenic mice, and CF patients suggest that the initiating event in CF airways disease pathogenesis is reduced airway surface liquid (ASL) volume, i.e., dehydration. CF ASL volume regulation depends on a single extracellular signaling system, ATP, which renders CF airways more vulnerable to disease-causing insults (e.g., viruses) than are normal airways, which regulate ASL volume by dual ATP and adenosine signaling pathways. Clinical studies have explored the hypothesis that treating the dehydration of CF airways will be therapeutically beneficial. Inhaled hypertonic saline osmotically draws water onto airway surfaces, improves mucus clearance and pulmonary function, and reduces acute exacerbations in CF patients. Thus, rehydration therapies may slow the progression of CF lung disease in patients with established bacterial infection and may prevent the onset of CF lung disease if initiated early in life.

Ten years of viral and non-bacterial serology in adults with cystic fibrosis

Viral infections are associated with pulmonary exacerbations in children with cystic fibrosis (CF), but few studies have addressed the frequency in adults. This paper investigates the frequency and impact of viral infections in adults with CF receiving intravenous antibiotics. Pre- and post-treatment spirometry, inflammatory markers and antibody titres against influenza A, influenza B, adenovirus, respiratory syncytial virus, Mycoplasma pneumoniae, Chlamydia psittaci, and Coxiella burnetti were analysed over a 10-year period. Non-bacterial infections were identified in 5.1% of 3156 courses of treatment. The annual incidence of admissions per patient associated with viral infection was 4.9%. The presence of viral infection in association with a pulmonary exacerbation did not adversely affect lung function or inflammatory markers in the short term. Adults with CF have a lower incidence of respiratory viral infections associated with pulmonary exacerbations requiring intravenous antibiotics compared to children and infants with CF.

Evidence for airway surface dehydration as the initiating event in CF airway disease

Cystic fibrosis (CF) lung disease reflects persistent bacterial infection of airway lumens. Several hypotheses have been advanced to link mutations in the CFTR gene to the failure of the CF lung to defend itself against bacterial infection. Amongst the most productive hypotheses at present is the ''low airway surface liquid (ASL) volume'' or ''dehydration'' hypothesis. This hypothesis predicts that airway surface dehydration produces the mucus adhesion, inflammation, and bacterial biofilm formation characteristic of CF. Clinical trials of inhaled hypertonic saline have demonstrated therapeutic benefit of manoeuvres designed to rehydrate CF airway surfaces.

Viral and atypical bacterial infections in the outpatient pediatric cystic fibrosis clinic

BACKGROUND

Respiratory viral and atypical bacterial infections are associated with pulmonary exacerbations and hospitalisations in cystic fibrosis patients. We wanted to study the impact of such infections on children attending the outpatient clinic.

METHODS

Seventy-five children were followed for 12 months at regular clinic visits. Routine sputum/laryngeal aspirations were tested with PCR for 7 respiratory viruses. Antibodies against C. pneumoniae, M. pneumoniae and B. pertussis were measured every 3-4 months. FEV-1, FEF(25-75) and specific airway resistance, "viral" symptoms and bacterial culture were recorded.

RESULTS

Ninety-seven viral and 21 atypical bacterial infections were found. FEV-1 was significantly reduced during viral infection (-12.5%, p=0.048), with the exception of rhinovirus infection. A small change in FEV-1 (-3%) was seen during atypical bacterial infection (p=0.039). Viral and atypical bacterial infections caused no change in type and frequency of bacterial culture. Positive predictive value of "viral symptoms" was low (0.64%). Eight patients received "unnecessary" antibiotics because of viral symptoms.

CONCLUSIONS

Some viral infections and atypical bacterial infections affect FEV-1 acutely. Viral infections did not precipitate bacterial infection or change of colonisation. Clinical symptoms failed to diagnose viral infection accurately. Routine surveillance for virus or atypical bacteria seems not to be justified in this patient category.

Viral respiratory infections in cystic fibrosis

Viral respiratory infections in CF patients are associated with an increase in morbidity at short and long term. Viral infections have a greater impact on CF patients compared to non-CF controls. They result in increased respiratory symptoms, deterioration of Shwachman and radiological scores, prolonged hospitalizations, a persistent decrease of pulmonary function, increased use of antibiotics and a higher frequency of exacerbations at follow-up. In addition, interaction between viruses and bacteria in CF is suggested. Some studies observe increased new bacterial colonization and raised antipseudomonal antibodies in episodes of viral respiratory infections. Experimental data suggest that increased virus replication, impaired specific anti-bacterial defense and increased adherence of bacteria play a role in the pathogenesis of viral respiratory infections in CF. Further knowledge about the role of viruses and interaction with bacteria in CF lung disease might result in new therapeutic strategies to improve prognosis of CF patients.