Impact of Host Genetics and Biological Response Modifiers on Respiratory Tract Infections

Respiratory Comorbidities Associated with Bronchiectasis in Patients with Common Variable Immunodeficiency in the USIDNET Registry

BACKGROUND

Bronchiectasis is a major respiratory complication in patients with common variable immunodeficiency (CVID) and is associated with recurrent pulmonary infections. However, it is unclear whether other infections or non-infectious respiratory conditions are related to its development.

OBJECTIVE

To identify respiratory comorbidities associated with bronchiectasis in patients with CVID.

METHODS

A total of 1470 CVID patients enrolled in the USIDNET registry were included in a cross-sectional analysis. The primary outcome of our study was to determine the clinical characteristics and other respiratory conditions associated with respiratory comorbidities and physician-reported bronchiectasis.

RESULTS

One hundred ninety-seven CVID patients were noted to have bronchiectasis (13.4%). Affected patients were significantly older than patients without bronchiectasis (median age 54 years vs. 49 years, p = 0.0004). These patients also had lower serum IgA (13 mg/dL IQR 60 mg/dL vs. 28.4 mg/dL IQR 66 mg/dL, p = 0.000). Notably, chronic rhinosinusitis (OR = 1.69 95%CI 1.05-2.75), sinusitis (OR = 2.06 95%CI 1.38-3.09), pneumonia (OR = 2.70 95%CI 1.88-3.88), COPD (OR = 2.66 95%CI 1.51-4.67), and interstitial lung disease (OR = 2.34 95%CI 1.41-3.91) were independently associated with the development of bronchiectasis in this population.

CONCLUSION

These data suggest that lower and upper respiratory infections, chronic lower airway disease, and interstitial lung diseases are independently associated with bronchiectasis in CVID patients. Further study into predisposing conditions related to the development of bronchiectasis in CVID patients may allow prediction and early intervention strategies to prevent the development of this complication.

Comparative analysis of machine learning approaches for predicting respiratory virus infection and symptom severity

Respiratory diseases are among the major health problems causing a burden on hospitals. Diagnosis of infection and rapid prediction of severity without time-consuming clinical tests could be beneficial in preventing the spread and progression of the disease, especially in countries where health systems remain incapable. Personalized medicine studies involving statistics and computer technologies could help to address this need. In addition to individual studies, competitions are also held such as Dialogue for Reverse Engineering Assessment and Methods (DREAM) challenge which is a community-driven organization with a mission to research biology, bioinformatics, and biomedicine. One of these competitions was the Respiratory Viral DREAM Challenge, which aimed to develop early predictive biomarkers for respiratory virus infections. These efforts are promising, however, the prediction performance of the computational methods developed for detecting respiratory diseases still has room for improvement. In this study, we focused on improving the performance of predicting the infection and symptom severity of individuals infected with various respiratory viruses using gene expression data collected before and after exposure. The publicly available gene expression dataset in the Gene Expression Omnibus, named GSE73072, containing samples exposed to four respiratory viruses (H1N1, H3N2, human rhinovirus (HRV), and respiratory syncytial virus (RSV)) was used as input data. Various preprocessing methods and machine learning algorithms were implemented and compared to achieve the best prediction performance. The experimental results showed that the proposed approaches obtained a prediction performance of 0.9746 area under the precision-recall curve (AUPRC) for infection (i.e., shedding) prediction (SC-1), 0.9182 AUPRC for symptom class prediction (SC-2), and 0.6733 Pearson correlation for symptom score prediction (SC-3) by outperforming the best leaderboard scores of Respiratory Viral DREAM Challenge (a 4.48% improvement for SC-1, a 13.68% improvement for SC-2, and a 13.98% improvement for SC-3). Additionally, over-representation analysis (ORA), which is a statistical method for objectively determining whether certain genes are more prevalent in pre-defined sets such as pathways, was applied using the most significant genes selected by feature selection methods. The results show that pathways associated with the 'adaptive immune system' and 'immune disease' are strongly linked to pre-infection and symptom development. These findings contribute to our knowledge about predicting respiratory infections and are expected to facilitate the development of future studies that concentrate on predicting not only infections but also the associated symptoms.

Airborne transmission of biological agents within the indoor built environment: a multidisciplinary review

The nature and airborne dispersion of the underestimated biological agents, monitoring, analysis and transmission among the human occupants into building environment is a major challenge of today. Those agents play a crucial role in ensuring comfortable, healthy and risk-free conditions into indoor working and leaving spaces. It is known that ventilation systems influence strongly the transmission of indoor air pollutants, with scarce information although to have been reported for biological agents until 2019. The biological agents' source release and the trajectory of airborne transmission are both important in terms of optimising the design of the heating, ventilation and air conditioning systems of the future. In addition, modelling via computational fluid dynamics (CFD) will become a more valuable tool in foreseeing risks and tackle hazards when pollutants and biological agents released into closed spaces. Promising results on the prediction of their dispersion routes and concentration levels, as well as the selection of the appropriate ventilation strategy, provide crucial information on risk minimisation of the airborne transmission among humans. Under this context, the present multidisciplinary review considers four interrelated aspects of the dispersion of biological agents in closed spaces, (a) the nature and airborne transmission route of the examined agents, (b) the biological origin and health effects of the major microbial pathogens on the human respiratory system, (c) the role of heating, ventilation and air-conditioning systems in the airborne transmission and (d) the associated computer modelling approaches. This adopted methodology allows the discussion of the existing findings, on-going research, identification of the main research gaps and future directions from a multidisciplinary point of view which will be helpful for substantial innovations in the field.

Electrospun-Based Membranes as a Key Tool to Prevent Respiratory Infections

The use of electrospun meshes has been proposed as highly efficient protective equipment to prevent respiratory infections. Those infections can result from the activity of micro-organisms and other small dust particles, such as those resulting from air pollution, that impair the respiratory tract, induce cellular damage and compromise breathing capacity. Therefore, electrospun meshes can contribute to promoting air-breathing quality and controlling the spread of such epidemic-disrupting agents due to their intrinsic characteristics, namely, low pore size, and high porosity and surface area. In this review, the mechanisms behind the pathogenesis of several stressors of the respiratory system are covered as well as the strategies adopted to inhibit their action. The main goal is to discuss the performance of antimicrobial electrospun nanofibers by comparing the results already reported in the literature. Further, the main aspects of the certification of filtering systems are highlighted, and the expected technology developments in the industry are also discussed.

Advances in diagnostic tools for respiratory tract infections. From tuberculosis to COVID19: changing paradigms?

Respiratory tract infections (RTI) are one of the commonest reasons for seeking healthcare, but are amongst the most challenging diseases in terms of clinical decision making. Proper and timely diagnosis is critical in order to optimize management and prevent further emergence of antimicrobial resistance by misuse, or overuse of antibiotics. Diagnostic tools for RTI include those involving syndromic and etiological diagnosis: from clinical and radiological features to laboratory methods targeting both pathogen detection and host biomarkers, as well as their combinations in terms of clinical algorithms. They also include tools for predicting severity and monitoring treatment response. Unprecedented milestones have been achieved in the context of the COVID-19 pandemic, involving the most recent applications of diagnostic technologies both at genotypic and phenotypic level, which have changed paradigms in infectious respiratory diseases in terms of why, how and where diagnostics are performed. The aim of this review is to discuss advances in diagnostic tools that impact clinical decision making, surveillance and follow-up of RTI and tuberculosis. If properly harnessed, recent advances in diagnostic technologies, including omics and digital transformation emerge as an unprecedented opportunity to tackle ongoing and future epidemics while handling antimicrobial resistance from a One Health perspective.

Genotypic and Phenotypic Characterization of Staphylococcus aureus Isolates from the Respiratory Tract in Mechanically-Ventilated Patients

Staphylococcus aureus is a commensal and frequent colonizer of the upper respiratory tract. When mechanical ventilation disrupts natural defenses, S. aureus is frequently isolated from the lower airways, but distinguishing between colonization and infection is difficult. The objectives of this study were (1) to investigate the bacterial genome sequence in consecutive isolates in order to identify changes related to the pathological adaptation to the lower respiratory tract and (2) to explore the relationship between specific phenotypic and genotypic features with the patient’s study group, persistence of the clinical isolate and clinical outcome. A set of 94 clinical isolates were selected and corresponded to 34 patients that were classified as having pneumonia (10), tracheobronchitis (11) and bronchial colonization (13). Clinical strains were phenotypically characterized by conventional identification and susceptibility testing methods. Isolates underwent whole genome sequencing using Illumina HiSeq4000. Genotypic characterization was performed with an in-house pipeline (BacterialTyper). Genomic variation arising within-host was determined by comparing mapped sequences and de novo assemblies. Virulence factors important in staphylococcal colonization and infection were characterized using previously established functional assays. (1) Toxin production was assessed using a THP-1 cytotoxicity assay, which reports on the gross cytotoxicity of individual isolates. In addition, we investigated the expression of the major virulence factor, alpha-toxin (Hla) by Western blot. (2) Adhesion to the important extracellular matrix molecule, fibronectin, was determined using a standardized microtitre plate assay. Finally, invasion experiments using THP-1 and A539 cell lines and selected clinical strains were also performed. Repeated isolation of S. aureus from endotracheal aspirate usually reflects persistence of the same strain. Within-host variation is detectable in this setting, but it shows no evidence of pathological adaptation related to virulence, resistance or niche adaptations. Cytotoxicity was variable among isolates with 14 strains showing no cytotoxicity, with these latter presenting an unaltered Fn binding capacity. No changes on cytotoxicity were reported when comparing study groups. Fn binding capacity was reported for almost all strains, with the exception of two strains that presented the lowest values. Strains isolated from patients with pneumonia presented a lower capacity of adhesion in comparison to those isolated during tracheobronchitis (p = 0.002). Hla was detected in 71 strains (75.5%), with most of the producer strains in pneumonia and bronchial colonization group (p = 0.06). In our cohort, Hla expression (presence or absence) in sequential isolates was usually preserved (70%) although in seven cases the expression varied over time. No relationship was found between low cytotoxicity and intracellular persistence in invasion experiments. In our study population, persistent S. aureus isolation from airways in ventilated patients does not reflect pathological adaptation. There is an important diversity of sequence types. Cytotoxicity is variable among strains, but no association with study groups was found, whereas isolates from patients with pneumonia had lower adhesion capability. Favorable clinical outcome correlated with increased bacterial adhesion in vitro. Most of the strains isolated from the lower airways were Hla producers and no correlation with an adverse outcome was reported. The identification of microbial factors that contribute to virulence is relevant to optimize patient management during lower respiratory tract infections.

Prevention of New Respiratory Episodes in Children with Recurrent Respiratory Infections: An Expert Consensus Statement

In healthy infants and young children, the development of respiratory tract infections (RTIs) is extremely common. In this paper, we present an international consensus of the available approaches for the prevention of recurrent RTIs in children, including the atopic/allergic ones as well as those with asthma. Few convincing measures for reducing the frequency and clinical relevance of recurrent respiratory episodes in RTI-prone children have been developed until now. Among the most recently suggested measures, immunotherapy is attractive, but only for OM-85 is there a sufficient number of well-conducted clinical trials confirming efficacy in RTIs prevention with an adequate safety profile. In the case of probiotics, it is not clear which bacteria can offer the best results and which dosage and schedule of administration are the most effective. The problems of dosage and the schedule of administration are not solved also for vitamin D, despite some promising efficacy results. While we wait for new knowledge, the elimination or reduction as much as possible of the environmental factors that favor RTIs, vaccination when available and/or indicated, and the systematic application of the traditional methods for infection prevention, such as hand washing, remain the best measures to prevent recurrent infections in RTI-prone children.

Triple RNA-Seq Reveals Synergy in a Human Virus-Fungus Co-infection Model

High-throughput RNA sequencing (RNA-seq) is routinely applied to study diverse biological processes; however, when performed separately on interacting organisms, systemic noise intrinsic to RNA extraction, library preparation, and sequencing hampers the identification of cross-species interaction nodes. Here, we develop triple RNA-seq to simultaneously detect transcriptomes of monocyte-derived dendritic cells (moDCs) infected with the frequently co-occurring pulmonary pathogens Aspergillus fumigatus and human cytomegalovirus (CMV). Comparing expression patterns after co-infection with those after single infections, our data reveal synergistic effects and mutual interferences between host responses to the two pathogens. For example, CMV attenuates the fungus-mediated activation of pro-inflammatory cytokines through NF-κB (nuclear factor κB) and NFAT (nuclear factor of activated T cells) cascades, while A. fumigatus impairs viral clearance by counteracting viral nucleic acid-induced activation of type I interferon signaling. Together, the analytical power of triple RNA-seq proposes molecular hubs in the differential moDC response to fungal/viral single infection or co-infection that contribute to our understanding of the etiology and, potentially, clearance of post-transplant infections.

Role of Genetic Variants and Gene Expression in the Susceptibility and Severity of COVID-19

Since its first report in December 2019, coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly emerged as a pandemic affecting nearly all countries worldwide. As the COVID-19 pandemic progresses, the need to identify genetic risk factors for susceptibility to this serious illness has emerged. Host genetic factors, along with other risk factors may help determine susceptibility to respiratory tract infections. It is hypothesized that the ACE2 gene, encoding angiotensin-converting enzyme 2 (ACE2), is a genetic risk factor for SARS-CoV-2 infection and is required by the virus to enter cells. Together with ACE2, transmembrane protease serine 2 (TMPRSS2) and dipeptidyl peptidase-4 (DPP4) also play an important role in disease severity. Evaluating the role of genetic variants in determining the direction of respiratory infections will help identify potential drug target candidates for further study in COVID-19 patients. We have summarized the latest reports demonstrating that ACE2 variants, their expression, and epigenetic factors may influence an individual’s susceptibility to SARS-CoV-2 infection and disease outcome.

Effects of host genetic variations on response to, susceptibility and severity of respiratory infections

The recent outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a global crisis, necessitating the identification of genetic factors that modulate the risk of disorder or its severity. The current data about the role of genetic risk factors in determination of rate of SARS-CoV-2 infection in each ethnic group and the severity of disorder is limited. Moreover, several confounding parameters such as the number of tests performed in each country, the structure of the population especially the age distribution, the presence of risk factors for respiratory disorders such as smoking and other environmental factors might be involved in the variability in disease course or prevalence of infection among different ethnic groups. However, assessment of the role of genetic variants in determination of the course of other respiratory infections might help in recognition of possible candidate for further analysis in patients affected with SARS-CoV-2. In the current review, we summarize the data showing the association between genomic variants and risk of acute respiratory distress syndrome, respiratory infections or severity of these conditions with an especial focus on the SARS-CoV-2.

Angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 and the pathophysiology of coronavirus disease 2019 (COVID-19)

Angiotensin-converting enzyme 2 (ACE2) has been established as the functional host receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the current devastating worldwide pandemic of coronavirus disease 2019 (COVID-19). ACE2 is abundantly expressed in a variety of cells residing in many different human organs. In human physiology, ACE2 is a pivotal counter-regulatory enzyme to ACE by the breakdown of angiotensin II, the central player in the renin-angiotensin-aldosterone system (RAAS) and the main substrate of ACE2. Many factors have been associated with both altered ACE2 expression and COVID-19 severity and progression, including age, sex, ethnicity, medication, and several co-morbidities, such as cardiovascular disease and metabolic syndrome. Although ACE2 is widely distributed in various human tissues and many of its determinants have been well recognised, ACE2-expressing organs do not equally participate in COVID-19 pathophysiology, implying that other mechanisms are involved in orchestrating cellular infection resulting in tissue damage. Reports of pathologic findings in tissue specimens of COVID-19 patients are rapidly emerging and confirm the established role of ACE2 expression and activity in disease pathogenesis. Identifying pathologic changes caused by SARS-CoV-2 infection is crucially important as it has major implications for understanding COVID-19 pathophysiology and the development of evidence-based treatment strategies. Currently, many interventional strategies are being explored in ongoing clinical trials, encompassing many drug classes and strategies, including antiviral drugs, biological response modifiers, and RAAS inhibitors. Ultimately, prevention is key to combat COVID-19 and appropriate measures are being taken accordingly, including development of effective vaccines. In this review, we describe the role of ACE2 in COVID-19 pathophysiology, including factors influencing ACE2 expression and activity in relation to COVID-19 severity. In addition, we discuss the relevant pathological changes resulting from SARS-CoV-2 infection. Finally, we highlight a selection of potential treatment modalities for COVID-19. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Moslea Herba flavonoids alleviated influenza A virus-induced pulmonary endothelial barrier disruption via suppressing NOX4/NF-κB/MLCK pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Moslae Herba, a common traditional Chinese herb with special flavor, has potential for treating respiratory and gastrointestinal diseases.

AIM OF THIS STUDY

Lung endothelial barrier dysfunction (LEBD) accelerates the pathogenesis of influenza A virus (IAV)-induced secondary acute lung injury. New strategies against LEBD provide benefits in prevention and treatment of IAV. Previous studies showed that flavonoids (MHF), main bioactivity fraction derived from M. Herba, exerted anti-inflammatory and antiviral activities, but the underlying protection of MHF against IAV-induced acute lung injury remained obscure. The present study was to investigate the protection of MHF against IAV-induced LEBD in vivo and in vitro.

MATERIALS AND METHODS

Mice were intranasally challenged with IAV and orally administered with MHF for 5 days. The pulmonary hyperpermeability of infected mice was evaluated by Evans Blue staining and in vivo imaging. Serum levels of inflammatory cytokines and mediators were detected by ELISA assay. The transepithelial electrical resistance (TER) of human pulmonary microvascular endothelial cells (HPMVECs) was measured by using TER meter. The expressions of key proteins in NOX4-mediated NF-κB/MLCK pathways were determined by western blotting.

RESULTS

MHF treatment reduced lung index, W/D ratios, and serum levels of inflammatory factors (IL-6, TNF-α, IL-1β, PLA₂, LBT₄ and ICAM-1) in IAV-infected mice. Evans blue staining and in vivo imaging results revealed that MHF alleviated IAV-induced barrier dysfunction and pulmonary hyperpermeability. Moreover, luteolin and kaempferol, the main activity compounds in MHF, significantly inhibited TNF-α-induced HPMVEC apoptosis, and downregulated NF-κB/MLCK pathway by targeting NOX4.

CONCLUSION

MHF attenuated IAV-induced barrier dysfunction by suppressing NOX4/NF-κB/MLCK pathway and may serve as a potential agent for the prevention of LEBD and IAV.

Respiratory syncytial virus infection: why does disease severity vary among individuals?

Introduction: Respiratory syncytial virus (RSV) is the most common cause of acute lower respiratory tract infections in infancy. While many infants are infected with RSV, the nature and severity of the disease vary among individuals. RSV causes bronchiolitis, pneumonia, and asthma exacerbation. However, most children infected with RSV have only mild upper airways disease and may be asymptomatic.Areas covered: Despite efforts to elucidate mechanisms for the various clinical responses to RSV infection, they remain largely unknown, suggesting that susceptibility and disease are influenced by multiple intrinsic and extrinsic factors. This article reviews the available literature on the field of RSV disease severity and discusses important factors associated to susceptibility and different disease outcome.Expert opinion: The severity of RSV-induced illness is a phenomenon that depends on a variety of graded mechanisms of interaction between the host, virus, and environment. This may lead to differences in the intensity of immune response in the lung and different courses of the disease. By characterizing, classifying, and grading the affecting factors in high-risk patients versus those who do not fall ill by RSV, we may find therapies or point to disease-limiting medications.