Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis

Microbial Community Analysis of Saliva and Biopsies in Patients With Oral Lichen Planus

The specific etiology and pathogenesis of oral lichen planus (OLP) remain elusive, and microbial dysbiosis may play an important role in OLP. We evaluated the saliva and tissue bacterial community of patients with OLP and identified the colonization of bacteria in OLP tissues. The saliva (n = 60) and tissue (n = 24) samples from OLP patients and the healthy controls were characterized by 16S rDNA gene sequencing and the bacterial signals in OLP tissues were detected by fluorescence in situ hybridization (FISH) targeting the bacterial 16S rDNA gene. Results indicate that the OLP tissue microbiome was different from the microbiota of OLP saliva. Compared with the healthy controls, Capnocytophaga and Gemella were higher in OLP saliva, while Escherichia–Shigella and Megasphaera were higher in OLP tissues, whereas seven taxa, including Carnobacteriaceae, Flavobacteriaceae, and Megasphaera, were enriched in both saliva and tissues of OLP patients. Furthermore, FISH found that the average optical density (AOD) of bacteria in the lamina propria of OLP tissues was higher than that of the healthy controls, and the AOD of bacteria in OLP epithelium and lamina propria was positively correlated. These data provide a different perspective for future investigation on the OLP microbiome.

Simultaneous profiling and cultivation of the skin microbiome of healthy young adult skin for the development of therapeutic agents

Background

Studies on the impact of the skin microbiota on human health have been gaining more attention. Bacteria are associated with various diseases, although certain strains of bacteria, which are known as probiotics, are considered beneficial. Mixtures of several bacteria (bacterial cocktail) isolated from targeted organs have shown promising modulatory activities for use in skin therapeutics. The objectives of this study were to determine and identify the microbial communities on the skin that can potentially be used as probiotics, as determined by bacterial isolation and cultivation, followed by next-generation sequencing (NGS).

Results

Samples were collected by swabbing on forehead and cheek skin. Genomic DNA from bacterial swab samples were directly extracted to be further processed into NGS. Cultivation of skin bacteria was carried out in subsequent medium. Thus, around twenty bacterial isolates with different characteristics were selected and identified by both culture-based method and 16sRNA sequencing. We found that Actinobacteria and Firmicutes are the most abundant phylum present on the skin as presented by NGS data, which constitute to 67% and 28.59% of the whole bacterial population, consecutively. However, Staphylococcus hominis, Staphylococcus warneri, and Micrococcus luteus (AN MK968325.1; AN MK968315.1; and MK968318.1 respectively) were able to be obtained in the samples of cultivable, and could be potentially developed as probiotics in skin microbiome therapeutic as well as for postbiotic formulation.

Conclusion

Skin microbiome is considered to provide several probiotics for skin therapeutic. However, some opportunistic pathogens were discovered in this study population. Thus, the promising formula of bacterial cocktail for skin microbiome therapeutic must be thoroughly elucidated to avoid unwanted species. Our study is the first human skin microbiome profile of Indonesia resulted from a Next Generation Sequencing as an effort to show a representative of tropical country profile.

Increased Risk of Chronic Periodontitis in Chronic Rhinosinusitis Patients: A Longitudinal Follow-Up Study Using a National Health-Screening Cohort

This study compared the risk of chronic periodontitis (CP) between chronic rhinosinusitis (CRS) and non-chronic rhinosinusitis (control) patients using a national cohort dataset from the Korean Health Insurance Review and Assessment Service. CRS (n = 5951) and control participants (n = 23,804) were selected after 1:4 ratio matching for age, sex, income, region of residence, and preoperative CP visits. Postoperative CP visits were measured between 2002 and 2015. The margin of equivalence of the difference between the CRS and control groups was set between -0.5 and 0.5. Statistical significance was noted in the post-index date (ID) of the third, fourth, and fifth year periods. In subgroup analyses according to age and sex, statistical significance was observed in 40-59-year-old males in post-ID third, fourth, and fifth year periods, ≥60-year-old males in post-ID third and fourth year periods, and ≥60-year-old females in post-ID fifth year period (p < 0.05, each). In another subgroup analysis based on the number of pre-ID CP visits, statistical significance was observed for pre-ID CP (0 time) in the third, fourth, and fifth year periods (p < 0.05, each). This study revealed that CRS participants were likely to receive CP diagnosis and treatment.

Chinese Society of Allergy and Chinese Society of Otorhinolaryngology-Head and Neck Surgery Guideline for Chronic Rhinosinusitis

The current document is based on a consensus reached by a panel of experts from the Chinese Society of Allergy and the Chinese Society of Otorhinolaryngology-Head and Neck Surgery, Rhinology Group. Chronic rhinosinusitis (CRS) affects approximately 8% of Chinese adults. The inflammatory and remodeling mechanisms of CRS in the Chinese population differ from those observed in the populations of European descent. Recently, precision medicine has been used to treat inflammation by targeting key biomarkers that are involved in the process. However, there are no CRS guidelines or a consensus available from China that can be shared with the international academia. The guidelines presented in this paper cover the epidemiology, economic burden, genetics and epigenetics, mechanisms, phenotypes and endotypes, diagnosis and differential diagnosis, management, and the current status of CRS in China. These guidelines-with a focus on China-will improve the abilities of clinical and medical staff during the treatment of CRS. Additionally, they will help international agencies in improving the verification of CRS endotypes, mapping of eosinophilic shifts, the identification of suitable biomarkers for endotyping, and predicting responses to therapies. In conclusion, these guidelines will help select therapies, such as pharmacotherapy, surgical approaches and innovative biotherapeutics, which are tailored to each of the individual CRS endotypes.

Corynebacterium tuberculostearicum, a human skin colonizer, induces the canonical nuclear factor-κB inflammatory signaling pathway in human skin cells

INTRODUCTION

Corynebacterium tuberculostearicum (C. t.) is a ubiquitous bacterium that colonizes human skin. In contrast to other members of the genus Corynebacterium, such as toxigenic Corynebacterium diphtheriae or the opportunistic pathogen Corynebacterium jeikeium, several studies suggest that C. t. may play a role in skin health and disease. However, the mechanisms underlying these effects remain poorly understood.

METHODS

To investigate whether C. t. induces inflammatory pathways in primary human epidermal keratinocytes (HEKs) and human cutaneous squamous carcinoma cells (SCCs), cell culture, reverse transcription-polymerase chain reaction (PCR), enzyme-linked immunosorbent assay, immunofluorescence microscopy, Western blot, chromatin immunoprecipitation-PCR, small interfering RNA knockdown and luciferase reporter expression system were used.

RESULTS

Herein, we demonstrate that C. t. upregulates the messenger RNA (mRNA) and protein levels of inflammatory mediators in two human skin cell lines, HEKs and SCCs. We further show activation of the canonical nuclear factor-κB (NF-κB) pathway in response to C. t. infection, including phosphorylation of the inhibitor of κB (IκB), the nuclear translocation of NF-κB subunit (NF-κB-P65 ) and the recruitment of NF-κB-P65 and RNA polymerase to the NF-κB response elements at the promoter region of the inflammatory genes. Lastly, the data confirm that C. t.-induced tumor necrosis factor mRNA expression in HEKs is toll-like receptor 2 (TLR2 ) dependent.

CONCLUSION

Our results offer a mechanistic model for C. t.-induced inflammation in human keratinocytes via TLR2 and activation of IκB kinase and downstream signaling through the canonical NF-κB pathway. Relevance to chronic inflammatory diseases of the skin and cutaneous oncology is discussed.

Association of the sinonasal bacterial microbiome with clinical outcomes in chronic rhinosinusitis: a systematic review

Background

The association between sinonasal microbiome and clinical outcomes of patients with chronic rhinosinusitis (CRS) is unclear. We performed a systematic review of prior studies evaluating the CRS microbiome in relation to clinical outcomes.

Methods

Computerized searches of PubMed/Medline, Cochrane, and EMBASE were updated through October 2019 revealing a total of 9 studies including 244 CRS patients. A systematic review of the literature was performed, including data extraction focusing on sample region, sequencing platforms, predominant organisms, and outcomes measures.

Results

Nine criterion‐meeting studies included 244 CRS patients, with varied results. Eight studies used 16s–ribosomal RNA (16s‐rRNA) gene sequencing to assess the sinonasal microbiome and 1 used 16s‐rRNA PhyloChip analysis. Seven studies used Sino‐Nasal Outcome Test scores, 1 applied another CRS symptom metric, and 1 used need for additional procedures/antibiotics as the primary clinical outcome. Three studies suggest that baseline abundance of phylum Actinobacteria (specifically genus Corynebacterium) was predictive of better surgical outcome. One study found C. tuberculostearicum was positively correlated with symptom severity. Another study revealed genus Escherichia was overrepresented in CRS and had positive correlation with increased symptom scores. In addition, 1 study identified Acinetobacter johnsonii to be associated with improvement in symptom scores while supporting Pseudomonas aeruginosa as having a negative impact on quality of life.

Conclusion

Microbiome data are varied in their association with clinical outcomes of CRS patients. Further research is required to identify if predominance of certain microbes within the microbiome is predictive of CRS patients’ outcomes.

The Microbiome and Chronic Rhinosinusitis

Chronic rhinosinusitis (CRS) is persistent inflammation and/or infection of the nasal cavity and paranasal sinuses. Recent advancements in culture-independent molecular techniques have enhanced understanding of interactions between sinus microbiota and upper airway microenvironment. The dysbiosis hypothesis-alteration of microbiota associated with perturbation of the local ecological landscape-is suggested as a mechanism involved in CRS pathogenesis. This review discusses the complex role of the microbiota in health and in CRS and considerations in sinus microbiome investigation, dysbiosis of sinus microbiota in CRS, microbial interactions in CRS, and development of preclinical models. The authors conclude with future directions for CRS-associated microbiome research.

Dual and Triple Epithelial Coculture Model Systems with Donor-Derived Microbiota and THP-1 Macrophages To Mimic Host-Microbe Interactions in the Human Sinonasal Cavities

Despite the relevance of the resident microbiota in sinonasal health and disease and the need for cross talk between immune and epithelial cells in the upper respiratory tract, these parameters have not been combined in a single in vitro model system. We have developed a coculture system of differentiated respiratory epithelium and natural nasal microbiota and incorporated an immune component. As indicated by absence of cytotoxicity and stable cytokine profiles and epithelial integrity, nasal microbiota from human origin appeared to be well tolerated by host cells, while microbial community composition remained representative for that of the human (sino)nasal cavity. Importantly, the introduction of macrophage-like cells enabled us to obtain a differential readout from the epithelial cells dependent on the donor microbial background to which the cells were exposed. We conclude that both model systems offer the means to investigate host-microbe interactions in the upper respiratory tract in a more representative way.

The epithelium of the human sinonasal cavities is colonized by a diverse microbial community, modulating epithelial development and immune priming and playing a role in respiratory disease. Here, we present a novel in vitro approach enabling a 3-day coculture of differentiated Calu-3 respiratory epithelial cells with a donor-derived bacterial community, a commensal species (Lactobacillus sakei), or a pathobiont (Staphylococcus aureus). We also assessed how the incorporation of macrophage-like cells could have a steering effect on both epithelial cells and the microbial community. Inoculation of donor-derived microbiota in our experimental setup did not pose cytotoxic stress on the epithelial cell layers, as demonstrated by unaltered cytokine and lactate dehydrogenase release compared to a sterile control. Epithelial integrity of the differentiated Calu-3 cells was maintained as well, with no differences in transepithelial electrical resistance observed between coculture with donor-derived microbiota and a sterile control. Transition of nasal microbiota from in vivo to in vitro conditions maintained phylogenetic richness, and yet a decrease in phylogenetic and phenotypic diversity was noted. Additional inclusion and coculture of THP-1-derived macrophages did not alter phylogenetic diversity, and yet donor-independent shifts toward higher Moraxella and Mycoplasma abundance were observed, while phenotypic diversity was also increased. Our results demonstrate that coculture of differentiated airway epithelial cells with a healthy donor-derived nasal community is a viable strategy to mimic host-microbe interactions in the human upper respiratory tract. Importantly, including an immune component allowed us to study host-microbe interactions in the upper respiratory tract more in depth.

IMPORTANCE Despite the relevance of the resident microbiota in sinonasal health and disease and the need for cross talk between immune and epithelial cells in the upper respiratory tract, these parameters have not been combined in a single in vitro model system. We have developed a coculture system of differentiated respiratory epithelium and natural nasal microbiota and incorporated an immune component. As indicated by absence of cytotoxicity and stable cytokine profiles and epithelial integrity, nasal microbiota from human origin appeared to be well tolerated by host cells, while microbial community composition remained representative for that of the human (sino)nasal cavity. Importantly, the introduction of macrophage-like cells enabled us to obtain a differential readout from the epithelial cells dependent on the donor microbial background to which the cells were exposed. We conclude that both model systems offer the means to investigate host-microbe interactions in the upper respiratory tract in a more representative way.

Personalized Medicine in Chronic Rhinosinusitis: Phenotypes, Endotypes, and Biomarkers

Chronic rhinosinusitis (CRS) is a heterogeneous disease process with a complex underlying cause. Improved understanding of CRS pathophysiology has facilitated new approaches to management of the patient with CRS that rely on targeting patient-specific characteristics and individual inflammatory pathways. A more personalized approach to care will ultimately incorporate a combination of phenotypic and endotypic classification systems to guide treatment. This review summarizes current evidence with respect to CRS phenotypes and endotypes, as well as the identification of potential biomarkers with potential to guide current and future treatment algorithms.

[Advances in the endotypes of chronic rhinosinusitis]

The pathogenesis of chronic rhinosinusitis（CRS） is complex. There are differences in the clinical manifestations and therapeutic effects of CRS dominated by different causes. At present, there is a lack of uniform classification standards in clinical practice. In this paper, the research progress in the endotype of CRS in recent years was discussed.

Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in critically ill patients

The purpose of this study was to assess the value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) for the diagnosis of severe respiratory diseases based on interpretation of sequencing results. BALF samples were harvested and used for mNGS as well as microbiological detection. Infectious bacteria or fungi were defined according to relative abundance and number of unique reads. We performed mNGS on 35 BALF samples from 32 patients. The positive rate reached 100% in the mNGS analysis of nine immunocompromised patients. Compared with the culture method, mNGS had a diagnostic sensitivity of 88.89% and a specificity of 74.07% with an agreement rate of 77.78% between these two methods. Compared with the smear method and PCR, mNGS had a diagnostic sensitivity of 77.78% and a specificity of 70.00%. In 13 cases, detection results were positive by mNGS but negative by culture/smear and PCR. The mNGS findings in 11/32 (34.4%) cases led to changes in treatment strategies. Linear regression analysis showed that diversity was significantly correlated with interval between disease onset and sampling. Dynamic changes in reads could indirectly reflect therapeutic effectiveness. BALF mNGS improves sensitivity of pathogen detection and provides guidance in clinical practice. Potential pathogens can be identified based on relative abundance and number of unique reads.

Anterior Nares Diversity and Pathobionts Represent Sinus Microbiome in Chronic Rhinosinusitis

It is generally believed that the microbiome plays a role in the pathophysiology of chronic rhinosinusitis (CRS), though its exact contribution to disease development and severity remains unclear. Here, samples were collected from the anterior nares, nasopharynx, and maxillary and ethmoid sinuses of 190 CRS patients and from the anterior nares and nasopharynx of 100 controls. Microbial communities were analyzed by Illumina sequencing of the V4 region of 16S rRNA. The phenotype and patient characteristics were documented, and several serum inflammatory markers were measured. Our data indicate a rather strong continuity for the microbiome in the different upper respiratory tract (URT) niches in CRS patients, with the microbiome in the anterior nares being most similar to the sinus microbiome. Bacterial diversity was reduced in CRS patients without nasal polyps compared to that in the controls but not in CRS patients with nasal polyps. Statistically significant differences in the presence/absence or relative abundance of several taxa were found between the CRS patients and the healthy controls. Of these, Dolosigranulum pigrum was clearly more associated with URT samples from healthy subjects, while the Corynebacterium tuberculostearicum, Haemophilus influenzae/H. aegyptius, and Staphylococcus taxa were found to be potential pathobionts in CRS patients. However, CRS versus health as a predictor explained only 1 to 2% of the variance in the microbiome profiles in an adonis model. A history of functional endoscopic sinus surgery, age, and sex also showed a minor association. This study thus indicates that functional studies on the potential beneficial versus pathogenic activity of the different indicator taxa found here are needed to further understand the pathology of CRS and its different phenotypes. (This study has been registered at ClinicalTrials.gov under identifier NCT02933983.)IMPORTANCE There is a clear need to better understand the pathology and specific microbiome features in chronic rhinosinusitis patients, but little is known about the bacterial topography and continuity between the different niches of the upper respiratory tract. Our work showed that the anterior nares could be an important reservoir for potential sinus pathobionts. This has implications for the diagnosis, prevention, and treatment of CRS. In addition, we found a potential pathogenic role for the Corynebacterium tuberculostearicum, Haemophilus influenzae/H. aegyptius, and Staphylococcus taxa and a potential beneficial role for Dolosigranulum Finally, a decreased microbiome diversity was observed in patients with chronic rhinosinusitis without nasal polyps compared to that in healthy controls but not in chronic rhinosinusitis patients with nasal polyps. This suggests a potential role for the microbiome in disease development or progression of mainly this phenotype.

Efficiency and Eco-Costs of Air Purifiers in Terms of Improving Microbiological Indoor Air Quality in Dwellings—A Case Study

Air pollution, a by-product of economic growth, generates an enormous environmental cost in Poland. The issue of healthy living spaces and indoor air quality (IAQ) is a global concern because people spend approximately 90% of their time indoors. An increasingly popular method to improve IAQ is to use air purifiers (APs). Indoor air is often polluted by bioaerosols (e.g., viruses, bacteria, fungi), which are a major concern for public health. This work presents research on culturable bacterial aerosol (CBA) samples collected from dwellings with or without active APs during the 2019 summer season. The CBA samples were collected using a six-stage Andersen cascade impactor (ACI). The CBA concentrations were expressed as Colony Forming Units (CFU) per cubic metre of air. The average concentration of CBA in dwellings when the AP was active was 450–570 CFU/m3, whereas the average concentration when the AP was not active was 920–1000 CFU/m3. IAQ, when the APs were active, was on average almost 50% better than in cases where there were no procedures to decrease the concentration of air pollutants. Moreover, the obtained results of the particle size distribution (PSD) of CBA indicate that the use of APs reduced the proportion of the respirable fraction (the particles < 3.3 µm) by about 16%. Life cycle assessment (LCA) was used to assess the ecological cost of air purification. Our conceptual approach addresses the impact of indoor air pollution on human health and estimates the ecological cost of APs and air pollution prevention policies.

Longitudinal study of the bacterial and fungal microbiota in the human sinuses reveals seasonal and annual changes in diversity

There is a pressing need for longitudinal studies which examine the stability of the sinonasal microbiota. In this study, we investigated bacterial and fungal community composition of the sinuses of four healthy individuals every month for one year, then once every three months for an additional year to capture seasonal variation. Sequencing of bacterial 16S rRNA genes and fungal ITS2 revealed communities that were mainly dominated by members of Actinobacteria and Basidiomycota, respectively. We observed overall shifts in both bacterial and fungal community diversity that were attributable to a combination of individual, seasonal and annual changes. The results suggest that each of the subjects possessed a strong bacterial sinonasal signature, but that fungal communities were less subject specific. Differences in fungal and bacterial diversity between subjects, and which OTUs may be correlated with seasonal differences, were investigated. A small core community that persisted throughout the two year sampling period was identified: Corynebacterium, Propionibacterium and Staphylococcus, and one type of fungus, Malassezia restricta. It is likely that bacterial and fungal airway microbiomes are dynamic and experience natural shifts in diversity with time. The underlying reasons for these shifts appear to be a combination of changes in environmental climate and host factors.

The microbiome of the upper respiratory tract in health and disease

The human upper respiratory tract (URT) offers a variety of niches for microbial colonization. Local microbial communities are shaped by the different characteristics of the specific location within the URT, but also by the interaction with both external and intrinsic factors, such as ageing, diseases, immune responses, olfactory function, and lifestyle habits such as smoking. We summarize here the current knowledge about the URT microbiome in health and disease, discuss methodological issues, and consider the potential of the nasal microbiome to be used for medical diagnostics and as a target for therapy.

Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma

BACKGROUND

In infants, distinct nasopharyngeal bacterial microbiotas differentially associate with the incidence and severity of acute respiratory tract infection and childhood asthma development.

OBJECTIVE

We hypothesized that distinct nasal airway microbiota structures also exist in children with asthma and relate to clinical outcomes.

METHODS

Nasal secretion samples (n = 3122) collected after randomization during the fall season from children with asthma (6-17 years, n = 413) enrolled in a trial of omalizumab (anti-IgE) underwent 16S rRNA profiling. Statistical analyses with exacerbation as the primary outcome and rhinovirus infection and respiratory illnesses as secondary outcomes were performed. Using A549 epithelial cells, we assessed nasal isolates of Moraxella, Staphylococcus, and Corynebacterium species for their capacity to induce epithelial damage and inflammatory responses.

RESULTS

Six nasal airway microbiota assemblages, each dominated by Moraxella, Staphylococcus, Corynebacterium, Streptococcus, Alloiococcus, or Haemophilus species, were observed. Moraxella and Staphylococcus species-dominated microbiotas were most frequently detected and exhibited temporal stability. Nasal microbiotas dominated by Moraxella species were associated with increased exacerbation risk and eosinophil activation. Staphylococcus or Corynebacterium species-dominated microbiotas were associated with reduced respiratory illness and exacerbation events, whereas Streptococcus species-dominated assemblages increased the risk of rhinovirus infection. Nasal microbiota composition remained relatively stable despite viral infection or exacerbation; only a few taxa belonging to the dominant genera exhibited relative abundance fluctuations during these events. In vitro, Moraxella catarrhalis induced significantly greater epithelial damage and inflammatory cytokine expression (IL-33 and IL-8) compared with other dominant nasal bacterial isolates tested.

CONCLUSION

Distinct nasal airway microbiotas of children with asthma relate to the likelihood of exacerbation, rhinovirus infection, and respiratory illnesses during the fall season.

The Therapeutic Effect of 1,8-Cineol on Pathogenic Bacteria Species Present in Chronic Rhinosinusitis

Chronic rhinosinusitis (CRS) is marked by an inflamed mucosa of sinuses and is accompanied by a significantly reduced quality of live. Since no guidelines for the treatment of CRS are available, long lasting clinical histories with health care costs adding up to dozens of billion $ annually are caused by CRS. The progression of CRS is often induced by bacterial infections and/or a shift in microbiome as well as biofilm formation. The exact microbiome alterations are still unclear and the impenetrable biofilm renders the treatment with common antibiotics ineffective. This study focuses on characterizing the microbiome changes in CRS and investigating the inhibition of biofilm growth by 1,8-Cineol, a small, non-polar and hence biofilm penetrating molecule with known antimicrobial potential. We performed MALDI-TOF MS based characterization of the microbiomes of healthy individuals and CRS patients (n = 50). The microbiome in our test group was shifted to pathogens (Staphylococcus aureus, Escherichia coli, and Moraxella catarrhalis). In contrast to published studies, solely based on cell culture techniques, we could not verify the abundance of Pseudomonas aeruginosa in CRS. The inhibition of bacterial proliferation and biofilm growth by 1,8-Cineol was measured for these three pathogens. Interestingly, S. aureus, the most prominent germ in CRS, showed a biofilm inhibition not simply correlated to its inhibition of proliferation. RT-qPCR confirmed that this was due to the downregulations of major key players in biofilm generation (agrA, SarA and σ^B) by 1,8-Cineol. Furthermore we verified this high biofilm inhibition potential in a model host system consisting out of S. aureus biofilm grown on mature respiratory epithelium. A second host model, comprising organotypic slices, was utilized to investigate the reaction of the innate immune system present in the nasal mucosa upon biofilm formation and treatment with 1,8-Cineol. Interestingly Staphylococcus epidermidis, the cause of very common catheter infections, possesses a biofilm generation pathway very similar to S. aureus and might be treatable in a similar fashion. The two presented in vitro model systems might be transferred to combinations of every biofilm forming bacterial with most kind of epithelium and mucosa.

Severe Obstructive Sleep Apnea Is Associated with Alterations in the Nasal Microbiome and an Increase in Inflammation

RATIONALE

Obstructive sleep apnea (OSA) is associated with recurrent obstruction, subepithelial edema, and airway inflammation. The resultant inflammation may influence or be influenced by the nasal microbiome.

OBJECTIVES

To evaluate whether the composition of the nasal microbiota is associated with obstructive sleep apnea and inflammatory biomarkers.

METHODS

Two large cohorts were used: 1) a discovery cohort of 472 subjects from the WTCSNORE (Seated, Supine and Post-Decongestion Nasal Resistance in World Trade Center Rescue and Recovery Workers) cohort, and 2) a validation cohort of 93 subjects rom the Zaragoza Sleep cohort. Sleep apnea was diagnosed using home sleep tests. Nasal lavages were obtained from cohort subjects to measure: 1) microbiome composition (based on 16S rRNA gene sequencing), and 2) biomarkers for inflammation (inflammatory cells, IL-8, and IL-6). Longitudinal 3-month samples were obtained in the validation cohort, including after continuous positive airway pressure treatment when indicated.

MEASUREMENTS AND MAIN RESULTS

In both cohorts, we identified that: 1) severity of OSA correlated with differences in microbiome diversity and composition; 2) the nasal microbiome of subjects with severe OSA were enriched with Streptococcus, Prevotella, and Veillonella; and 3) the nasal microbiome differences were associated with inflammatory biomarkers. Network analysis identified clusters of cooccurring microbes that defined communities. Several common oral commensals (e.g., Streptococcus, Rothia, Veillonella, and Fusobacterium) correlated with apnea-hypopnea index. Three months of treatment with continuous positive airway pressure did not change the composition of the nasal microbiota.

CONCLUSIONS

We demonstrate that the presence of an altered microbiome in severe OSA is associated with inflammatory markers. Further experimental approaches to explore causal links are needed.

Sub-Inhibitory Clindamycin and Azithromycin reduce S. aureus Exoprotein Induced Toxicity, Inflammation, Barrier Disruption and Invasion

Background: Chronic rhinosinusitis (CRS) is defined as a chronic inflammation of the nose and paranasal sinus mucosa associated with relapsing infections—particularly with S. aureus. Long-term treatments with protein synthesis inhibitor antibiotics have been proposed to reduce inflammation in the context chronic severe inflammatory airway pathologies, including CRS. This study assessed the effect of subinhibitory clindamycin and azithromycin on S. aureus exoprotein induced inflammation, toxicity and invasiveness. Methods: S. aureus ATCC51650 and two clinical isolates grown in planktonic and biofilm form were treated with subinhibitory clindamycin and azithromycin. Exoproteins were collected and applied to primary human nasal epithelial cells (HNECs) in monolayers and at air-liquid interface. This was followed by lactate dehydrogenase (LDH), enzyme-linked immunosorbent assay (ELISA), Transepithelial Electrical Resistance (TEER) and paracellular permeability assays to assess the effect on cell toxicity, inflammatory cytokine production and mucosal barrier structure and function, respectively. The effect of these treatments was tested as well on the S. aureus invasiveness of HNECs. Results: Subinhibitory clindamycin reduced S. aureus exoprotein production in planktonic and biofilm form, thereby blocking exoprotein-induced toxicity, reversing its detrimental effects on mucosal barrier structure and function and modulating its inflammatory properties. Sub-inhibitory azithromycin had similar effects—albeit to a lesser extent. Furthermore, clindamycin—but not azithromycin—treated S. aureus lost its invasive capacity of HNECs. Conclusion: Subinhibitory clindamycin and azithromycin reduce S. aureus exoprotein production, thereby modulating the inflammatory cascade by reducing exoprotein-induced toxicity, inflammation, mucosal barrier disruption and invasiveness.

Analysis of Sinonasal Microbiota in Exacerbations of Chronic Rhinosinusitis Subgroups

Objective

Microbiome analyses now allow precise determination of the sinus microbiota of patients with exacerbations of chronic rhinosinusitis (CRS). The aim of this report is to describe the sinus microbiota of acute exacerbations in CRS clinical subgroups (with nasal polyps [CRSwNP], without nasal polyps [CRSsNP], and allergic fungal rhinosinusitis [AFRS]).

Study Design

Retrospective chart review.

Setting

Tertiary rhinology practice.

Subjects and Methods

A retrospective review was performed of all patients whose sinus microbiota were assayed via a commercially available microbiome technology during an acute CRS exacerbation during the 2-year period ending December 31, 2016. All samples were sinus aspirates collected under endoscopic visualization in clinic.

Results

Samples from a total of 134 patients (65 CRSsNP, 55 CRSwNP, and 14 AFRS) were reviewed. The observed richness (number of taxa >2% relative abundance) ranged between 1 and 11 taxa, with an average of 3 taxa per specimen. The most common bacteria in all groups were Staphylococcal spp (including Staphylococcus aureus), Streptococcus spp, Pseudomonas spp, and Escherichia spp. S aureus had an increased prevalence in CRSsNP and AFRS as compared with CRSwNP. Otherwise, the sinus microbiota were markedly similar among all 3 clinical subgroups.

Conclusions

Many bacterial types are identified during acute CRS exacerbation according to DNA-based detection techniques. Bacterial richness was remarkably low in all samples. Few differences in the patterns among clinical subgroups were observed. Further investigation is warranted to determine the clinical significance of these observations and their role in current clinical algorithms.

Community analysis and co-occurrence patterns in airway microbial communities during health and disease

Ecological relationships between bacteria are important when considering variation in bacterial communities in humans, with such variation playing an important role in both health and disease.

Using high-throughput sequence data of the 16S rRNA marker-gene, we analysed the prevalence of taxa in the airways of a number of health- and disease-associated cohorts and determined the main drivers of community variance and bacterial co-occurrence.

A number of facultative and obligately anaerobic bacterial taxa are commonly associated with the upper airways, forming the main “core” microbiota, e.g. Streptococcus spp., Veillonella spp., Prevotella spp., Granulicatella spp. and Fusobacterium spp. Opportunistic pathogenic bacteria associated with chronic airways disease, such as Pseudomonas spp. (Pseudomonas aeruginosa), Burkholderia spp. (Burkholderia cepacia complex) and Haemophilus spp. (Haemophilus influenzae) demonstrated poor correlation with other members of their respective communities (ρ<0.5; p>0.005), indicating probable independent acquisition and colonisation. Furthermore, our findings suggest that intra-genus variation between health and disease may affect community assemblies.

Improved understanding of how bacteria assemble in time and space during health and disease will enable the future development of tailored treatment according to the patient's own signature microbiota, potentially providing benefit to patients suffering from airway diseases characterised by chronic infection.

Within the airways, “core” community structures are formed between microbial taxa in both health and disease, with a number of common opportunistic pathogens not being members of such core communitieshttp://bit.ly/2Kau3ni

Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda

Febrile illness is a major burden in African children, and non-malarial causes of fever are uncertain. In this retrospective exploratory study, we used metagenomic next-generation sequencing (mNGS) to evaluate serum, nasopharyngeal, and stool specimens from 94 children (aged 2–54 months) with febrile illness admitted to Tororo District Hospital, Uganda. The most common microbes identified were Plasmodium falciparum (51.1% of samples) and parvovirus B19 (4.4%) from serum; human rhinoviruses A and C (40%), respiratory syncytial virus (10%), and human herpesvirus 5 (10%) from nasopharyngeal swabs; and rotavirus A (50% of those with diarrhea) from stool. We also report the near complete genome of a highly divergent orthobunyavirus, tentatively named Nyangole virus, identified from the serum of a child diagnosed with malaria and pneumonia, a Bwamba orthobunyavirus in the nasopharynx of a child with rash and sepsis, and the genomes of two novel human rhinovirus C species. In this retrospective exploratory study, mNGS identified multiple potential pathogens, including 3 new viral species, associated with fever in Ugandan children.

Laryngotracheal Microbiota in Adult Laryngotracheal Stenosis

Laryngotracheal stenosis is an obstructive respiratory disease that leads to voicing difficulties and dyspnea with potential life-threatening consequences. The majority of incidences are due to iatrogenic etiology from endotracheal tube intubation; however, airway scarring also has idiopathic causes. While recent evidence suggests a microbial contribution to mucosal inflammation, the microbiota associated with different types of stenosis has not been characterized. High-throughput sequencing of the V4 region of the16S rRNA gene was performed to characterize the microbial communities of 61 swab samples from 17 iatrogenic and 10 adult idiopathic stenosis patients. Nonscar swabs from stenosis patients were internal controls, and eight swabs from four patients without stenosis represented external controls. Significant differences in diversity were observed between scar and nonscar samples and among sample sites, with decreased diversity detected in scar samples and the glottis region. Permutational analysis of variance (PERMANOVA) results revealed significant differences in community composition for scar versus nonscar samples, etiology type, sample site, groups (iatrogenic, idiopathic, and internal and external controls), and individual patients. Pairwise Spearman's correlation revealed a strong inverse correlation between Prevotella and Streptococcus among all samples. Finally, bacteria in the family Moraxellaceae were found to be distinctly associated with idiopathic stenosis samples in comparison with external controls. Our findings suggest that specific microbiota and community shifts are present with laryngotracheal stenosis in adults, with members of the family Moraxellaceae, including the known pathogens Moraxella and Acinetobacter, identified in idiopathic scar. Further work is warranted to elucidate the contributing role of bacteria on the pathogenesis of laryngotracheal stenosis.IMPORTANCE The laryngotracheal region resides at the intersection between the heavily studied nasal cavity and lungs; however, examination of the microbiome in chronic inflammatory conditions of the subglottis and trachea remains scarce. To date, studies have focused on the microbiota of the vocal folds, or the glottis, for laryngeal carcinoma, as well as healthy larynges, benign vocal fold lesions, and larynges exposed to smoking and refluxate. In this study, we seek to examine the structure and composition of the microbial community in adult laryngotracheal stenosis of various etiologies. Due to the heterogeneity among the underlying pathogenesis mechanisms and clinical outcomes seen in laryngotracheal stenosis disease, we hypothesized that different microbial profiles will be detected among various stenosis etiology types. Understanding differences in the microbiota for subglottic stenosis subtypes may shed light upon etiology-specific biomarker identification and offer novel insights into management approaches for this debilitating disease.

The pH Value as a Factor Modifying Bacterial Colonization of Sinonasal Mucosa in Healthy Persons

OBJECTIVE

The aim of the present study is to determine and compare the range of pH value in nasal and sinus cavities in vivo regarding the presence of bacteria colonizing sinonasal mucosa among healthy subjects.

METHODS

The nasal pH value measurement using a portable pH meter (Dx-pH System, Restech) and the microbiological culture swab were taken from beneath the middle turbinate and in the sinus cavity in 39 healthy subjects during maxillary bone corrective osteotomy with the Le Fort I technique.

RESULTS

The mean pH value (independently of sex, P = .441) in the healthy sinus cavity was statistically higher than in the nasal middle meatus: 7.96 (SD ± 0.29) versus 7.83 (SD ± 0.30) (P = .032). Forty-eight strains of bacteria were cultured from sinus maxillaries cavities-aerobic 36.8%, aerobic and anaerobic 52.6%, anaerobic only 10.5%-and 23 strains from the nasal meatus-aerobic 25%, aerobic and anaerobic 75%. A statistically significant correlation was found between the type and location of 8 microorganisms, especially Propionibacterium acnes, identified only in the sinus cavities.

CONCLUSIONS

Differences in the pH value between the middle nasal meatus and the maxillary sinus are characteristic of healthy subjects and could be associated with the diverse bacterial flora. The role of bacteria Propionibacterium acnes seems to be crucial for the pH range and sinus flora in healthy subjects.

Inflammation and Endotyping in Chronic Rhinosinusitis-A Paradigm Shift

Chronic rhinosinusitis (CRS) is a heterogeneous chronic inflammatory condition of the paranasal sinuses and nasal passage. It is characterized as inflammation of the sinonasal passage, presenting with two or more symptoms (nasal blockage, secretions, facial pain and headaches) for more than 12 weeks consecutively. The disease is phenotypically differentiated based on the presence of nasal polyps; CRS with nasal polyps (CRSwNP) and CRS without nasal polyps (CRSsNP). Traditionally, CRSwNP has been associated with a type 2 inflammatory profile, while CRSsNP has been associated with a type 1 inflammatory profile. Extensive work in characterizing the inflammatory profiles of CRS patients has challenged this dichotomy, with great variation both between and within populations described. Recent efforts of endotyping CRS based on underlying pathophysiology have further highlighted the heterogeneity of the disease, revealing mixed inflammatory profiles coordinated by a number of inflammatory cell types. This review will highlight the current understanding of inflammation in CRS, and discuss the importance and impact of refining this understanding in the development of appropriate treatment options for CRS sufferers.

The Role of Staphylococcus aureus in Patients with Chronic Sinusitis and Nasal Polyposis

PURPOSE OF REVIEW

Staphylococcus aureus (S. aureus) is correlated with the development of persistent severe inflammatory disease of the upper airway including chronic rhinosinusitis with nasal polyps (CRSwNP). The presence of S. aureus is associated with atopic disease including allergic rhinitis and atopic dermatitis and is associated with poor outcomes.

RECENT FINDINGS

Several different strains of S. aureus generate different toxins and gene products that can account for organism pathogenicity. S. aureus bacteria and its antigens shape the bacterial and fungal microbiome and the mucosal niche which generates host responses that can account for inflammation. The multiple disease phenotypes and molecular endotypes seen in CRSwNP can be characterized by T-helper cell environment within the inflammatory milieu, the presence of epithelial barrier dysfunction, aberrant eicosanoid metabolism, poor wound healing, and dysfunctional host-bacteria interactions which lead to recalcitrant disease and worse surgical outcomes. Understanding the pathomechanisms that S. aureus utilizes to promote nasal polyp formation, prolonged tissue inflammation, and bacterial dysbiosis are essential in our efforts to identify new therapeutic approaches to resolve this chronic inflammatory process.

Association Between Culture and Culture-Independent Microtyping in Recalcitrant Chronic Rhinosinusitis

BACKGROUND:

Many different etiologies have been proposed to be responsible for the pathogenesis of chronic rhinosinusitis, including dysbiosis of the sinus microbiome. Attempts have recently been made to identify a pathogenic organism via advanced culture mechanisms. The purpose of this study is to use culture-dependent and culture-independent means of microtyping to determine whether any association exists between the quantity and quality of bacteria identified in patients with recalcitrant chronic rhinosinusitis.

METHODS:

Medical records were retrospectively reviewed for patients with a history of revision sinus surgery and persistent symptoms who underwent endoscopically directed culture and underwent quantitative polymerase chain reaction analysis of the 16S ribosomal RNA of bacteria and fungi from February 1, 2014, to January 1, 2017. A total of 21 patients met the inclusion criteria. Medical records were reviewed to determine the number of bacterial isolates and relative abundance of bacteria and fungi on culture and polymerase chain reaction.

RESULTS:

Using culture-independent techniques of examining purulent secretions in patients with recalcitrant chronic rhinosinusitis, an average of 3.61 isolates were identified per specimen, compared with culture-dependent methods that revealed 2.10 isolates per specimen ( P < .05). The dominant species identified on each culture was rarely the most abundant species identified using polymerase chain reaction techniques.

CONCLUSIONS:

Traditional culture methodologies may fail to identify potential pathogens or the dominant pathogen in patients with recalcitrant chronic rhinosinusitis with acute exacerbations.

Biofilm Formations in Pediatric Respiratory Tract Infection : Part 1: Biofilm Structure, Role of Innate Immunity in Protection Against and Response to Biofilm, Methods of Biofilm Detection, Pediatric Respiratory Tract Diseases Associated with Mucosal Biofilm Formation

PURPOSE OF REVIEW

Biofilm represents an organized structure of microorganisms within an extracellular matrix attached to a surface. While the importance of biofilm in prosthetic heart valve and catheter-related infections has been known since the 1980s, the role of mucosal biofilm in human disease pathogenesis has only recently been elucidated. It is now clear that mucosal biofilm is present in both healthy and pathologic states. The purpose of this review is to examine the role of mucosal biofilm in pediatric respiratory infections.

RECENT FINDINGS

Mucosal biofilm has been implicated in relationship to several pediatric respiratory infections, including tonsillitis, adenoiditis, otitis media with effusion, chronic rhinosinusitis, persistent endobronchial infection, and bronchiectasis. In these conditions, core pathogens are detected in the biofilm, biofilm organisms are often detected by molecular techniques when conventional cultures are negative, and biofilm presence is more extensive in relation to disease than in healthy tissues. In chronic rhinosinusitis, the presence of polymicrobial biofilm is also a predictor of poorer outcome following sinus surgery. Biofilm in the tonsillar and adenoidal compartments plays a distinct role in contributing to disease in the middle ear and sinuses. Key observations regarding the relevance of biofilm to pediatric respiratory infections include (1) the association between the presence of biofilm and persistent/recurrent and more severe disease in these tissues despite antibiotic treatment, (2) linkage between biofilm core pathogens and acute infections, and (3) interrelationship between biofilm presence in one tissue and persistent or recurrent infection in an adjacent tissue. A greater understanding of the significance of mucosal biofilm will undoubtedly emerge with the development of effective means of eradicating mucosal biofilm.

Identification and Analysis of Human Microbe-Disease Associations by Matrix Decomposition and Label Propagation

Studies have shown that microbes exist widely in the human body and are closely related to human complex diseases. Predicting potential associations between microbes and diseases is conducive to understanding the mechanisms of complex diseases and can also facilitate the diagnosis and prevention of human diseases. In this paper, we put forward the Matrix Decomposition and Label Propagation for Human Microbe-Disease Association prediction (MDLPHMDA) on the basis of the dataset of known microbe-disease associations collected from the database of HMDAD and the Gaussian interaction profile kernel similarity for diseases and microbes, disease symptom similarity. Moreover, the performance of our model was evaluated by means of leave-one-out cross validation and five-fold cross validation, and the corresponding AUCs of 0.9034 and 0.8954 ± 0.0030 were gained, respectively. In case studies, 10, 9, 9, and 8 out of the top 10 predicted microbes for asthma, colorectal carcinoma, liver cirrhosis, and type 1 diabetes were confirmed by literatures, respectively. Overall, evaluation results showed that MDLPHMDA has good performance in potential microbe-diseasepositive free parameter, which associations prediction.

The difference in nasal bacterial microbiome diversity between chronic rhinosinusitis patients with polyps and a control population

BACKGROUND

Little is known regarding the role of the microbiome of the paranasal sinuses and its contribution to sinus mucosal health and disease. Consequently, we examined the microbiome of chronic rhinosinusitis patients with polyps (CRSwNP) and a control population to provide new insights into the microbiota associated with the pathogenesis of CRSwNP.

METHODS

Fifty-nine CRSwNP patients and 27 controls were enrolled in the study. The bacterial communities of the middle meatus were detected using 16S ribosomal RNA (rRNA)-targeted Illumina MiSeq sequencing after microbial DNA was extracted from swabs.

RESULTS

Although there was no difference in diversity between the 2 groups, richness was lower in the CRSwNP group than in the control group (p = 0.03). At the phylum level, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were predominant in both groups; however, the relative abundance was different, with the proportions of Actinobacteria (predominantly Corynebacterium) and Dolosigranulum being significantly higher in the control group than in the CRSwNP group.

CONCLUSION

These results support the theory of microbial dysbiosis as the pathogenesis of CRSwNP. The reduction in the proportions of potentially protective bacteria may decrease the overall stability of the sinonasal bacterial community.

Microbiological Aspects of Acute and Chronic Pediatric Rhinosinusitis

The microbiology of acute and chronic rhinosinusitis has been extensively studied, but there are still some differences of view concerning the etiology of the former, and many disagreements regarding the microbiology of the latter. Establishing the concomitant distribution of the causative micro-organisms in cases that involve multiple sinuses is scientifically and practically important. The main problems are the variety of aerobes and anaerobes that may be involved, and the fact that different tracts of the sinuses of the same patient may be simultaneously affected. Rhinosinusitis may also involve the formation of biofilm, which may play a significant role in its pathogenesis and persistence. Biofilms have a number of advantages in terms of bacterial survival, and their perpetuation can create a certain degree of instability in host-bacteria interactions. Sinonasal microflora may further complicate pathogenesis and the identification of the pathogen(s) involved. Furthermore, the concentration, uniformity, and type/number of strains of nasal microbiota may vary from one site to another. The relative and total micro-organism counts can also be affected by various factors, and microbiota can modulate the course of both acute and chronic rhinosinusitis.

Metagenomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota

Accurate and informative microbiological testing is essential for guiding diagnosis and management of pneumonia in patients who are critically ill. Sampling of tracheal aspirate (TA) is less invasive compared with mini-bronchoalveolar lavage (mBAL) and is now recommended as a frontline diagnostic approach in patients who are mechanically ventilated, despite the historical belief that TA was suboptimal due to contamination from oral microbes. Advancements in metagenomic next-generation sequencing (mNGS) now permit assessment of airway microbiota without a need for culture and, as such, provide an opportunity to examine differences between mBAL and TA at a resolution previously unachievable. Here, we engaged shotgun mNGS to assess quantitatively the airway microbiome in matched mBAL and TA specimens from a prospective cohort of critically ill adults. We observed moderate differences between sample types across all subjects; however, we found significant compositional similarity in subjects with bacterial pneumonia, whose microbial communities were characterized by dominant pathogens. In contrast, in patients with noninfectious acute respiratory illnesses, significant differences were observed between sample types. Our findings suggest that TA sampling provides a similar assessment of airway microbiota as more invasive testing by mBAL in patients with pneumonia.

Use of Dipstick Assay and Rapid PCR-DNA Analysis of Nasal Secretions for Diagnosis of Bacterial Sinusitis in Children With Chronic Cough

BACKGROUND

Chronic cough in children is a diagnostic challenge.

OBJECTIVE

To discover the utility of nasal dipsticks and polymerase chain reaction (PCR)-DNA analysis in differentiating bacterial sinusitis from other causes of chronic cough and identifying pathogens from the nasal cavity.

METHOD

We recruited 22 patients under 15 years of age with cough lasting longer than 4 weeks (group 1), 7 controls with allergic rhinitis (group 2), and 10 controls without respiratory symptoms (group 3). Based on symptoms, the results of nasal secretion assays, and nasal endoscopy, a diagnosis of clinical bacterial sinusitis was made. We identified potential pathogens by quantitative PCR of nasal secretions.

RESULTS

Group 1A (cough with clinical bacterial sinusitis n = 10): Eight (80%) patients had bacterial sinusitis associated with dominant potential pathogenic bacteria (PPB): Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. Group 1B (cough without clinical bacterial sinusitis n = 12): None had dominant PPB. Group 2 (allergic rhinitis n = 7): None had dominant PPB. Group 3 (asymptomatic n = 10): None had dominant PPB. Twenty to 57% of all groups were colonized with Staphylococcus aureus. Fifty to 70% were colonized with Staphylococcus epidermidis, Corynebacterium pseudodiphtheriticum, and Dolosigranulum pigrum.

CONCLUSION

In children with chronic cough, clinicians can utilize a simple and inexpensive nasal secretion dipstick assay for rapid diagnosis of sinusitis and identify PPB by DNA-PCR test for specific antibiotic treatment.

Quantitative analysis of Staphylococcus aureus in patients with chronic rhinosinusitis under continuous ultrasound treatment

BACKGROUND AND OBJECTIVES

Bacterial pathogens, in particular drug resistant strains, involved in chronic rhinosinusitis may result in treatment failure. Ultrasound waves are able to destroy bacterial population in sinus cavities and can recover patients.

MATERIALS AND METHODS

Twelve patients with chronic sinusitis and 10 healthy controls were treated by continuous ultrasound waves. Clinical specimens were collected before and after treatment. Serial diluted specimens were cultured on blood agar, chocolate and MacConkey agar plates for bacterial isolation. Bacterial DNA was extracted and used for Staphylococcus aureus detection using quantitative PCR.

RESULTS

S. aureus was the most isolated bacterium (10 patients), which was eradicated from 8 patients after treatment. Using phenotypic methods at the beginning, 3 out of 10 healthy individuals were found to be positive. From 11 positive patients for S. aureus identified by real time qPCR, 9 showed significant reduction after treatment. In the healthy group, S. aureus was detected in 4 samples using qPCR, but they were clean at the second sampling.

CONCLUSION

According to our phenotypic and molecular experiments, continuous ultrasound treatment effectively reduced the bacterial population in studied patients (p < 0.01). This was a hopeful basis for doing more studies with ultrasound therapy as a treatment option.

Chronic Rhinosinusitis in Children

Purpose of review

Pediatric chronic rhinosinusitis (CRS) is a common condition that is often misdiagnosed and can be challenging to treat. This review aims to 1) Review definitions, presentation, complications, and management of CRS in children. 2) Highlight the paucity of evidence in the management of pediatric CRS.

Recent findings

There are few studies supporting the usual recommended medical therapy for pediatric CRS (antibiotics, nasal saline irrigations, intranasal steroid). Adenoidectomy remains a mainstay of surgical treatment, but recent evidence demonstrates the utility of balloon sinuplasty and functional endoscopic sinus surgery (FESS) for patients who fail adenoidectomy alone.

Summary

Pediatric CRS is distinct from ARS and adult CRS. It is a common problem that is poorly studied, in part because of significant symptomatic overlap with related conditions. Recent evidence supports the use of surgical treatment in children who fail medical management. However, further outcome studies are needed to better evaluate the effectiveness of current medical and surgical management protocols.

Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults

Lower respiratory tract infections (LRTIs) are the leading cause of infectious disease-related deaths worldwide yet remain challenging to diagnose because of limitations in existing microbiologic tests. In critically ill patients, noninfectious respiratory syndromes that resemble LRTIs further complicate diagnosis and confound targeted treatment. To address this, we developed a metagenomic sequencing-based approach that simultaneously interrogates three core elements of acute airway infections: the pathogen, airway microbiome, and host response. We studied this approach in a prospective cohort of critically ill patients with acute respiratory failure and found that combining pathogen, microbiome, and host gene expression metrics achieved accurate LRTI diagnosis and identified etiologic pathogens in patients with clinically identified infections but otherwise negative testing.

Lower respiratory tract infections (LRTIs) lead to more deaths each year than any other infectious disease category. Despite this, etiologic LRTI pathogens are infrequently identified due to limitations of existing microbiologic tests. In critically ill patients, noninfectious inflammatory syndromes resembling LRTIs further complicate diagnosis. To address the need for improved LRTI diagnostics, we performed metagenomic next-generation sequencing (mNGS) on tracheal aspirates from 92 adults with acute respiratory failure and simultaneously assessed pathogens, the airway microbiome, and the host transcriptome. To differentiate pathogens from respiratory commensals, we developed a rules-based model (RBM) and logistic regression model (LRM) in a derivation cohort of 20 patients with LRTIs or noninfectious acute respiratory illnesses. When tested in an independent validation cohort of 24 patients, both models achieved accuracies of 95.5%. We next developed pathogen, microbiome diversity, and host gene expression metrics to identify LRTI-positive patients and differentiate them from critically ill controls with noninfectious acute respiratory illnesses. When tested in the validation cohort, the pathogen metric performed with an area under the receiver-operating curve (AUC) of 0.96 (95% CI, 0.86–1.00), the diversity metric with an AUC of 0.80 (95% CI, 0.63–0.98), and the host transcriptional classifier with an AUC of 0.88 (95% CI, 0.75–1.00). Combining these achieved a negative predictive value of 100%. This study suggests that a single streamlined protocol offering an integrated genomic portrait of pathogen, microbiome, and host transcriptome may hold promise as a tool for LRTI diagnosis.

Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia

Influenza and other respiratory viral infections are the most common type of acute respiratory infection. Viral infections predispose patients to secondary bacterial infections, which often have a more severe clinical course. The mechanisms underlying post-viral bacterial infections are complex, and include multifactorial processes mediated by interactions between viruses, bacteria, and the host immune system. Studies over the past 15 years have demonstrated that unique microbial communities reside on the mucosal surfaces of the gastrointestinal tract and the respiratory tract, which have both direct and indirect effects on host defense against viral infections. In addition, antiviral immune responses induced by acute respiratory infections such as influenza are associated with changes in microbial composition and function (“dysbiosis”) in the respiratory and gastrointestinal tract, which in turn may alter subsequent immune function against secondary bacterial infection or alter the dynamics of inter-microbial interactions, thereby enhancing the proliferation of potentially pathogenic bacterial species. In this review, we summarize the literature on the interactions between host microbial communities and host defense, and how influenza, and other acute respiratory viral infections disrupt these interactions, thereby contributing to the pathogenesis of secondary bacterial infections.

Nasopharyngeal Lactobacillus is associated with a reduced risk of childhood wheezing illnesses following acute respiratory syncytial virus infection in infancy

BACKGROUND

Early life acute respiratory infection (ARI) with respiratory syncytial virus (RSV) has been strongly associated with the development of childhood wheezing illnesses, but the pathways underlying this association are poorly understood.

OBJECTIVE

To examine the role of the nasopharyngeal microbiome in the development of childhood wheezing illnesses following RSV ARI in infancy.

METHODS

We conducted a nested cohort study of 118 previously healthy, term infants with confirmed RSV ARI by RT-PCR. We used next-generation sequencing of the V4 region of the 16S ribosomal RNA gene to characterize the nasopharyngeal microbiome during RSV ARI. Our main outcome of interest was 2-year subsequent wheeze.

RESULTS

Of the 118 infants, 113 (95.8%) had 2-year outcome data. Of these, 46 (40.7%) had parental report of subsequent wheeze. There was no association between the overall taxonomic composition, diversity, and richness of the nasopharyngeal microbiome during RSV ARI with the development of subsequent wheeze. However, the nasopharyngeal detection and abundance of Lactobacillus was consistently higher in infants who did not develop this outcome. Lactobacillus also ranked first among the different genera in a model distinguishing infants with and without subsequent wheeze.

CONCLUSIONS

The nasopharyngeal detection and increased abundance of Lactobacillus during RSV ARI in infancy are associated with a reduced risk of childhood wheezing illnesses at age 2 years.

The microbiome and chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is a multifactorial condition in which the microbiota plays a pathogenic role. The nature of the interaction between the microbiota and the local immune system is very complex and has not been fully elucidated. Recent improvements in the microbiological techniques have greatly advanced our understanding of the complex nature of this interaction. This paper summarizes the current state of the rapidly evolving research on this subject. Defining the nature of the role of the microbiota in CRS is important because of the associated therapeutic implications.

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes

BACKGROUND

Pan-bacterial 16S rRNA microbiome surveys performed with massively parallel DNA sequencing technologies have transformed community microbiological studies. Current 16S profiling methods, however, fail to provide sufficient taxonomic resolution and accuracy to adequately perform species-level associative studies for specific conditions. This is due to the amplification and sequencing of only short 16S rRNA gene regions, typically providing for only family- or genus-level taxonomy. Moreover, sequencing errors often inflate the number of taxa present. Pacific Biosciences' (PacBio's) long-read technology in particular suffers from high error rates per base. Herein, we present a microbiome analysis pipeline that takes advantage of PacBio circular consensus sequencing (CCS) technology to sequence and error correct full-length bacterial 16S rRNA genes, which provides high-fidelity species-level microbiome data.

RESULTS

Analysis of a mock community with 20 bacterial species demonstrated 100% specificity and sensitivity with regard to taxonomic classification. Examination of a 250-plus species mock community demonstrated correct species-level classification of > 90% of taxa, and relative abundances were accurately captured. The majority of the remaining taxa were demonstrated to be multiply, incorrectly, or incompletely classified. Using this methodology, we examined the microgeographic variation present among the microbiomes of six sinonasal sites, by both swab and biopsy, from the anterior nasal cavity to the sphenoid sinus from 12 subjects undergoing trans-sphenoidal hypophysectomy. We found greater variation among subjects than among sites within a subject, although significant within-individual differences were also observed. Propiniobacterium acnes (recently renamed Cutibacterium acnes) was the predominant species throughout, but was found at distinct relative abundances by site.

CONCLUSIONS

Our microbial composition analysis pipeline for single-molecule real-time 16S rRNA gene sequencing (MCSMRT, https://github.com/jpearl01/mcsmrt ) overcomes deficits of standard marker gene-based microbiome analyses by using CCS of entire 16S rRNA genes to provide increased taxonomic and phylogenetic resolution. Extensions of this approach to other marker genes could help refine taxonomic assignments of microbial species and improve reference databases, as well as strengthen the specificity of associations between microbial communities and dysbiotic states.

Chronic rhinosinusitis: pathogenesis, therapy options, and more

INTRODUCTION

When rhinosinusitis - the inflammation of the nasal cavity and paranasal sinuses - persists for over 12 weeks, it is termed 'chronic rhinosinusitis' (CRS). Both innate and adaptive immunity contribute to the heterogeneous inflammatory pathogenesis of CRS, which is driven by genetic and environmental factors and the microbiome. CRS is classified by the presence of polyps. Molecular mechanisms in CRS with nasal polyps are similar to those in atopic diseases.

AREAS COVERED

This review focuses on the immune pathogenesis of CRS, differences between the two CRS subtypes, and latest treatments that may aid in the provision of personalized medicine.

EXPERT OPINION

Basic research in the last decade has helped significantly in enhancing our knowledge of the pathophysiologic processes of CRS, due to which there is now a better understanding of the associated natural history, physiopathology, novel treatments, and prevention strategies. Treatment success depends on the clarification of the underlying pathogenesis and disease-contributing factors. The exploration of disease endotypes and introduction of novel agents are important advancements. Prior studies performed without disease-endotyping resulted in the inefficiency of certain drugs and insignificant results. The identification of biomarkers, development of personalized approaches, and utilization of disease algorithms are required for CRS therapy success.

Pathophysiologic mechanisms of chronic rhinosinusitis and their roles in emerging disease endotypes

OBJECTIVE

Chronic rhinosinusitis (CRS) is a heterogeneous disorder with distinct pathophysiologic mechanisms. Based on transcription factor expression and cytokine production patterns in different innate lymphoid cell (ILC) types, in parallel with those of adaptive CD4⁺ T-helper (T_H) cells and CD8⁺ cytotoxic T (Tc) cells, new perspectives on endotypes of patients are emerging for the immune response deviation into type 1 (orchestrated by ILC1s and Tc1, and T_H1 cells), type 2 (characterized by ILC2s and Tc2 and T_H2 cells), and type 3 (mediated by ILC3s and Tc17 and T_H17 cells). In addition, cluster analysis has been applied to endotyping of CRS in recent years, which has provided additional novel insights into CRS pathogenesis. This review assessed pathologic mechanisms of CRS based on type 1, 2, and 3 immune responses and how they inform us to begin to understand CRS endotypes. This review also assessed recent cluster analysis studies of CRS endotypes. The impact of endotype on therapeutic management of CRS also is summarized.

DATA SOURCES

Review of published literature.

STUDY SELECTIONS

Relevant literature concerning CRS endotypes and possible underlying mechanisms was obtained from a PubMed search and summarized.

RESULTS AND CONCLUSION

CRS with and without nasal polyps are composed of distinct endotypes with distinct deviated immune responses, pathogenic mechanisms, and different responses to medical and surgical treatment. An endotype of CRS with prominent type 2 immune responses is the best-studied endotype and generally can benefit from treatment with steroids and specific type 2 disrupting biologics.

Loss of Microbial Niche Specificity Between the Upper and Lower Airways in Patients With Cystic Fibrosis

OBJECTIVES/HYPOTHESIS

To determine the relationship between mucosal-associated sinus and bronchial microbiota in cystic fibrosis (CF) patients compared to non-CF patients with chronic rhinosinusitis (CRS).

STUDY DESIGN

Case series.

METHODS

We examined the microbial composition of 52 paired sinus and bronchial brushings from 26 patients with CRS. Paired airway samples from nine subjects with CF were compared with samples from 17 non-CF-CRS disease control patients. The Illumina MiSeq platform was used to sequence the V4 region of the 16S rRNA gene. Sequences were analyzed using QIIME 1.9.0.

RESULTS

CF patients demonstrate increased severity of sinus inflammation (Lund-Mackay score 16.3 vs. 12.4, P = .023) and diminished diversity of microbial communities in both the sinuses (Shannon diversity 0.98 vs. 3.3, P = .009) and lungs (Shannon diversity 2.2 vs. 4.0, P = .042) relative to non-CF-CRS. Non-CF-CRS sinus and lung microbiota were distinct and clustered by niche (sinus vs. lung, P = .004). However, CF airway microbiota demonstrated a loss of niche specificity (sinus vs. lung, P = .492). Two CF patients underwent lung transplantation at 4.5 and 9 months prior to sampling. Sinus and lung samples from these two patients demonstrated distinct microbial communities.

CONCLUSIONS

Patients with CF undergoing surgery for CRS exhibit substantial bacterial community collapse in the sinuses and a loss of niche specificity between the upper and lower airways compared to non-CF patients with CRS. These results extend previous studies elucidating the lower airway microbiome in cystic fibrosis and provide support for the concept of microbial translocation in the cystic fibrosis airways.

LEVEL OF EVIDENCE

4 Laryngoscope, 129:544-550, 2019.

Probiotics for the airways: Potential to improve epithelial and immune homeostasis

Probiotics are live microorganisms that, when administered in adequate amounts, confer health benefit on the host. The therapeutic effects of probiotics have been mostly studied in the gastrointestinal tract, but recent evidence points toward the potential of these bacteria to prevent and/or treat chronic airway diseases. In this review, possible mechanisms of action of probiotics in the airways are described, with a particular focus on their capacity to modulate the epithelial barrier function and their mode of interaction with the immune system. Indeed, probiotic bacteria, mostly lactobacilli, can promote the expression and regulation of tight junctions and adherence junctions, resulting in the restoration of a defective epithelial barrier. These bacteria interact with the epithelial barrier and immune cells through pattern recognition receptors, such as Toll-like receptors, which upon activation can stimulate or suppress various immune responses. Finally, the clinical potential of probiotics to treat inflammatory diseases of the upper and lower respiratory tract, and the difference between their mode of application (eg, oral or nasal) are discussed here.