Fungal and Bacterial Microbiome in Sinus Mucosa of Patients with and without Chronic Rhinosinusitis

OBJECTIVES

Dysbiosis of the sinonasal microbiome has been implicated in the pathogenesis of chronic rhinosinusitis (CRS). However, the mycobiome remains largely understudied, and microbial alterations associated with specific CRS subtypes have yet to be delineated. The objective of this study is to investigate the fungal and bacterial microbiome of sinus mucosa in CRS patients with and without nasal polyposis (CRSwNP and CRSsNP) versus healthy controls.

METHODS

Sinus mucosa was obtained from 92 patients (31 CRSsNP, 31 CRSwNP, and 30 controls) undergoing endoscopic sinus/skull base surgery. Data regarding demographics, Lund-MacKay scores, and histopathology were collected. Fungal and bacterial microbiome analysis was performed utilizing internal transcribed spacer amplicon and 16S rRNA sequencing.

RESULTS

Beta diversity of the sinonasal mycobiome differed significantly between CRS and controls (p = 0.001) and between CRSwNP and controls (p = 0.049), but not between CRSwNP and CRSsNP (p = 0.32) nor between CRSsNP and controls (p = 0.06). With respect to the bacterial microbiome, significantly lower alpha diversity was observed between CRS and controls (p < 0.001), CRSwNP versus controls (p < 0.001), and CRSsNP versus controls (p < 0.001). Beta diversity was also significantly different at the genus level between CRSwNP and CRSsNP (p = 0.019), CRSwNP and controls (p = 0.002)), and CRSsNP and controls (p < 0.001). However, alpha and beta diversity did not differ significantly between CRS patients with/without eosinophils or correlate with Lund-MacKay scores.

CONCLUSIONS

Differences in mycobiota diversity in CRS patients in comparison with controls suggest that alterations in the mycobiome may contribute to disease pathogenesis. Our findings also confirmed that diminished diversity among bacterial communities is associated with CRS and that significant differences are present in microbial composition between CRSwNP and CRSsNP.

LEVEL OF EVIDENCE

3 Laryngoscope, 134:1054-1062, 2024.

Nasal microbiome in chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is defined as an inflammatory disorder of the paranasal sinuses and of the nasal mucosa that lasts 12 weeks or longer. In CRS microbes contribute to the disease pathogenesis. Clinical microbiology is focused on finding single pathogens that causes the disease and the main goal is the use of antibiotics to kill bacteria. Efforts to achieve a better understanding of CRS include the study of the sinus microbiome, and to evaluate the ability of probiotics to augment homeostasis and modulate the immune response of the host mucosa. This review provides an update on the role of the microbiome in CRS. The study was conducted using two databases: PubMed and Science Direct. We searched for articles in English that matched the review topic. We first used the abstracts of articles to assess whether they met the inclusion criteria. We also reviewed the references of the selected articles and read those with titles that might be of interest. Several studies have shown that endogenous microbiome dysbiosis can impact mucosa health and disease severity. Some bacterial species presenting protective or pathogenic effect. Antimicrobial agents can create a similar disruption and impact the nasal microbiome balance. On the other hand, probiotics offers a promising avenue for developing systemic and topical therapies geared towards strategic manipulation of the biological host load, thereby augmenting immune homeostasis. A better comprehension of sinus-nasal microbiome in healthy and in CRS patients and the link with different CRS phenotype can help in developing new prognostics, diagnostics, and therapeutics strategies. Going forward, the use of probiotics can restore the native sinus ecology with significant therapeutic and preventive implications.

Molecular analysis of dominant paranasal sinus bacteria in patients with and without chronic rhinosinusitis

Recent studies have established the possible role of microbiota in developing various diseases. In this regard, attention has shifted to the evaluation of microbiota changes in the paranasal sinuses and its relationship to chronic rhinosinusitis (CRS), especially CRS with nasal polyposis (CRSwNP). This study aimed to examine the bacterial communities of the sphenoidal sinus in Iranian patients with and without CRS. The investigation included 36 subjects, including 18 patients with CRSwNP who underwent Functional Endoscopic Sinus Surgery (FESS) and 18 non-CRS patients who underwent Endoscopic Endonasal Approach (EEA) for pituitary adenoma. The surgeries were performed under general anesthesia, and the sphenoidal sinus was sampled using sterile rayon-tipped swabs coated with a sheet. TaqMan quantitative real-time polymerase chain reaction (qPCR) method (the 16S rDNA gene from bacteria) was used for detection of bacterial communities in different samples. Staphylococcus haemolyticus and Pseudomonas aeruginosa were significantly more prevalent in CRS patients than non-CRS patients (P value ≤ 0.05). However, no significant difference in the frequency of Corynebacterium spp. and Staphylococcus aureus was observed between the two groups, and no Streptococcus pneumoniae or Haemophilus influenza species were isolated from any of the samples. The current study's findings indicated a significant difference in the frequency of certain bacterial species in patients with CRS vs. non-CRS patients. By establishing a link between microbial burden and CRS, it is possible to develop effective treatments or even prevent disorders in this body area.

The Microbiology of Acute Exacerbations in Chronic Rhinosinusitis - A Systematic Review

Background

Acute exacerbations (AE) in chronic rhinosinusitis (CRS) are a common and important clinical issue. However, relatively little is known regarding the underlying microbiology that drives exacerbations or how it relates to the microbiome of CRS. The purpose of this study is to examine the literature to characterize the microbiome associated with acute exacerbations in a chronic rhinosinusitis setting. Understanding this disease process may facilitate targeted antibiotic therapy, reduced antibiotic resistance, and offer more effective disease control and treatment efficacy.

Objective

To characterize the microbiome associated with acute exacerbations of chronic rhinosinusitis (AECRS).

Methods

We conducted a systematic review of the literature on Medline, Embase, and Web of Science databases from January 1990-June 2021 to identify studies related to AE in CRS. Exclusion criteria include non-English, non-human studies, and case reports. Studies without culture or PCR data were also excluded.

Results

Fourteen studies were identified which provided detailed data regarding sinus microbiome in AECRS patients. In these patients, a total of 1252 individual isolates were identified. While common acute pathogens were identified in high frequencies in the sinonasal cultures (Staphylococcus pneumonia, Haemophilus influenza), the predominant bacteria were Staphylococcus aureus (including methicillin-sensitive Staphylococcus aureus) and Pseudomonas aeruginosa. Patient characteristics that may represent higher risk phenotypes were not consistently collected in the studies. Discussion of antimicrobial sensitivities and/or resistance were included in 7/14 studies.

Conclusions

This systematic review identifies the predominant microbiology species that may contribute to AECRS. Further studies are needed to understand the pathogenic role of bacteria and viruses in AECRS and to identify associated comorbidities and patient phenotypes that may predispose to AE. The optimal treatment regimen for AECRS remains unclear.

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.

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.

Staphylococcus aureus Nasal Colonization and Asthma in Adults: Systematic Review and Meta-Analysis

BACKGROUND

Staphylococcus aureus (SA) is a frequent colonizer in humans, and it is known to be associated with chronic allergic diseases including asthma. Recent individual studies suggested that nasal SA colonization may be positively associated with asthma.

OBJECTIVE

To examine relationships between nasal SA colonization and asthma prevalence and activity in adults.

METHODS

Electronic databases were searched for studies published until June 2018. Studies that reported nasal SA colonization prevalence and asthma outcome (prevalence and disease activity) in general adult populations or patients with chronic rhinosinusitis (CRS) were included. Random effects meta-analyses were performed to calculate pooled odds ratio (OR) of the relationships. Subgroup analysis was conducted for the presence of nasal polyps within CRS populations.

RESULTS

A total of 21 cross-sectional studies were identified, and the data from 16 studies using culture methods for SA detection were meta-analyzed (5 general population-based studies and 11 studies of patients with CRS). In studies of general populations, nasal SA colonization had significant relationships with asthma prevalence (OR 1.19; 95% confidence interval [CI] 1.06-1.34; I² = 1%). In studies of patients with CRS, positive associations were also found but had a considerable heterogeneity (OR 1.87; 95% CI 1.18-2.97; I² = 72%). However, the results were comparable between CRS with and without nasal polyps.

CONCLUSIONS

This study demonstrated modest but significant relationships between nasal SA colonization and asthma, supporting potential roles of SA in adult patients with asthma. Further longitudinal cohort and intervention studies are warranted to identify host determinants and to clarify causality of the relationships.

Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites

Chronic rhinosinusitis (CRS) is an inflammatory condition that affects up to 12% of the human population in developed countries. Previous studies examining the potential role of the sinus bacterial microbiota within CRS infections have found inconsistent results, possibly because of inconsistencies in sampling strategies. The aim of this study was to determine whether the sinus microbiome is altered in CRS and additionally if the middle meatus is a suitable representative site for sampling the sinus microbiome. Swab samples were collected from 12 healthy controls and 21 CRS patients, including all eight sinuses for CRS patients and between one and five sinuses for control subjects. The left and right middle meatus and nostril swabs were also collected. Significant differences in the sinus microbiomes between CRS and control samples were revealed using high-throughput 16S rRNA gene sequencing. The genus Escherichia was over-represented in CRS sinuses, and associations between control patients and Corynebacterium and Dolosigranulum were also identified. Comparisons of the middle meatuses between groups did not reflect these differences, and the abundance of the genus Escherichia was significantly lower at this location. Additionally, intra-patient variation was lower between sinuses than between sinus and middle meatus, which together with the above results suggests that the middle meatus is not an effective representative sampling site.

Bacterial microbiome in the nose of healthy cats and in cats with nasal disease

Background

Traditionally, changes in the microbial population of the nose have been assessed using conventional culture techniques. Sequencing of bacterial 16S rRNA genes demonstrated that the human nose is inhabited by a rich and diverse bacterial microbiome that cannot be detected using culture-based methods. The goal of this study was to describe the nasal microbiome of healthy cats, cats with nasal neoplasia, and cats with feline upper respiratory tract disease (FURTD).

Methodology/Principal findings

DNA was extracted from nasal swabs of healthy cats (n = 28), cats with nasal neoplasia (n = 16), and cats with FURTD (n = 15), and 16S rRNA genes were sequenced. High species richness was observed in all samples. Rarefaction analysis revealed that healthy cats living indoors had greater species richness (observed species p = 0.042) and Shannon diversity (p = 0.003) compared with healthy cats living outdoors. Higher species richness (observed species p = 0.001) and Shannon diversity (p<0.001) were found in middle-aged cats in comparison to healthy cats in different age groups. Principal coordinate analysis revealed separate clustering based on similarities in bacterial molecular phylogenetic trees of 16S rRNA genes for indoor and outdoor cats. In all groups examined, the most abundant phyla identified were Proteobacteria, Firmicutes, and Bacteroidetes. At the genus level, 375 operational taxonomic units (OTUs) were identified. In healthy cats and cats with FURTD, Moraxella spp. was the most common genus, while it was unclassified Bradyrhizobiaceae in cats with nasal neoplasia. High individual variability was observed.

Conclusion

This study demonstrates that the nose of cats is inhabited by much more variable and diverse microbial communities than previously shown. Future research in this field might help to develop new diagnostic tools to easily identify nasal microbial changes, relate them to certain disease processes, and help clinicians in the decision process of antibiotic selection for individual patients.

A systematic review of the sinonasal microbiome in chronic rhinosinusitis

BACKGROUND

The interaction between the host and microorganisms in chronic rhinosinusitis (CRS) is poorly understood and is a growing area of interest. More recently, methodologies have been developed to assess the microbiome without the use of culture by analyzing the bacterial 16S ribosomal RNA gene. We reviewed the microbiome literature to better understand the role of microbes in CRS.

METHODS

Systematic review of studies that used the 16S ribosomal RNA gene deep sequencing.

RESULTS

Nine publications met the search criteria. Eight studies evaluated the microbiome in controls (total, 83 subjects; range, 3-28 per study), whereas six of the studies included patients with CRS (total, 121 patients; range, 7-43 per study). Various sequencing techniques, primers, sample sites, and extraction methods were used. Of the articles that specified the number of taxa in controls, an average of 1587 taxa were identified (range, 911-2330). Significant heterogeneity was noted among the studies; however, Firmicutes, Actinobacteria, and Bacteroides phyla were identified in every sample of control patients and patients with CRS. Three of the studies showed enrichment to some degree of Staphylococcus aureus in patients with CRS. The total bacterial burden in CRS was similar to the controls. One study demonstrated a decrease in diversity, whereas other studies did not show any changes in CRS when compared with controls.

CONCLUSION

Although there are common phyla present in both control patients and patients with CRS, no consistent enrichment of any particular taxon was identified. Our findings indicated that there was no clear single causative microbe in CRS. More studies are needed to better understand the significance of the host interaction with the microbiome and the role it plays in CRS.

Microbiology of otitis media in Indigenous Australian children: review

Objectives:

To review research addressing the polymicrobial aetiology of otitis media in Indigenous Australian children in order to identify research gaps and inform best practice in effective prevention strategies and therapeutic interventions.

Methods:

Literature review.

Results:

Studies of aspirated middle-ear fluid represented a minor component of the literature reviewed. Most studies relied upon specimens from middle-ear discharge or the nasopharynx. Culture-based middle-ear discharge studies have found that non-typeableHaemophilus influenzaeandStreptococcus pneumoniaepredominate, withMoraxella catarrhalis, Staphylococcus aureusandStreptococcus pyogenesisolated in a lower proportion of samples.Alloiococcus otitidiswas detected in a number of studies; however, its role in otitis media pathogenesis remains controversial. Nasopharyngeal colonisation is a risk factor for otitis media in Indigenous infants, and bacterial load of otopathogens in the nasopharynx can predict the ear state of Indigenous children.

Conclusion:

Most studies have used culture-based methods and specimens from middle-ear discharge or the nasopharynx. Findings from these studies are consistent with international literature, but reliance on culture may incorrectly characterise the microbiology of this condition. Advances in genomic technologies are now providing microbiologists with the ability to analyse the entire mixed bacterial communities (‘microbiomes’) of samples obtained from Indigenous children with otitis media.

Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis

BACKGROUND

Chronic rhinosinusitis (CRS) is a multifactorial inflammatory airway disorder in which bacteria are implicated in the initiation and/or sustenance of disease in some patients. The sinuses are colonized by bacteria even in health, and the potential for sinus-specific niches harboring unique microbial consortia raises questions for clinical and research investigation. The objective was to determine the degree to which resident upper airways microbiota differ between individuals and anatomic sites, in order to determine the optimal site of microbial sampling for study in CRS.

METHODS

Eight CRS patients undergoing primary surgery were sampled bilaterally at the anterior nares, middle meatus, nasopharynx, maxillary sinus, frontal sinus, and sphenoid sinus for investigation using broad-range bacterial 16S ribosomal RNA (rRNA) sequencing.

RESULTS

Between-subject variability in bacterial microbiota was substantially greater than within-subject variability. The middle meatus was fairly representative of the underlying sinuses, although corynebacteria were detected at higher abundances in the middle meatus, relative to the maxillary (p < 0.1), frontal (p < 0.05), or sphenoid (p < 0.1) sinuses.

CONCLUSION

Interpersonal variation of the upper airway microbiome greatly outweighs niche-specific differences. The middle meatus is a fair representation of the underlying sinuses and may be considered for use as a simple single site for sampling in longitudinal studies or in subjects who have not undergone sinus surgery.

Microbiome of the paranasal sinuses: Update and literature review

BACKGROUND

Our understanding of the resident microbiome of the paranasal sinuses has changed considerably in recent years. Once presumed to be sterile, healthy sinus cavities are now known to harbor a diverse assemblage of microorganisms, and, it is hypothesized that alterations in the kinds and quantities of these microbes may play a role in the pathogenesis of chronic rhinosinusitis (CRS).

OBJECTIVES

To review the current literature regarding the sinus microbiome and collate research findings from relevant studies published to date.

METHODS

A systematic literature review was performed on all molecular studies that investigated the microbial communities of the paranasal sinuses. Methods of detection, microbiome composition, and comparative profiling between patients with and without CRS were explored.

RESULTS

A complex consortium of microorganisms has been demonstrated in the sinuses of both patients with and without CRS. However, the latter generally have been characterized by reduced biodiversity compared with controls, with selective enrichment of particular microbes (e.g., Staphylococcus aureus). Such disruptions in the resident microbiome may contribute to disease pathogenesis by enhancing the virulence of potential pathogens and adversely modulating immune responses.

CONCLUSION

The advent of culture-independent molecular approaches has led to a greater appreciation of the intricate microbial ecology of the paranasal sinuses. Microbiota composition, distribution, and abundance impact mucosal health and influence pathogen growth and function. A deeper understanding of the host-microbiome relationship and its constituents may encourage development of new treatment paradigms for CRS, which target restoration of microbiome homeostasis and cultivation of optimal microbial communities.

The sinonasal bacterial microbiome in health and disease

PURPOSE OF REVIEW

The development of culture-independent bacterial DNA sequencing techniques and integration into research practice has led to a burgeoning interest in the microbiome and its relevance to human health and disease. Introduction into the study of chronic rhinosinusitis in the past few years has shaped current thinking on the role of bacteria in the disease process.

RECENT FINDINGS

Rich and diverse populations of bacteria inhabit the sinonasal cavity at all times. Decreased bacterial richness and diversity may be associated with disease state and outcomes.

SUMMARY

Although there is much to be explored, the sinus microbiome appears to have potentially promising roles in many aspects of sinus health and disease.

Chronic rhinosinusitis: the rationale for current treatments

INTRODUCTION

Chronic rhinosinusitis (CRS) is a broad clinical syndrome linked by mucosal inflammation. Primary treatment modalities are corticosteroids and antibiotics with surgery an option for failures, but the level of supporting evidence is generally low. The primary reason is that CRS is a symptom complex and not a specific disease. Areas covered: The primary treatment modalities for CRS are corticosteroids, antibiotics and surgery. Corticosteroids, which have very broad anti-inflammatory properties, also have the strongest evidence for efficacy. Antibiotics are likely effective in a subpopulation of patients but the various phenotypes and endotypes that make up CRS have thus far been poorly defined. Early surgery as well as biologics may also be more efficacious and cost effective in some phenotypes as well. Expert commentary: A better understanding of the inflammatory pathways that drive CRS will permit investigators to separate patient groups. This will allow for clinical trials that target specific subpopulations and more personalized therapy for CRS patients in the future.

Effects of a honeybee lactic acid bacterial microbiome on human nasal symptoms, commensals, and biomarkers

BACKGROUND

Lactic acid bacteria (LAB) can restore commensal microbiomes and prevent infections. Arguably, nasal administrations of LAB may therefore be beneficial in chronic rhinosinusitis (CRS). Previous studies have examined effects of topical/nasal LAB in children with secretory otitis media, but little is as yet known about their effects on the human nasal airway. The aim of this pilot study was to examine effects on nasal symptoms and commensal bacteria in healthy subjects of nasal administration of a honeybee LAB microbiome; ie, a mixture of 9 Lactobacillus spp. and 4 Bifidobacterium spp. obtained from the honeybee Apis mellifera. Furthermore, we aimed to assess whether or not the honeybee LAB produced a local inflammatory response.

METHODS

Twenty-two healthy subjects received a single administration of honeybee LAB in a sham-controlled, double-blinded, and crossover design. Using questionnaires, microbiological methods, and nasal lavages, they were assessed regarding symptoms, changes to commensal bacteria, and inflammatory products in nasal lavage fluids.

RESULTS

The honeybee LAB did not produce any symptoms or other untoward effects. No changes were observed of commensal bacteria by the honeybee LAB, and no inflammatory response was detected (compared to sham); ie, unaffected nasal lavage fluid levels of monocyte chemoattractant protein-1 (MCP-1), interleukin-8 (IL-8), monokine induced by interferon-γ (MIG), interleukin-15 (IL-15), epidermal growth factor (EGF), eotaxin, interferon gamma-induced protein-10 (IP-10), and interleukin-1 receptor antagonist (IL-1RA).

CONCLUSION

A single human nasal administration of a honeybee LAB microbiome is well tolerated. Specifically, it does not affect commensal bacteria and does not produce an inflammatory response.

Dead or alive: Deoxyribonuclease I sensitive bacteria and implications for the sinus microbiome

BACKGROUND

Recently, there has been tremendous interest in the sinus microbiome and how it relates to disease. However, a lack of a standardized sample collection and DNA extraction methods makes comparison of results across studies nearly impossible. Furthermore, current techniques fail to identify which components of the microbiome are actually alive within the host at the time of sampling.

OBJECTIVE

To develop and optimize a method to differentiate which bacterial species in the human sinus microbiome are live versus dead.

METHODS

Duplicate samples from the middle meatus of patients with healthy sinus tissue and those patients with chronic rhinosinusitis were collected by using brushes (n = 12), swabs (n = 27), and tissue biopsy (n = 8) methods. One sample from each pair was either deoxyribonuclease I- or control-treated before DNA extraction. The relative bacterial versus human composition of each sample was determined. A 16S ribosomal RNA gene analysis was performed on a six-paired sample from patients with healthy sinus tissue.

RESULTS

We found that swabs and brushes collected a higher percentage of bacterial DNA than did tissue biopsy. We also determined that as much as 50% of the bacteria collected in these samples was already dead at the time of collection. The 16S ribosomal RNA gene analysis found significant changes in the relative abundance of taxa identified in the live versus dead bacterial communities of healthy human sinuses.

CONCLUSIONS

Our findings indicated that swabs provided the best quality microbiome samples and that a large portion of the bacteria identified in the sinus were deoxyribonuclease I sensitive. These results highlighted the need for improved techniques such as those presented here, which can differentiate between living and dead bacteria in a sample, a potentially critical distinction when examining changes in sinus innate immune function because both components play important, but distinct, functions. Further studies will determine how these living and dead bacterial populations shift in different disease states and after clinical intervention.

Enzyme-assisted target recycling (EATR) for nucleic acid detection

Fast, reliable and sensitive methods for nucleic acid detection are of growing practical interest with respect to molecular diagnostics of cancer, infectious and genetic diseases. Currently, PCR-based and other target amplification strategies are most extensively used in practice. At the same time, such assays have limitations that can be overcome by alternative approaches. There is a recent explosion in the design of methods that amplify the signal produced by a nucleic acid target, without changing its copy number. This review aims at systematization and critical analysis of the enzyme-assisted target recycling (EATR) signal amplification technique. The approach uses nucleases to recognize and cleave the probe-target complex. Cleavage reactions produce a detectable signal. The advantages of such techniques are potentially low sensitivity to contamination and lack of the requirement of a thermal cycler. Nucleases used for EATR include sequence-dependent restriction or nicking endonucleases or sequence independent exonuclease III, lambda exonuclease, RNase H, RNase HII, AP endonuclease, duplex-specific nuclease, DNase I, or T7 exonuclease. EATR-based assays are potentially useful for point-of-care diagnostics, single nucleotide polymorphisms genotyping and microRNA analysis. Specificity, limit of detection and the potential impact of EATR strategies on molecular diagnostics are discussed.

The Etiology and Pathogenesis of Chronic Rhinosinusitis: a Review of Current Hypotheses

Chronic rhinosinusitis (CRS) is a broad clinical syndrome that is characterized by prolonged mucosal inflammation of the nose and paranasal sinuses, and is typically divided into two subtypes based on the presence or absence of nasal polyps. The etiology and pathogenesis of both forms remain areas of active research. Over the last 15 years, a number of hypotheses have been proposed to explain all or part of the clinical CRS spectrum. These hypotheses reflect the concept that CRS results from a dysfunctional interplay between individual host characteristics and factors exogenous to the host. Six broad theories on CRS etiology and pathogenesis are discussed as follows: (1) the "fungal hypothesis," (2) the "superantigen hypothesis," (3) the "biofilm hypothesis," and (4) the "microbiome hypothesis," all of which emphasize key environmental factors, and (5) the "eicosanoid hypothesis" and (6) the "immune barrier hypothesis," which describe specific host factors. These theories are reviewed, and the evidence supporting them is critically appraised.

Sinus microbiota varies among chronic rhinosinusitis phenotypes and predicts surgical outcome

BACKGROUND

Chronic rhinosinusitis (CRS) is a prevalent multifactorial disease process in which bacteria are believed to play a role in the propagation of inflammation. Multiple subtypes of CRS have been described based on clinical and pathologic features, but a detailed examination of the sinus microbiota in patients with CRS and its clinical subtypes has yet to be performed.

OBJECTIVE

We sought to examine the resident microbiota of CRS subtypes and determine whether bacterial diversity is a predictor of disease outcomes.

METHODS

Sinus swabs from patients with CRS and healthy subjects collected during endoscopic sinus surgery were analyzed by means of molecular phylogenetic analysis of 16S rDNA pyrosequences.

RESULTS

Fifty-six patients with CRS and 26 control subjects were studied. Biodiversity was similar between the CRS and control groups. Among the CRS subtypes examined, only 2 conditions (presence of purulence and comorbid condition of asthma) were associated with significant alterations in microbial community composition. In 27 patients with CRS who were followed postoperatively, those with better outcomes had more diverse bacterial communities present at the time of surgery, along with higher relative abundances of Actinobacteria.

CONCLUSION

Analysis of microbiota in a large cohort reveals that particular CRS phenotypes (asthma and purulence) are characterized by distinct compositions of resident bacterial communities. We found that bacterial diversity and composition are predictors of surgical outcome, promoting the concept of community ecology in patients with CRS.

The prevalence of bacterial infection in acute rhinosinusitis: a Systematic review and meta-analysis

OBJECTIVES/HYPOTHESIS

To systematically assess the prevalence of bacterial infection in adults with acute rhinosinusitis (ARS).

METHODS

Electronic databases were systematically searched for relevant studies published up to June 2012.

RESULTS

Twenty-nine articles, evaluating a total of 9,595 patients with a clinical diagnosis of ARS, were included in the study. Of these, 14 (48%) studies required radiographic confirmation of sinusitis, one study (3%) required evidence of purulence, 10 studies (35%) required both for inclusion in the study population, and four studies (14%) required neither. The random effects model estimate of prevalence of bacterial growth on all cultures was 53.7% (CI 48.4%-59.0%), ranging from 52.5% (CI 46.7%-58.3%) in studies requiring radiographic confirmation of sinusitis to 61.1% (CI 54.0%-68.1%) in studies requiring neither radiographic evidence nor purulence on exam. Studies that obtained cultures from antral swab had a prevalence of bacterial growth of 61.0% (CI 54.7%-67.2%), whereas those utilizing endoscopic meatal sampling had a prevalence of 32.9% (CI 19.0%-46.8%).

CONCLUSIONS

Few studies evaluate the recovery of bacteria via culture in adults with a diagnosis of ABRS or ARS based on clinical criteria alone. With radiographic and/or endoscopic confirmation, antral puncture and endoscopically guided cultures produce positive bacterial cultures in approximately one-half of patients. Opportunities exist to improve diagnostic accuracy for bacterial infection in ARS.

The microbiome of the middle meatus in healthy adults

Rhinitis and rhinosinusitis are multifactorial disease processes in which bacteria may play a role either in infection or stimulation of the inflammatory process. Rhinosinusitis has been historically studied with culture-based techniques, which have implicated several common pathogens in disease states. More recently, the NIH Human Microbiome Project has examined the microbiome at a number of accessible body sites, and demonstrated differences among healthy and diseased patients. Recent DNA-based sinus studies have suggested that healthy sinuses are not sterile, as was previously believed, but the normal sinonasal microbiome has yet to be thoroughly examined. Middle meatus swab specimens were collected from 28 consecutive patients presenting with no signs or symptoms of rhinosinusitis. Bacterial colonization was assessed in these specimens using quantitative PCR and 16S rRNA pyrosequencing. All subjects were positive for bacterial colonization of the middle meatus. Staphylococcus aureus, Staphylococcus epidermidis and Propionibacterium acnes were the most prevalent and abundant microorganisms detected. Rich and diverse bacterial assemblages are present in the sinonasal cavity in the normal state, including opportunistic pathogens typically found in the nasopharynx. This work helps establish a baseline for understanding how the sinonasal microbiome may impact diseases of the upper airways.

Confounding factors in rhinological research

PURPOSE OF REVIEW

Basic science studies directed at understanding the inflammatory mechanisms in chronic rhinosinusitis (CRS) are increasing, yet their relevance to the underlying disease process is often conflicting and confounded by the enrollment of a heterogeneous CRS population. This review is aimed at exploring the issues affecting the basic science mucosal studies of CRS patients, with special attention to the inclusion criteria for CRS and the control group, and the site from which the mucosal tissue sample is obtained.

RECENT FINDINGS

A common confounding factor is an inadequate documentation of selection criteria for patients, controls, and tissue sites examined. Inconsistent definitions for CRS and for maximum medical therapy, and a lack of histopathology confirmation of mucosal inflammation (eosinophilic or neutrophilic) can bias the disease population entering a given study. Further confounding factors include the influence of coexisting diseases, pollution and cigarette smoke, and a need for same-site tissue comparisons, meticulous selection of relevant controls, and consensus on 'nondiseased' mucosal inflammatory cell populations and microbiology.

SUMMARY

Documentation of well defined patient and control groups, standardized specimen collection methods, and detection assays are critical in minimizing the bias and conflicting findings among investigators. With standardized sampling of tissue sites and tight controls on subcategories of CRS patients enrolled, studies will more likely identify the findings that can increase our understanding of the disparate group of CRS patients and identify new therapeutic targets in the CRS subcategories.

Genomics, the origins of agriculture, and our changing microbe-scape: time to revisit some old tales and tell some new ones

Though agriculture is often viewed as one of humanity's crowning achievements, skeletal evidence indicates that dependence on domesticated plants and animals was accompanied by an increase in infectious disease. Scientists have proposed that many important infections emerged in the period following the advent of agriculture, as a result of newly dense populations and novel proximity to domestic animals that served as reservoirs for novel pathogens. Here, we review genomic evidence regarding pathogen origins, analyzing these data using the epidemiological transition framework. Genetic information has forced us to reconsider how and when many important pathogens emerged; it appears that a number of infections thought to result from contact with domesticated animals arose much earlier than agriculture was adopted. We also consider the broader effect of agriculture upon the microbiome, exploring potential consequences for human health. We end by discussing the changes in the human microbe-scape we are likely to see in the future.

The impact of culturable bacterial community on histopathology in chronic rhinosinusitis

BACKGROUND

The influence of the microbial community on inflammatory subtype in chronic rhinosinusitis (CRS) has been proposed. Superantigen mechanisms potentially create a T helper 2 (Th-2)/eosinophilic dominated inflammation as a product of local flora rather than an intrinsic mucosal process. The associations between culturable bacteria and the histopathology and clinical features of CRS patients are described.

METHODS

A cross-sectional study involving patients with CRS undergoing surgery was undertaken. Middle meatal swabs were performed at surgery for microbiological evaluation. Mucosal biopsies were taken and a blinded histopathological profile was performed. Disease specific quality of life and nasal symptom scores were recorded. The presence of culturable organisms and particular pathogens were compared with histopathology and clinical outcomes.

RESULTS

A total of 95 patients were assessed (48.4% female, mean age 45.6 ± 14.0 years), of which 47.3% had a culturable organism. Tissue eosinophilia (>10/high-power field [HPF]) was found in 46.1% of these patients and 30.3% had neutrophilic infiltrate, with the presence of neither Gram-positive organisms, Gram-negative organisms, nor species correlating to pathology subtype. A culturable pathogen was a predictor of subepithelial fibrosis (χ(2) = 6.36, p = 0.04) and Gram-negative bacteria had the strongest association (χ(2) = 18.82, p < 0.01). There were no other significant associations with other clinical outcomes.

CONCLUSION

The culturable bacterial community has little impact on histopathology in CRS. While more sensitive tests may detect bacteria in the sinuses, the impact of the simple "culturable" bacteria on the underlying pathologic process is limited. Changes, such as subepithelial fibrosis, suggest colonization may lead to undesirable local mucosal damage and remodeling.

Bacteriology of normal frontal sinuses

PURPOSE

The aim of this cross-sectional trial was to identify the bacterial flora and to quantify the level of bacterial presence in healthy adult frontal sinus cavities.

MATERIALS AND METHODS

Ninety five consecutive patients undergoing craniotomy of the anterior cranial fossa were enrolled. All patients were evaluated preoperatively by a sino-nasal questionnaire, nasal endoscopy and CT scan. Exclusion criteria were patients with sinus tumours, presenting a cold in the past 8 weeks, having signs or symptoms suggestive of sinus disease, history suggestive of allergic rhinitis and/or asthma, having undergone hospitalization or an outpatient clinic visit within the past 12 months, patients with known systemic disease, having previous sinus or nose surgery, history of trauma of the sino-nasal region, or having used systemic antibiotics, steroids, or nasal spray in the past 8 weeks. Lavages were obtained from frontal sinuses before craniotomy through trephination of the anterior wall. The sinus was irrigated with sterile saline followed by aspiration. Specimens were inoculated for aerobic and anaerobic organisms.

RESULTS

After applying the exclusion criteria, 42 patients (84 sinuses) were finally included in the study. Bacterial organisms were recovered in 12 of 84 (14.28%) sinuses. However, 85.72% of the sinuses were found to be sterile. Bacteria recovered included three different coagulase-negative staphylococci, one Citrobacter diversus and two Micrococcus spp. No anaerobic organism was isolated.

CONCLUSIONS

This study demonstrated that the majority of frontal sinuses of asymptomatic adults with normal CT and endoscopic appearance are sterile.

The bacteriology of chronic rhinosinusitis and the pre-eminence of Staphylococcus aureus in revision patients

BACKGROUND

The role of bacteria in the etiopathogenesis of chronic rhinosinusitis (CRS) remains an area of interest. The impact of surgery and factors such as the presence of polyps, asthma, and aspirin sensitivity on the bacterial state are poorly understood. To determine the effect of these factors, this study examines the culture results from a large cohort of CRS patients.

METHODS

This retrospective study used the culture results from 513 CRS patients, which were analyzed for species growth and compared to factors such as previous surgery, presence of polyps, aspirin sensitivity, and asthma. Univariate and multivariate logistic regression models were used for statistical analysis.

RESULTS

Eighty-three percent (83%) of patients had a positive culture result. The average number of isolates detected per patient was 0.95. S. aureus was the most frequently cultured organism (35%), followed by P. aeruginosa (9%), Haemophilus spp. (7%), and S. pneumonia (5%). Revision patients were more likely to grow S. aureus (p = 0.001), P. aeruginosa (p = 0.044) and have a positive culture (p = 0.001). Asthma was correlated with a positive culture (p = 0.039). No difference was determined between polyp and nonpolyp patients for any of the bacterial outcomes.

CONCLUSION

This study highlights important factors in the bacteriology of CRS patients. S. aureus was the most prevalent species identified in our cohort, followed by P. aeruginosa. S. aureus rates of isolation were also significantly higher in patients undergoing revision surgery. No association was found between the presence of nasal polyposis and culture rates.

Prevalence and abundance of Staphylococcus aureus in the middle meatus of patients with chronic rhinosinusitis, nasal polyps, and asthma

BACKGROUND

Chronic rhinosinusitis (CRS) is an idiosyncratic and multifactorial disease process. Bacteria play a role in some patients, by infection or stimulation of inflammation. Staphylococcus aureus (SA) appears to be implicated in a number of infectious and inflammatory mechanisms, and may be particularly relevant in CRS patients with nasal polyps and asthma.

METHODS

Middle meatus swabs from control and CRS patients collected during endoscopic sinus surgery were analyzed by quantitative polymerase chain reaction (QPCR). Total bacterial count, SA prevalence, and SA abundance were examined with respect to patient demographics and disease characteristics.

RESULTS

Total bacteria, as measured by QPCR, was not statistically different between controls, CRS without nasal polyps (CRSsNP), CRS with nasal polyps (CRSwNP), or CRS with asthma groups (p < 0.09). Total bacterial counts did not correlate with disease severity as measured by Lund-Mackay computed tomography (CT) scores (p = 0.65). The prevalence of SA was similar between groups (15-25%); however, the abundance increased in CRS patients with allergic rhinitis, nasal polyps, and asthma.

CONCLUSION

The paranasal sinuses are not sterile. SA is implicated in a subset of CRS patients with nasal polyps and/or asthma. Further study is required to predict this subset of patients, and to define the mechanisms of SA pathogenesis.

Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis

OBJECTIVES/HYPOTHESIS

The aim of this study was to compare microbiological culture-based and culture-independent (16S rRNA gene sequencing) methodologies for pathogen identification in chronic rhinosinusitis (CRS) patients. We hypothesized that bacterial culture and DNA sequencing would yield largely concurrent results, although sequencing would detect greater bacterial diversity, and the sinonasal microbiomes of CRS patients would differ in composition and diversity compared with non-CRS controls.

STUDY DESIGN

Cross-sectional observational study.

METHODS

Middle meatus swabs from CRS patients collected during endoscopic sinus surgery were analyzed by both clinical culture and broad-range analysis of 16S rRNA gene pyrosequences.

RESULTS

A total of 21 swab samples from 15 CRS patients and five non-CRS controls were analyzed. One CRS patient was also swabbed 3 weeks postoperatively due to evidence of purulence during a clinical visit. All subjects had positive bacterial cultures, with a mean of 2.8 isolates per subject. The most prevalent cultivars were coagulase-negative staphylococci (15/20 specimens, 75%), Staphylococcus aureus (10/20, 50%), and Propionibacterium acnes (6/20, 30%). Among 57,407 pyrosequences generated, the most prevalent were from coagulase-negative staphylococci (21/21 specimens, 100%), Corynebacterium spp (18/21, 85.7%), P acnes (16/21, 76.2%), and S aureus (14/21, 66.7%). Bacterial diversity correlated with recent antibiotic use, asthma, prior sinus surgery, and relative abundance of S aureus.

CONCLUSIONS

DNA pyrosequencing revealed greater biodiversity than culture, although in most cases culture results represented a subset of the abundant DNA sequence types. CRS patients were characterized by altered microbial composition (P = .02) and greater abundance of S aureus (P = .03).