Bacterial Pathogens and the Microbiome

Microbial Analysis in Chronic Rhinosinusitis Patients with Chronic Kidney Disease and End-Stage Renal Disease

INTRODUCTION

This study aimed to elucidate the bacterial profile of chronic rhinosinusitis (CRS) in patients with end-stage renal disease (ESRD) and chronic kidney disease (CKD) compared with nonrenal patients, guiding antibiotic selection for clinicians.

METHODS

We retrospectively analyzed 13,906 inpatients from the Chang Gung Research Database who underwent sinus surgery (2004-2018). Patients were categorized into ESRD-CRS, CKD-CRS, and non-CKD-CRS based on the estimated glomerular filtration rate. Bacterial cultures from surgical samples were classified as facultative anaerobes or aerobes (e.g., Klebsiella pneumoniae [KP], Pseudomonas aeruginosa [Ps.a]), anaerobes, and fungi and ranked by prevalence.

RESULTS

Data from 47 ESRD-CRS, 230 CKD-CRS, and 13,123 non-CKD-CRS patients were analyzed. In ESRD-CRS, the predominant species were KP (31.6%), Ps.a (21.1%), and Coagulase-negative Staphylococcus (CoNS, 15.8%). CKD-CRS showed Staphylococcus epidermidis (27.7%), CoNS (20.5%), and Ps.a (20.5%). Non-CKD-CRS had Staphylococcus epidermidis (29.8%), CoNS (25.0%), and Staphylococcus aureus (15.5%). For anaerobes, ESRD-CRS was dominated by Fusobacterium nucleatum (10.5%) and Peptostreptococcus micros (10.5%), whereas CKD-CRS and non-CKD-CRS showed Propionibacterium acnes as a primary strain (14.5% and 28.7%, respectively).

CONCLUSION

For CRS in ESRD, antibiotics targeting KP and Fusobacterium nucleatum are recommended. In CKD-CRS, a focus on Staphylococcus epidermidis and Propionibacterium acnes is suggested.

LEVEL OF EVIDENCE

4 Laryngoscope, 134:3499-3507, 2024.

Bacterial colonization differences between central compartment atopic disease and eosinophilic chronic rhinosinusitis

KEY POINTS

Culturable bacterial colonization is similar between type 2 CRS phenotypes Staphylococcus aureus coinfection is similar between eosinophilic CRS and CCAD Patients with CCAD were younger, consistent with current knowledge of the disease.

The difference in pathogenic bacteria between chronic rhinosinusitis in patients with and without Sjogren's syndrome: a retrospective case-control study

Background

Chronic rhinosinusitis (CRS) affects the quality of life of many people worldwide and can cause comorbidities. Our previous research proved that Sjogren’s syndrome (SS) is a predisposing factor for CRS, with a 2.5-fold associated risk. Antibiotics are important in CRS treatment; however, there is a paucity of research on the pathogenic bacteria of SS-CRS in the past. We conducted this study to investigate the pathogenic difference of SS-CRS and non-SS-CRS and aimed to give clinicians references when selecting antibiotics to treat SS-CRS.

Materials and methods

A total of 14,678 patients hospitalized for CRS operation from 2004 to 2018 were identified from the Chang Gung Research Database. These CRS cases were classified as either SS-CRS or non-SS-CRS. We analyzed their bacterial distribution by studying the results of the pus cultures performed alongside surgery.

Results

The top three facultative anaerobic or aerobic isolated bacteria in the SS-CRS group were coagulase-negative Staphylococcus (CoNS: 34.3%), Pseudomonas aeruginosa (28.6%), methicillin-sensitive Staphylococcus aureus (MSSA: 20%), and Staphylococcus epidermidis (20%). In the non-SS-CRS group, S. epidermidis (29.3%), CoNS (25.7%), and MSSA (14.2%) were identified. The top three anaerobic bacterial genera were Cutibacterium (54.3%), Peptostreptococcus (11.4%), and Fusobacterium (11.4%) in the SS-CRS group and Cutibacterium (53.8%), Peptostreptococcus (25%), and Prevotella (12.9%) in the non-SS-CRS group.

Conclusions

P.aeruginosa is a major pathogen in SS-CRS patients. In addition, physicians should be aware of potential Fusobacterium and antibiotic-resistant bacterial infection in patients with SS-CRS.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07652-4.

Investigation and Functional Enrichment Analysis of the Human Host Interaction Network with Common Gram-Negative Respiratory Pathogens Predicts Possible Association with Lung Adenocarcinoma

Haemophilus influenzae (Hi), Moraxella catarrhalis (MorCa) and Pseudomonas aeruginosa (Psa) are three of the most common gram-negative bacteria responsible for human respiratory diseases. In this study, we aimed to identify, using the functional enrichment analysis (FEA), the human gene interaction network with the aforementioned bacteria in order to elucidate the full spectrum of induced pathogenicity. The Human Pathogen Interaction Database (HPIDB 3.0) was used to identify the human proteins that interact with the three pathogens. FEA was performed via the ToppFun tool of the ToppGene Suite and the GeneCodis database so as to identify enriched gene ontologies (GO) of biological processes (BP), cellular components (CC) and diseases. In total, 11 human proteins were found to interact with the bacterial pathogens. FEA of BP GOs revealed associations with mitochondrial membrane permeability relative to apoptotic pathways. FEA of CC GOs revealed associations with focal adhesion, cell junctions and exosomes. The most significantly enriched annotations in diseases and pathways were lung adenocarcinoma and cell cycle, respectively. Our results suggest that the Hi, MorCa and Psa pathogens could be related to the pathogenesis and/or progression of lung adenocarcinoma via the targeting of the epithelial cellular junctions and the subsequent deregulation of the cell adhesion and apoptotic pathways. These hypotheses should be experimentally validated.

Low-dose and long-term azithromycin significantly decreases Staphylococcus aureus in the microbiome of refractory CRS patients

BACKGROUND

The sinonasal microbiome is believed to play an important role in the pathophysiology of refractory chronic rhinosinusitis (CRS). We evaluated changes in the microbiome following a 4-month course of low-dose azithromycin. Assessing microbiome alterations following such a treatment may help identify underlying mechanisms of this drug.

METHODS

A total of 48 adults with refractory CRS were enrolled in a double-blind, randomized, placebo-controlled trial. Patients were randomized to 250 mg of azithromycin or placebo 3 times weekly for 4 months. During this time, daily budesonide saline irrigations were continued. Sinonasal swabs were collected by endoscopically-assisted method prior to treatment initiation and at the end of it, and sent for 16S ribosomal RNA gene sequencing. High-resolution ANCHOR pipeline was used to infer and annotate putative species. The 2 patient groups were compared using DESeq2 differential abundance analysis.

RESULTS

From initiation to the end of azithromycin treatment, patients showed a significant difference in beta diversity analysis (p = 0.0004) along with a significant decrease in 71 different operational taxonomic units (OTUs) of Staphylococcus aureus (false discovery rate [FDR] < 0.05) obtained from the differential abundance analysis. This was not observed in placebo-treated patients. By the end of treatments, azithromycin-treated patients had a significant decrease in 29 different OTUs of S. aureus (FDR < 0.05) when compared to placebo.

CONCLUSION

A 4-month course of 250 mg of azithromycin 3 times weekly in patients with refractory CRS significantly decreases S. aureus abundance in the sinonasal microbiome. Considering the pathogenic role of S. aureus in the refractory CRS population, azithromycin may constitute an additional therapeutic option to help control this 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.

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.

Determinants of the Nasal Microbiome: Pilot Study of Effects of Intranasal Medication Use

Introduction

A role for bacteria and other microbes has long been suspected in the chronic inflammatory sinonasal diseases. Recent studies utilizing culture-independent, sequence-based identification have demonstrated aberrant shifts in the sinus microbiota of chronic rhinosinusitis subjects, compared with ostensibly healthy controls. Examining how such microbiota shifts occur and the potential for physician-prescribed interventions to influence microbiota dynamics are the topics of the current article.

Methods

The nasal cavity microbiota of 5 subjects was serially examined over an 8-week period using pan-bacterial 16S rRNA gene sequencing. Four of the subjects were administered topical mometasone furoate spray, while 1 subject underwent a mupirocin decolonization procedure in anticipation of orthopedic surgery.

Results

Measures of microbial diversity were unaffected by intranasal treatment in 2 patients and were markedly increased in the remaining 3. The increase in microbial diversity was related to clearance of Moraxella spp. and a simultaneous increase in members of the phylum Actinobacteria. Both effects persisted at least 2 weeks beyond cessation of treatment. Transient changes in the relative abundance of several bacterial genera, including Staphylococcus and Priopionibacteria, were also observed during treatment.

Conclusions

The effects of intranasal steroids on the sinonasal microbiome are poorly understood, despite their widespread use in treating chronic sinonasal inflammatory disorders. In this longitudinal study, administration of intranasal mometasone furoate or mupirocin resulted in shifts in microbial diversity that persisted to some degree following treatment cessation. Further characterization of these effects as well as elucidation of the mechanism(s) underlying these changes is needed.

Characteristics of meningitis following transsphenoidal endoscopic surgery: a case series and a systematic literature review

BACKGROUND

Meningitis occurs in 0.8-1.5% of patients undergoing neurosurgery. The aim of the study was to evaluate the characteristics of meningitis after endoscopic endonasal transsphenoidal surgery (EETS) comparing the findings retrieved to those highlighted by literature search.

MATERIALS AND METHODS

Patients treated by EETS during an 18-year period in the Department of Neurosurgery of 'Federico II' University of Naples were evaluated and included in the study if they fulfilled criteria for meningitis. Epidemiological, demographic, laboratory, and microbiological findings were evaluated. A literature research according to PRISMA methodology completed the study.

RESULTS

EETS was performed on 1450 patients, 8 of them (0.6%) had meningitis [median age 46 years (range 33-73)]. Endoscopic surgery was performed 1-15 days (median 4 days) before diagnosis. Meningeal signs were always present. CSF examination revealed elevated cells [median 501 cells/μL (range 30-5728)], high protein [median 445 mg/dL (range 230-1210)], and low glucose [median 10 mg/dL (range 1-39)]. CSF culture revealed Gram-negative bacteria in four cases (Klebsiella pneumoniae, Escherichia coli, Alcaligenes spp., and Haemophilus influenzae), Streptococcus pneumoniae in two cases, Aspergillus fumigatus in one case. An abscess occupying the surgical site was observed in two cases. Six cases reported a favorable outcome; two died. Incidence of meningitis approached to 2%, as assessed by the literature search.

CONCLUSIONS

Incidence of meningitis after EETS is low despite endoscope goes through non-sterile structures; microorganisms retrieved are those present within sinus microenvironment. Meningitis must be suspected in patients with persistent fever and impaired conscience status after EETS.

Examination of high-antibiotic users in a multi-institutional cohort of chronic rhinosinusitis patients

BACKGROUND

In addition to known concerns regarding antibiotic overuse, recent research indicates that excessive antibiotic use is associated with poorer long-term health. Given that rhinosinusitis is the leading condition accounting for antibiotic prescriptions in the ambulatory setting, we aimed to evaluate characteristics associated with greater antibiotic use in chronic rhinosinusitis (CRS).

METHODS

Adult CRS patients enrolled in a prospective, multi-institutional, observational cohort study evaluating treatment outcomes were included in this analysis. Study participants were asked to report the number of days out of the previous 90 days that systemic antibiotics were taken for sinus disease. Patient demographics, disease characteristics, and measures of disease severity were evaluated.

RESULTS

A total of 561 patients from 4 institutions were included in the analysis, with mean antibiotic use of 17.4 ± 22.4 out of the prior 90 days. No differences between antibiotic-use groups were found for objective measures of disease severity (computed tomography [CT], endoscopy, Brief Smell Identification Test [BSIT] scores), however, increased patient-reported symptom burden (22-item Sino-Nasal Outcome Test [SNOT-22], Rhinosinusitis Disability Index [RSDI]) was associated with more antibiotic use. Patients reporting the most antibiotic use were older (p = 0.004) but no ethnic or gender differences were seen. Comorbid diagnoses of allergy, asthma, diabetes, depression, or fibromyalgia were not associated with increased antibiotic use. In accordance with literature recommendations, CRS with nasal polyps (CRSwNP) patients were less likely to have used antibiotics. Endoscopic sinus surgery (ESS) significantly decreased antibiotic use.

CONCLUSION

Variability in antibiotic use in CRS appears to be driven by symptom burden, independent of objective measures of disease severity, patient demographics, and presence of comorbid disease. Clear guidelines are essential to define appropriate antibiotic use in CRS.

Effects of glucocorticoid on the expression and regulation of aquaporin 5 in the paranasal sinus of rats with chronic rhinosinusitis

Aquaporins (AQPs) are water-specific membrane channel proteins that regulate water homeostasis for cells and organisms. AQP5 serves an important role in the maintenance of mucosal water homeostasis, and potentially contributes to mucosal edema and inflammation formation in chronic rhinosinusitis (CRS). The aim of the present study was to explore the expression pattern of AQP5 and the effect of glucocorticoids on AQP5 expression in rats with CRS. The rats were randomly divided into three equal groups, as follows: CRS, dexamethasone (dexa) treatment and control groups. A polyvinyl acetal material containing Staphylococcus aureus was inserted into the left nasal cavity of each rat from the CRS and dexa groups. On the 90th post-operative day, the dexa group received dexamethasone (2 mg/kg/day) via intraperitoneal injection for 7 days. The controls did not receive any treatment. The expression of AQP5 in the sinonasal mucosa was determined using immunohistochemistry and quantitative PCR. The immunoreactivities of AQP5 were primarily noted in the epithelial lining and glandular cells, the vascular endothelium and in the goblet cells in the sinonasal mucosa. The AQP5 mRNA expression level was significantly higher in the dexa group than in the control and CRS groups (P=0.006 and P=0.014, respectively). However, no significant difference was indicated between the CRS and control groups (P=0.760). In conclusion, the current study suggests that glucocorticoids induce AQP5 expression in the sinonasal mucosa of CRS rats, which highlights AQP5 as a potential target in the diagnosis and treatment of CRS.

Characterization of Sinus Microbiota by 16S Sequencing from Swabs

New culture-independent microbiology methods are leading to a paradigm shift in our understanding of how the microbial community at the mucosal surface impacts sinonasal health and disease. Whereas traditional culture-based protocols were designed to identify specific pathogens in order to direct antibiotic therapies and eradicate bacteria, newer molecular techniques allow for the identification of both culturable and nonculturable bacteria in diverse communities. As a result of the recent explosion in the use of molecular techniques, we are gaining an understanding of how commensal bacteria may help modulate the host immune response and promote homeostasis. Here, we describe the general workflow of microbiome sequencing including the detailed methods for extracting mixed-community genomic DNA from sinonasal swabs, amplifying bacterial 16S rRNA genes using quantitative PCR, and preparing the samples for next-generation sequencing on the most commonly used sequencing platforms.