A comparison of sampling methods for examining the laryngeal microbiome

Primary ciliary dyskinesia in Volendam: Diagnostic and phenotypic features in patients with a CCDC114 mutation

Primary ciliary dyskinesia (PCD) is a heterogeneous disease, with impaired mucociliary clearance causing respiratory tract infections. A founding CCDC114 mutation has led to a relatively homogeneous and large Dutch PCD population in Volendam. Our aim was to describe their phenotype. Therefore, all Volendam PCD patients seen at the Amsterdam UMC were included in this study. Data were collected on lung function, microbiology, radiology, and ear‐nose‐throat (ENT) symptoms. A mixed effects model estimated lung function decline in %point per year (95% confidence interval [CI]). Thirty‐three (60%) out of approximately 56 Volendam PCD patients were treated at our center and included in this study. Only 30% of patients had situs inversus. FEV₁ declined in children (−1.43%/year, CI: −1.80/−1.05), but not in adults (0.01%/year, CI: −0.36/0.38). Pseudomonas aeruginosa was cultured in 21% of children and 60% of adults, respectively. Patients who have been infected at some point with P. aeruginosa had a steeper decline in FEV₁ as compared to patients that have never been infected. Neonatal symptoms (79%) and ENT problems (94%) were common; fertility issues however, were not (11%) common. Compared to other PCD cohorts, the Volendam/CCDC114 patients have a moderately severe phenotype with lung function decline predominantly occurring in childhood.

Use of a transnasal flexible laryngoscope tip for laryngeal culturing: A novel in-office technique

BACKGROUND

In-office culture of the larynx using a flexible laryngoscope tip can help identify laryngeal pathogens in cases of laryngitis.

OBJECTIVE

This retrospective case series aimed to investigate the feasibility of in-office laryngoscope tip culture to identify laryngeal pathogens and help guide medical treatment.

METHODS

This case series consists of 8 patients who underwent 11 in-office laryngeal cultures using the tip of the flexible laryngoscope. Concurrent nasal cultures were performed on two patients to assess for possible nasal contamination of these laryngoscope tip cultures.

RESULTS

Nine patients underwent laryngeal culture with laryngoscope tip in-office, with two patients undergoing repeat swabs for a total of eleven swabs. Then, 8 of 11 swabs (73%) grew methicillin-sensitive Staphylococcus aureus, while 1 of 11 (9.1%) swabs grew methicillin-resistant S. aureus. Three of eleven swabs (27%) grew Candida species. Concurrent culture was performed of the contralateral nasal cavity in two patients to assess for the possibility of nasal contamination of laryngoscope tip cultures. Concurrent contralateral nasal cultures grew distinct pathogens compared to the laryngeal cultures, suggesting that nasal contamination did not occur.

CONCLUSION

In-office laryngoscope tip culture allows safe identification of laryngeal pathogens in an ambulatory setting. In-office laryngoscope tip culture can help guide medical treatment of laryngeal infections.

LEVEL OF EVIDENCE

4.

Alterations of bacterial communities of vocal cord mucous membrane increases the risk for glottic laryngeal squamous cell carcinoma

Bacteria are among the important factors that play a role in the balance of human health, and their relationship with some tumors has been well established. However, the association between bacteria colonizing the vocal cords and glottic laryngeal squamous cell carcinoma (GLSCC) remains unclear. Here, we investigated whether bacterial communities of the vocal cord mucous membrane play a role in the development of GLSCC. We collected tumor tissue and normal adjacent tissue (NAT) samples from 19 GLSCC patients, and the bacterial communities were compared with control samples (control) from 21 vocal cord polyps using 16S rRNA high-throughput pyrosequencing. We detected 41 phyla, 93 classes, 188 orders, 373 families, and 829 genera in the vocal cord mucous membrane. A comparison of the bacterial communities in the NAT samples showed higher α‐diversity than in the tumor samples. In the tumor samples, seven groups of bacteria, i.e., the phylum Fusobacteria, the class Fusobacteriia, the order Fusobacteriales, the family Fusobacteriaceae, and the genera Fusobacterium, Alloprevotella, and Prevotella, were significantly enriched, as revealed by linear discriminant analysis coupled with effect size measurements (LEfSe). However, bacteria from the phylum Firmicutes were most significantly enriched in the vocal cord polyp tissues. These findings suggest alterations in the bacterial community structure of the vocal cord mucous membrane of GLSCC patients and that seven groups of bacteria are related to GLSCC, indicating that imbalances in bacterial communities increase the risk for the development of GLSCC.

The porcine respiratory microbiome: recent insights and future challenges

Understanding the structure of the respiratory microbiome and its complex interactions with opportunistic pathogenic bacteria has become a topic of great scientific and economic interest in livestock production, given the severe consequences of respiratory disease on animal health and welfare. The present review focuses on the microbial structures of the porcine upper and lower airways, and the factors that influence microbiome development and onset of respiratory disease. Following a literature search on PubMed and Scopus, 21 articles were selected based on defined exclusion criteria (20 studies performed by 16S rRNA gene sequencing and one by shotgun metagenomics). Analysis of the selected literature indicated that the microbial structure of the upper respiratory tract undergoes a remarkable evolution after birth and tends to stabilise around weaning. Antimicrobial treatment, gaseous ammonia concentration, diet and floor type are amongst the recognized environmental factors influencing microbiome structure. The predominant phyla of the upper respiratory tract are Proteobacteria and Firmicutes with significant differences at the genus level between the nasal and the oropharyngeal cavity. Only five studies investigated the lower respiratory tract and their results diverged in relation to the relative abundance of these two phyla and even more in the composition of the lung microbiome at the genus level, likely because of methodological differences. Reduced diversity and imbalanced microbial composition are associated with an increased risk of respiratory disease. However, most studies presented methodological pitfalls concerning specimen collection, sequencing target and depth, and lack of quality control. Standardization of sampling and sequencing procedures would contribute to a better understanding of the structure of the microbiota inhabiting the lower respiratory tract and its relationship with pig health and disease.

Daily HIV pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate-emtricitabine reduced Streptococcus and increased Erysipelotrichaceae in rectal microbiota

Daily PrEP is highly effective at preventing HIV-1 acquisition, but risks of long-term tenofovir disoproxil fumarate plus emtricitabine (TDF-FTC) include renal decline and bone mineral density decrease in addition to initial gastrointestinal side effects. We investigated the impact of TDF-FTC on the enteric microbiome using rectal swabs collected from healthy MSM before PrEP initiation and after 48 to 72 weeks of adherent PrEP use. The V4 region of the 16S ribosomal RNA gene sequencing showed that Streptococcus was significantly reduced from 12.0% to 1.2% (p = 0.036) and Erysipelotrichaceae family was significantly increased from 0.79% to 3.3% (p = 0.028) after 48–72 weeks of daily PrEP. Catenibacterium mitsuokai, Holdemanella biformis and Turicibacter sanguinis were increased within the Erysipelotrichaceae family and Streptococcus agalactiae, Streptococcus oralis, Streptococcus mitis were reduced. These changes were not associated with host factors including PrEP duration, age, race, tenofovir diphosphate blood level, any drug use and drug abuse, suggesting that the observed microbiome shifts were likely induced by daily PrEP use. Long-term PrEP resulted in increases of Catenibacterium mitsuokai and Holdemanella biformis, which have been associated with gut microbiome dysbiosis. Our observations can aid in characterizing PrEP’s side effects, which is likely to improve PrEP adherence, and thus HIV-1 prevention.

Variation in treatment strategies for the eradication of Pseudomonas aeruginosa in primary ciliary dyskinesia across European centers

Primary ciliary dyskinesia (PCD) is a rare disease causing motile cilia dysfunction, recurrent airway infection, and bronchiectasis. Airway infection management strategies are borrowed from cystic fibrosis. The aim of this study is to describe the management of airway infection with Pseudomonas aeruginosa (PA) in children and adults with PCD across European centers. An online survey questionnaire was sent electronically using SurveyMonkey® to 55 PCD centers in 36 European countries. Fifty-two responded from 43 centers in 26 countries, a response rate of 70%. Most (89%) countries did not have written guidelines for PCD management. Airway sampling for infection detection at each clinic visit was more likely when follow-up was frequent. Eighty-seven percent of centers chose to treat the first PA isolate, most prescribing combined oral ciprofloxacin and inhaled colistimethate sodium (43%, n = 18). The preferred treatment for chronic infection with PA was nebulized colistimethate in 51% (n = 22). In summary, considerable variation exists across European centers in the frequency of patient follow-up and airway sampling for infection, treatment goals, and the management of PA infection. Few centers had written guidelines for PCD management. Clinical trials to determine optimal treatment of PA in PCD patients are urgently needed.

[The Microbiome - The Unscheduled Parameter for Future Therapies]

The microbiome is defined as the total of cellular microorganisms of baczerial, viral or e. g., parasite origin living on the surface of a body. Within the anatomical areas of otorhinolaryngology, a significant divergence and variance can be demonstrated. For ear, nose, throat, larynx and cutis different interactions of microbiome and common factors like age, diet and live style factors (e. g., smoking) have been detected in recent years. Besides, new insights hint at a passible pathognomic role of the microbiome towards diseases in the ENT area. This review article resumes the present findings of this rapidly devloping scientific area.