Paired analysis of the microbiota between surface tissue swabs and biopsies from pediatric patients undergoing adenotonsillectomy

Paired qualitative and quantitative analysis of bacterial microcolonies in the tonsils of patients with tonsillar hyperplasia

The discovery of bacterial microcolonies in tonsillar tissue of patients with tonsillar hyperplasia has raised the question of their role in provoking the local immune response. Tonsils collected from patients undergoing tonsillectomy were stained for three clinically relevant bacterial taxa and lymphocytes. The bacterial composition and abundance of microcolonies was investigated using a combination of laser-microdissection, amplicon sequencing and Droplet Digital polymerase chain reaction. Microcolonies were detected in most samples (32/35) with a high prevalence of Haemophilus influenzae (78% of samples). B and T cell lymphocytes were significantly higher in the epithelium adjacent to microcolonies compared to epithelium distal to microcolonies. Furthermore, significant positive and negative correlations were identified between bacterial taxa and lymphocytes. Genus Streptococcus, which includes Group A Streptococcus (traditionally described as the main pathogen of tonsillar hyperplasia), was found in low abundance in this study. These results suggest other potential pathogens may be involved in stimulating the local immune response leading to tonsillar hyperplasia.

Identifying the Microbiome of the Adenoid Surface of Children Suffering from Otitis Media with Effusion and Children without Middle Ear Effusion Using 16S rRNA Genetic Sequencing

BACKGROUND

The upper respiratory tract harbors diverse communities of commensal, symbiotic, and pathogenic organisms, originating from both the oral and nasopharyngeal microbiota. Among the primary sites of microbial colonization in the upper airways are the adenoids. Alterations in the adenoid microbiota have been implicated in the development of various conditions, including secretory otitis media.

AIM

This study aims to employ 16S rRNA genetic sequencing to identify the most common bacteria present on the surface of adenoids in children with otitis media with effusion and compare them with children without pathologies in the tympanic cavity. Additionally, we seek to determine and compare the bacterial diversity in these two study groups.

MATERIALS AND METHODS

A total of nineteen samples from the adenoid surfaces were collected, comprising two groups: thirteen samples from children without middle ear effusion and six samples from children with secretory otitis media. The libraries of the V3-V4 hypervariable region of the bacterial 16S rRNA gene was made and sequenced using MiSeq platform.

RESULTS

The most prevalent phyla observed in both groups were Proteobacteria, Firmicutes, and Bacteroidetes. The most common bacterial genera identified in both groups were Haemophilus, Streptococcus, Moraxella, Fusobacterium, and Bordetella, with Fusobacterium and Moraxella being more prevalent in the groups that had no middle ear effusion, while Haemophulus and Streptococcus were more prevalent in the otitis media with effusion group, although not in a statistically significant way. Statistical analysis shows a trend towards bacterial composition and beta diversity being similar between the study groups; however, due to the limited sample size and unevenness between groups, we should approach this data with caution.

CONCLUSION

The lack of prolific difference in bacterial composition between the study groups suggests that the role of the adenoid microbiome in the development of otitis media with effusion may be less significant.

PI16+ reticular cells in human palatine tonsils govern T cell activity in distinct subepithelial niches

Fibroblastic reticular cells (FRCs) direct the interaction and activation of immune cells in discrete microenvironments of lymphoid organs. Despite their important role in steering innate and adaptive immunity, the age- and inflammation-associated changes in the molecular identity and functional properties of human FRCs have remained largely unknown. Here, we show that human tonsillar FRCs undergo dynamic reprogramming during life and respond vigorously to inflammatory perturbation in comparison to other stromal cell types. The peptidase inhibitor 16 (PI16)-expressing reticular cell (PI16⁺ RC) subset of adult tonsils exhibited the strongest inflammation-associated structural remodeling. Interactome analysis combined with ex vivo and in vitro validation revealed that T cell activity within subepithelial niches is controlled by distinct molecular pathways during PI16⁺ RC-lymphocyte interaction. In sum, the topological and molecular definition of the human tonsillar stromal cell landscape reveals PI16⁺ RCs as a specialized FRC niche at the core of mucosal immune responses in the oropharynx.

Changes in the oral and nasal microbiota in pediatric obstructive sleep apnea

Background

Several clinical studies have demonstrated that pediatric obstructive sleep apnea (OSA) is associated with dysbiosis of airway mucosal microbiota. However, how oral and nasal microbial diversity, composition, and structure are altered in pediatric OSA has not been systemically explored.

Methods

30 polysomnography-confirmed OSA patients with adenoid hypertrophy, and 30 controls who did not have adenoid hypertrophy, were enrolled. Swabs from four surface oral tissue sites (tongue base, soft palate, both palatine tonsils, and adenoid) and one nasal swab from both anterior nares were collected. The 16S ribosomal RNA (rRNA) V3-V4 region was sequenced to identify the microbial communities.

Results

The beta diversity and microbial profiles were significantly different between pediatric OSA patients and controls at the five upper airway sites. The abundances of Haemophilus, Fusobacterium, and Porphyromonas were higher at adenoid and tonsils sites of pediatric patients with OSA. Functional analysis revealed that the differential pathway between the pediatric OSA patients and controls involved glycerophospholipids and amino acid metabolism.

Conclusions

In this study, the oral and nasal microbiome of pediatric OSA patients exhibited certain differences in composition compared with the controls. However, the microbiota data could be useful as a reference for studies on the upper airway microbiome.

The Effect of Amoxicillin with Clavulanate on the Microbiota of Tonsillar Tissue in Disease: a Randomized Control Trial

Despite antibiotics being the primary medical treatment for recurrent tonsillitis, the impact of antibiotics on the tonsillar microbiome is not well understood. This study aimed to determine the effect of amoxicillin with clavulanate on the composition and quantity of bacteria in the tonsils of children with recurrent tonsillitis. A multicenter randomized clinical trial in Auckland, New Zealand was undertaken between August 1, 2017, and June 30, 2018. Sixty children undergoing tonsillectomy for the indication of recurrent tonsillitis were recruited for this study. Following random allocation, 30 participants were prescribed amoxicillin with clavulanate for the week before surgery. The remaining 30 received no antibiotics. Immediately following surgery, the crypts of the right and left tonsils were swabbed. Bacterial 16S rRNA gene-targeted amplicon sequencing and histological techniques were utilized. In the control group, there were significantly higher relative abundances of Haemophilus, Streptococcus, Neisseria, and Porphyromonas. Members from the genera Fusobacterium and Treponema were found to be significantly more abundant in the antibiotic group. There were no significant differences in the absolute quantities of bacteria between the groups. Microscopic examination found fewer bacterial microcolonies present in the tonsillar crypts of participants in the antibiotic group. Streptococcus pyogenes was not present in these bacterial microcolonies. These results suggest that a single course of antibiotics has a significant impact on the tonsil microbiota composition. The duration of this effect and the effect that the altered microbiome has on the course of the condition need to be determined. IMPORTANCE Several studies have identified the presence of multiple pathogenic bacteria in hyperplastic adenoids and palatine tonsils. However, there are currently no studies that utilize this technology to investigate the effect of oral antibiotics in children with recurrent tonsillitis on the tonsillar microbiome. This is the first study to investigate the effect of antibiotics on the microbiome of tonsillar tissue in children with recurrent tonsillitis using molecular techniques. This study has shown that participants who received amoxicillin with clavulanate immediately before tonsillectomy had a significantly reduced number of bacterial taxa commonly associated with recurrent tonsillitis, as well as the number of bacterial microcolonies observed in the tonsillar crypts. This novel finding suggests that either the effect of antibiotics is not sustained or that they are not an effective treatment for recurrent tonsillitis.

Distinct microbial communities colonize tonsillar squamous cell carcinoma

Squamous cell carcinoma of the tonsil is one of the most frequent cancers of the oropharynx. The escalating rate of tonsil cancer during the last decades is associated with the increase of high risk-human papilloma virus (HR-HPV) infections. While the microbiome in oropharyngeal malignant diseases has been characterized to some extent, the microbial colonization of HR-HPV-associated tonsil cancer remains largely unknown. Using 16S rRNA gene amplicon sequencing, we have characterized the microbiome of human palatine tonsil crypts in patients suffering from HR-HPV-associated tonsil cancer in comparison to a control cohort of adult sleep apnea patients. We found an increased abundance of the phyla Firmicutes and Actinobacteria in tumor patients, whereas the abundance of Spirochetes and Synergistetes was significantly higher in the control cohort. Furthermore, the accumulation of several genera such as Veillonella, Streptococcus and Prevotella_7 in tonsillar crypts was associated with tonsil cancer. In contrast, Fusobacterium, Prevotella and Treponema_2 were enriched in sleep apnea patients. Machine learning-based bacterial species analysis indicated that a particular bacterial composition in tonsillar crypts is tumor-predictive. Species-specific PCR-based validation in extended patient cohorts confirmed that differential abundance of Filifactor alocis and Prevotella melaninogenica is a distinct trait of tonsil cancer. This study shows that tonsil cancer patients harbor a characteristic microbiome in the crypt environment that differs from the microbiome of sleep apnea patients on all phylogenetic levels. Moreover, our analysis indicates that profiling of microbial communities in distinct tonsillar niches provides microbiome-based avenues for the diagnosis of tonsil cancer.

Tissue microbiota in nasopharyngeal adenoid and its association with pneumococcal carriage

The microbial colonization in the nasopharynx is a prerequisite for the onset of infectious diseases. For successful infection, pathogens should overcome host defenses as well as compete effectively with the resident microbiota. Hence, elucidating the richness and diversity of the microbiome at the site of pathogen colonization is pivotal. Here, we investigated the adenoidal tissue microbiota collected through adenoidectomy to evaluate the impact of Streptococcus pneumoniae. Prospectively, children with sleep-disordered breathing (SDB) and otitis media with effusion (OME) were enrolled. During adenoidectomy, the nasopharyngeal swab and adenoid tissues were collected to determine the pneumococcal carriage and tissue microbiota, using multiplex PCR and 16S ribosomal RNA (16S rRNA) pyrosequencing. A total of 66 pediatric patients comprising 38 children with SDB and 28 children with OME were enrolled. There was no difference between the bacterial cultures from the surface of the nasopharyngeal adenoid in the SDB and OME groups. Thirty-four samples (17 SDB and 17 OME) underwent 16S rRNA pyrosequencing and fulfilled the criteria for further analysis. The Shannon diversity index for the samples from the SDB patients was found to be higher than that observed for the samples from OME patients, although the difference was not significant (p = 0.095). The Shannon diversity index for the samples negative for the pneumococcal carriage was significantly higher than that for the samples positive for pneumococcal carriage (p = 0.038). Alloprevotella, Staphylococcus, Moraxella, and Neisseriaceae were significantly dominant in the samples positive for the pneumococcal carriage. Dialister was significantly less present in the adenoid tissue positive for the pneumococcal carriage. Streptococcus pneumoniae, one of the most common pathogens of the airway, significantly influences the composition and diversity of the microbiota in the nasopharyngeal adenoid. Thus, bacterial community analysis based on 16S rRNA pyrosequencing allows for better understanding of the relationship between the adenoidal microbial communities.

Tonsillar Microbiota: a Cross-Sectional Study of Patients with Chronic Tonsillitis or Tonsillar Hypertrophy

Chronic tonsillitis (CT) and tonsillar hypertrophy (TH) are common tonsillar diseases that are related to infection and inflammation. Little is known about tonsillar microbiota and its role in CT and TH. This study aims to identify palatine tonsillar microbiota both on the surface and in the core tissues of CT and TH patients. In total, 22 palatine tonsils were removed and collected from CT and TH patients who underwent surgery. The surface and core microbiota in the tonsils of CT and TH patients were compared using 16S rRNA gene sequencing of V3-V4 regions. Differential tonsillar microbiotas were found in the CT versus TH patients and surface versus core tissues. Further, a higher relative abundance of bacterial genera, including Haemophilus, Streptococcus, Neisseria, Capnocytophaga, Kingella, Moraxella, and Lachnospiraceae [G-2] in patients with TH and Dialister, Parvimonas, Bacteroidales [G-2], Aggregatibacter, and Atopobium in patients with CT, was observed. Of these, the differential genera of Dialister, Parvimonas, and Neisseria served as key factors in the tonsillar microbiota network. Notably, four representable tonsillar microbial types were identified, with one, consisting of a higher abundance of Haemophilus and Neisseria, exclusively detected in the TH patients. This study analyzed the different tonsillar microbiota from the surface and core tissues of CT and TH patients. Several bacteria and various microbial types related to CT and TH were identified, along with potential bacterial networks and related immune pathways.

IMPORTANCE The human microbiota has been shown to be functionally connected to infectious and inflammation-related diseases. So far, only limited studies had been performed on tonsillar microbiota, although tonsils play an essential role in the human immune defense system and encountered numerous microorganisms. Our work presented different tonsillar microbiota from surface and core tissues of chronic tonsillitis (CT) and tonsillar hypertrophy (TH) patients. Notably, one tonsillar microbiota type, which contains a higher abundance of Haemophilus and Neisseria, was only detected in the TH patients. Furthermore, certain bacteria, such as Haemophilus, Neisseria, Dialister, and Parvimonas, may serve as microbial biomarkers to discriminate CT patients from TH patients. These data provide important microbiota data in the tonsillar research area and are highly useful for researchers both in the oral microbiome field and clinical field.

Pediatric oropharyngeal microbiome: Mapping in chronic tonsillitis and tonsillar hypertrophy

OBJECTIVES

Aim of our study was to map the adenotonsillar lymphoid tissues' microbiome identifying its potential etiopathogenetic role in children affected by chronic tonsillitis or tonsillar hypertrophy with Obstructive Sleep Apnea Syndrome (OSAS).

METHODS

In our study, we examined tonsillar swabs from healthy children and children affected by chronic tonsillitis or by tonsillar hypertrophy with Obstructive Sleep Apnea Syndrome (OSAS). Microbiome's analysis was performed and bacterial 16Sr RNA gene was sequenced according to metagenomic principles. Variability was described according to the biodiversity concept, indicating species found in a certain environment and changes they undergo adapting to different environmental conditions.

RESULTS

The most significant differences concern variation of microbes in a single sample (alpha diversity) of some phyla in children affected by chronic tonsillitis compared with alpha diversity in healthy children and in children affected by OSAS with tonsillar hyperplasia. Proteobacteria are prevalent in chronic tonsillitis group, Fusobacteria and Spirochete in OSAS and Firmicutes, Actinobacteria, and Bacteroidetes were found in healthy children. Finally, comparison between the groups showed that children with OSAS with tonsillar hypertrophy had a higher presence of the Fusobacterium genus.

CONCLUSION

Recurrent upper airway inflammatory and/or infectious processes are polymicrobial; chronicity of such processes appear to be related to variations in microbiome's composition and interaction among various taxonomic units. Knowledge of the microbiomes' composition together with traditional clinical biomarkers can also determine relationships between oropharyngeal microbiome and systemic pathologies to determine preventive changes in lifestyle, eating habits, environmental exposure and use of probiotics.

Correlations Between the Adenotonsillar Microbiome and Clinical Characteristics of Pediatric Patients With Snoring

Objectives

Few studies have reported combined analyses of the microbiome of the adenoids and tonsils in pediatric patients with snoring, and correlations of the adenotonsillar microbiome with clinical characteristics have not been evaluated to date. The aim of this study was to characterize the adenotonsillar microbiome and to determine its correlations with the subjective symptoms of pediatric patients with snoring and with levels of regional mucosal immune molecules.

Methods

Twenty-four children who underwent tonsillectomy with adenoidectomy owing to snoring were enrolled in this cross-sectional study conducted between August 2017 and December 2018. The microbiome of the adenoids and tonsils was characterized, and its alpha- and beta-diversity was determined. Clinical characteristics, including subjective discomfort during sleep (assessed using the obstructive sleep apnea-18 questionnaire), the presence of allergic rhinitis, concentrations of heat shock protein (Hsp)27, Hsp70, and interleukin-8 (IL-8) in lavage fluids, and white blood cell (WBC) counts, were measured.

Results

At the phylum level, the microbiome was not significantly different between the adenoids and tonsils; the alpha and beta indices were likewise not significantly different between these two regions. The alpha-diversity of the entire adenotonsillar microbiome was associated with sex, emotional stress, and IL-8 levels in the tonsil lavage fluids. Beta-diversity was associated with Hsp27 levels in the tonsil lavage fluids and WBC counts. Multiple allergen simultaneous test results were not significant, although total serum immunoglobulin E levels were significantly associated with the beta-diversity of the adenotonsillar microbiome.

Conclusion

The data reported herein suggest, for the first time, that the adenotonsillar microbiome interacts with the regional mucosal immune system. The observed association of the microbiome with subjective discomfort is a novel finding that warrants further investigation.

Comparative analysis of the tonsillar microbiota in IgA nephropathy and other glomerular diseases

Immunoglobulin A nephropathy (IgAN) involves repeated events of gross haematuria with concurrent upper airway infections. The mucosal immune system, especially the tonsil, is considered the initial site of inflammation, although the role of the tonsillar microbiota has not been established in IgAN. In this study, we compared the tonsillar microbiota of patients with IgAN (n = 21) and other glomerular diseases (n = 36) as well as, healthy controls (n = 23) from three medical centres in Korea. The microbiota was analysed from tonsil swabs using the Illumina MiSeq system based on 16S rRNA gene. Tonsillar bacterial diversity was higher in IgAN than in other glomerular diseases, although it did not differ from that of healthy controls. Principal coordinates analysis revealed differences between the tonsillar microbiota of IgAN and both healthy and disease controls. The proportions of Rahnella, Ruminococcus_g2, and Clostridium_g21 were significantly higher in patients with IgAN than in healthy controls (corrected p < 0.05). The relative abundances of several taxa were correlated with the estimated glomerular filtration rate, blood urea nitrogen, haemoglobin, and serum albumin levels. Based on our findings, tonsillar microbiota may be associated with clinical features and possible immunologic pathogenesis of IgAN.

Pathogen reservoir hypothesis investigated by analyses of the adenotonsillar and middle ear microbiota

INTRODUCTION

Adenotonsillar and middle ear diseases result in some of the most frequently performed operations in the pediatric population worldwide. The pathogen reservoir hypothesis (PRH) suggests that the adenoids act as a reservoir of bacteria which play a potential pathogenic role in otitis media. Evidence supporting this hypothesis is limited. This study sought to comprehensively determine and compare associations between the adenotonsillar and middle ear bacterial microbiota within individual patients via next-generation sequencing and microbial network analyses.

METHODS

Bacterial 16S rRNA gene-targeted amplicon sequencing was used to determine the bacterial composition of ten pediatric patients undergoing adenotonsillectomy and ventilation tube insertion for otitis media with effusion. At the time of surgery, swabs were taken from the adenoid surface, tonsil crypts and middle ear clefts (through the myringotomy incision).

RESULTS

The most abundant sequences within the bacterial community at genus level across all anatomical sites were Fusobacterium, Haemophilus, Neisseria, and Porphyromonas. There was an observable difference in the relative abundance of bacterial communities, with a higher proportion of Haemophilus and Moraxella in the adenoid when compared with the middle ear. Furthermore, only one module (consisting of 4 bacterial OTUs) from one patient was identified through microbial network analyses to be significantly associated between middle ear and adenoid. In addition, microbial network analysis revealed that the adenoid and tonsil microbiota share greater similarity than do the adenoid and middle ear.

CONCLUSION

The results of this study suggest that the adenoid microenvironment does not correlate to the middle ear microenvironment. A future study at the species level, and over time, is required to further investigate whether the differing relationship between the microbiota of the adenoid and middle ear rejects the pathogen reservoir hypothesis.

The bacterial community and local lymphocyte response are markedly different in patients with recurrent tonsillitis compared to obstructive sleep apnoea

INTRODUCTION

Obstructive sleep apnea (OSA) is now a more common indication for tonsillectomy than recurrent tonsillitis (RT) [1,2]. Few studies have addressed possible differences in pathogenesis between these two conditions. Children with RT and OSA are often being treated in the community with multiple courses of antibiotics before surgery. Current understanding of the role of bacteria in disorders of the tonsils is mainly based on the culture of tonsil swabs. Swab cultures reflect only a very small fraction of the bacteria present on the mucosal surface and may not represent the bacterial communities within the tonsil crypts [3,4]. This study aimed to evaluate the local lymphocyte response and associations with bacterial community composition using molecular techniques of the tonsils removed from children for RT or OSA.

METHOD

The palatine tonsils were removed by extracapsular dissection from 24 patients with age range one to ten years, 14 of whom had RT and 10 had OSA. The fixed tonsil tissues were evaluated for bacteria by Gram-staining and presence of connective tissue by safranin staining. B lymphocytes and T lymphocytes were also measured immunohistochemically. Finally, previously published bacterial community data for this cohort were reassessed for associations with RT and OSA, and with the observed lymphocyte patterns.

RESULTS

In tonsils from patients with RT, large micro-colonies of bacteria were observed in the tonsil crypts, and a large number of B and T lymphocytes were noted immediately adjacent to the tonsil crypt itself. In marked contrast, the tonsils from patients with OSA had no bacteria identified, and no significant skewing of lymphocytes based on site (such as follicles or crypts). We observed that the majority of lymphocytes surrounding the bacterial micro-colonies were B lymphocytes with a mean ratio of 109:55 (B lymphocytes: T lymphocytes). Bacterial community diversity was not different between the two cohorts; however, there were significant differences in bacterial community composition. Children with RT had a higher relative abundance of members from the genera Parvimonas, Prevotella, and Treponema. While children with OSA had a higher relative abundance of Haemophilus, and Capnocytophaga.

CONCLUSION

These results demonstrate significant differences in the local lymphocyte response and bacterial community composition in tonsil tissue between RT and OSA patients. It suggests that the response to antibiotics used in the treatment of these two conditions may be different. Furthermore, the presence of lymphocytes in RT within the tonsil crypt outside the tonsil epithelium is a unique observation of the location of these cells.