Panel 4: Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures

Draft genome sequence of novel Candidatus Ornithobacterium hominis carrying antimicrobial resistance genes in Egypt

BACKGROUND

Candidatus Ornithobacterium hominis (O. hominis), which was identified in nasopharyngeal swabs from Egypt, has been associated with respiratory disorders in humans. O. hominis, a recently identified member of the Flavobacteriaceae family, belongs to the largest family within the Bacteroidetes phylum. This family includes hundreds of species and 90 genera, including major human pathogens such as Capnocytophaga canimorsus and Elizabethkingia meningoseptica. Herein, we presented two draft genome assemblies of O. hominis that were extracted from metagenomic data using the Illumina sequencing method. The alignment of reads against the O. hominis genome was accomplished using BLASTN, and the reads with significant hits were extracted using Seqtk and assembled using SPAdes. The primary goal of this study was to obtain a more profound understanding of the genomic landscape of O. hominis, with an emphasis on identifying the associated virulence, antimicrobial genes, and distinct defense mechanisms to shed light on the potential role of O. hominis in human respiratory infections.

RESULTS

The genome size was estimated to be 1.84 Mb, including 1,931,660 base pairs (bp), with 1,837 predicted coding regions and a G+C content of 35.62%. Genes encoding gliding motility, antibiotic resistance (20 genes), and the toxA gene were all included in the genome assembly. Gliding motility lipoproteins (GldD, GldJ, GldN, and GldH) and the gliding motility-associated ABC transporter substrate-binding protein, which acts as a crucial virulence mechanism in Flavobacterium species, were identified. The genome contained unique genes encoding proteins, such as the ParE1 toxin that defend against the actions of quinolone and other antibiotics. The cobalt-zinc-cadmium resistance gene encoding the protein CzcB, which is necessary for metal resistance, urease regulation, and colonization, was also detected. Several multidrug resistance genes encoding proteins were identified, such as MexB, MdtK, YheI, and VanC.

CONCLUSION

Our study focused on identifying virulence factors, and antimicrobial resistance genes present in the core genome of O. hominis. These findings provide valuable insights into the potential pathogenicity and antibiotic susceptibility of O. hominis.

Realising respiratory microbiomic meta-analyses: time for a standardised framework

In microbiome fields of study, meta-analyses have proven to be a valuable tool for identifying the technical drivers of variation among studies and results of investigations in several diseases, such as those of the gut and sinuses. Meta-analyses also represent a powerful and efficient approach to leverage existing scientific data to both reaffirm existing findings and generate new hypotheses within the field. However, there are currently limited data in other fields, such as the paediatric respiratory tract, where extension of original data becomes even more critical due to samples often being difficult to obtain and process for a range of both technical and ethical reasons. Performing such analyses in an evolving field comes with challenges related to data accessibility and heterogeneity. This is particularly the case in paediatric respiratory microbiomics - a field in which best microbiome-related practices are not yet firmly established, clinical heterogeneity abounds and ethical challenges can complicate sharing of patient data. Having recently conducted a large-scale, individual participant data meta-analysis of the paediatric respiratory microbiota (n = 2624 children from 20 studies), we discuss here some of the unique barriers facing these studies and open and invite a dialogue towards future opportunities. Video Abstract.

A Brief Review of Local Bacteriotherapy for Preventing Respiratory Infections

Recurrent respiratory infections (RRIs) account for relevant economic and social implications and significantly affect family life. Local Bacteriotherapy (LB) represents an innovative option in preventing RRIs. Local bacteriotherapy consists of administering “good” and safe bacteria (probiotics) by nasal or oral route. In particular, two strains (Streptococcus salivarius 24SMB and Streptococcus oralis 89a) are commonly used. The present article presents and discusses the literature concerning LB. Infections of airways include the upper and lower respiratory tract. A series of clinical trials investigated the preventive role of LB in preventing upper and lower RIs. These studies demonstrated that LB safely reduced the prevalence and severity of RIs, the use of antibiotics, and absences from school. Therefore, Local Bacteriotherapy may be considered an interesting therapeutic option in RRI prevention.

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.

The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes

Otitis media (OM) and externa (OE) are painful, recurrent ear conditions. As most otitis publications focus on the bacterial content of childhood ears, there remains a dearth of information regarding the adult ear microbiome including both bacteria and fungi. This study compares the outer ear microbiome of healthy adults to adults affected by OE and OM using both intergenic-transcribed-spacer (ITS) and 16S-rDNA sequencing. The adult ear core microbiome consists of the prokaryote Cutibacterium acnes and the eukaryotic Malassezia arunalokei, M. globosa, and M. restricta. The healthy ear mycobiome is dominated by Malassezia and can be divided into two groups, one dominated by M. arunalokei, the other by M. restricta. Microbiome diversity and biomass varied significantly between healthy and diseased ears, and analyses reveal the presence of a potential mutualistic, protective effect of Malassezia species and C. acnes. The healthy ear core microbiome includes the bacteria Staphylococcus capitis and S. capitis/caprae, while the diseased ear core is composed of known bacterial and fungal pathogens including Aspergillus sp., Candida sp., Pseudomonas aeruginosa, S. aureus, and Corynebacterium jeikeium. The data presented highlight the need for early detection of the cause of otitis to direct more appropriate, efficient treatments. This will improve patient outcomes and promote improved antimicrobial stewardship.

Innate Immunity in the Middle Ear Mucosa

Otitis media (OM) encompasses a spectrum of clinical presentations ranging from the readily identifiable Acute OM (AOM), which is characterised by otalgia and fever, to chronic otitis media with effusion (COME) where impaired hearing due to middle ear effusion may be the only clinical symptom. Chronic suppurative OM (CSOM) presents as a more severe form of OM, involving perforation of the tympanic membrane. The pathogenesis of OM in these varied clinical presentations is unclear but activation of the innate inflammatory responses to viral and/or bacterial infection of the upper respiratory tract performs an integral role. This localised inflammatory response can persist even after pathogens are cleared from the middle ear, eustachian tubes and, in the case of respiratory viruses, even the nasal compartment. Children prone to OM may experience an over exuberant inflammatory response that underlies the development of chronic forms of OM and their sequelae, including hearing impairment. Treatments for chronic effusive forms of OM are limited, with current therapeutic guidelines recommending a "watch and wait" strategy rather than active treatment with antibiotics, corticosteroids or other anti-inflammatory drugs. Overall, there is a clear need for more targeted and effective treatments that either prevent or reduce the hyper-inflammatory response associated with chronic forms of OM. Improved treatment options rely upon an in-depth understanding of OM pathogenesis, particularly the role of the host innate immune response during acute OM. In this paper, we review the current literature regarding the innate immune response within the middle ear to bacterial and viral otopathogens alone, and as co-infections. This is an important consideration, as the role of respiratory viruses as primary pathogens in OM is not yet fully understood. Furthermore, increased reporting from PCR-based diagnostics, indicates that viral/bacterial co-infections in the middle ear are more common than bacterial infections alone. Increasingly, the mechanisms by which viral/bacterial co-infections may drive or maintain complex innate immune responses and inflammation during OM as a chronic response require investigation. Improved understanding of the pathogenesis of chronic OM, including host innate immune response within the middle ear is vital for development of improved diagnostic and treatment options for our children.

Human nasal microbiota

The human nasal passages host a distinct community of microbes. Katherine P. Lemon describes this distinct community, and why it matters so much for human health.

Upper Respiratory Microbiota in Relation to Ear and Nose Health Among Australian Aboriginal and Torres Strait Islander Children

BACKGROUND

We explored the nasal microbiota in Indigenous Australian children in relation to ear and nasal health.

METHODS

In total, 103 Indigenous Australian children aged 2-7 years (mean 4.7 years) were recruited from 2 Queensland communities. Children's ears, nose, and throats were examined and upper respiratory tract (URT) swabs collected. Clinical histories were obtained from parents/medical records. URT microbiota were characterized using culturomics with Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification. Real-time PCR was used to quantify otopathogen (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) loads and detect respiratory viruses. Data were analyzed using beta diversity measures, regression modeling, and a correlation network analysis.

RESULTS

Children with historical/current otitis media (OM) or URT infection (URTI) had higher nasal otopathogen detection and loads and rhinovirus detection compared with healthy children (all P < .04). Children with purulent rhinorrhea had higher nasal otopathogen detection and loads and rhinovirus detection (P < .04) compared with healthy children. High otopathogen loads were correlated in children with historical/current OM or URTI, whereas Corynebacterium pseudodiphtheriticum and Dolosigranulum pigrum were correlated in healthy children.

CONCLUSIONS

Corynebacterium pseudodiphtheriticum and D. pigrum are associated with URT and ear health. The importance of the main otopathogens in URT disease/OM was confirmed, and their role relates to co-colonization and high otopathogens loads.

Targeting host-microbial interactions to develop otitis media therapies

Otitis media (OM; middle ear infection) is the most common reason for pre-school children to visit a doctor, be prescribed antimicrobials, or undergo surgery. Recent Cochrane reviews of clinical trials have identified that antibiotics and grommet surgery are only moderately effective in treating OM, with recurrent or persistent infection observed in one-third of children. Research efforts are focusing on developing improved therapies to treat OM and prevent disease recurrence. The recurrent nature of OM is mostly due to the persistence of bacterial pathogens within established biofilm in the middle ear. Promising novel therapies are harnessing host-microbe interactions to disrupt middle ear biofilm and permit antibiotics to work more effectively. New approaches are also being developed to prevent OM, including new vaccines and mining the host respiratory microbiome to develop novel bacterial therapies. This review describes how our improved knowledge of human and microbial interactions is driving development of OM therapies to improve health outcomes for children in Australia and worldwide.

Local Bacteriotherapy - a promising preventive tool in recurrent respiratory infections

INTRODUCTION

Children with recurrent respiratory infections (RRI) represent a social issue for the economic burden and the negative family impact. Local Bacteriotherapy is an attractive therapeutic strategy that could be potentially effective in preventing infections. The current article remarks on the existing evidence of preventing RRI by Local Bacteriotherapy.

AREAS COVERED

The literature search methodology was based on the articles cited by PubMed from 1980 to 2020. Respiratory infections include rhino-pharyngitis, otitis media, rhinosinusitis, pharyngo-tracheitis, bronchitis, and pneumonia. Several studies were performed to investigate the effects of Local Bacteriotherapy in children with RRI. Both intranasal and oral Local Bacteriotherapy were evaluated. The findings showed that Local Bacteriotherapy significantly reduced the number of RI episodes, their severity, the use of antibiotics, and school absences.

EXPERT OPINION

Local Bacteriotherapy is a promising approach to RRI prevention and could be a profitable strategy to contrast infections in the future.

Review of otitis media microbiome studies: What do they tell us?

OBJECTIVES

To provide a state of the art review on accruing studies focused on defining the middle ear microbiome, highlighting the relationship of the microbiome to disease pathophysiology.

DATA SOURCES

Pubmed indexed peer-reviewed articles and published textbooks.

REVIEW METHODS

Comprehensive review of the literature using the following search terms: "microbiome" "bacterial pathogens" with the term "otitis media," and "middle ear."

RESULTS

A multitude of microbiome studies have been published in the recent past. In general findings from these studies underscore distinct profiles based on disease category. The adenoidal reservoir theory may not explain all etiologies of middle ear effusion production. The host immune system appears to be associated to the bacterial population identified in the middle ear space. Atopic respiratory diseases correlate to the middle ear microbiome. Some novel middle ear bacterial genera may be protective in terms of disease.

CONCLUSION

The understanding of otitis media disease progression pathophysiology is evolving, informed by accruing middle ear microbiomic data. The functional implications of middle ear microbiome findings need to be studied further. This may help counterbalance probiotic vs antibiotic approaches to disease mitigation.

Oral bacteriotherapy in children with recurrent respiratory infections: a real-life study

Children with recurrent respiratory infections (RRI) represent a social issue for the economic burden and the familiar negative impact. Bacteriotherapy, such as the administration of “good” bacteria, is a new therapeutic strategy that could be potentially effective in preventing infections. The current study tested the hypothesis of preventing RRI by oral Bacteriotherapy in a real-life setting. This open study was conducted in an outpatient clinic, enrolling 51 children (27 males, mean age 4.8 ± 2.6 years) suffering from RRI. Children were treated with an oral spray, containing Streptococcus salivarius 24SMB and Streptococcus oralis89a (125 x 10⁹ CFU/g), 2 puffs per os once/day for 30 consecutive days; this course was repeated for 3 months. The evaluated parameters were: RI number and school absences reported in the current year; these outcomes were compared with those recorded in the past year. The mean number of RI significantly diminished: from 5.17 (2.30) in the past year to 2.25 (2.43) after the treatment (p<0.0001). The mean number of school absences significantly diminished (from 3.35 to 1.86; p<0.0001). In conclusion, this real-life study suggests that oral Bacteriotherapy with Streptococcus salivarius 24SMB and Streptococcus oralis89a could efficaciously and safely prevent RRI in children. (www.actabiomedica.it)