The Microbiome of the Nose-Friend or Foe?

Human nasal microbiota shifts in healthy and chronic respiratory disease conditions

BACKGROUND

An increasing number of studies investigate various human microbiotas and their roles in the development of diseases, maintenance of health states, and balanced signaling towards the brain. Current data demonstrate that the nasal microbiota contains a unique and highly variable array of commensal bacteria and opportunistic pathogens. However, we need to understand how to harness current knowledge, enrich nasal microbiota with beneficial microorganisms, and prevent pathogenic developments.

RESULTS

In this study, we have obtained nasal, nasopharyngeal, and bronchoalveolar lavage fluid samples from healthy volunteers and patients suffering from chronic respiratory tract diseases for full-length 16 S rRNA sequencing analysis using Oxford Nanopore Technologies. Demographic and clinical data were collected simultaneously. The microbiome analysis of 97 people from Lithuania suffering from chronic inflammatory respiratory tract disease and healthy volunteers revealed that the human nasal microbiome represents the microbiome of the upper airways well.

CONCLUSIONS

The nasal microbiota of patients was enriched with opportunistic pathogens, which could be used as indicators of respiratory tract conditions. In addition, we observed that a healthy human nasal microbiome contained several plant- and bee-associated species, suggesting the possibility of enriching human nasal microbiota via such exposures when needed. These candidate probiotics should be investigated for their modulating effects on airway and lung epithelia, immunogenic properties, neurotransmitter content, and roles in maintaining respiratory health and nose-brain interrelationships.

A neonatal piglet model reveals interactions between nasal microbiota and influenza A virus pathogenesis

While vaccination and therapeutics for prevention/treatment of influenza are available, new strategies are needed to combat influenza disease in susceptible populations, particularly young children and newborns. Host associated microbiota play an important role in modulating the virulence of numerous pathogens, including the influenza A virus. In this study, we examined microbiome-influenza interactions in a neonatal piglet model system. The nasal microbiome of newborn piglets was longitudinally sampled before and after intranasal infection with recombinant viruses expressing hemagglutinins (HAs) derived from distinct zoonotic H1 subtypes. We found that viruses expressing different parental HAs manifested unique patterns of pathogenicity, and varied impacts on microbial community diversity. Despite these virus specific differences, a consistent microbial signature of viral infection was detected. Our results indicate that influenza A virus infection associates with the restructuring of nasal microbiome and such shifts in microbial diversity may contribute to outcomes of viral infection in neonatal piglets.

In vitro photoinactivation effectiveness of a portable LED device aimed for intranasal photodisinfection and a photosensitizer formulation comprising methylene blue and potassium iodide against bacterial, fungal, and viral respiratory pathogens

Antimicrobial photodynamic therapy (aPDT) can be a viable option for management of intranasal infections. However, there are light delivery, fluence, and photosensitizer-related challenges. We report in vitro effectiveness of an easily fabricated, low-cost, portable, LED device and a formulation comprising methylene blue (MB) and potassium iodide (KI) for photoinactivation of pathogens of the nasal cavity, namely, methicillin-resistant Staphylococcus aureus, antibiotic-resistant Klebsiella pneumoniae, multi-antibiotic-resistant Pseudomonas aeruginosa, Candida spp., and SARS-CoV-2.In a 96-well plate, microbial suspensions incubated with 0.005% MB alone or MB and KI formulation were exposed to different red light (~ 660 ± 25 nm) fluence using the LED device fitted to each well. Survival loss in bacteria and fungi was quantified using colony-forming unit assay, and SARS-CoV-2 photodamage was assessed by RT-PCR.The results suggest that KI addition to MB leads to KI concentration-dependent potentiation (up to ~ 5 log10) of photoinactivation in bacteria and fungi. aPDT in the presence of 25 or 50 mM KI shows the following photoinactivation trend; Gm + ve bacteria  > Gm - ve bacteria > fungi  > virus. aPDT in the presence of 100 mM KI, using 3- or 5-min red light exposure, results in complete eradication of bacteria or fungi, respectively. For SARS-CoV-2, aPDT using MB-KI leads to a ~ 6.5 increase in cycle threshold value.The results demonstrate the photoinactivation effectiveness of the device and MB-KI formulation, which may be helpful in designing of an optimized protocol for future intranasal photoinactivation studies in clinical settings.

Effect of nasal carriage of Bacillus species on COVID-19 severity: a cross-sectional study

Intranasal sprays containing Bacillus species are being researched for treating viral respiratory tract infections. The aim of this study was to assess the relationship between the nasal carriage of Bacillus and COVID-19 severity. This was a cross-sectional study that collected nasopharyngeal samples from adults 18 years and above visiting two COVID-19 testing centers in Lagos, Nigeria, between September 2020 and September 2021. Bacillus species were cultured from the samples and confirmed using 16 s rRNA gene sequencing. The dependent variable was COVID-19 status classified as negative, asymptomatic, mild, or severe. The independent variable was the nasal carriage of Bacillus species. Multinomial regression analysis was done to determine the association between nasal carriage of Bacillus and COVID-19 severity after adjusting for age, sex, and co-morbidity status. A total of 388 participants were included in the study with mean (standard deviation) age of 40.05 (13.563) years. Sixty-one percent of the participants were male, 100 (25.8%) had severe COVID-19, 130 (33.5%) had pre-existing comorbidity, and 76 (19.6%) had Bacillus cultured from their nasopharyngeal specimen. Bacillus species presence was significantly associated with higher odds of severe COVID-19 compared to having a negative COVID-19 status (AOR = 3.347, 95% CI: 1.359, 8.243). However, the presence of Bacillus species was significantly associated with lower odds of severe COVID-19 compared to having a mild COVID-19 status. The study suggests that nasal carriage of Bacillus species is associated with the clinical course of COVID-19 and supports the exploration of Bacillus species in the management of viral respiratory tract infections.IMPORTANCEWith the introduction of intranasal spray containing Bacillus species for the treatment of viral respiratory tract infections, such as COVID-19 and respiratory syncytial virus, identifying the association between the nasal carriage of Bacillus species and COVID-19 susceptibility and severity will help further substantiate the investigation of these bacteria for COVID-19 prevention and treatment. This study evaluated the association between the carriage of Bacillus species in the nasopharyngeal tract and COVID-19 severity and found that the presence of Bacillus species in the nasopharynx may significantly impact the clinical course of COVID-19.

The nasopharyngeal microbiome in COVID-19

The development of novel culture-independent techniques of microbial identification has allowed a rapid progress in the knowledge of the nasopharyngeal microbiota and its role in health and disease. Thus, it has been demonstrated that the nasopharyngeal microbiota defends the host from invading pathogens that enter the body through the upper airways by participating in the modulation of innate and adaptive immune responses. The current COVID-19 pandemic has created an urgent need for fast-track research, especially to identify and characterize biomarkers to predict the disease severity and outcome. Since the nasopharyngeal microbiota diversity and composition could potentially be used as a prognosis biomarker for COVID-19 patients, which would pave the way for strategies aiming to reduce the disease severity by modifying such microbiota, dozens of research articles have already explored the possible associations between changes in the nasopharyngeal microbiota and the severity or outcome of COVID-19 patients. Unfortunately, results are controversial, as many studies with apparently similar experimental designs have reported contradictory data. Herein we put together, compare, and discuss all the relevant results on this issue reported to date. Even more interesting, we discuss in detail which are the limitations of these studies, that probably are the main sources of the high variability observed. Therefore, this work is useful not only for people interested in current knowledge about the relationship between the nasopharyngeal microbiota and COVID-19, but also for researchers who want to go further in this field while avoiding the limitations and variability of previous works.

Nasal microbes in allergic rhinitis children with or without sublingual immunotherapy

The mechanism of allergic rhinitis (AR) remains unclear. Most researchers believe that AR is the result of a combination of environmental and genetic factors. Sublingual immunotherapy (SLIT) is a treatment that can change the natural course of AR through immunomodulatory mechanism and maintain efficacy after the treatment. Nasal cavity is the main site where AR patients contact with external allergens, produce inflammatory reactions and nasal symptoms. Therefore, in this study, we investigate the nasal microbiome in AR patients, and the changes after SLIT. In this cross-sectional study, nasal swabs for microbiome analysis were collected from 3 groups: SLIT-naïve AR patients (AR group), AR patients undergoing SLIT treatment over 2 years (SLIT group) and a control group (CG). The characteristics of nasal microbiome of each groups were produced by 16s-rDNA sequencing technology. The Simpson index of AR group was significantly higher than that of CG and SLIT groups, but not different between SLIT group and CG group. The abundance of Bacteroidete and Firmicutes remarkably increased in the AR group, but Bacteroidete reduced to CG level after SLIT. AR patients have different nasal microbiome composition, but we do not know how it happened and whether the AR condition affected nasal microbiome composition or nasal microbiome affected AR.

Maternal constipation is associated with allergic rhinitis in the offspring: A nationwide retrospective cohort study

Allergic rhinitis (AR) is a common atopic disease worldwide, and it was found that babies with constipation in their early life might have an increased risk of atopic diseases, including AR. Furthermore, recent studies also indicate that the maternal gut microbiota may influence babies. Thus, we extended the definition of early life in utero and evaluated the association between maternal constipation and the risk of AR in their babies. Using the Longitudinal Health Insurance Database, a subset of Taiwan's National Health Insurance Research Database, we identified 102,820 constipated mothers and 102,820 matched controls between 2005 and 2015. Propensity score analysis was used to match birth year, child sex, birth weight, gestational age, mode of delivery, maternal comorbidities, and children antibiotics taken. Multiple Cox regression and subgroup analyzes were conducted to estimate the adjusted hazard ratio of childhood AR. The incidence of childhood AR was 83.47 per 1,000 person-years in constipated mothers. Adjusting children's sex, birth weight, gestational age, mode of delivery, maternal comorbidities, and children antibiotic use, the results showed that the children whose mothers had constipation had a 1.20-fold risk of AR compared to children of mothers without constipation. Maternal constipation was associated with an increased risk of AR. Therefore, it is important to pay close attention to pregnant mothers with constipation.

Exposure to cooking fumes is associated with perturbations in nasal microbiota composition: A pilot study

Air pollution is one of the leading causes of overall mortality globally. Cooking emissions are a major source of fine particulate matter (PM2.5). However, studies on their potential perturbations on the nasal microbiota as well as their association with respiratory health are lacking. This pilot study aims to assess the environmental air quality among occupational cooks and its associations with nasal microbiota and respiratory symptoms. A total of 20 cooks (exposed) and 20 unexposed controls (mainly office workers), were recruited in Singapore from 2019 to 2021. Information on sociodemographic factors, cooking methods, and self-reported respiratory symptoms were collected using a questionnaire. Personal PM2.5 concentrations and reactive oxygen species (ROS) levels were measured using portable sensors and filter samplers. DNA was extracted from nasal swabs and sequenced using 16s sequencing. Alpha-diversity and beta-diversity were calculated, and between-group variation analysis of species was performed. Multivariable logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for associations between exposure groups and self-reported respiratory symptoms. Higher daily mean PM2.5 (P = 2 × 10-7) and environmental ROS exposure (P = 3.25 × 10-7) were observed in the exposed group. Alpha diversity of the nasal microbiota between the two groups was not significantly different. However, beta diversity was significantly different (unweighted UniFrac P = 1.11 × 10-5, weighted UniFrac P = 5.42 × 10-6) between the two exposure groups. In addition, certain taxa of bacteria were slightly more abundant in the exposed group compared to unexposed controls. There were no significant associations between the exposure groups and self-reported respiratory symptoms. In summary, the exposed group had higher PM2.5 and ROS exposure levels and altered nasal microbiotas as compared to unexposed controls, though further studies are required to replicate these findings in a larger population.

Human Knee Has A Distinct Microbiome: Implications for Periprosthetic Joint Infection

INTRODUCTION

Pathogens causing prosthetic joint infection are thought to gain access to the knee during surgery or from a remote site in the body. Recent studies have shown that there is a distinct microbiome in various sites of the body. This prospective study, and first of its kind, was set up to investigate the presence of possible microbiome in human knee and compare the profile in different knee conditions.

METHODS

This transversal study prospectively obtained synovial fluid from 65 knees (55 patients) with various conditions that included normal knee, osteoarthritis, aseptic revision, and those undergoing revision for periprosthetic joint infection (PJI). The contralateral knee of patients who had a PJI were also aspirated to compare the composition of the PJI knee with uninfected contralateral knee. A minimum of 3 milliliters (ml) of synovial fluid was collected per joint. Then, the samples were aliquoted for culture and next generation sequencing (NGS) analysis.

RESULTS

The highest number of species was found in native osteoarthritic knees (P≤0.035). Cutibacterium, Staphylococcus, and Paracoccus species were dominant in native non-osteoarthritic knees, and meanwhile a markedly high abundance of Proteobacteria was observed in the osteoarthritic joints. Moreover, the contralateral and aseptic revision knees showed a similar trend in bacterial composition (P=0.75). The NGS analysis of patients who had PJI diagnosis, confirmed the culture results.

DISCUSSION/CONCLUSION

Distinct knee microbiome profiles can be detected in patients who have osteoarthritis and other knee conditions. The distinct microbiome in the knee joint and the close host-microbe relationships within the knee joint may play a decisive role in the development of osteoarthritis and periprosthetic joint infection.

Effect of Antibiotic Eye Drops on the Nasal Microbiome in Healthy Subjects—A Pilot Study

Background: Antibiotic eye drops are frequently used in clinical practice. Due to the anatomical connection via the nasolacrimal duct, it seems possible that they have an influence on the nasal/pharyngeal microbiome. This was investigated by using two different commonly used antibiotic eye drops. Methods: 20 subjects were randomized to four groups of five subjects receiving eye drops containing gentamicin, ciprofloxacin, or, as controls, unpreserved povidone or benzalkonium chloride-preserved povidone. Nasal and pharyngeal swabs were performed before and after the instillation period. Swabs were analyzed by Illumina next-generation sequencing (NGS)-based 16S rRNA analysis. Bacterial culture was performed on solid media, and bacterial isolates were identified to the species level by MALDI-TOF MS. Species-dependent antimicrobial susceptibility testing was performed using single isolates and pools of isolates. Results: Bacterial richness in the nose increased numerically from 163 ± 30 to 243 ± 100 OTUs (gentamicin) and from 114 ± 17 to 144 ± 45 OTUs (ciprofloxacin). Phylogenetic diversity index (pd) of different bacterial strains in the nasal microbiome increased from 12.4 ± 1.0 to 16.9 ± 5.6 pd (gentamicin) and from 10.2 ± 1.4 to 11.8 ± 3.1 pd (ciprofloxacin). Unpreserved povidone eye drops resulted in minimal changes in bacterial counts. Preservative-containing povidone eye drops resulted in no change. A minor increase (1–2-fold) in the minimal inhibitory concentration (MIC) was observed in single streptococcal isolates. Conclusions: Antibiotic eye drops could affect the nasal microbiome. After an instillation period of seven days, an increase in the diversity and richness of bacterial strains in the nasal microbiome was observed.

In vitro assembly of plasmid DNA for direct cloning in Lactiplantibacillus plantarum WCSF1

Lactobacilli are gram-positive bacteria that are growing in importance for the healthcare industry and genetically engineering them as living therapeutics is highly sought after. However, progress in this field is hindered since most strains are difficult to genetically manipulate, partly due to their complex and thick cell walls limiting our capability to transform them with exogenous DNA. To overcome this, large amounts of DNA (>1 μg) are normally required to successfully transform these bacteria. An intermediate host, like E. coli, is often used to amplify recombinant DNA to such amounts although this approach poses unwanted drawbacks such as an increase in plasmid size, different methylation patterns and the limitation of introducing only genes compatible with the intermediate host. In this work, we have developed a direct cloning method based on in-vitro assembly and PCR amplification to yield recombinant DNA in significant quantities for successful transformation in L. plantarum WCFS1. The advantage of this method is demonstrated in terms of shorter experimental duration and the possibility to introduce a gene incompatible with E. coli into L. plantarum WCFS1.

Local allergic rhinitis: considerations

The term "local allergic rhinitis" has gained popularity as a clinical entity in recent years. Despite the apparent contradiction in the definitions of "nasal" and "local," we offer insights based on our extensive experience in the field. Local allergic rhinitis has been recognized and treated for many years, so it is not a new discovery. The nasal provocation test, which was introduced in the 1980s, was critical in identifying allergic rhinitis cases with suggestive symptoms but negative allergy tests. Our reflections aim to contribute to a precise terminological decision that is consistent with various points of view.

Rapid separation of bacteria from primary nasal samples using inertial microfluidics

Microbial populations play a crucial role in human health and the development of many diseases. These diseases often arise from the explosive proliferation of opportunistic bacteria, such as those in the nasal cavity. Recently, there have been increases in the prevalence of these opportunistic pathogens displaying antibiotic resistance. Thus, the study of the nasal microbiota and its bacterial diversity is critical in understanding pathogenesis and developing microbial-based therapies for well-known and emerging diseases. However, the isolation and analysis of these populations for clinical study complicates the already challenging task of identifying and profiling potentially harmful bacteria. Existing methods are limited by low sample throughput, expensive labeling, and low recovery of bacteria with ineffective removal of cells and debris. In this study, we propose a novel microfluidic channel with a zigzag configuration for enhanced isolation and detection of bacteria from human clinical nasal swabs. This microfluidic zigzag channel separates the bacteria from epithelial cells and debris by size differential focusing. As such, pure bacterial cell fractions devoid of large contaminating debris or epithelial cells are obtained. DNA sequencing performed on the separated bacteria defines the diversity and species present. This novel method of bacterial separation is simple, robust, rapid, and cost-effective and has the potential to be used for the rapid identification of bacterial cell populations from clinical samples.

Nasopharyngeal microbiome of COVID-19 patients revealed a distinct bacterial profile in deceased and recovered individuals

The bacterial co-infections in SARS-CoV-2 patients remained the least explored subject of clinical manifestations that may also determine the disease severity. Nasopharyngeal microbial community structure within SARS-CoV-2 infected patients could reveal interesting microbiome dynamics that may influence the disease outcomes. Here, in this research study, we analyzed distinct nasopharyngeal microbiome profile in the deceased (n = 48) and recovered (n = 29) COVID-19 patients and compared it with control SARS-CoV-2 negative individuals (control) (n = 33). The nasal microbiome composition of the three groups varies significantly (PERMANOVA, p-value <0.001), where deceased patients showed higher species richness compared to the recovered and control groups. Pathogenic genera, including Corynebacterium (LDA score 5.51), Staphylococcus, Serratia, Klebsiella and their corresponding species were determined as biomarkers (p-value <0.05, LDA cutoff 4.0) in the deceased COVID-19 patients. Ochrobactrum (LDA score 5.79), and Burkholderia (LDA 5.29), were found in the recovered group which harbors ordinal bacteria (p-value <0.05, LDA-4.0) as biomarkers. Similarly, Pseudomonas (LDA score 6.19), and several healthy nasal cavity commensals including Veillonella, and Porphyromonas, were biomarkers for the control individuals. Healthy commensal bacteria may trigger the immune response and alter the viral infection susceptibility and thus, may play important role and possible recovery that needs to be further explored. This research finding provide vital information and have significant implications for understanding the microbial diversity of COVID-19 patients. However, additional studies are needed to address the microbiome-based therapeutics and diagnostics interventions.

Altered Nasal Microbiome in Atrophic Rhinitis: A Novel Theory of Etiopathogenesis and Therapy

Background: Atrophic rhinitis (AtR) is a chronic nasal condition with polygenic and polybacterial etiology. We investigated the clinical outcomes of honey therapy and the associated nasal microbiome in AtR. Methods: For eight weeks, a nonrandomized control trial using a nasal spray of 10% manuka honey and saline on the right and left sides of the nose was conducted on 19 primary AtR patients. A nasal endoscopy was performed and a mucosal biopsy were taken before and after the intervention. Five of the nineteen patients were selected for microbiome and GPR43 expression studies. Results: We used manuka honey to describe an effective prebiotic treatment for atrophic rhinitis. There were nine males and ten females with an average (±SD) age of 33.8 (±10.7) years. Endoscopic scores and clinical symptoms improved in honey-treated nasal cavities (p < 0.003). There was a significant decrease in inflammation, restoration of mucus glands, and increased expression of GPR43 in the nasal cavities with honey therapy. The nasal microbiome composition before and after treatment was documented. Particularly, short chain fatty acid (SCFA) producers were positively enriched after honey therapy and correlated with improved clinical outcomes like nasal crusting, congestion, and discharge. Conclusion: Our approach to treating AtR patients with manuka honey illustrated effective clinical outcomes such as (1) decreased fetid smell, (2) thickening of the mucosa, (3) decreased inflammation with healed mucosal ulcers, (4) increased concentration of the mucosal glands, (5) altered nasal microbiome, and (6) increased expression of SCFA receptors. These changes are consequent to resetting the nasal microbiome due to honey therapy.

Nasal Microbiome and Its Interaction with the Host in Childhood Asthma

Childhood asthma is a major chronic non-communicable disease in infants and children, often triggered by respiratory tract infections. The nasal cavity is a reservoir for a broad variety of commensal microbes and potential pathogens associated with respiratory illnesses including asthma. A healthy nasal microenvironment has protective effects against respiratory tract infections. The first microbial colonisation in the nasal region is initiated immediately after birth. Subsequently, colonisation by nasal microbiota during infancy plays important roles in rapidly establishing immune homeostasis and the development and maturation of the immune system. Dysbiosis of microbiota residing in the mucosal surfaces, such as the nasopharynx and guts, triggers immune modulation, severe infection, and exacerbation events. Nasal microbiome dysbiosis is related to the onset of symptomatic infections. Dynamic interactions between viral infections and the nasal microbiota in early life affect the later development of respiratory infections. In this review, we summarise the existing findings related to nasal microbiota colonisation, dynamic variations, and host–microbiome interactions in childhood health and respiratory illness with a particular examination of asthma. We also discuss our current understanding of biases produced by environmental factors and technical concerns, the importance of standardised research methods, and microbiome modification for the prevention or treatment of childhood asthma. This review lays the groundwork for paying attention to an essential but less emphasized topic and improves the understanding of the overall composition, dynamic changes, and influence of the nasal microbiome associated with childhood asthma.

Investigation of nasopharyngeal microbiota in children with asthma and allergic rhinitis comorbidity

Aim: The goal of this study was to compare the nasopharyngeal bacterial microbiota of healthy children with asthma and allergic rhinitis, identify potential microbial dysbiosis in patients. Materials and Methods: The study included a total of 15 patients. There were five patients with asthma, five with allergic rhinitis, and five healthy controls. The upper respiratory tract microbiota were identified using 16S metagenomics analysis of nasal lavage samples. Results: Firmucutes was the most prevalent phylum in the upper respiratory tract microbiota of asthma patients, while Proteobacteria were found in the healthy control and allergic rhinitis groups. Dolosigranulum was identified as the most dominant genus in the upper respiratory tract microbiota of asthma patients. Moraxella was the most prevalent genera in the upper respiratory tract microbiota of the healthy control group. When asthma patients were compared to the control group, the ratio of the Moraxella genus decreased while the ratios of Staphylococcus, Streptococcus, and Corynebacterium species increased. Conclusion: In conclusion, it has not been determined that upper respiratory tract microbiota has a role in determining the pathogenesis of allergic rhinitis and asthma in childhood. The fact that there is a proportional difference between groups’ supports that there may be a possible difference if the entire airway microbiome is studied.

From the nose to the lungs: the intricate journey of airborne pathogens amidst commensal bacteria

The recent COVID-19 pandemic has dramatically brought the pitfalls of airborne pathogens to the attention of the scientific community. Not only viruses but also bacteria and fungi may exploit air transmission to colonize and infect potential hosts and be the cause of significant morbidity and mortality in susceptible populations. The efforts to decipher the mechanisms of pathogenicity of airborne microbes have brought to light the delicate equilibrium that governs the homeostasis of mucosal membranes. The microorganisms already thriving in the permissive environment of the respiratory tract represent a critical component of this equilibrium and a potent barrier to infection by means of direct competition with airborne pathogens or indirectly via modulation of the immune response. Moving down the respiratory tract, physicochemical and biological constraints promote site-specific expansion of microbes that engage in cross talk with the local immune system to maintain homeostasis and promote protection. In this review, we critically assess the site-specific microbial communities that an airborne pathogen encounters in its hypothetical travel along the respiratory tract and discuss the changes in the composition and function of the microbiome in airborne diseases by taking fungal and SARS-CoV-2 infections as examples. Finally, we discuss how technological and bioinformatics advancements may turn microbiome analysis into a valuable tool in the hands of clinicians to predict the risk of disease onset, the clinical course, and the response to treatment of individual patients in the direction of personalized medicine implementation.

Chronic and Recurrent Sinusitis in Children, as Manifestation of Immune Dysfunction and Atopic Background

Rhinosinusitis in children, as in adults, can be classified by duration (acute, recurrent, and chronic) and by cause (viral, bacterial, and inflammatory) and needs to be treated accordingly after careful investigation which include through clinical history, laboratory tests, and, if necessary, nasal endoscopy and imaging studies.

Nasopharyngeal Bacterial Microbiota Composition and SARS-CoV-2 IgG Antibody Maintenance in Asymptomatic/Paucisymptomatic Subjects

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19), ranging from asymptomatic conditions to severe/fatal lung injury and multi-organ failure. Growing evidence shows that the nasopharyngeal microbiota composition may predict the severity of respiratory infections and may play a role in the protection from viral entry and the regulation of the immune response to the infection. In the present study, we have characterized the nasopharyngeal bacterial microbiota (BNM) composition and have performed factor analysis in a group of 54 asymptomatic/paucisymptomatic subjects who tested positive for nasopharyngeal swab SARS-CoV-2 RNA and/or showed anti-RBD-IgG positive serology at the enrolment. We investigated whether BNM was associated with SARS-CoV-2 RNA positivity and serum anti-RBD-IgG antibody development/maintenance 20–28 weeks after the enrolment. Shannon’s entropy α-diversity index [odds ratio (OR) = 5.75, p = 0.0107] and the BNM Factor1 (OR = 2.64, p = 0.0370) were positively associated with serum anti-RBD-IgG antibody maintenance. The present results suggest that BNM composition may influence the immunological memory against SARS-CoV-2 infections. To the best of our knowledge, this is the first study investigating the link between BNM and specific IgG antibody maintenance. Further studies are needed to unveil the mechanisms through which the BNM influences the adaptive immune response against viral infections.

Investigation of Bacterial Isolations and Antimicrobial Susceptibility of Chronic Rhinitis in Cats

Chronic rhinitis is a quite common upper respiratory tract (URT) disease in cats. As a result of unclear etiology, frequently, multidrug-resistant bacteria are identified. This study investigated bacterial isolations and an antimicrobial susceptibility test (AST) in chronic rhinitis in cats. The medical records of 395 cats with chronic URT signs were reviewed at the Kasetsart University Veterinary Teaching Hospital (KUVTH) between 2016 and 2021 to survey the underlying causes of URT. Then, apart from rhinitis, other causes were excluded to identify the bacterial species and antimicrobial susceptibility. The results indicated that the most frequent finding was neoplasia, followed by rhinitis and anatomical defects. Furthermore, the only significant association was between the age range and disease group, with gender, FIV, or FeLV infection not being significant. Rhinitis was 4.7 times more likely to occur than neoplasia in younger and young adult cats in the age range < 1−3 years compared to the group > 10 years. The main bacterial species was the Pseudomonas species. Antimicrobials with a susceptibility rate of more than 90% were amikacin, gentamicin, ciprofloxacin, norfloxacin, marbofloxacin, imipenem, and meropenem. In conclusion, rhinitis was the second most common chronic URT disease in cats and was more common in younger and young adult cats. The predominant bacteria with AST in this study reflect the antimicrobial resistance situation. Thus, antimicrobial usage should follow antimicrobial use guidelines first.

Alloiococcus otitidis-Cause of Nonspecific Acute Sinusitis: First Case Report and Review of Literature

Although most sinus infections are viral, potential bacterial pathogens such as Streptococcus pneumoniae, Haemophilus influenza and Moraxella catarrhalis can migrate during a viral respiratory infection from the nasopharynx into the sinus cavity causing sinusitis. Alloiococcus otitidis is a commensal of the external auditory canal and is considered one of the potential middle ear pathogens. Unlike most otopathogens, A. otitidis is rarely found in the nasopharynx of healthy individuals. This difficult-to-culture organism has not previously been described as a causative agent of sinusitis. Here we describe one case of acute sinusitis due to A. otitidis and review previous knowledge of this controversial organism based on recent literature.

The Impact of Alcohol-Induced Dysbiosis on Diseases and Disorders of the Central Nervous System

The human digestive tract contains a diverse and abundant microbiota that is important for health. Excessive alcohol use can disrupt the balance of these microbes (known as dysbiosis), leading to elevated blood endotoxin levels and systemic inflammation. Using QIAGEN Ingenuity Pathway Analysis (IPA) bioinformatics tool, we have confirmed that peripheral endotoxin (lipopolysaccharide) mediates various cytokines to enhance the neuroinflammation signaling pathway. The literature has identified alcohol-mediated neuroinflammation as a possible risk factor for the onset and progression of neurodegenerative diseases, including Alzheimer's disease (AD) and Parkinson's disease (PD), and psychiatric disorders such as addiction to alcohol and other drugs. In this review, we discuss alcohol-use-induced dysbiosis in the gut and other body parts as a causal factor in the progression of Central Nervous System (CNS) diseases including neurodegenerative disease and possibly alcohol use disorder.

Review: The Nose as a Route for Therapy. Part 2 Immunotherapy

The nose provides a route of access to the body for inhalants and fluids. Unsurprisingly it has a strong immune defense system, with involvement of innate (e.g., epithelial barrier, muco- ciliary clearance, nasal secretions with interferons, lysozyme, nitric oxide) and acquired (e.g., secreted immunoglobulins, lymphocytes) arms. The lattice network of dendritic cells surrounding the nostrils allows rapid uptake and sampling of molecules able to negotiate the epithelial barrier. Despite this many respiratory infections, including SARS-CoV2, are initiated through nasal mucosal contact, and the nasal mucosa is a significant "reservoir" for microbes including Streptococcus pneumoniae, Neisseria meningitidis and SARS -CoV-2. This review includes consideration of the augmentation of immune defense by the nasal application of interferons, then the reduction of unnecessary inflammation and infection by alteration of the nasal microbiome. The nasal mucosa and associated lymphoid tissue (nasopharynx-associated lymphoid tissue, NALT) provides an important site for vaccine delivery, with cold-adapted live influenza strains (LAIV), which replicate intranasally, resulting in an immune response without significant clinical symptoms, being the most successful thus far. Finally, the clever intranasal application of antibodies bispecific for allergens and Intercellular Adhesion Molecule 1 (ICAM-1) as a topical treatment for allergic and RV-induced rhinitis is explained.

Drug-Free Nasal Spray as a Barrier against SARS-CoV-2 and Its Delta Variant: In Vitro Study of Safety and Efficacy in Human Nasal Airway Epithelia

The nasal epithelium is a key portal for infection by respiratory viruses such as SARS-CoV-2 and represents an important target for prophylactic and therapeutic interventions. In the present study, we test the safety and efficacy of a newly developed nasal spray (AM-301, marketed as Bentrio) against infection by SARS-CoV-2 and its Delta variant on an in vitro 3D-model of the primary human nasal airway epithelium. Safety was assessed in assays for tight junction integrity, cytotoxicity and cilia beating frequency. Efficacy against SARS-CoV-2 infection was evaluated in pre-viral load and post-viral load application on airway epithelium. No toxic effects of AM-301 on the nasal epithelium were found. Prophylactic treatment with AM-301 significantly reduced viral titer vs. controls over 4 days, reaching a maximum reduction of 99% in case of infection from the wild-type SARS-CoV-2 variant and more than 83% in case of the Delta variant. When AM-301 administration was started 24 h after infection, viral titer was reduced by about 12-folds and 3-folds on Day 4. The results suggest that AM-301 is safe and significantly decelerates SARS-CoV-2 replication in cell culture inhibition assays of prophylaxis (pre-viral load application) and mitigation (post-viral load application). Its physical (non-pharmaceutical) mechanism of action, safety and efficacy warrant additional investigations both in vitro and in vivo for safety and efficacy against a broad spectrum of airborne viruses and allergens.

Rhinosinusitis: clinical-based phenotyping

Rhinosinusitis (RS) is a common disease and is currently classified into two main types: acute RS (ARS) and chronic RS (CRS), which in turn includes CRS with or without nasal polyps. Different guidelines consider this classification. However, in clinical practice, other phenotypes exist. The current article would propose new clinical-based phenotyping of RS, including the following clinical phenotypes: simple catarrhal RS, Acute RS, acute bacterial RS, severe (complicated) acute RS, chronic RS, and recurrent chronic RS. Treatment strategy should be tailored considering the clinical phenotype and could include phytomedicines, intranasal non-pharmacological remedies, and local bacteriotherapy. In conclusion, RS requires thorough diagnostic work-up, and the therapeutic approach should be mainly based on appropriate management.

The Effect of Radiation and Chemoradiation Therapy on the Head and Neck Mucosal Microbiome: A Review

Radiation (RT) and chemoradiation therapy (CRT) play an essential role in head and neck cancer treatment. However, both cause numerous side effects in the oral cavity, paranasal sinuses, and pharynx, having deleterious consequences on patients’ quality of life. Concomitant with significant advances in radiation oncology, much attention has turned to understanding the role of the microbiome in the pathogenesis of treatment-induced tissue toxicity, to ultimately explore microbiome manipulation as a therapeutic intervention. This review sought to discuss current publications investigating the impact of RT and CRT-induced changes on the head and neck microbiome, using culture-independent molecular methods, and propose opportunities for future directions. Based on 13 studies derived from a MEDLINE, EMBASE, and Web of Science search on November 7, 2021, use of molecular methods has uncovered various phyla and genera in the head and neck microbiome, particularly the oral microbiome, not previously known using culture-based methods. However, limited research has investigated the impact of RT/CRT on subsites other than the oral cavity and none of the studies aimed to examine the relationship between the head and neck microbiome and treatment effectiveness. Findings from this review provide helpful insights on our current understanding of treatment-induced oral mucositis, dental plaque, and caries formation and highlight the need for future research to examine the effect of RT/CRT on the sinonasal and oropharyngeal microbiome. In addition, future research should use larger cohorts, examine the impact of the microbiome on treatment response, and study the effect of manipulating the microbiome to overcome therapy resistance.

The Role of Probiotics in Chronic Rhinosinusitis Treatment: An Update of the Current Literature

Chronic rhinosinusitis (CRS) is a significant health problem. It affects 5–12% of the general population. The causes that underlie the onset of CRS are not yet well known. However, many factors may contribute to its onset, such as environmental factors and the host’s general condition. Medical treatment mainly uses local corticosteroids, nasal irrigation, and antibiotics. In recent years, a new therapeutic approach that employs the use of probiotics emerged. Probiotics have been extensively studied as a therapy for dysbiosis and inflammatory pathologies of various parts of the body. We aimed to examine the studies in vivo and in vitro and clinicals reports in the existing literature to update probiotics’ role in rhinosinusitis chronic medical treatment.

Mucormycosis in COVID-19 pandemic: Risk factors and linkages

Mucormycosis is a serious and potentially fatal fungal infection caused by a type of rare but opportunistic fungal pathogen called mucormycetes. Recently, mucormycosis, also known as black fungus, made severe chaos in India during the second wave (between April and June 2021) of the tragical COVID-19 epidemic by its sudden and devastating surge with up to 50% mortality rate. While the exact cause of its sharp rise suddenly and specifically during the second wave still remains debatable, it has been noted that the people who are diabetic and have recovered from COVID-19 infection are more predisposed to mucormycosis. Nevertheless, the precise reason and mechanism(s) underlying the surge of this deadly infection needs to be investigated to comprehend its pathogenesis and pathological elements and discover rationale preventative/ therapeutic solutions. It is speculated that the indiscriminate use of steroids, antibiotics and zinc as a self-medication practice that increased during the COVID-19 epidemic may have promoted the dysbiosis of gut microbiota thereby inducing immune-suppression and making the risk group highly susceptible to this mycotic disease. In these contexts, this timely article attempts to contemplate and discuss some of the possible factors and potential mechanisms that can help to understand and explain the conundrum of sudden, steep and deadly upsurge of mucormycosis infections during the second wave of COVID-19 epidemic.

Composition of nasal bacterial community and its seasonal variation in health care workers stationed in a clinical research laboratory

The microorganisms at the workplace contribute towards a large portion of the biodiversity a person encounters in his or her life. Health care professionals are often at risk due to their frontline nature of work. Competition and cooperation between nasal bacterial communities of individuals working in a health care setting have been shown to mediate pathogenic microbes. Therefore, we investigated the nasal bacterial community of 47 healthy individuals working in a clinical research laboratory in Kuwait. The taxonomic profiling and core microbiome analysis identified three pre-dominant genera as Corynebacterium (15.0%), Staphylococcus (10.3%) and, Moraxella (10.0%). All the bacterial genera exhibited seasonal variations in summer, winter, autumn and spring. SparCC correlation network analysis revealed positive and negative correlations among the classified genera. A rich set of 16 genera (q < 0.05) were significantly differentially abundant (LEfSe) across the four seasons. The highest species counts, richness and evenness (P < 0.005) were recorded in autumn. Community structure profiling indicated that the entire bacterial population followed a seasonal distribution (R2-0.371; P < 0.001). Other demographic factors such as age, gender and, ethnicity contributed minimally towards community clustering in a closed indoor laboratory setting. Intra-personal diversity also witnessed rich species variety (maximum 6.8 folds). Seasonal changes in the indoor working place in conjunction with the outdoor atmosphere seems to be important for the variations in the nasal bacterial communities of professionals working in a health care setting.

Effects of nasopharyngeal microbiota in respiratory infections and allergies

The human microbiome, which consists of a collective cluster of commensal, symbiotic, and pathogenic microorganisms living in the human body, plays a key role in host health and immunity. The human nasal cavity harbors commensal bacteria that suppress the colonization of opportunistic pathogens. However, dysbiosis of the nasal microbial community is associated with many diseases, such as acute respiratory infections including otitis media, sinusitis and bronchitis and allergic respiratory diseases including asthma. The nasopharyngeal acquisition of pneumococcus, which exists as a pathobiont in the nasal cavity, is the initial step in virtually all pneumococcal diseases. Although the factors influencing nasal colonization and elimination are not fully understood, the adhesion of opportunistic pathogens to nasopharyngeal mucosa receptors and the eliciting of immune responses in the host are implicated in addition to bacterial microbiota properties and colonization resistance dynamics. Probiotics or synbiotic interventions may show promising and effective roles in the adjunctive treatment of dysbiosis; however, more studies are needed to characterize how these interventions can be applied in clinical practice in the future.

Chronic Rhinosinusitis and Alzheimer's Disease-A Possible Role for the Nasal Microbiome in Causing Neurodegeneration in the Elderly

Among millions of sufferers of chronic rhinosinusitis (CRS), the challenge is not only constantly coping with CRS-related symptoms, such as congested nose, sinus pain, and headaches, but also various complications, such as attention difficulties and possible depression. These complications suggest that neural activity in the central nervous system may be altered in those patients, leading to unexpected conditions, such as neurodegeneration in elderly patients. Recently, some studies linked the presence of CRS and cognitive impairments that could further develop into Alzheimer’s disease (AD). AD is the leading cause of dementia in the elderly and is characterised by progressive memory loss, cognitive behavioural deficits, and significant personality changes. The microbiome, especially those in the gut, has been recognised as a human organ and plays an important role in the development of various conditions, including AD. However, less attention has been paid to the microbiome in the nasal cavity. Increased nasal inflammatory responses due to CRS may be an initial event that changes local microbiome homeostasis, which may further affect neuronal integrity in the central nervous system resulting in AD. Evidence suggests a potential of β-amyloid deposition starting in olfactory neurons, which is then expanded from the nasal cavity to the central nervous system. In this paper, we reviewed currently available evidence that suggests this potential mechanism to advise the need to investigate the link between these two conditions.

Particulate Matter Exposure and Allergic Rhinitis: The Role of Plasmatic Extracellular Vesicles and Bacterial Nasal Microbiome

Particulate matter (PM) exposure is linked to the worsening of respiratory conditions, including allergic rhinitis (AR), as it can trigger nasal and systemic inflammation. To unveil the underlying molecular mechanisms, we investigated the effects of PM exposure on the release of plasmatic extracellular vesicles (EV) and on the complex cross-talk between the host and the nasal microbiome. To this aim, we evaluated the effects of PM₁₀ and PM_2.5 exposures on both the bacteria-derived-EV portion (bEV) and the host-derived EVs (hEV), as well as on bacterial nasal microbiome (bNM) features in 26 AR patients and 24 matched healthy subjects (HS). In addition, we assessed the role exerted by the bNM as a modifier of PM effects on the complex EV signaling network in the paradigmatic context of AR. We observed that PM exposure differently affected EV release and bNM composition in HS compared to AR, thus potentially contributing to the molecular mechanisms underlying AR. The obtained results represent the first step towards the understanding of the complex signaling network linking external stimuli, bNM composition, and the immune risponse.

Influence of the Microbiome on Chronic Rhinosinusitis With and Without Polyps: An Evolving Discussion

Chronic rhinosinusitis (CRS) is widely prevalent within the population and often leads to decreased quality of life, among other related health complications. CRS has classically been stratified by the presence of nasal polyps (CRSwNP) or the absence nasal polyps (CRSsNP). Management of these conditions remains a challenge as investigators continue to uncover potential etiologies and therapeutic targets. Recently, attention has been given to the sinunasal microbiota as both an inciting and protective influence of CRS development. The healthy sinunasal microbiologic environment is largely composed of bacteria, with the most frequent strains including Staphylococcus aureus, Streptococcus epidermidis, and Corynebacterium genera. Disruptions in this milieu, particularly increases in S. aureus concentration, have been hypothesized to perpetuate both Th1 and Th2 inflammatory changes within the nasal mucosa, leading to CRS exacerbation and potential polyp formation. Other contributors to the sinunasal microbiota include fungi, viruses, and bacteriophages which may directly contribute to underlying inflammation or impact bacterial prevalence. Modifiable risk factors, such as smoking, have also been linked to microbiota alterations. Research interest in CRS continues to expand, and thus the goal of this review is to provide clinicians and investigators alike with a current discussion on the microbiologic influence on CRS development, particularly with respect to the expression of various phenotypes. Although this subject is rapidly evolving, a greater understanding of these potential factors may lead to novel research and targeted therapies for this often difficult to treat condition.

Respiratory Nasal Mucosa in Chronic Rhinosinusitis with Nasal Polyps versus COVID-19: Histopathology, Electron Microscopy Analysis and Assessing of Tissue Interleukin-33

(1) Background: Chronic rhinosinusitis with nasal polyps (CRSwNP) is one of the most studied rhinological disorders. Modifications of the respiratory nasal mucosa in COVID-19 patients are so far unknown. This paper presents a comparative morphological characterization of the respiratory nasal mucosa in CRSwNP versus COVID-19 and tissue interleukin (IL)-33 concentration. (2) Methods: We analyzed CRSwNP and COVID-19 samples through histopathology, scanning and transmission electron microscopy and performed proteomic determination of IL-33. (3) Results: Histopathologically, stromal edema (p < 0.0001) and basal membrane thickening (p = 0.0768) were found more frequently in CRSwNP than in COVID-19. Inflammatory infiltrate was mainly eosinophil-dominant in CRSwNP and lymphocyte-dominant in COVID-19 (p = 0.3666). A viral cytopathic effect was identified in COVID-19. Scanning electron microscopy detected biofilms only in CRSwNP, while most COVID-19 samples showed microbial aggregates (p = 0.0148) and immune cells (p = 0.1452). Transmission electron microscopy of CRSwNP samples identified biofilms, mucous cell hyperplasia (p = 0.0011), eosinophils, fibrocytes, mastocytes, and collagen fibers. Extracellular suggestive structures for SARS-CoV-2 and multiple Golgi apparatus in epithelial cells were detected in COVID-19 samples. The tissue IL-33 concentration in CRSwNP (210.0 pg/7 μg total protein) was higher than in COVID-19 (52.77 pg/7 μg total protein) (p < 0.0001), also suggesting a different inflammatory pattern. (4) Conclusions: The inflammatory pattern is different in each of these disorders. Results suggested the presence of nasal dysbiosis in both conditions, which could be a determining factor in CRSwNP and a secondary factor in COVID-19.

Acute SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa in the nose

Research conducted on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis and coronavirus disease 2019 (COVID-19) generally focuses on the systemic host response, especially that generated by severely ill patients, with few studies investigating the impact of acute SARS-CoV-2 at the site of infection. We show that the nasal microbiome of SARS-CoV-2-positive patients (CoV⁺, n = 68) at the time of diagnosis is unique when compared to CoV⁻ healthcare workers (n = 45) and CoV⁻ outpatients (n = 21). This shift is marked by an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa, which is also positively associated with viral RNA load. Additionally, we observe a robust host transcriptional response in the nasal epithelia of CoV⁺ patients, indicative of an antiviral innate immune response and neuronal damage. These data suggest that the inflammatory response caused by SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens in the nasal cavity that could contribute to increased incidence of secondary bacterial infections.

Pathophysiology of SARS-CoV-2 Infection in the Upper Respiratory Tract and Its Relation to Breath Volatile Organic Compounds

Among the many products of metabolic processes are volatile organic compounds (VOCs). In the airways, these volatile metabolites are emitted through breathing and thus are easily sampled for analysis. Recent work has connected the functions and structure of the human microbiome with health and disease. Alteration in microbial function in this context can result in differences in metabolite composition, including that of VOCs, presenting the possibility of a new noninvasive method for clinical diagnosis. Screening methods that assess VOCs arising from changes in the airway microbiome could be highly useful in diagnosing viral upper respiratory tract infections (URTIs), e.g., COVID-19, which are highly contagious and have an enormous public health impact worldwide. A rapid noninvasive screening test for URTIs would pose major advantages in containing the disease. As early evidence shows that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection alters the human microbiome (both in the gut and the respiratory tract), we propose that detection of a VOC signature of an altered nasal microbiome could be fruitful as a rapid noninvasive measure of URTI in general and of SARS-CoV-2 in particular.

Characteristics of the bacterial microbiota in the upper respiratory tract of children

PURPOSE

The respiratory tract microbiota are deemed as the gatekeeper to health. Consequently, microbiota dysbiosis can lead to the development of diseases. To identify the exact origins of the localized pathogenic bacteria, we investigated bacterial composition in the upper airway tract.

METHODS

Separate mucosal swabs were collected from nostril or oropharynx of each participant. Meanwhile, the lymphoid tissues including adenoids and tonsils were collected during operation. DNAs were exacted from all the samples for the following 16S rRNA analysis.

RESULTS

At the phylum level, the basic bacterial structures in the adenoids, tonsils, oropharynx, and nostrils were generally similar: five main phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria form the majority of the microbiota. However, across these four sites, the microbiota composition differed. More specifically, the bacterial composition in the nostrils was unique. There, Firmicutes and Actinobacteria were the most abundant phyla, while Bacteroides and Fusobacteria were the least abundant. At the genus level, Staphylococcus, Dolosigranulum, Corynebacterium, and Moraxella were the most plentiful, while Fusobacteria was the least ample. Across all sites, Streptococcus displayed similar abundances. Fusobacteria exhibited higher abundances in the lymphoid tissues and oropharynx. Haemophilus and Neisseria were more plentiful in the tonsils and oropharynx. Notably, Klebsiella, which is normally localized to the gut, was abundant in the adenoids and tonsils.

CONCLUSION

Our data indicate that promising pathogenic bacteria originate from all sites in the upper airway. The upper tract lymphoid tissues, normally considered as immune organs, may also serve as reservoirs for pathogenic bacteria.

The Nasal Microbiome in ANCA-Associated Vasculitis: Picking the Nose for Clues on Disease Pathogenesis

PURPOSE OF REVIEW

The onset and progression of small vessel vasculitis associated with anti-neutrophil cytoplasmic antibodies has been linked to microbial infections. Here, we provide a brief overview of the association of nasal colonization of Staphylococcus aureus with ANCA-associated vasculitis (AAV) and discuss several recent studies mapping the nasal microbiome in AAV patients in particular.

RECENT FINDINGS

Nasal microbiome studies revealed dysbiosis as a common trait in active AAV which tends to normalize upon immunosuppressive treatment and quiescent disease. However, due to differences in study design, patient selection, and methodology, the reported microbiome profiles differ considerably precluding conclusions on causal relationships. The microbiome is an emerging area of research in AAV warranting further investigation. Ideally, such studies should be combined with mechanistic studies to unravel key elements related to host-microbe interactions and their relevance for AAV pathogenesis.

Probiotics in Pediatrics. A Review and Practical Guide

The potential benefit of the administration of probiotics in children has been studied in many settings globally. Probiotics products contain viable micro-organisms that confer a health benefit on the host. Beneficial effects of selected probiotic strains for the management or prevention of selected pediatric conditions have been demonstrated. The purpose of this paper is to provide an overview of current available evidence on the efficacy of specific probiotics in selected conditions to guide pediatricians in decision-making on the therapeutic or prophylactic use of probiotic strains in children. Evidence to support the use of certain probiotics in selected pediatric conditions is often available. In addition, the administration of probiotics is associated with a low risk of adverse events and is generally well tolerated. The best documented efficacy of certain probiotics is for treatment of infectious gastroenteritis, and prevention of antibiotic-associated, Clostridioides difficile-associated and nosocomial diarrhea. Unfortunately, due to study heterogeneity and in some cases high risk of bias in published studies, a broad consensus is lacking for specific probiotic strains, doses and treatment regimens for some pediatric indications. The current available evidence thus limits the systematic administration of probiotics. The most recent meta-analyses and reviews highlight the need for more well-designed, properly powered, strain-specific and dedicated-dose response studies.

Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including Pseudomonas Aeruginosa

Much of the research conducted on SARS-CoV-2 and COVID-19 has focused on the systemic host response, especially that generated by severely ill patients. Very few studies have investigated the impact of acute SARS-CoV-2 within the nasopharynx, the site of initial infection and viral replication. In this study we profiled changes in the nasal microbial communities as well as in host transcriptional profile during acute SARS-CoV-2 infection using 16S amplicon sequencing and RNA sequencing. These analyses were coupled to viral genome sequencing. Our microbiome analysis revealed that the nasal microbiome of COVID patients was unique and was marked by an expansion of bacterial pathogens. Some of these microbes (i.e. Acinetobacter ) were shared with COVID negative health care providers from the same medical center but absent in COVID negative outpatients seeking care at the same institutions suggesting acquisition of nosocomial respiratory pathogens. Specifically, we report a distinct increase in the prevalence and abundance of the pathogen Pseudomonas aeruginosa in COVID patients that correlated with viral RNA load. These data suggest that the inflammatory environment caused by SARS-CoV-2 infection and potentially exposure to the hospital environment leads to an expansion of bacterial pathogens in the nasal cavity that could contribute to increased incidence of secondary bacterial infections. Additionally, we observed a robust host transcriptional response in the nasal epithelia of COVID patients, indicative of an antiviral innate immune repones and neuronal damage. Finally, analysis of viral genomes did not reveal an association between viral loads and viral sequences.

Noninvasive and minimally invasive techniques for the diagnosis and management of allergic diseases

Allergic diseases of the (upper and lower) airways, the skin and the gastrointestinal tract, are on the rise, resulting in impaired quality of life, decreased productivity, and increased healthcare costs. As allergic diseases are mostly tissue-specific, local sampling methods for respective biomarkers offer the potential for increased sensitivity and specificity. Additionally, local sampling using noninvasive or minimally invasive methods can be cost-effective and well tolerated, which may even be suitable for primary or home care sampling. Non- or minimally invasive local sampling and diagnostics may enable a more thorough endotyping, may help to avoid under- or overdiagnosis, and may provide the possibility to approach precision prevention, due to early diagnosis of these local diseases even before they get systemically manifested and detectable. At the same time, dried blood samples may help to facilitate minimal-invasive primary or home care sampling for classical systemic diagnostic approaches. This EAACI position paper contains a thorough review of the various technologies in allergy diagnosis available on the market, which analytes or biomarkers are employed, and which samples or matrices can be used. Based on this assessment, EAACI position is to drive these developments to efficiently identify allergy and possibly later also viral epidemics and take advantage of comprehensive knowledge to initiate preventions and treatments.

Prevention and Management with Pro-, Pre and Synbiotics in Children with Asthma and Allergic Rhinitis: A Narrative Review

Allergic diseases including allergic rhinitis and asthma are increasing in the developing world, related to a westernizing lifestyle, while the prevalence is stable and decreasing in the industrialized world. This paper aims to answer the question if prevention and/or treatment of allergic rhinitis and asthma can be achieved by administrating pro-, pre- and/or synbiotics that might contribute to stabilizing the disturbed microbiome that influences the immune system through the gut-lung axis. We searched for relevant English articles in PubMed and Google Scholar. Articles interesting for the topic were selected using subject heading and key words. Interesting references in included articles were also considered. While there is substantial evidence from animal studies in well controlled conditions that selected probiotic strains may offer benefits in the prevention of wheezing and asthma, outcomes from clinical studies in infants (including as well pre- and postnatal administration) are disappointing. The latter may be related to the multiple confounding factors such as environment, strain selection and dosage, moment of administration and genetic background. There is little evidence to recommend administration of pro, pre- or synbiotics in the prevention of asthma and allergic rhinitis in children.

Markers Associated with COVID-19 Susceptibility, Resistance, and Severity

In December 2019, the latest member of the coronavirus family, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan, China, leading to the outbreak of an unusual viral pneumonia known as coronavirus disease 2019 (COVID-19). COVID-19 was then declared as a pandemic in March 2020 by the World Health Organization (WHO). The initial mortality rate of COVID-19 declared by WHO was 2%; however, this rate has increased to 3.4% as of 3 March 2020. People of all ages can be infected with SARS-CoV-2, but those aged 60 or above and those with underlying medical conditions are more prone to develop severe symptoms that may lead to death. Patients with severe infection usually experience a hyper pro-inflammatory immune reaction (i.e., cytokine storm) causing acute respiratory distress syndrome (ARDS), which has been shown to be the leading cause of death in COVID-19 patients. However, the factors associated with COVID-19 susceptibility, resistance and severity remain poorly understood. In this review, we thoroughly explore the correlation between various host, viral and environmental markers, and SARS-CoV-2 in terms of susceptibility and severity.

Alterations in the conjunctival surface bacterial microbiome in bacterial keratitis patients

Microbial keratitis is an infectious disease of the eye, in which the cornea is inflamed. Under severe conditions, keratitis can lead to significant loss of vision and enucleation of the eye. Ocular trauma is the major risk factor causing keratitis and microorganisms viz., bacteria, fungi, viruses are the causative agents. The current study characterized the conjunctival bacterial microbiomes of healthy individuals and individuals with bacterial keratitis (BK) and assessed whether ocular microbiome dysbiosis is prevalent in BK patients. Ocular bacterial microbiomes were generated from the conjunctival swabs of healthy controls (HC-SW) and conjunctival swabs (BK-SW) and corneal scrapings (BK-CR) of BK patients using V3-V4 amplicon sequencing and data analysed using QIIME and R software. The Alpha diversity indices, diversity and abundance of different phyla and genera, heat map analysis, NMDS plots and inferred functional pathway analysis clearly discriminated the bacterial microbiomes of conjunctival swabs of healthy controls from that of BK patients. Preponderance of negative interactions in the hub genera were observed in BK-CR and BK-SW compared to HC-SW. In addition, a consistent increase in the abundance of pathogenic bacteria, as inferred from published literature, was observed in the conjunctiva of BK patients compared to HC and this may be related to causing or exacerbating ocular surface inflammation. This is the first study demonstrating dysbiosis in the ocular bacterial microbiome of conjunctiva of bacterial keratitis patients compared to the eye of healthy controls. The bacterial microbiome associated with the corneal scrapings of keratitis individuals is also described for the first time.

The Microbiota/Host Immune System Interaction in the Nose to Protect from COVID-19

Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is characterized by variable clinical presentation that ranges from asymptomatic to fatal multi-organ damage. The site of entry and the response of the host to the infection affect the outcomes. The role of the upper airways and the nasal barrier in the prevention of infection is increasingly being recognized. Besides the epithelial lining and the local immune system, the upper airways harbor a community of microorganisms, or microbiota, that takes an active part in mucosal homeostasis and in resistance to infection. However, the role of the upper airway microbiota in COVID-19 is not yet completely understood and likely goes beyond protection from viral entry to include the regulation of the immune response to the infection. Herein, we discuss the hypothesis that restoring endogenous barriers and anti-inflammatory pathways that are defective in COVID-19 patients might represent a valid strategy to reduce infectivity and ameliorate clinical symptomatology.

Cutaneous Bacteria in the Gut Microbiome as Biomarkers of Systemic Malodor and People Are Allergic to Me (PATM) Conditions: Insights From a Virtually Conducted Clinical Trial

Background

The skin is a dynamic ecosystem of microbes and the source of many chemical compounds that affect human health. Skin-microbiome interactions can cause persistent, psychosocially devastating body smell despite good hygiene. Since odor production is often transient, malodors may not be perceptible during medical examinations. Therefore, having odor complaints can be diagnosed as body dysmorphic disorder and referred for psychological evaluations. Development of simple at-home tests and virtual care programs could improve the diagnosis and management of socially debilitating malodor conditions.

Objective

The aim of this study was to assess potential effectiveness of at-home gut microbiome testing in the diagnosis and management of idiopathic body and breath odor and in people are allergic to me (PATM) syndrome.

Methods

We contacted participants of prior metabolic body odor (MEBO) and PATM studies and online support groups by email or social media. Individuals who consented to participate were mailed test kits for at-home collection of gut microbiome samples. Participants completed an online survey (specially developed for this study) addressing their symptoms and other quality-of-life indicators at baseline and after sampling. Participants collected stool samples after flare-ups or symptom improvements and mailed them to the laboratory to be processed and analyzed. We evaluated between-group differences in symptom severity, as well as symptom improvement observations for the same individuals. For differential abundance testing of microbial taxa, we performed nonparametric statistical analyses using Mann-Whitney U tests for unpaired samples and Wilcoxon signed rank test for paired samples.

Results

A total of 112 individuals from 21 countries consented to participate. About half the participants had been tested for the metabolic disorder trimethylaminuria, and about half of those tested were diagnosed with the disorder. The levels of bacteria previously associated with cutaneous body odor were significantly elevated in gut samples. For the combination of species from Anaerococcus, Corynebacterium, Campylobacter, and Propionibacterium genera, the differences were P=.002 for active (73 participants, 182 samples) versus regression or remission groups (30 participants, 51 samples); P=.01 for those experiencing symptoms most or all of the time (46 participants, 88 samples) versus those who had symptoms sometimes, rarely, or never (25 participants, 74 samples); and P<.001 for improvement of symptoms in the same individuals (22 participants, 43 sets of matched samples). Changes in microbial diversity were significant for between- but not within-participant comparisons.

Conclusions

Changes in the gut microbiome composition affect MEBO and PATM severity. In particular, an increase in intestinal bacteria producing odor when in skin flexures was associated with increased intensity of self-reported symptoms. The changes were consistent in the within-group and between-group analyses. Our findings support the feasibility of remote and decentralized clinical studies of malodor conditions. Supplementary sample collection procedures may help to meet established research quality standards.

Trial Registration

ClinicalTrials.gov NCT03582826; http://clinicaltrials.gov/ct2/show/NCT03582826

International Registered Report Identifier (IRRID)

RR2-10.1101/2020.08.21.20179242