Insights into the role of the respiratory tract microbiome in defense against bacterial pneumonia

Respiratory dysbiosis as prognostic biomarker of disease severity for adults with community-acquired pneumonia requiring mechanical ventilation

OBJETIVES

To ascertain the role of the lung microbiome in the development of severe pneumonia and its potential as a biomarker for disease progression.

METHODS

BAL samples from 34 adults with severe community-acquired pneumonia (CAP) (17 viral, 8 viral coinfected with bacteria and 9 bacterial) admitted to the ICU for acute respiratory failure between 2019 and 2021 were collected within the first 48 h of admission to the ICU. The microbiome was characterized via the Ion 16S Metagenomics Kit and the Ion Torrent sequencing platform. Clinical factors, including survival, mechanical ventilation duration, blood biomarkers and organ failure in terms of acute respiratory distress syndrome (ARDS), shock or acute renal failure, were correlated with microbiome characteristics.

RESULTS

The microbiome diversity in patients with viral pneumonia was significantly greater than that in patients with bacterial or coinfected pneumonia: the Shannon diversity index was 3.75 (Q1-Q3: 2.5-4.1) versus 0.4 (Q1-Q3: 0.2-1.3) and 0.48 (Q1-Q3: 0.3-1.1), respectively (p < 0.05). The microbiome diversity index was associated with severity-of-illness (APACHE II), independent of the etiology of pneumonia (B coefficient -1.845; p < 0.01). Patients with severe viral CAP who developed ARDS had a lower presence of Proteobacteria, and those who were complicated with ventilator-associated pneumonia had a higher prevalence of Acinetobacter at admission. The mortality of patients with bacterial or coinfected pneumonia was 35%. In coinfected patients, the diversity index was associated with the development of shock.

CONCLUSION

Patients with severe CAP have low respiratory microbiome diversity, indicating that respiratory microbiome diversity is a potential biomarker of disease severity.

The Respiratory Tract Microbiome and Human Health

The respiratory tract microbiome (RTM) is a multi-kingdom microbial ecosystem that inhabits various niches of the respiratory system. While previously overlooked, there is now sufficient evidence that the RTM plays a crucial role in human health related to immune system training and protection against pathogens. Accordingly, dysbiosis or disequilibrium of the RTM has been linked to several communicable and non-communicable respiratory diseases, highlighting the need to unveil its role in health and disease. Here, we define the RTM and its place in microbiome medicine. Moreover, we outline the challenges of RTM research, emphasising the need for combining methodologies, including multi-omics and computational tools. We also discuss the RTM's potential for diagnosing, preventing and treating respiratory diseases and developing novel microbiome-based therapies to improve pulmonary health.

Profiling the nasopharyngeal Microbiome in patients with community-acquired pneumonia caused by Streptococcus pneumoniae: diagnostic challenges and ecological insights

Community-acquired pneumonia (CAP) is a significant health threat for adults. Although conjugate vaccines have reduced pneumococcal CAP incidence in children, Streptococcus pneumoniae-related CAP remains prevalent among older adults. The nasopharynx acts as a reservoir for S. pneumoniae, yet the interplay between this pathogen and the nasopharyngeal microbiome during and after pneumonia remains poorly understood. This study included 61 adult patients diagnosed with pneumococcal CAP and 61 matched healthy controls. An S. pneumoniae-specific PCR, urine antigen tests and bacterial cultures were performed. Nasopharyngeal swabs collected at admission and three months post-infection were analyzed for microbiome dynamics through 16 S rRNA gene amplicon sequencing. 16 S rRNA gene amplicon sequencing revealed Streptococcus spp. in the majority of all nasopharyngeal samples during infection compared to the other diagnostic test performed. While overall bacterial biomass did not differ between groups, patients exhibited higher alpha diversity (p = 0.012) and lower microbiome stability post-infection. Beta diversity analysis distinguished infection from healthy status (p = 0.002). Taxonomic analysis showed similar core microbiota across groups, but Streptococcus spp. was significantly more abundant during infection, particularly in those patients with viral co-infections. Notably, unique significant bacterial interactions were identified both during and after infection, as well as in healthy states. A negative correlation was observed between Corynebacterium and Streptococcus spp. in infected patients, suggesting a potential antagonistic interaction between these taxa. The nasopharyngeal microbiome in patients with pneumococcal CAP demonstrates persistent disruption post-infection, characterized by lower resilience three months after acute illness. Additionally, we identified specific bacterial interplays during and after infection that differed from those in healthy donors. These bacterial dynamics might play critical roles in pathogen colonization resistance and infection prevention. Thus, our findings highlight the need for further investigation into microbial interactions and potential microbiome-based therapies for respiratory infections, particularly in vulnerable populations.

From Microbial Ecology to Clinical Challenges: The Respiratory Microbiome's Role in Antibiotic Resistance

Antibiotic resistance represents a growing public health threat, with airborne drug-resistant strains being especially alarming due to their ease of transmission and association with severe respiratory infections. The respiratory microbiome plays a pivotal role in maintaining respiratory health, influencing the dynamics of antibiotic resistance among airborne pathogenic microorganisms. In this context, this review proposes the exploration of the complex interplay between the respiratory microbiota and antimicrobial resistance, highlighting the implications of microbiome diversity in health and disease. Moreover, strategies to mitigate antibiotic resistance, including stewardship programs, alternatives to traditional antibiotics, probiotics, microbiota restoration techniques, and nanotechnology-based therapeutic interventions, are critically presented, setting an updated framework of current management options. Therefore, through a better understanding of respiratory microbiome roles in antibiotic resistance, alongside emerging therapeutic strategies, this paper aims to shed light on how the global health challenges posed by multi-drug-resistant pathogens can be addressed.

The impact of environmental factors on respiratory tract microbiome and respiratory system diseases

The respiratory tract microbiome, a complex ecosystem of microorganisms colonizing the respiratory mucous layers and epithelial surfaces along with their associated microenvironment, plays a vital role in maintaining respiratory function and promoting the maturation of the respiratory immune system. Current research suggests that environmental changes can disrupt the respiratory microbiota, potentially leading to disease. This review summarizes existing research on the impact of environmental factors on the respiratory microbiome and associated diseases, aiming to offer new insights into the prevention and treatment of respiratory disease.

Beyond the present: current and future perspectives on the role of infections in pediatric PCD

Introduction

Primary Ciliary Dyskinesia (PCD) is a rare genetic disorder affecting motile cilia, leading to impaired mucociliary clearance and increased susceptibility to respiratory infections. These infections contribute to long-term complications such as bronchiectasis and lung function decline.

Objectives

This review explores both the acute and long-term impact of respiratory infections in children with PCD, while highlighting the multiple contributors to infection susceptibility. The review also evaluates emerging personalized approaches such as gene and mRNA therapy that hold promise for restoring ciliary function and reducing the burden of acute infections in pediatric PCD.

Key findings and conclusions

Acute respiratory infections have a significant impact on morbidity in pediatric PCD, driving progressive airway remodeling. While current treatment strategies focus on managing infections directly, emerging therapies targeting inflammation and genetic causes hold promise for reducing infection burden and improving long-term outcomes. Future advances in personalized medicine could further enhance therapeutic approaches in this population.

Oropharyngeal Staphylococcus aureus is linked to higher mortality in long-term aged care residents

BACKGROUND

Biological ageing, healthcare interactions, and pharmaceutical and environmental exposures in later life alter the characteristics of the oropharyngeal (OP) microbiome. These changes, including an increased susceptibility to colonisation by pathobiont species, have been linked with diverse health outcomes.

OBJECTIVES

To investigate the relationship between OP microbiome characteristics and all-cause mortality in long-term aged care residents.

METHODS

OP swabs were collected from 190 residents of five aged care facilities in South Australia. Microbiota composition was assessed by shotgun metagenomics and related to health outcomes during a 12-month follow-up period. OP carriage of Staphylococcus aureus and methicillin resistance was confirmed by qPCR.

RESULTS

OP carriage of S. aureus was identified in 13 (6.8%) residents. Detection of S. aureus was significantly associated with an increased risk of mortality (adjusted HR [95% CI]: 9.7 [3.8-24.9], P < .0001), compared with non-carriers, independent of methicillin resistance. Staphylococcus aureus carriage demonstrated a stronger association with mortality risk than the total number of comorbidities at the univariate level (S. aureus HR [95% CI]: 7.2 [3.4-15.5], P < .0001 vs. comorbidity count HR [95% CI]: 1.1 [1.0-1.3], P = .03), and remained significant after multivariable adjustment. Staphylococcus aureus detection was significantly associated with total number of comorbidities (adjusted OR [95% CI]: 1.4 [1.0-2.0], P = .04).

CONCLUSION

OP S. aureus carriage predicts all-cause mortality in long-term aged care. We speculate that S. aureus carriage represents a marker of general health, including prior healthcare exposures. OP S. aureus carriage could contribute to estimations of general health in older individuals and thereby inform care strategies.

Nasal microbiota transplantation: a gateway to novel treatments

Two recent studies have highlighted the potential of nasal microbiota transplantation (NMT) to treat chronic rhinosinusitis (CRS). Here we evaluate these findings and propose that lessons from fecal microbiota transplantation (FMT) could guide NMT development, with possible implications for combating antimicrobial resistance in respiratory infections.

Airway Corynebacterium interfere with Streptococcus pneumoniae and Staphylococcus aureus infection and express secreted factors selectively targeting each pathogen

The composition of the respiratory tract microbiome is a notable predictor of infection-related morbidities and mortalities among both adults and children. Species of Corynebacterium, which are largely present as commensals in the upper airway and other body sites, are associated with lower colonization rates of opportunistic bacterial pathogens such as Streptococcus pneumoniae and Staphylococcus aureus. In this study, Corynebacterium-mediated protective effects against S. pneumoniae and S. aureus were directly compared using in vivo and in vitro models. Pre-exposure to Corynebacterium pseudodiphtheriticum reduced the ability of S. aureus and S. pneumoniae to infect the lungs of mice, indicating a broadly protective effect. Adherence of both pathogens to human respiratory tract epithelial cells was significantly impaired following pre-exposure to C. pseudodiphtheriticum or Corynebacterium accolens, and this effect was dependent on live Corynebacterium colonizing the epithelial cells. However, Corynebacterium-secreted factors had distinct effects on each pathogen. Corynebacterium lipase activity was bactericidal against S. pneumoniae, but not S. aureus. Instead, the hemolytic activity of pore-forming toxins produced by S. aureus was directly blocked by a novel Corynebacterium-secreted factor with protease activity. Taken together, these results suggest diverse mechanisms by which Corynebacterium contribute to the protective effect of the airway microbiome against opportunistic bacterial pathogens.

Corynebacteria from the respiratory microbiota modulate inflammatory responses and associate with a reduced pneumococcal burden in the lungs

Background

Certain species from the normal respiratory tract microbiota have recently been proposed to positively influence human health. Corynebacterium propinquum and C. pseudodiphtheriticum (Corynebacteria) are two Gram-positive species that frequently colonize the upper respiratory tract and strongly associate with a reduced incidence of respiratory tract infections. The specific role of Corynebacteria during respiratory health and disease is, however, largely uncharacterized.

Method

Respiratory tract epithelial cells NCI-H292 and BALB/cByJ mice were inoculated with Corynebacteria (C. propinquum 2018M3 and 2019M4, and C. pseudodiphtheriticum 2019M8 and 2020M12) alone or with subsequent challenge with Streptococcus pneumoniae (pneumococci). The inflammatory response and the bacterial burden of both species over time were determined by Western blot, luciferase assay, cytokine bead array, flow cytometry and viable plate counts on blood agar plates.

Results

Clinical isolates of Corynebacteria were well tolerated by human cells and mice. Corynebacteria induced a transient inflammatory response during healthy conditions in the absence of known pathogens. Pre-exposure or nasal priming with Corynebacteria did not affect subsequent acquisition of pneumococci but were associated with a modulated inflammatory response in vitro and in vivo as well as with a reduced pneumococcal burden in the respiratory tract of mice. This indicates that the presence of C. propinquum or C. pseudodiphtheriticum may protect against severe pneumococcal infections.

Conclusions

In this study, we delineate the role of Corynebacteria from the normal microbiota that epidemiologically associate with respiratory health. We show that the presence of Corynebacteria modulates the inflammatory response to pneumococci and associate with faster decrease in pneumococcal burden, primarily in the lower respiratory tract. Our data indicate that Corynebacteria has potential to protect against severe pneumococcal infections.

Diagnosing and engineering gut microbiomes

The microbes, nutrients and toxins that we are exposed to can have a profound effect on the composition and function of the gut microbiome. Thousands of peer-reviewed publications link microbiome composition and function to health from the moment of birth, right through to centenarians, generating a tantalizing glimpse of what might be possible if we could intervene rationally. Nevertheless, there remain relatively few real-world examples where successful microbiome engineering leads to beneficial health effects. Here we aim to provide a framework for the progress needed to turn gut microbiome engineering from a trial-and-error approach to a rational medical intervention. The workflow starts with truly understanding and accurately diagnosing the problems that we are trying to fix, before moving on to developing technologies that can achieve the desired changes.

Staphylococcus aureus Phenol-Soluble Modulins Mediate Interspecies Competition with Upper Respiratory Commensal Bacteria

In chronic rhinosinusitis (CRS) disease, microbial dysbiosis is considered a key contributor to inflammation and pathogenicity, with increased prevalence of upper respiratory tract (URT) pathogens concomitant with decreased abundance of commensal species. Staphylococcus aureus is a common URT pathobiont associated with higher carriage rates in CRS. S. aureus secreted toxins are implicated in CRS pathogenesis, and toxins and antibodies to S. aureus secreted factors have been observed in tissue from CRS subjects. CRS disease severity is positively correlated with immune reactivity to S. aureus proteins. Prior studies have examined polymicrobial interactions between S. aureus and URT commensals, however, no studies to date have described possible methods employed by S. aureus to outcompete commensals leading to a S. aureus- dominant microbiome as seen in CRS. This study addresses this gap in knowledge by characterizing how a CRS-associated secreted toxin from S. aureus can inhibit aggregation in commensal URT species. Using a model URT commensal, Corynebacterium pseudodiphtheriticum , we identified a CRS-associated secreted protein from S. aureus , δ-toxin (Hld), that can inhibit C. pseudodiphtheriticum aggregation at biologically relevant concentrations. Furthermore, we observed recombinant δ-toxin reduces C. pseudodiphtheriticum adherence and aggregation on human nasal epithelial cells in an air-liquid interface cell culture model. These results define a novel mechanism by which S. aureus can disrupt URT commensal lifestyles of microbial competitors, contributing to the establishment of microbial dysbiosis.

IMPORTANCE

Microbial dysbiosis in the upper respiratory tract (URT) is associated with disease pathogenicity in chronic rhinosinusitis (CRS). There are significant links between Staphylococcus aureus and worse CRS outcomes, but no studies to date have demonstrated if S. aureus outcompetes other URT microbes through direct interactions. Here, we report that S. aureus δ-toxin, a secreted protein found in CRS patient tissue, can inhibit the ability of commensal bacteria to aggregate, adhere to, and grow in association with human nasal epithelial cells. These results suggest a potential mechanism for S. aureus to establish dominance in the URT microbiome through direct antagonism of commensals with a disease-associated toxin.

MASS cohort: Multicenter, longitudinal, and prospective study of the role of microbiome in severe pneumonia and host susceptibility

The MASS cohort comprises 2000 ICU patients with severe pneumonia, covering community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia, sourced from 19 hospitals across 10 cities in three provinces. A wide array of samples including bronchoalveolar lavage fluid, sputum, feces, and whole blood are longitudinally collected throughout patients' ICU stays. The cohort study seeks to uncover the dynamics of lung and gut microbiomes and their associations with severe pneumonia and host susceptibility, integrating deep metagenomics and transcriptomics with detailed clinical data.

Current Management of Allergic Rhinitis

Allergic rhinitis (AR) is the most common allergic disease worldwide and one of the most common chronic diseases in general. Allergic rhinitis is caused by inhalant allergens from outdoor and indoor environments with varying significance of different allergens in global regions. We provide options for the current management for AR including pharmacological treatments and nonpharmacological options and allergen immunotherapy (AIT). A literature review has been conducted in Medline, Pubmed, as well as the national and international study (ClinicalTrials.gov) and guideline registers and the Cochrane Library. Human studies published on the topic in the period up to and including November 2023 were taken into account. Allergen avoidance measures, pharmacotherapy, and AIT are the cornerstones of AR treatment. Nonpharmacological measures and behavioral recommendations should be adequately added. Tools of precision medicine are already playing a significant role and will be part of the diagnostic and therapeutic standard in the future. Patients benefit most in a network of different pharmacological and nonpharmacological treatment measures including AIT. Application of precision medicine tools for diagnosis and treatment will improve standards of care.

Microbiota and Immunity during Respiratory Infections: Lung and Gut Affair

Bacterial and viral respiratory tract infections are the most common infectious diseases, leading to worldwide morbidity and mortality. In the past 10 years, the importance of lung microbiota emerged in the context of pulmonary diseases, although the mechanisms by which it impacts the intestinal environment have not yet been fully identified. On the contrary, gut microbial dysbiosis is associated with disease etiology or/and development in the lung. In this review, we present an overview of the lung microbiome modifications occurring during respiratory infections, namely, reduced community diversity and increased microbial burden, and of the downstream consequences on host-pathogen interaction, inflammatory signals, and cytokines production, in turn affecting the disease progression and outcome. Particularly, we focus on the role of the gut-lung bidirectional communication in shaping inflammation and immunity in this context, resuming both animal and human studies. Moreover, we discuss the challenges and possibilities related to novel microbial-based (probiotics and dietary supplementation) and microbial-targeted therapies (antibacterial monoclonal antibodies and bacteriophages), aimed to remodel the composition of resident microbial communities and restore health. Finally, we propose an outlook of some relevant questions in the field to be answered with future research, which may have translational relevance for the prevention and control of respiratory infections.