Exploring the microbiota of upper respiratory tract during the development of pneumonia in a mouse model

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.

Animal models of Klebsiella pneumoniae mucosal infections

Klebsiella pneumoniae is among the most relevant pathogens worldwide, causing high morbidity and mortality, which is worsened by the increasing rates of antibiotic resistance. It is a constituent of the host microbiota of different mucosa, that can invade and cause infections in many different sites. The development of new treatments and prophylaxis against this pathogen rely on animal models to identify potential targets and evaluate the efficacy and possible side effects of therapeutic agents or vaccines. However, the validity of data generated is highly dependable on choosing models that can adequately reproduce the hallmarks of human diseases. The present review summarizes the current knowledge on animal models used to investigate K. pneumoniae infections, with a focus on mucosal sites. The advantages and limitations of each model are discussed and compared; the applications, extrapolations to human subjects and future modifications that can improve the current techniques are also presented. While mice are the most widely used species in K. pneumoniae animal studies, they present limitations such as the natural resistance to the pathogen and difficulties in reproducing the main steps of human mucosal infections. Other models, such as Drosophila melanogaster (fruit fly), Caenorhabditis elegans, Galleria mellonella and Danio rerio (zebrafish), contribute to understanding specific aspects of the infection process, such as bacterial lethality and colonization and innate immune system response, however, they but do not present the immunological complexity of mammals. In conclusion, the choice of the animal model of K. pneumoniae infection will depend mainly on the questions being addressed by the study, while a better understanding of the interplay between bacterial virulence factors and animal host responses will provide a deeper comprehension of the disease process and aid in the development of effective preventive/therapeutic strategies.

Pathophysiology of acute lung injury in patients with acute brain injury: the triple-hit hypothesis

It has been convincingly demonstrated in recent years that isolated acute brain injury (ABI) may cause severe dysfunction of peripheral extracranial organs and systems. Of all potential target organs and systems, the lung appears to be the most vulnerable to damage after ABI. The pathophysiology of the bidirectional brain-lung interactions is multifactorial and involves inflammatory cascades, immune suppression, and dysfunction of the autonomic system. Indeed, the systemic effects of inflammatory mediators in patients with ABI create a systemic inflammatory environment ("first hit") that makes extracranial organs vulnerable to secondary procedures that enhance inflammation, such as mechanical ventilation (MV), surgery, and infections ("second hit"). Moreover, accumulating evidence supports the knowledge that gut microbiota constitutes a critical superorganism and an organ on its own, potentially modifying various physiological functions of the host. Furthermore, experimental and clinical data suggest the existence of a communication network among the brain, gastrointestinal tract, and its microbiome, which appears to regulate immune responses, gastrointestinal function, brain function, behavior, and stress responses, also named the "gut-microbiome-brain axis." Additionally, recent research evidence has highlighted a crucial interplay between the intestinal microbiota and the lungs, referred to as the "gut-lung axis," in which alterations during critical illness could result in bacterial translocation, sustained inflammation, lung injury, and pulmonary fibrosis. In the present work, we aimed to further elucidate the pathophysiology of acute lung injury (ALI) in patients with ABI by attempting to develop the "double-hit" theory, proposing the "triple-hit" hypothesis, focused on the influence of the gut-lung axis on the lung. Particularly, we propose, in addition to sympathetic hyperactivity, blast theory, and double-hit theory, that dysbiosis and intestinal dysfunction in the context of ABI alter the gut-lung axis, resulting in the development or further aggravation of existing ALI, which constitutes the "third hit."

Distinctive features of the oropharyngeal microbiome in Inuit of Nunavik and correlations of mild to moderate bronchial obstruction with dysbiosis

Inuit of Nunavik are coping with living conditions that can influence respiratory health. Our objective was to investigate associations between respiratory health in Inuit communities and their airway microbiome. Oropharyngeal samples were collected during the Qanuilirpitaa? 2017 Inuit Health Survey and subjected to metagenomic analyses. Participants were assigned to a bronchial obstruction group or a control group based on their clinical history and their pulmonary function, as monitored by spirometry. The Inuit microbiota composition was found to be distinct from other studied populations. Within the Inuit microbiota, differences in diversity measures tend to distinguish the two groups. Bacterial taxa found to be more abundant in the control group included candidate probiotic strains, while those enriched in the bronchial obstruction group included opportunistic pathogens. Crossing taxa affiliation method and machine learning consolidated our finding of distinct core microbiomes between the two groups. More microbial metabolic pathways were enriched in the control participants and these were often involved in vitamin and anti-inflammatory metabolism, while a link could be established between the enriched pathways in the disease group and inflammation. Overall, our results suggest a link between microbial abundance, interactions and metabolic activities and respiratory health in the Inuit population.

A novel hamster model of SARS-CoV-2 respiratory infection using a pseudotyped virus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a biosafety level (BSL)-3 pathogen; therefore, its research environment is limited. Pseudotyped viruses that mimic the infection of SARS-CoV-2 have been widely used for in vitro evaluation because they are available in BSL-2 containment laboratories. However, in vivo application is inadequate. Therefore, animal models instigated with animal BSL-2 will provide opportunities for in vivo evaluation. Hamsters (6–10-week-old males) were intratracheally inoculated with luciferase-expressing vesicular stomatitis virus (VSV)-based SARS-CoV-2 pseudotyped virus. The lungs were harvested 24–72 h after inoculation and luminescence was measured using an in vivo imaging system. Lung luminescence after inoculation with the SARS-CoV-2 pseudotyped virus increased in a dose-dependent manner and peaked at 48 h. The VSV-G (envelope G) pseudotyped virus also induced luminescence; however, a 100-fold concentration was required to reach a level similar to that of the SARS-CoV-2 pseudotyped virus. The SARS-CoV-2 pseudotyped virus is applicable to SARS-CoV-2 respiratory infections in a hamster model. Because of the single-round infectious virus, the model can be used to study the steps from viral binding to entry, which will be useful for future research on SARS-CoV-2 entry without using live SARS-CoV-2 or transgenic animals.

Understanding the Complexities and Changes of the Astronaut Microbiome for Successful Long-Duration Space Missions

During space missions, astronauts are faced with a variety of challenges that are unique to spaceflight and that have been known to cause physiological changes in humans over a period of time. Several of these changes occur at the microbiome level, a complex ensemble of microbial communities residing in various anatomic sites of the human body, with a pivotal role in regulating the health and behavior of the host. The microbiome is essential for day-to-day physiological activities, and alterations in microbiome composition and function have been linked to various human diseases. For these reasons, understanding the impact of spaceflight and space conditions on the microbiome of astronauts is important to assess significant health risks that can emerge during long-term missions and to develop countermeasures. Here, we review various conditions that are caused by long-term space exploration and discuss the role of the microbiome in promoting or ameliorating these conditions, as well as space-related factors that impact microbiome composition. The topics explored pertain to microgravity, radiation, immunity, bone health, cognitive function, gender differences and pharmacomicrobiomics. Connections are made between the trifecta of spaceflight, the host and the microbiome, and the significance of these interactions for successful long-term space missions.

Microbiology and Outcomes of Institutionalized Patients With Stroke-Associated Pneumonia: An Observational Cohort Study

Background: The attributable mortality and microbial etiology of stroke-associated pneumonia (SAP) vary among different studies and were inconsistent. Purpose: To determine the microbiology and outcomes of SAP in the lower respiratory tract (LRT) for patients with invasive mechanical ventilation (MV). Methods: In this observational study, included patients were divided into SAP and non-SAP based on a comprehensive analysis of symptom, imaging, and laboratory results. Baseline characteristics, clinical characteristics, microbiology, and outcomes were recorded and evaluated. Results: Of 200 patients, 42.5% developed SAP after the onset of stroke, and they had a lower proportion of non-smokers (p = 0.002), lower GCS score (p < 0.001), higher serum CRP (p < 0.001) at ICU admission, and a higher proportion of males (p < 0.001) and hypertension (p = 0.039) than patients with non-SAP. Gram-negative aerobic bacilli were the predominant organisms isolated (78.8%), followed by Gram-positive aerobic cocci (29.4%). The main pathogens included K. pneumoniae, S. aureus, H. influenzae, A. baumannii, P. aeruginosa, E. aerogenes, Serratia marcescens, and Burkholderia cepacia. SAP prolonged length of MV (p < 0.001), duration of ICU stay (p < 0.001) and hospital stay (p = 0.027), shortened MV-free days by 28 (p < 0.001), and caused elevated vasopressor application (p = 0.001) and 60-day mortality (p = 0.001). Logistic regression analysis suggested that patients with coma (p < 0.001) have a higher risk of developing SAP. Conclusion: The microbiology of SAP is similar to early phase of HAP and VAP. SAP prolongs the duration of MV and length of ICU and hospital stays, but also markedly increases 60-day mortality.

Conjunctival Sac Microbiome in Infectious Conjunctivitis

Acute bacterial conjunctival infections are common, and this study identified the conjunctival bacterial community in infectious conjunctivitis cases seen at the outpatient clinic of Khanh Hoa General Hospital in Nha Trang, Vietnam from October 2016 through December 2017. Conjunctival swabs were collected and tested using conventional culture, PCR, and 16S ribosomal RNA sequencing. The study included 47 randomly selected patients. More than 98% of all DNA reads represented five bacterial phyla. Three of these phyla constituted 92% of all sequences (Firmicutes (35%), Actinobacteria (31%), and Proteobacteria (26%)). At the genus level, there were 12 common genera that constituted about 61% of all sequence reads. Seven of those genera were common (Streptococcus (10%), Cutibacterium (10%), Staphylococcus (7%), Nocardioides (7%), Corynebacterium 1 (5%), Anoxybacillus (5%), and Acinetobacter (5%)), which encompassed 49% of all reads. As for diversity analysis, there was no difference on PERMANOVA analysis (unweighted UniFrac) for sex (p = 0.087), chemosis (p = 0.064), and unclassified eyedrops (p = 0.431). There was a significant difference in cases with bilateral conjunctivitis (p = 0.017) and for using antibiotics (p = 0.020). Of the predominant phyla, Firmicutes had the highest abundance in bacterial conjunctivitis in this study. Pseudomonas as a resident commensal microbiota may have an important role in the prevention of infection.

From Klebsiella pneumoniae Colonization to Dissemination: An Overview of Studies Implementing Murine Models

Klebsiella pneumoniae is a Gram-negative pathogen responsible for community-acquired and nosocomial infections. The strains of this species belong to the opportunistic group, which is comprised of the multidrug-resistant strains, or the hypervirulent group, depending on their accessory genome, which determines bacterial pathogenicity and the host immune response. The aim of this survey is to present an overview of the murine models mimicking K. pneumoniae infectious processes (i.e., gastrointestinal colonization, urinary, pulmonary, and systemic infections), and the bacterial functions deployed to colonize and disseminate into the host. These in vivo approaches are pivotal to develop new therapeutics to limit K. pneumoniae infections via a modulation of the immune responses and/or microbiota.

Impact of daily wearing of fabric gloves on the management of hand eczema: A pilot study in health-care workers

Hand eczema is a major occupational disease, especially in medical workers, reducing their quality of life (QOL) and work productivity. Daily wearing of fabric gloves to prevent loss of moisture and lipids from the surface of the hands has been regarded as good in the management of hand eczema. However, limited evidence is available regarding the efficacy of moisturizing care with daily gloves on hand eczema. This pilot study was performed to evaluate the efficacy of moisturizing intervention with daily wearing of fabric gloves on skin barrier function, disease severity, and microbiome in health-care workers with hand eczema. Study 1: Nurses in the neonatal intensive care unit or growing care unit with and without hand eczema were recruited in the study. Subjects were instructed to apply moisturizer and wear two types of fabric gloves, common cotton gloves and moisturizing fabric gloves containing malate, for 4 weeks. Study 2: Physicians and health-care workers were recruited and instructed to wear a cotton glove on one hand at nighttime for 4 weeks. Disease severity, skin barrier function, QOL, and hand microbiome (Study 1) were evaluated. Study 1 found that daily wearing of both types of fabric gloves accompanied by use of topical moisturizers reduced the severity of hand eczema without changing the variation of microbiome. Study 2 found no apparent change between wearing and not wearing cotton gloves. In summary, topical moisturizer is of fundamental importance, and concomitant use of fabric gloves may merely enhance the efficacy of moisturizer in the management of hand eczema.

Temporal Characteristics of the Oropharyngeal and Nasal Microbiota Structure in Crewmembers Stayed 180 Days in the Controlled Ecological Life Support System

Confined experiments are carried out to simulate the closed environment of space capsule on the ground. The Chinese Controlled Ecological Life Support System (CELSS) is designed including a closed-loop system supporting 4 healthy volunteers surviving for 180 days, and we aim to reveal the temporal characteristics of the oropharyngeal and nasal microbiota structure in crewmembers stayed 180 days in the CELSS, so as to accumulate the information about microbiota balance associated with respiratory health for estimating health risk in future spaceflight. We investigated the distribution of microorganisms and their dynamic characteristics in the nasal cavity and oropharynx of occupants with prolonged confinement. Based on the 16S rDNA v3–v4 regions using Illumina high-throughput sequencing technology, the oropharyngeal and nasal microbiota were monitored at eight time points during confinement. There were significant differences between oropharyngeal and nasal microbiota, and there were also individual differences among the same site of different volunteers. Analysis on the structure of the microbiota showed that, in the phylum taxon, the nasal bacteria mainly belonged to Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, etc. In addition to the above phyla, in oropharyngeal bacteria Fusobacterial accounted for a relatively high proportion. In the genus taxon, the nasal and oropharyngeal bacteria were independent. Corynebacterium and Staphylococcus were dominant in nasal cavity, and Corynebacterium, Streptococcus, and Neisseria were dominant in oropharynx. With the extension of the confinement time, the abundance of Staphylococcus in the nasal cavity and Neisseria in the oropharynx increased, and the index Chao fluctuated greatly from 30 to 90 days after the volunteers entered the CELSS.

Conclusion: The structure and diversity of the nasal and oropharyngeal microbiota changed in the CELSS, and there was the phenomenon of migration between occupants, suggesting that the microbiota structure and health of the respiratory tract could be affected by living in a closed environment for a long time.