Nasal commensal Staphylococcus epidermidis counteracts influenza virus

Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro

Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen Coccidioides. Unfortunately, patients are often misdiagnosed with bacterial pneumonia, leading to inappropriate antibiotic treatment. The soil Bacillus subtilis-like species exhibits antagonistic properties against Coccidioides in vitro; however, the antagonistic capabilities of host microbiota against Coccidioides are unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth of Coccidioides in vitro. We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth of Coccidioides, while partial in vitro depletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2×GYE (GYE) and Columbia colistin and nalidixic acid with 5% sheep's blood agar inhibited the growth of Coccidioides, but microbiota grown on chocolate agar did not. Partial depletion of the microbiota through antibiotic disk diffusion revealed diminished inhibition and comparable growth of Coccidioides to controls. To characterize the bacteria grown and identify potential candidates contributing to the inhibition of Coccidioides, 16S rRNA sequencing was performed on tracheal and intestinal agar cultures and murine lung extracts. We found that the host bacteria likely responsible for this inhibition primarily included Lactobacillus and Staphylococcus. The results of this study demonstrate the potential of the host microbiota to inhibit the growth of Coccidioides in vitro and suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growth in vivo.

IMPORTANCE

Coccidioidomycosis is caused by a fungal pathogen that invades the host lungs, causing respiratory distress. In 2019, 20,003 cases of Valley fever were reported to the CDC. However, this number likely vastly underrepresents the true number of Valley fever cases, as many go undetected due to poor testing strategies and a lack of diagnostic models. Valley fever is also often misdiagnosed as bacterial pneumonia, resulting in 60%-80% of patients being treated with antibiotics prior to an accurate diagnosis. Misdiagnosis contributes to a growing problem of antibiotic resistance and antibiotic-induced microbiome dysbiosis; the implications for disease outcomes are currently unknown. About 5%-10% of symptomatic Valley fever patients develop chronic pulmonary disease. Valley fever causes a significant financial burden and a reduced quality of life. Little is known regarding what factors contribute to the development of chronic infections and treatments for the disease are limited.

Mucosal Immunity against SARS-CoV-2 in the Respiratory Tract

The respiratory tract, the first-line defense, is constantly exposed to inhaled allergens, pollutants, and pathogens such as respiratory viruses. Emerging evidence has demonstrated that the coordination of innate and adaptive immune responses in the respiratory tract plays a crucial role in the protection against invading respiratory pathogens. Therefore, a better understanding of mucosal immunity in the airways is critical for the development of novel therapeutics and next-generation vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses. Since the coronavirus disease 2019 pandemic, our knowledge of mucosal immune responses in the airways has expanded. In this review, we describe the latest knowledge regarding the key components of the mucosal immune system in the respiratory tract. In addition, we summarize the host immune responses in the upper and lower airways following SARS-CoV-2 infection and vaccination, and discuss the impact of allergic airway inflammation on mucosal immune responses against SARS-CoV-2.

Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro

Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen Coccidioides. Unfortunately, patients are often misdiagnosed with bacterial pneumonia leading to inappropriate antibiotic treatment. Soil bacteria B. subtilis-like species exhibits antagonistic properties against Coccidioides in vitro; however, the antagonistic capabilities of host microbiota against Coccidioides are unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth of Coccidioides in vitro. We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth of Coccidioides while partial in vitro depletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2xGYE (GYE) and CNA w/ 5% sheep's blood agar (5%SB-CNA) inhibited the growth of Coccidioides, but that grown on chocolate agar does not. Partial depletion of the microbiota through antibiotic disk diffusion revealed that microbiota depletion leads to diminished inhibition and comparable growth of Coccidioides growth to controls. To characterize the bacteria grown and narrow down potential candidates contributing to the inhibition of Coccidioides, 16s rRNA sequencing of tracheal and intestinal agar cultures and murine lung extracts was performed. The identity of host bacteria that may be responsible for this inhibition was revealed. The results of this study demonstrate the potential of the host microbiota to inhibit the growth of Coccidioides in vitro and suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growth in vivo.

Randomized, Double-Blind, Placebo-Controlled Trial of a Throat Spray with Selected Lactobacilli in COVID-19 Outpatients

Primary care urgently needs treatments for coronavirus disease 2019 (COVID-19) patients because current options are limited, while these patients who do not require hospitalization encompass more than 90% of the people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we evaluated a throat spray containing three Lactobacillaceae strains with broad antiviral properties in a randomized, double-blind, placebo-controlled trial. Before the availability of vaccines, 78 eligible COVID-19 patients were randomized to verum (n = 41) and placebo (n = 37) within 96 h of a positive PCR-based SARS-CoV-2 diagnosis, and a per-protocol analysis was performed. Symptoms and severity were reported daily via an online diary. Combined nose-throat swabs and dried blood spots were collected at regular time points in the study for microbiome, viral load, and antibody analyses. The daily reported symptoms were highly variable, with no added benefit for symptom resolution in the verum group. However, based on 16S V4 amplicon sequencing, the acute symptom score (fever, diarrhea, chills, and muscle pain) was significantly negatively associated with the relative abundance of amplicon sequence variants (ASVs) that included the applied lactobacilli (P < 0.05). Furthermore, specific monitoring of these applied lactobacilli strains showed that they were detectable via quantitative PCR (qPCR) analysis in 82% of the patients in the verum group. At the end of the trial, a trend toward lower test positivity for SARS-CoV-2 was observed for the verum group (2/30; 6.7% positive) than for the placebo group (7/27; 26% positive) (P = 0.07). These data indicate that the throat spray with selected antiviral lactobacilli could have the potential to reduce nasopharyngeal viral loads and acute symptoms but should be applied earlier in the viral infection process and substantiated in larger trials. IMPORTANCE Viral respiratory tract infections result in significant health and economic burdens, as highlighted by the COVID-19 pandemic. Primary care patients represent 90% of those infected with SARS-CoV-2, yet their treatment options are limited to analgesics and antiphlogistics, and few broadly acting antiviral strategies are available. Microbiome or probiotic therapy is a promising emerging treatment option because it is based on the multifactorial action of beneficial bacteria against respiratory viral disease. In this study, an innovative topical throat spray with select beneficial lactobacilli was administered to primary COVID-19 patients. A remote study setup (reducing the burden on hospitals and general practitioners) was successfully implemented using online questionnaires and longitudinal self-sampling. Our results point toward the potential mechanisms of action associated with spray administration at the levels of viral loads and microbiome modulation in the upper respiratory tract and pave the way for future clinical applications of beneficial bacteria against viral diseases.

Role of Microbiota in Viral Infections and Pathological Progression

Viral infections are influenced by various microorganisms in the environment surrounding the target tissue, and the correlation between the type and balance of commensal microbiota is the key to establishment of the infection and pathogenicity. Some commensal microorganisms are known to resist or promote viral infection, while others are involved in pathogenicity. It is also becoming evident that the profile of the commensal microbiota under normal conditions influences the progression of viral diseases. Thus, to understand the pathogenesis underlying viral infections, it is important to elucidate the interactions among viruses, target tissues, and the surrounding environment, including the commensal microbiota, which should have different relationships with each virus. In this review, we outline the role of microorganisms in viral infections. Particularly, we focus on gaining an in-depth understanding of the correlations among viral infections, target tissues, and the surrounding environment, including the commensal microbiota and the gut virome, and discussing the impact of changes in the microbiota (dysbiosis) on the pathological progression of viral infections.

Colonization of nasal cavities by Staphylococcus epidermidis mitigates SARS‐CoV‐2 nucleocapsid phosphoprotein‐induced interleukin (IL)‐6 in the lung

Infection by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) can trigger excessive interleukin (IL)‐6 signalling, leading to a myriad of biological effects including a cytokine storm that contributes to multiple organ failure in severe coronavirus disease 2019 (COVID‐19). Using a mouse model, we demonstrated that nasal inoculation of nucleocapsid phosphoprotein (NPP) of SARS‐CoV‐2 increased IL‐6 content in bronchoalveolar lavage fluid (BALF). Nasal administration of liquid coco‐caprylate/caprate (LCC) onto Staphylococcus epidermidis (S. epidermidis)‐colonized mice significantly attenuated NPP‐induced IL‐6. Furthermore, S. epidermidis‐mediated LCC fermentation to generate electricity and butyric acid that promoted bacterial colonization and activated free fatty acid receptor 2 (Ffar2) respectively. Inhibition of Ffar2 impeded the effect of S. epidermidis plus LCC on the reduction of NPP‐induced IL‐6. Collectively, these results suggest that nasal S. epidermidis is part of the first line of defence in ameliorating a cytokine storm induced by airway infection of SARS‐CoV‐2.

The potential application of probiotics for the prevention and treatment of COVID-19

Background

Given the severe infection, poor prognosis, and the low number of available effective drugs, potential prevention and treatment strategies for COVID-19 need to be urgently developed.

Main body

Herein, we present and discuss the possible protective and therapeutic mechanisms of human microbiota and probiotics based on the previous and recent findings. Microbiota and probiotics consist of mixed cultures of living microorganisms that can positively affect human health through their antiviral, antibacterial, anti-inflammatory, and immunomodulatory effect. In the current study, we address the promising advantages of microbiota and probiotics in decreasing the risk of COVID-19.

Conclusions

Thus, we recommend further studies be conducted for assessing and evaluating the capability of these microbes in the battle against COVID-19.

Mapping bacterial diversity and metabolic functionality of the human respiratory tract microbiome

Background

The Human Respiratory Tract (HRT) is colonized by various microbial taxa, known as HRT microbiota, in a manner that is indicative of mutualistic interaction between such microorganisms and their host.

Aim

To investigate the microbial composition of the HRT and its possible correlation with the different compartments of the respiratory tract.

Methods

In the current study, we performed an in-depth meta‐analysis of 849 HRT samples from public shotgun metagenomic datasets obtained through several distinct collection methods.

Results

The statistical robustness provided by this meta-analysis allowed the identification of 13 possible HRT-specific Community State Types (CSTs), which appear to be specific to each anatomical region of the respiratory tract. Furthermore, functional characterization of the metagenomic datasets revealed specific microbial metabolic features correlating with the different compartments of the respiratory tract.

Conclusion

The meta-analysis here performed suggested that the variable presence of certain bacterial species seems to be linked to a location-related abundance gradient in the HRT and seems to be characterized by a specific microbial metabolic capability.

Staphylococcus epidermidis Controls Opportunistic Pathogens in the Nose, Could It Help to Regulate SARS-CoV-2 (COVID-19) Infection?

Staphylococcus epidermidis is more abundant in the anterior nares than internal parts of the nose, but its relative abundance changes along with age; it is more abundant in adolescents than in children and adults. Various studies have shown that S. epidermidis is the guardian of the nasal cavity because it prevents the colonization and infection of respiratory pathogens (bacteria and viruses) through the secretion of antimicrobial molecules and inhibitors of biofilm formation, occupying the space of the membrane mucosa and through the stimulation of the host’s innate and adaptive immunity. There is a strong relationship between the low number of S. epidermidis in the nasal cavity and the increased risk of serious respiratory infections. The direct application of S. epidermidis into the nasal cavity could be an effective therapeutic strategy to prevent respiratory infections and to restore nasal cavity homeostasis. This review shows the mechanisms that S. epidermidis uses to eliminate respiratory pathogens from the nasal cavity, also S. epidermidis is proposed to be used as a probiotic to prevent the development of COVID-19 because S. epidermidis induces the production of interferon type I and III and decreases the expression of the entry receptors of SARS-CoV-2 (ACE2 and TMPRSS2) in the nasal epithelial cells.

Ocular benzalkonium chloride exposure: problems and solutions

Preservatives in multidose formulations of topical ophthalmic medications are crucial for maintaining sterility but can be toxic to the ocular surface. Benzalkonium chloride (BAK)-used in approximately 70% of ophthalmic formulations-is well known to cause cytotoxic damage to conjunctival and corneal epithelial cells, resulting in signs and symptoms of ocular surface disease (OSD) including ocular surface staining, increased tear break-up time, and higher OSD symptom scores. These adverse effects are more problematic with chronic exposure, as in lifetime therapy for glaucoma, but can also manifest after exposure as brief as seven days. Multiple strategies are available to minimize or eliminate BAK exposure, among them alternative preservatives, preservative-free formulations including sustained release drug delivery platforms, and non-pharmacological therapies for common eye diseases and conditions. In this paper, we review the cytotoxic and clinical effects of BAK on the ocular surface and discuss existing and emerging options for ocular disease management that can minimize or eliminate BAK exposure.

Virus Infection Is an Instigator of Intestinal Dysbiosis Leading to Type 1 Diabetes

In addition to genetic predisposition, environmental determinants contribute to a complex etiology leading to onset of type 1 diabetes (T1D). Multiple studies have established the gut as an important site for immune modulation that can directly impact development of autoreactive cell populations against pancreatic self-antigens. Significant efforts have been made to unravel how changes in the microbiome function as a contributor to autoimmune responses and can serve as a biomarker for diabetes development. Large-scale longitudinal studies reveal that common environmental exposures precede diabetes pathology. Virus infections, particularly those associated with the gut, have been prominently identified as risk factors for T1D development. Evidence suggests recent-onset T1D patients experience pre-existing subclinical enteropathy and dysbiosis leading up to development of diabetes. The start of these dysbiotic events coincide with detection of virus infections. Thus viral infection may be a contributing driver for microbiome dysbiosis and disruption of intestinal homeostasis prior to T1D onset. Ultimately, understanding the cross-talk between viral infection, the microbiome, and the immune system is key for the development of preventative measures against T1D.

Circadian Rhythm Modulation of Microbes During Health and Infection

Circadian rhythms, referring to 24-h daily oscillations in biological and physiological processes, can significantly regulate host immunity to pathogens, as well as commensals, resulting in altered susceptibility to disease development. Furthermore, vaccination responses to microbes have also shown time-of-day-dependent changes in the magnitude of protective immune responses elicited in the host. Thus, understanding host circadian rhythm effects on both gut bacteria and viruses during infection is important to minimize adverse effects on health and identify optimal times for therapeutic administration to maximize therapeutic success. In this review, we summarize the circadian modulations of gut bacteria, viruses and their interactions, both in health and during infection. We also discuss the importance of chronotherapy (i.e., time-specific therapy) as a plausible therapeutic administration strategy to enhance beneficial therapeutic responses.

Nasopharyngeal Microbiome Community Composition and Structure Is Associated with Severity of COVID-19 Disease and Breathing Treatment

Viral infections are known to modulate the upper respiratory tract microbiome, but few studies have addressed differences in the nasopharyngeal microbiome following SARS-CoV-2 infection. Using nasopharyngeal swab medical waste samples from 79 confirmed SARS-CoV-2 positive and 20 SARS-CoV-2 negative patients, we assessed microbiome composition with metagenomic sequencing. COVID-19 status and breathing assistive device use was associated with differences in beta diversity, principal component analyses, community composition and abundance of several species. Serratia more frequently appeared in COVID-19 patient samples compared to negative patient samples, and Serratia, Streptococcus, Enterobacter, Veillonella, Prevotella, and Rothia appeared more frequently in samples of those who used breathing assistive devices. Smoking and age were associated with differences in alpha diversity. Cross-sectional differences in the microbiome were apparent with SARS-CoV-2 infection, but longitudinal studies are needed to understand the dynamics of viral and breathing treatment modulation of microbes.

The effect of topical ocular moxifloxacin on conjunctival and nasal mucosal flora

To determine the short-term effect of topically administered ocular moxifloxacin on conjunctival and nasal bacterial mucosal flora. The study included 20 patients with newly diagnosed age-related macular degeneration. Each patient’s diseased eye was selected as the treatment eye and the fellow eye was selected as the control eye. All treatment eyes constituted the treatment group and all controls eyes constituted the control group. All patients received intravitreal injection of ranibizumab. Cultures were obtained from the inferior conjunctival fornix and the nostrils in all patients. Patients were instructed to administer moxifloxacin eye drops to the treatment eye 4 times daily for 1 week. The patients were instructed to come for a follow-up exam 1 week post intravitreal injection. The bacterial culture positivity rate and the bacteria isolated from the conjunctiva and nostrils were recorded in the 2 groups before and after use of topical ocular moxifloxacin. Mean age of the patients (12 female and 8 male) was 64.9 years. Before use of topical ocular moxifloxacin the conjunctival and nasal culture positivity rates in the treatment group were both 100%, versus 90% and 95%, respectively, in the control group. At the follow-up exam the conjunctival and nasal mucosa culture positivity rates in the treatment group decreased to 20% (4/20) and 30% (6/20), respectively (P < 0.001), versus 85% (17/20) and 80% (16/20), respectively, in the control group (P = 0.68 and P = 0.72 for conjunctival and nasal). This is the first study to show that moxifloxacin applied to the ocular surface topically has a significant effect on nasal flora. Daily administration of topical ocular moxifloxacin for 1 week significantly reduces the nasal bacterial flora in addition to conjunctival flora.

Vancomycin use and cytomegalovirus reactivation after allogeneic hematopoietic cell transplantation

Vancomycin exposure in the pre-engraftment period was associated with an increased risk for CMV reactivation after allogeneic HCT. Some gram-positive bacteria may protect against CMV reactivation.

Topical Microbial Therapeutics against Respiratory Viral Infections

Emerging evidence suggests that microbial therapeutics can prevent and treat respiratory viral diseases, especially when applied directly to the airways. This review presents established beneficial effects of locally administered microbial therapeutics against respiratory viral diseases and the inferred related molecular mechanisms. Several mechanisms established in the intestinal probiotics field as well as novel, niche-specific insights are relevant in the airways. Studies at cellular and organism levels highlight biologically plausible but strain-specific and host and virus context-dependent mechanisms, underlying the potential of beneficial bacteria. Large-scale clinical studies can now be rationally designed to provide a bench-to-bedside translation of the multifactorial bacterial mechanisms within the host respiratory tract, to diminish the incidence and severity of viral infections and the concomitant complications.

Non-epidermidis coagulase-negative Staphylococcus isolated from farm animals can inhibit the hemagglutinating activity of Newcastle disease virus and bovine parainfluenza virus type 3

The Embp protein of Staphylococcus epidermidis inhibits the hemagglutination of the H1N1 influenza virus and protects birds from a viral respiratory infection. Several species of Coagulase-negative Staphylococcus (CoNS) are present in the respiratory cavity, particularly in nostrils. We hypothesize that non-epidermidis CoNS found in animals can have the same function as observed in S. epidermidis. Thirty Non-epidermidis CoNS isolates were obtained from poultry, sheep, goat, pig, and dairy cow nostrils. Haemagglutination inhibition (HI) activity was assayed in bacteria-free supernatants from non-epidermidis CoNS against Newcastle disease virus (NDV) and bovine parainfluenza virus type 3 (BPIV). In 13 of the 30 strains (43.3 %), bacteria-free supernatants showed HI activity for NDV and BPIV-3. Staphylococcus xylosus supernatants from poultry (one isolate), sheep (two isolates), goat (one isolate), and dairy cow (three isolates) had the highest frequency of HI activity on NDV and BPIV-3, followed by Staphylococcus sp. supernatants from goat (one isolate), dairy cow (two isolates), and finally Staphylococcus equorum, Staphylococcus chromogens and Staphylococcus gallinarum supernatants with single isolation from poultry, pig and poultry, respectively. Nine isolates had the homologous gene to the embp gene of S. epidermidis, and it was associated with HI activity in the studied viruses. By Pulsed-field gel electrophoresis, S. xylosus isolates showed to be different clones and related to the origin of isolation and HI activity. These results demonstrate that non-epidermidis CoNS supernatants from different animals and origins have the ability of HI on NDV and BPIV-3, indicating that not only S. epidermidis has the same function.

Letter to the Editor: Microbiota in the Respiratory System-A Possible Explanation to Age and Sex Variability in Susceptibility to SARS-CoV-2

The Human respiratory tract is colonized by a variety of microbes and the microbiota change as we age. In this perspective, literature support is presented for the hypothesis that the respiratory system microbiota could explain the differential age and sex breakdown amongst COVID-19 patients. The number of patients in the older and elderly adult group is higher than the other age groups. The perspective presents the possibility that certain genera of bacteria present in the respiratory system microbiota in children and young adults could be directly or through eliciting an immune response from the host, prevent full-fledged infection of SARS-CoV-2. The possibility also exists that the microbiota in older adults and the elderly population have bacteria that make it easier for the virus to cause infection. I call upon the scientific community to investigate the link between human microbiota and SARS-CoV-2 susceptibility to further understand the viral pathogenesis.

Dual and mutual interaction between microbiota and viral infections: a possible treat for COVID-19

All of humans and other mammalian species are colonized by some types of microorganisms such as bacteria, archaea, unicellular eukaryotes like fungi and protozoa, multicellular eukaryotes like helminths, and viruses, which in whole are called microbiota. These microorganisms have multiple different types of interaction with each other. A plethora of evidence suggests that they can regulate immune and digestive systems and also play roles in various diseases, such as mental, cardiovascular, metabolic and some skin diseases. In addition, they take-part in some current health problems like diabetes mellitus, obesity, cancers and infections. Viral infection is one of the most common and problematic health care issues, particularly in recent years that pandemics like SARS and COVID-19 caused a lot of financial and physical damage to the world. There are plenty of articles investigating the interaction between microbiota and infectious diseases. We focused on stimulatory to suppressive effects of microbiota on viral infections, hoping to find a solution to overcome this current pandemic. Then we reviewed mechanistically the effects of both microbiota and probiotics on most of the viruses. But unlike previous studies which concentrated on intestinal microbiota and infection, our focus is on respiratory system's microbiota and respiratory viral infection, bearing in mind that respiratory system is a proper entry site and residence for viruses, and whereby infection, can lead to asymptomatic, mild, self-limiting, severe or even fatal infection. Finally, we overgeneralize the effects of microbiota on COVID-19 infection. In addition, we reviewed the articles about effects of the microbiota on coronaviruses and suggest some new therapeutic measures.

Skin Viral Infections: Host Antiviral Innate Immunity and Viral Immune Evasion

The skin is an active immune organ that functions as the first and largest site of defense to the outside environment. Serving as the primary interface between host and pathogen, the skin’s early immune responses to viral invaders often determine the course and severity of infection. We review the current literature pertaining to the mechanisms of cutaneous viral invasion for classical skin-tropic, oncogenic, and vector-borne skin viruses. We discuss the skin’s evolved mechanisms for innate immune viral defense against these invading pathogens, as well as unique strategies utilized by the viruses to escape immune detection. We additionally explore the roles that demographic and environmental factors, such as age, biological sex, and the cutaneous microbiome, play in altering the host immune response to viral threats.

Is a healthy microbiome responsible for lower mortality in COVID-19?

The novel severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is the cause of an ongoing pandemic with significant case fatality ratio (CFR) worldwide. Although SARS-CoV-2 primarily causes respiratory infection by binding to ACE2 receptors present on alveolar epithelial cells, studies have been published linking the disease to the small intestine enterocytes and its microbiome. Dysbiosis of microbiome, mainly intestinal and lung, can affect the course of the disease. Environmental factors, such as reduced intake of commensal bacteria from the environment or their products in the diet, play an important role in microbiome formation, which can significantly affect the immune response. In elderly, obese or chronically ill people, the microbiota is often damaged. Therefore, we speculate that a good microbiome may be one of the factors responsible for lower CFR from the coronavirus disease 2019 (COVID-19). An approach using tailored nutrition and supplements known to improve the intestinal microbiota and its immune function might help minimize the impact of the disease at least on people at higher risk from coronavirus.

Anti-Influenza Protective Efficacy of a H6 Virus-Like Particle in Chickens

H6 avian influenza viruses (AIVs) have a worldwide distribution, and they pose a potential concern for public health. In Taiwan, H6 AIVs have circulated in domestic chickens for more than 40 years, and certain strains have crossed the species barrier to infect mammals. With the goal of containing the disease, there is a pressing need to develop a safe and effective vaccine for pandemic preparedness. In this study, we prepared a virus-like particle (VLP) that consisted of the hemagglutinin (HA) and matrix protein 1 (M1) derived from a H6 AIV as a vaccine antigen, and we examined the immunogenicity and protective efficacy when combined with an adjuvant in a chicken model. Full-length HA and M1 protein genes were cloned and expressed using a baculovirus expression system, and VLPs were purified from the supernatant of insect cell cultures. We performed nanoparticle-tracking analysis and transmission electron microscopy to validate that the particle structure and properties resembled the native virions. In animal experiments, specific-pathogen-free chickens that received the H6 VLPs in combination with an adjuvant showed superior H6N1 virus-specific serum IgG and hemagglutination-inhibition antibody responses, which lasted more than 112 days. Following the H6N1 viral challenge, the vaccinated chickens showed reduced viral replication in the lungs, kidneys and conjunctival/cloacal shedding. The antibodies induced in the chickens by the vaccine were able to cross-react with the H6N1 human isolate and drifted avian H6N1 isolates. In summary, the H6 VLP vaccine elicited superb immunogenicity in vivo, and the use of an adjuvant further enhanced the antiviral protective efficacy. This vaccine formulation could potentially be used to manage H6 influenza virus infections in chickens.

Bioengineered Nisin Derivative M17Q Has Enhanced Activity against Staphylococcus epidermidis

Staphylococcus epidermidis is frequently implicated in medical device-related infections. As a result of this, novel approaches for control of this opportunistic pathogen are required. We examined the ability of the natural peptide nisin A, produced by Lactococcus lactis, to inhibit S. epidermidis. In addition, a bank of 29 rationally selected bioengineered L. lactis strains were examined with the aim of identifying a nisin derivative with enhanced antimicrobial activity. Agar-based deferred antagonism assays revealed that wild type nisin A inhibited all 18 S. epidermidis strains tested. Larger zones of inhibition than those obtained from the nisin A producing L. lactis strain were observed for each derivative producer against at least one S. epidermidis strain tested. Six derivative producing strains, (VGA, VGT, SGK, M21A, M17Q, AAA), gave larger zones against all 18 strains compared to the wildtype producing strain. The enhanced bioactivity of M17Q was confirmed using well diffusion, minimum inhibitory concentration (MIC) and a broth-based survival assays. Biofilm assays were performed with plastic microtiter plates and medical device substrates (stainless-steel coupons and three catheter materials). The presence of nisin A significantly reduce the amount of biofilm formed on all surfaces. M17Q was significantly better at reducing biofilm production than nisin A on plastic and stainless-steel. Finally, M17Q was significantly better than nisin A at reducing bacterial numbers in a simulated wound fluid. The findings of this study suggest that nisin and bioengineered derivatives warrant further investigation as potential strategies for the control of S. epidermidis.

SARS-CoV-2 spike glycoprotein-binding proteins expressed by upper respiratory tract bacteria may prevent severe viral infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a major global challenge. The virus infects host cells using its spike glycoprotein (S-protein) and has significantly higher infectivity and mortality rates among the aged population. Here, based on bioinformatic analysis, I provide evidence that some members of the upper respiratory tract (URT) commensal bacteria express viral S-protein -binding proteins. Based on this analysis and available data showing a decline in the population of these bacteria in the elderly, I propose that some URT commensal bacteria hamper SARS-CoV-2 infectivity and that a decline in the population of these bacteria contributes to the severity of infection. Further studies should provide a better understanding of the interaction of URT bacteria and SARS-CoV-2, which may lead to new therapeutic approaches.

Strengthening the Immune System and Reducing Inflammation and Oxidative Stress through Diet and Nutrition: Considerations during the COVID-19 Crisis

The coronavirus-disease 2019 (COVID-19) was announced as a global pandemic by the World Health Organization. Challenges arise concerning how to optimally support the immune system in the general population, especially under self-confinement. An optimal immune response depends on an adequate diet and nutrition in order to keep infection at bay. For example, sufficient protein intake is crucial for optimal antibody production. Low micronutrient status, such as of vitamin A or zinc, has been associated with increased infection risk. Frequently, poor nutrient status is associated with inflammation and oxidative stress, which in turn can impact the immune system. Dietary constituents with especially high anti-inflammatory and antioxidant capacity include vitamin C, vitamin E, and phytochemicals such as carotenoids and polyphenols. Several of these can interact with transcription factors such as NF-kB and Nrf-2, related to anti-inflammatory and antioxidant effects, respectively. Vitamin D in particular may perturb viral cellular infection via interacting with cell entry receptors (angiotensin converting enzyme 2), ACE2. Dietary fiber, fermented by the gut microbiota into short-chain fatty acids, has also been shown to produce anti-inflammatory effects. In this review, we highlight the importance of an optimal status of relevant nutrients to effectively reduce inflammation and oxidative stress, thereby strengthening the immune system during the COVID-19 crisis.

Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection

Infection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation. The effects of influenza infection on the upper respiratory tract (URT) microbiome are largely unknown. Here, we report a longitudinal study to assess the temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes have stable healthy ecostate communities both within and between individuals. In contrast, infected patients and ferrets exhibit large changes in bacterial community composition over time and between individuals. The unhealthy ecostates of infected individuals progress towards the healthy ecostate, coinciding with viral clearance and recovery. Pseudomonadales associate statistically with the disturbed microbiomes of infected individuals. The dynamic and resilient microbiome during influenza virus infection in multiple hosts provides a compelling rationale for the maintenance of the microbiome homeostasis as a potential therapeutic target to prevent IAV associated bacterial co-infections.

Influenza A virus (IAV) infection can be exacerbated by bacterial co-infections but the effect of IAV on the upper respiratory tract (URT) microbiome remains unclear. Here, the authors compare the dynamics of the UTR microbiome in IAV-infected ferrets and humans, finding similar trends at the ecosystem and individual taxon level in both hosts.

Viral strategies predisposing to respiratory bacterial superinfections

Acute respiratory infections are amongst the leading causes of childhood morbidity and mortality globally. Viruses are the predominant cause of such infections, but mixed etiologies with bacteria has for decades raised the question of the interplay between them in causality and determination of the outcome of such infections. In this review, we examine recent microbiological, biochemical, and immunological advances that contribute to elucidating the mechanisms by which infections by specific viruses enable bacterial infections in the airway, and exacerbate them. We analyze specific domains in which viruses play such facilitating role including enhancement of bacterial adhesion by unmasking cryptic receptors and upregulation of adhesion proteins, disruption of tight junction integrity favoring paracellular transmigration of bacteria and loss of epithelial barrier integrity, increased availability of nutrient, such as mucins and iron, alteration of innate and adaptive immune responses, and disabling defense against bacteria, and lastly, changes in airway microbiome that render the lung more vulnerable to pathogens. Separate exhaustive analysis of each domain focuses on individuals with cystic fibrosis (CF), in whom viruses may play a key role in paving the way for the primary injury that leads to permanence of bacterial pathogens, viruses may then serve as triggers for "CF exacerbations"; these constituting the signature and ultimately the outcome determinants of these patients.

Screening of antibiotic-resistant staphylococci in the nasal cavity of patients and healthy individuals

The normal microbiota play critical roles in the general health of an individual and the functions of the microbiota colonized the nasal cavity in maintaining the health of the respiratory tract are well known. The nasal cavity is one of the potential bio-sources of the pathogenic opportunistic bacteria that have the ability to resist standard antibiotics. My aim was an evaluation of the prevalence of antibiotic-resistant staphylococci in the nasal cavity of healthy individuals and compared them with the strains isolated from patients. The work was designed as prospective, descriptive study in Medical University Hospital (MUH) and Botany and Microbiology Department, King Saud University (KSU), Riyadh, respectively. Strain isolation, purification, and preservation were performed according to standard protocols and the identification of pure bacterial cultures was carried out using a fully automatic system (VITEK 2 system). The isolates identified as Staphylococcus spp. were subjected to investigation. In patients, 34 out of 6668 isolates were Staphylococcus spp. obtained from the nasal cavity, while 32 out of 320 isolates from the nasal cavity of healthy individuals were Staphylococcus spp. The results confirmed that all the isolates were resistant to ampicillin and benzylpenicillin, but showed susceptibility to vancomycin, fusidic acid, gentamicin, linezolid, rifampicin, teicoplanin, tetracycline, and trimethoprim/sulfamethoxazole. A significant association (P < 0.05) was observed between all the isolates resistant to ampicillin and clindamycin in patients and healthy individuals. The antibiotic-resistant staphylococci are prevalent in the nasal cavity among healthy individuals and patients, and a statistically significant association exists between sources of bacterial isolates and antibiotic resistance.

Severe Obstructive Sleep Apnea Is Associated with Alterations in the Nasal Microbiome and an Increase in Inflammation

RATIONALE

Obstructive sleep apnea (OSA) is associated with recurrent obstruction, subepithelial edema, and airway inflammation. The resultant inflammation may influence or be influenced by the nasal microbiome.

OBJECTIVES

To evaluate whether the composition of the nasal microbiota is associated with obstructive sleep apnea and inflammatory biomarkers.

METHODS

Two large cohorts were used: 1) a discovery cohort of 472 subjects from the WTCSNORE (Seated, Supine and Post-Decongestion Nasal Resistance in World Trade Center Rescue and Recovery Workers) cohort, and 2) a validation cohort of 93 subjects rom the Zaragoza Sleep cohort. Sleep apnea was diagnosed using home sleep tests. Nasal lavages were obtained from cohort subjects to measure: 1) microbiome composition (based on 16S rRNA gene sequencing), and 2) biomarkers for inflammation (inflammatory cells, IL-8, and IL-6). Longitudinal 3-month samples were obtained in the validation cohort, including after continuous positive airway pressure treatment when indicated.

MEASUREMENTS AND MAIN RESULTS

In both cohorts, we identified that: 1) severity of OSA correlated with differences in microbiome diversity and composition; 2) the nasal microbiome of subjects with severe OSA were enriched with Streptococcus, Prevotella, and Veillonella; and 3) the nasal microbiome differences were associated with inflammatory biomarkers. Network analysis identified clusters of cooccurring microbes that defined communities. Several common oral commensals (e.g., Streptococcus, Rothia, Veillonella, and Fusobacterium) correlated with apnea-hypopnea index. Three months of treatment with continuous positive airway pressure did not change the composition of the nasal microbiota.

CONCLUSIONS

We demonstrate that the presence of an altered microbiome in severe OSA is associated with inflammatory markers. Further experimental approaches to explore causal links are needed.

B. Teles R, Montoya D, O. Scumpia P, Nunes Sarno E, Ochoa MT, Ma F, Pellegrini M, Modlin RL. The cell fate regulator NUPR1 is induced by Mycobacterium leprae via type I interferon in human leprosy

The initial interaction between a microbial pathogen and the host immune response influences the outcome of the battle between the host and the foreign invader. Leprosy, caused by the obligate intracellular pathogen Mycobacterium leprae, provides a model to study relevant human immune responses. Previous studies have adopted a targeted approach to investigate host response to M. leprae infection, focusing on the induction of specific molecules and pathways. By measuring the host transcriptome triggered by M. leprae infection of human macrophages, we were able to detect a host gene signature 24-48 hours after infection characterized by specific innate immune pathways involving the cell fate mechanisms autophagy and apoptosis. The top upstream regulator in the M. leprae-induced gene signature was NUPR1, which is found in the M. leprae-induced cell fate pathways. The induction of NUPR1 by M. leprae was dependent on the production of the type I interferon (IFN), IFN-β. Furthermore, NUPR1 mRNA and protein were upregulated in the skin lesions from patients with the multibacillary form of leprosy. Together, these data indicate that M. leprae induces a cell fate program which includes NUPR1 as part of the host response in the progressive form of leprosy.

The Commensal Microbiota and Viral Infection: A Comprehensive Review

The human body is inhabited by a diverse microbial community that is collectively coined as commensal microbiota. Recent research has greatly advanced our understanding of how the commensal microbiota affects host health. Among the various kinds of pathogenic infections of the host, viral infections constitute one of the most serious public health problems worldwide. During the infection process, viruses may have substantial and intimate interactions with the commensal microbiota. A plethora of evidence suggests that the commensal microbiota regulates and is in turn regulated by invading viruses through diverse mechanisms, thereby having stimulatory or suppressive roles in viral infections. Furthermore, the integrity of the commensal microbiota can be disturbed by invading viruses, causing dysbiosis in the host and further influencing virus infectivity. In the present article, we discuss current insights into the regulation of viral infection by the commensal microbiota. We also draw attention to the disruption of microbiota homeostasis by several viruses.

Nasal commensal Staphylococcus epidermidis enhances interferon-λ-dependent immunity against influenza virus

BACKGROUND

Staphylococcus epidermidis is one of the most abundant colonizers of healthy human mucosa including that in the respiratory tract. As the respiratory microbiome has been linked to host immune responses, this study sought to determine the role of nasal mucosa-associated S. epidermidis in innate immune responses against the influenza A virus (IAV). S. epidermidis strains were isolated from nasal mucus samples of healthy individuals. The effects of these mucosa-derived commensal strains on interferon (IFN)-dependent innate immunity and IAV infection dynamics were tested in vitro using normal human nasal epithelial (NHNE) cells and human turbinate mucosa. The effects of S. epidermidis on antiviral immunity were also tested in vivo using an acute IAV infection mouse model.

RESULTS

Exposure of NHNE cells to nasal mucosa-derived S. epidermidis increased IFN-λ mRNA and secreted protein levels in the absence of viral stimulation. In the context of IAV infection, NHNE exposure to S. epidermidis prevented an increase in the viral burden, as revealed by IAV PA mRNA abundance, IAV nucleoprotein levels, and viral titers. S. epidermidis also enhanced transcription of IFN-stimulated genes independently of Toll-like receptor 2 and further induced IFN-λ production in IAV-infected cells by promoting phosphorylation of interferon regulatory factor 7. In a murine infection model, S. epidermidis prevented the spread of IAV to the lungs by stimulating IFN-λ innate immunity and suppressing IAV replication in the nasal mucosa.

CONCLUSION

The human nasal commensal S. epidermidis mediates front-line antiviral protection against IAV infection through modulation of IFN-λ-dependent innate immune mechanisms in the nasal mucosa, thereby demonstrating the role of host-bacterial commensalism in shaping human antiviral responses.

Cultivated Human Vaginal Microbiome Communities Impact Zika and Herpes Simplex Virus Replication in ex vivo Vaginal Mucosal Cultures

The human vaginal microbiome (VMB) is a complex bacterial community that interacts closely with vaginal epithelial cells (VECs) impacting the mucosal phenotype and its responses to pathogenic insults. The VMB and VEC relationship includes nutrient exchange and regulation of signaling molecules that controls numerous host functions and defends against invading pathogens. To better understand infection and replication of sexually transmitted viral pathogens in the human vaginal mucosa we used our ex vivo VEC multilayer culture system. We tested the hypothesis that selected VMB communities could be identified that alter the replication of sexually transmitted viruses consistent with reported clinical associations. Sterile VEC multilayer cultures or those colonized with VMB dominated by specific Lactobacillus spp., or VMB lacking lactobacilli, were infected with Zika virus, (ZIKV) a single stranded RNA virus, or Herpes Simplex Virus type 2 (HSV-2), a double stranded DNA virus. The virus was added to the apical surface of the cultured VEC multilayer to model transmission during vaginal intercourse. Viral replication was measured 48 h later by qPCR. The results indicated that VEC cultures colonized by VMB containing Staphylococcus spp., previously reported as inflammatory, significantly reduced the quantity of viral genomes produced by ZIKV. HSV-2 titers were decreased by nearly every VMB tested relative to the sterile control, although Lactobacillus spp.-dominated VMBs caused the greatest reduction in HSV-2 titer consistent with clinical observations. To explore the mechanism for reduced ZIKV titers, we investigated inflammation created by ZIKV infection, VMB colonization or pre-exposure to selected TLR agonists. Finally, expression levels of human beta defensins 1–3 were quantified in cultures infected by ZIKV and those colonized by VMBs that impacted ZIKV titers. Human beta defensins 1–3 produced by the VEC showed no association with ZIKV titers. The data presented expands the utility of this ex vivo model system providing controlled and reproducible methods to study the VMB impact on STIs and indicated an association between viral replication and specific bacterial species within the VMB.

Controlling the Growth of Staphylococcus epidermidis by Layer-By-Layer Encapsulation

Commensal skin bacteria such as Staphylococcus epidermidis are currently being considered as possible components in skin-care and skin-health products. However, considering the potentially adverse effects of commensal skin bacteria if left free to proliferate, it is crucial to develop methodologies that are capable of maintaining bacteria viability while controlling their proliferation. Here, we encapsulate S. epidermidis in shells of increasing thickness using layer-by-layer assembly, with either a pair of synthetic polyelectrolytes or a pair of oppositely charged polysaccharides. We study the viability of the cells and their delay of growth depending on the composition of the shell, its thickness, the charge of the last deposited layer, and the degree of aggregation of the bacteria which is varied using different coating procedures-among which is a new scalable process that easily leads to large amounts of nonaggregated bacteria. We demonstrate that the growth of bacteria is not controlled by the mechanical properties of the shell but by the bacteriostatic effect of the polyelectrolyte complex, which depends on the shell thickness and charge of its outmost layer, and involves the diffusion of unpaired amine sites through the shell. The lag times of growth are sufficient to prevent proliferation for daily topical applications.

The Effect of Topical Ocular Anesthetic Proparacaine on Conjunctival and Nasal Mucosal Flora in Dry Eye Disease Patients

The aim of this study was to investigate the effect of topically applied ocular anesthetic proparacaine on conjunctival and nasal bacterial mucosal flora in patients with dry eye disease. A Schirmer test was done with (group 1) and without (group 2) topical anesthetic proparacaine to 40 patients in each group. Conjunctival and nasal cultures were obtained before and 10 min after performing the Schirmer test. The bacterial culture results and the isolated bacteria were recorded in two groups. Patients' mean age was 62 years (70 female, 10 male). Before the application of topical anesthetic, 50 (62.5%) and 62 (77.5%) had positive conjunctival and nasal culture, respectively, with the most commonly isolated organism being coagulase-negative Staphylococcus in each group. In group 1 the conjunctival bacterial culture positivity rate decreased from 26 (65%) to six (15%) eyes (p < 0.001); however, this rate decreased slightly from 24 (60%) to 20 (50%) eyes in group 2 (p > 0.05). For the nasal cultures, the bacterial culture positivity rate decreased from 80% to 20% and from 75% to 65% in groups 1 (p < 0.001) and 2 (p > 0.05), respectively. Topical ocular anesthetic proparacaine has antibacterial activity in both conjunctival and nasal flora in patients with dry eye disease.

The effect of ocular lubricants containing benzalkonium chloride on nasal mucosal flora

PURPOSE

The effect of ocular artificial teardrop containing benzalkonium chloride (BAC) on nasal mucosa was investigated.

MATERIALS AND METHODS

There were two different treatment trial groups. Each dry eye syndrome (DES) patient received the ocular lubricant treatment four times a day in both groups (one group containing BAC, the other group was not). Moistened sterile cotton-tipped applicators were placed in both nostrils and were immediately cultured prior to ocular lubricant treatment and at the end of treatment trial. The bacterial culture-positivity rate, species of bacteria, and drug sensitivity were recorded in the two groups during pre-treatment and post-treatment.

RESULTS

There were 20 patients in each group with a mean age of 53.14 years (36 female, 4 male). At the beginning of the treatment trial, Staphylococcus epidermidis was the most frequently isolated organism from the nasal cavity accounting in 24/40 patients (60%). Of the 40 organisms isolated from the nares prior to treatment trial, 37 (92.5%) were sensitive to gentamycin. At the end of 1 month of treatment trial in patients who were treated with ocular lubricants containing BAC, none of the nasal cultures showed growth of any organisms. However, patients who were treated with ocular lubricants not containing BAC demonstrated persistent positive nasal cultures with the same species and the same antibiotic susceptibility profile at the end of the treatment trial period.

CONCLUSION

Topically applied ocular lubricants including BAC has an anti-bacterial activity on nasal flora in DES patients.

Manipulating the microbiome: evolution of a strategy to prevent S. aureus disease in children

Hospitalized infants have the highest rates of invasive Staphylococcus aureus disease of any population and infection control strategies such as decolonization have been insufficient. For decades, researchers began studying the microbiome in search of new prevention strategies. The resident microbiota was found to be closely associated with susceptibility and at times, resistance to S. aureus colonization. The evolution of nucleic acid based techniques has enhanced our understanding of the complex relationship between the nasal microbiota and S. aureus colonization. We review what is known about bacterial communities in the nasal cavity of infants and discuss how future microbiome studies may help identify novel interventions to protect high-risk infants from S. aureus disease.

Targeting and Enrichment of Viral Pathogen by Cell Membrane Cloaked Magnetic Nanoparticles for Enhanced Detection

Attachment to cellular surfaces is a major attribute among infectious pathogens for initiating disease pathogenesis. In viral infections, viruses exploit receptor-ligand interactions to latch onto cellular exterior prior to subsequent entry and invasion. In light of the selective binding affinity between viral pathogens and cells, nanoparticles cloaked in cellular membranes are herein employed for virus targeting. Using the influenza virus as a model, erythrocyte membrane cloaked nanoparticles are prepared and modified with magnetic functionalities (RBC-mNP) for virus targeting and isolation. To maximize targeting and isolation efficiency, density gradient centrifugation and nanoparticle tracking analysis were applied to minimize the presence of uncoated particles and membrane vesicles. The resulting nanoparticles possess a distinctive membrane corona, a sialylated surface, and form colloidally stable clusters with influenza viruses. Magnetic functionality is bestowed to the nanoparticles through encapsulation of superparamagnetic iron-oxide particles, which enable influenza virus enrichment via magnetic extraction. Viral samples enriched by the RBC-mNPs result in significantly enhanced virus detection by multiple virus quantification methods, including qRT-PCR, immunnochromatographic strip test, and cell-based titering assays. The demonstration of pathogen targeting and isolation by RBC-mNPs highlights a biologically inspired approach toward improved treatment and diagnosis against infectious disease threats. The work also sheds light on the efficient membrane cloaking mechanism that bestows nanoparticles with cell mimicking functionalities.

Multi-antigen avian influenza a (H7N9) virus-like particles: particulate characterizations and immunogenicity evaluation in murine and avian models

BACKGROUND

Human infection with avian influenza A virus (H7N9) was first reported in China in March 2013. Since then, hundreds of cases have been confirmed showing severe symptoms with a high mortality rate. The virus was transmitted from avian species to humans and has spread to many neighboring areas, raising serious concerns over its pandemic potential. Towards containing the disease, the goal of this study is to prepare a virus-like particle (VLP) that consists of hemagglutinin (HA), neuraminidase (NA) and matrix protein 1 (M1) derived from the human isolate A/Taiwan/S02076/2013(H7N9) for potential vaccine development.

RESULTS

Full length HA, NA, and M1 protein genes were cloned and expressed using a baculoviral expression system, and the VLPs were generated by co-infecting insect cells with three respective recombinant baculoviruses. Nanoparticle tracking analysis and transmission electron microscopy were applied to verify the VLPs' structure and antigenicity, and the multiplicity of infection of the recombinant baculoviruses was adjusted to achieve the highest hemagglutination activity. In animal experiments, BALB/c mice and specific-pathogen-free chickens receiving the VLP immunization showed elevated hemagglutination inhibition serum titer and antibodies against NA and M1 proteins. In addition, examination of cellular immunity showed the VLP-immunized mice and chickens exhibited an increased splenic antigen-specific cytokines production.

CONCLUSIONS

The H7N9 VLPs possess desirable immunogenicity in vivo and may serve as a candidate for vaccine development against avian influenza A (H7N9) infection.