Yeast species in the respiratory samples of COVID-19 patients; molecular tracking of Candida auris.

Introduction: Although the existence of Candida species in the respiratory tract is often considered commensal, it is crucial to recognize the significance of Candida colonization in immunocompromised or COVID-19 patients. The emergence of Candida auris as an emerging pathogen further emphasizes the importance of monitoring yeast infection/colonization, particularly in COVID-19 patients. Methods: In this study, respiratory samples mainly from COVID-19 patients, primarily those suspected of having a fungal infection, were cultured on Sabouraud dextrose agar plates and the yeast colonies were identified using a two-step multiplex PCR method. The samples suspected of C. auris underwent specific nested PCR followed by sequence analysis. Results: A total of 199 respiratory samples were collected from 73 women and 126 men, ranging in age from 1.6 to 88 years. Among the patients, 141 had COVID-19, 32 had cancer, 5 were hospitalized in ICU, 2 had chronic obstructive pulmonary disease)COPD(, and others were patients with combination diseases. From these samples, a total of 334 yeast strains were identified. C. albicans (n=132, 39.52%) was the most common species, followed by C. tropicalis (n=67, 20%), C. glabrata (n=56, 16.76%), C. krusei (n=18, 5.4%), C. parapsilosis (n=17, 5.08%), Saccharomyces cerevisiae (n=10, 3%), C. kefyr (n=9, 2.6%), C. dubliniensis (n=7, 2.1%), C. lusitaniae (n=5, 1.5%), C. auris (n=3, 0.9%), C. guilliermondii (n=2, 0.6%), C. rugosa (n=1, 0.3%), C. intermedia (n=1, 0.3%), and Trichosporon spp. (n=1, 0.3%). C. auris was detected in a patient in ICU and two COVID-19 patients. While its presence was confirmed through sequence analysis, our extensive efforts to isolate C. auris were unsuccessful. Conclusion: While C. albicans colonization remains prevalent, our study found no evidence of Candida lung infection. Since the role of Candida colonization in airway secretions remains ambiguous due to limited research, further studies are imperative to shed light on this matter.

Microbial and clinical epidemiology of invasive fungal rhinosinusitis in hospitalized COVID-19 patients, the divergent causative agents.

Since COVID-19 spread worldwide, invasive fungal rhinosinusitis (IFRS) has emerged in immunocompromised patients as a new clinical challenge. In this study, clinical specimens of 89 COVID-19 patients who presented clinical and radiological evidence suggestive of IFRS were examined by direct microscopy, histopathology, and culture, and the isolated colonies were identified through DNA sequence analysis. Fungal elements were microscopically observed in 84.27% of the patients. Males (53.9%) and patients over 40 (95.5%) were more commonly affected than others. Headache (94.4%) and retro-orbital pain (87.6%) were the most common symptoms, followed by ptosis/proptosis/eyelid swelling (52.8%), and 74 patients underwent surgery and debridement. The most common predisposing factors were steroid therapy (n = 83, 93.3%), diabetes mellitus (n = 63, 70.8%), and hypertension (n = 42, 47.2%). The culture was positive for 60.67% of the confirmed cases, and Mucorales were the most prevalent (48.14%) causative fungal agents. Different species of Aspergillus (29.63%) and Fusarium (3.7%) and a mix of two filamentous fungi (16.67%) were other causative agents. For 21 patients, no growth was seen in culture despite a positive result on microscopic examinations. In PCR-sequencing of 53 isolates, divergent fungal taxons, including 8 genera and 17 species, were identified as followed: Rhizopus oryzae (n = 22), Aspergillus flavus (n = 10), A. fumigatus (n = 4), A. niger (n = 3), R. microsporus (n = 2), Mucor circinelloides, Lichtheimia ramosa, Apophysomyces variabilis, A. tubingensis, A. alliaceus, A. nidulans, A. calidoustus, Fusarium fujikuroi/proliferatum, F. oxysporum, F. solani, Lomentospora prolificans, and Candida albicans (each n = 1). In conclusion, a diverse set of species involved in COVID-19-associated IFRS was observed in this study. Our data encourage specialist physicians to consider the possibility of involving various species in IFRS in immunocompromised and COVID-19 patients. In light of utilizing molecular identification approaches, the current knowledge of microbial epidemiology of invasive fungal infections, especially IFRS, may change dramatically.

Invasive fungal rhinosinusitis (IFRS) may infect people with diabetes, cancer, or COVID-19. In this study, various types of fungi were identified from COVID-19-associated-IFRS, encouraging physicians to consider specific treatments.

Deep-AFPpred: identifying novel antifungal peptides using pretrained embeddings from seq2vec with 1DCNN-BiLSTM.

Fungal infections or mycosis cause a wide range of diseases in humans and animals. The incidences of community acquired; nosocomial fungal infections have increased dramatically after the emergence of COVID-19 pandemic. The increase in number of patients with immunodeficiency / immunosuppression related diseases, resistance to existing antifungal compounds and availability of limited therapeutic options has triggered the search for alternative antifungal molecules. In this direction, antifungal peptides (AFPs) have received a lot of interest as an alternative to currently available antifungal drugs. Although the AFPs are produced by diverse population of living organisms, identifying effective AFPs from natural sources is time-consuming and expensive. Therefore, there is a need to develop a robust in silico model capable of identifying novel AFPs in protein sequences. In this paper, we propose Deep-AFPpred, a deep learning classifier that can identify AFPs in protein sequences. We developed Deep-AFPpred using the concept of transfer learning with 1DCNN-BiLSTM deep learning algorithm. The findings reveal that Deep-AFPpred beats other state-of-the-art AFP classifiers by a wide margin and achieved approximately 96% and 94% precision on validation and test data, respectively. Based on the proposed approach, an online prediction server is created and made publicly available at https://afppred.anvil.app/. Using this server, one can identify novel AFPs in protein sequences and the results are provided as a report that includes predicted peptides, their physicochemical properties and motifs. By utilizing this model, we identified AFPs in different proteins, which can be chemically synthesized in lab and experimentally validated for their antifungal activity.

Circulating acetylated polyamines correlate with Covid-19 severity in cancer patients.

Cancer patients are particularly susceptible to the development of severe Covid-19, prompting us to investigate the serum metabolome of 204 cancer patients enrolled in the ONCOVID trial. We previously described that the immunosuppressive tryptophan/kynurenine metabolite anthranilic acid correlates with poor prognosis in non-cancer patients. In cancer patients, we observed an elevation of anthranilic acid at baseline (without Covid-19 diagnosis) and no further increase with mild or severe Covid-19. We found that, in cancer patients, Covid-19 severity was associated with the depletion of two bacterial metabolites, indole-3-proprionate and 3-phenylproprionate, that both positively correlated with the levels of several inflammatory cytokines. Most importantly, we observed that the levels of acetylated polyamines (in particular N1-acetylspermidine, N1,N8-diacetylspermidine and N1,N12-diacetylspermine), alone or in aggregate, were elevated in severe Covid-19 cancer patients requiring hospitalization as compared to uninfected cancer patients or cancer patients with mild Covid-19. N1-acetylspermidine and N1,N8-diacetylspermidine were also increased in patients exhibiting prolonged viral shedding (>40 days). An abundant literature indicates that such acetylated polyamines increase in the serum from patients with cancer, cardiovascular disease or neurodegeneration, associated with poor prognosis. Our present work supports the contention that acetylated polyamines are associated with severe Covid-19, both in the general population and in patients with malignant disease. Severe Covid-19 is characterized by a specific metabolomic signature suggestive of the overactivation of spermine/spermidine N1-acetyl transferase-1 (SAT1), which catalyzes the first step of polyamine catabolism.

Coinfection in SARS-CoV-2 Infected Children Patients.

INTRODUCTION: The aim of this study is to determine the coinfections with other respiratory pathogens in SARS-CoV-2 infected children patients in a pediatric unit in Istanbul. METHODOLOGY: This retrospective descriptive study was conducted in a 1000-bedded tertiary education and research hospital in Istanbul. All children hospitalized with the diagnosis of SARS-CoV-2 infection had been investigated for respiratory agents in nasopharyngeal secretions. Laboratory confirmation of SARS-CoV-2 and the other respiratory pathogens were performed using reverse transcriptase-polymerase chain reaction (RT-PCR). RESULTS: A total of 209 hospitalized children with suspected SARS-CoV-2 infection between March 2020-May 2020 were enrolled in this study. Among 209 children, 93 (44.5%) were RT-PCR positive for SARS-CoV-2 infection, and 116 (55.5%) were RT-PCR negative. The most common clinical symptoms in all children with SARS-CoV-2 infection were fever (68.8%) and cough (57.0%). The other clinical symptoms in decreasing rates were headache (10.8%), myalgia (5.4%), sore throat (3.2%), shortness of breath (3.2%), diarrhea (2.2%) and abdominal pain in one child. In 7 (7.5%) patients with SARS-CoV-2 infection, coinfection was detected. Two were with rhinovirus/enterovirus, two were with Coronavirus NL63, one was with adenovirus, and one was with Mycoplasma pneumoniae. In one patient, two additional respiratory agents (rhinovirus/enterovirus and adenovirus) were detected. There was a significantly longer hospital stay in patients with coinfection (p = 0.028). CONCLUSIONS: Although the coinfection rate was low in SARS-CoV-2 infected patients in our study, we found coinfection as a risk factor for length of hospital stay in the coinfected patient group.

Identification of Lung and Blood Microbiota Implicated in COVID-19 Prognosis.

The implications of the microbiome on Coronavirus disease 2019 (COVID-19) prognosis has not been thoroughly studied. In this study we aimed to characterize the lung and blood microbiome and their implication on COVID-19 prognosis through analysis of peripheral blood mononuclear cell (PBMC) samples, lung biopsy samples, and bronchoalveolar lavage fluid (BALF) samples. In all three tissue types, we found panels of microbes differentially abundant between COVID-19 and normal samples correlated to immune dysregulation and upregulation of inflammatory pathways, including key cytokine pathways such as interleukin (IL)-2, 3, 5-10 and 23 signaling pathways and downregulation of anti-inflammatory pathways including IL-4 signaling. In the PBMC samples, six microbes were correlated with worse COVID-19 severity, and one microbe was correlated with improved COVID-19 severity. Collectively, our findings contribute to the understanding of the human microbiome and suggest interplay between our identified microbes and key inflammatory pathways which may be leveraged in the development of immune therapies for treating COVID-19 patients.

Probiotics, Photobiomodulation, and Disease Management: Controversies and Challenges.

In recent decades, researchers around the world have been studying intensively how micro-organisms that are present inside living organisms could affect the main processes of life, namely health and pathological conditions of mind or body. They discovered a relationship between the whole microbial colonization and the initiation and development of different medical disorders. Besides already known probiotics, novel products such as postbiotics and paraprobiotics have been developed in recent years to create new non-viable micro-organisms or bacterial-free extracts, which can provide benefits to the host with additional bioactivity to probiotics, but without the risk of side effects. The best alternatives in the use of probiotics and postbiotics to maintain the health of the intestinal microbiota and to prevent the attachment of pathogens to children and adults are highlighted and discussed as controversies and challenges. Updated knowledge of the molecular and cellular mechanisms involved in the balance between microbiota and immune system for the introspection on the gut-lung-brain axis could reveal the latest benefits and perspectives of applied photobiomics for health. Multiple interconditioning between photobiomodulation (PBM), probiotics, and the human microbiota, their effects on the human body, and their implications for the management of viral infectious diseases is essential. Coupled complex PBM and probiotic interventions can control the microbiome, improve the activity of the immune system, and save the lives of people with immune imbalances. There is an urgent need to seek and develop innovative treatments to successfully interact with the microbiota and the human immune system in the coronavirus crisis. In the near future, photobiomics and metabolomics should be applied innovatively in the SARS-CoV-2 crisis (to study and design new therapies for COVID-19 immediately), to discover how bacteria can help us through adequate energy biostimulation to combat this pandemic, so that we can find the key to the hidden code of communication between RNA viruses, bacteria, and our body.

Case report: histopathology and molecular pathology analysis on enteric tissue of a COVID-19 patient.

AIMS: Patients with COVID-19 can also have enteric symptoms. Here we analyzed the histopathology of intestinal detachment tissue from a patient with COVID-19. METHODS: The enteric tissue was examined by hematoxylin & eosin stain, PAS (Periodic acid-Schiff) staining, Gram staining, Ziehl-Neelsen stain and Grocott's Methenamine Silver (GMS) Stain. The distribution of CD3, CD4, CK20 and CD68, cytomegalovirus (CMV) and Herpes Simplex Virus (HSV) antigen were determined by immunohistochemistry. In situ hybridization (ISH) of SARS-CoV-2 and Epstein-Barr virus-encoded small RNA (EBER) were also performed. RESULTS: We observed mucosal epithelium shedding, intestinal mucosal erosion, focal inflammatory necrosis with hemorrhage, massive neutrophil infiltration, macrophage proliferation accompanied by minor lymphocyte infiltration. Fungal spores and gram positive cocci but not mycobacteria tuberculosis were identified. Immunohistochemistry staining showed abundant CD68+ macrophages but few lymphocytes infiltration. HSV, CMV and EBV were negative. ISH of SARS-CoV-2 RNA showed positive signal which mostly overlapped with CD68 positivity. CONCLUSIONS: The in situ detection of SARS-CoV-2 RNA in intestinal macrophages implicates a possible route for gastrointestinal infection. Further study is needed to further characterize the susceptibility of enteric cells to SARS-CoV-2 infection.

Extensive microbiological respiratory tract specimen characterization in critically ill COVID-19 patients.

Microbial co-infections may contribute to the pulmonary deterioration in COVID-19 patients needing intensive care treatment. The present study portrays the extent of co-infections in COVID-19 ICU patients. Conventional culture, molecular detections for atypical aetiologies, QiaStat-Dx® respiratory panel V2 detecting 21 respiratory pathogens and ribosomal DNA genes 16S/18S amplicon-based microbiome analyses were performed on respiratory samples from 34 COVID-19 patients admitted to the ICU. Potential pathogens were detected in seven patients (21%) by culturing, in four patients (12%) by microbiome analysis and in one patient (3%) by respiratory panel. Among 20 patients receiving antibiotics prior to ICU admission, fungi (3 Candida albicans, 1 C. tropicalis, 1 C. dubliniensis) were cultured in 5 (15%) endotracheal aspirates. Among 14 patients who were antibiotic-naive at ICU admission, two patients (6%) had bacterial respiratory pathogens (Staphylococcus aureus, Streptococcus pseudopneumoniae) cultured in their endotracheal aspirates. Microbiome analysis recognized four potential respiratory pathogens (3 Haemophilus influenza, 1 Fusobacterium necrophorum) isolated in samples from four other patients (12%). QiaStat-Dx® respiratory panel V2 detected adenovirus in one patient (3%). The prevalence of pulmonary microbial co-infections is modest among COVID-19 patients upon admission to ICU. Microbiome analysis complements conventional microbial diagnostics in characterization of respiratory co-infections.

Virtualized clinical studies to assess the natural history and impact of gut microbiome modulation in non-hospitalized patients with mild to moderate COVID-19 a randomized, open-label, prospective study with a parallel group study evaluating the physiologic effects of KB109 on gut microbiota structure and function: a structured summary of a study protocol for a randomized controlled study.

OBJECTIVES: These 2 parallel studies (K031 and K032) aim to evaluate the safety of KB109 in addition to supportive self-care (SSC) compared with SSC alone in outpatients with mild to moderate coronavirus disease 2019 (COVID-19). KB109 is a novel synthetic glycan that was formulated to modulate the gut microbiome composition and metabolic output in order to increase beneficial short-chain fatty acid (SCFA) production in the gut. The K031 study is designed to evaluate the safety of KB109 and characterize its impact on the natural progression of COVID-19 in patients with mild to moderate disease. The K032 study is evaluating the effect of KB109 on the gut microbiota structure and function in this same patient population. Additionally, both studies are evaluating measures of health care utilization, quality of life (QOL), laboratory indices, biomarkers of inflammation, and serological measures of immunity in patients who received SSC alone or with KB109. Noteworthy aspects of these outpatient studies include study design measures aimed at limiting in-person interactions to minimize the risk of infection spread, such as use of online diaries, telemedicine, and at-home sample collection. STUDY DESIGN: K031 and K032 are randomized, controlled, open-label, clinical food studies. PARTICIPANTS: Inclusion Criteria: • Adults ≥18 years of age • Patients willing and able to give informed consent • Screening/randomization telemedicine visit within 2 days of testing positive test for COVID-19 ○ In K031 study, symptomatic patients at COVID-19 testing must report new or worsening symptoms at baseline that have not been present for more than 5 days ▪ Cardinal COVID-19 symptoms include fever, chills/repeated shaking with chills, cough, shortness of breath, headache, muscle pain, anosmia/ageusia, and sore throat. The 5 additional symptoms include gastrointestinal (GI) disturbance/symptoms (other than diarrhea), diarrhea, fatigue, nasal congestion, and chest tightness ○ In K031, at COVID-19 testing, pre-symptomatic patients must report new cardinal COVID-19 symptoms within 7 days of a positive test and they must be screened and randomized within 5 days of developing symptoms • Mild to moderate COVID-19 and self-reported outpatient management ○ In K032, mild to moderate COVID-19 was defined as having the following symptoms for no more than 72 hours before COVID-19 testing: a self- reported fever or cough (new or exacerbated) or presence of at least 2 of the following: anosmia, sore throat, or nasal congestion • Ability to adhere to the study visit schedule and other protocol requirements • Consistent internet or cell phone access with a data plan and access to a smartphone, tablet, or computer • The K031 and K032 studies are currently being conducted at 17 clinical institutions throughout the United States. EXCLUSION CRITERIA: • In the primary investigator's (PI) judgement, patients likely to require hospitalization for COVID-19 • Patients who are hospitalized for in-patient treatment or currently being evaluated for potential hospitalization at the time of informed consent for conditions other than COVID-19 • History of chronic lung disease with chronic hypoxia • History of documented cirrhosis or end-stage liver disease • Ongoing requirement for oxygen therapy • Shortness of breath in resting position • Diagnosis of sleep apnea requiring bilevel positive airway pressure (BIPAP)/continuous positive airway pressure (CPAP) • Female patients who are pregnant, trying to become pregnant, or lactating • Concurrent use of immunomodulatory agent within 12 months; systemic antibiotics, antifungals, or antivirals for treatment of active infection within 28 days; systemic immunosuppressive therapy within 3 months; or drugs or other compounds that modulate GI motility (eg, stool softeners, laxatives, or fiber supplements) taken currently, or within 7 days. Antacid (histamine 2 blockers and proton pump inhibitors) and antidiarrheal agents are not prohibited • History of GI surgery (6 months prior to randomization), including but not limited to bariatric surgery and bowel resection, or history of, or active GI disease(s) that may affect assessment of tolerability, including but not limited to inflammatory bowel disease, irritable bowel syndrome, autoimmune disease, or GI malignancy • Participation in an interventional clinical trial or use of any investigational agent within 30 days before randomization • Clinically significant or uncontrolled concomitant medical condition that would put the patient at risk or jeopardize the objectives of the study in the opinion of the PI • In the opinion of the PI, patient unlikely for any reason to be able to comply with study procedures • Contraindications, sensitivities, or known allergy to the use of the study product or its components INTERVENTION AND COMPARATOR: Patients will be randomized (1,1) to receive either SSC and KB109 or SSC alone. During SSC, patients should follow the steps as instructed by their healthcare provider to care for themselves and protect other people in the home and community from potentially contracting COVID-19. Management of COVID-19-related symptoms with over-the-counter cough, cold, and anti-pyretic medications by patients is permitted in accordance with the medications' respective drug facts label or as instructed by the patient's healthcare provider. Following randomization, patients assigned to receive KB109 and SSC will receive a Kaleido Biosciences, Inc at-home study kit including a thermometer, pulse oximeter, and KB109. During the Intake Period (days 1-14), KB109 will be reconstituted in water by the patient and consumed by the patient twice daily (at least 8 hours apart), following an up-titration dosing schedule: Days 1 to 2: 9 g twice daily for a total daily dose of 18 g Days 3 to 4: 18 g twice daily for a total daily dose of 36 g Days 5 to 14: 36 g twice daily for a total daily dose of 72 g During the intake period, patients will record their daily COVID-19-related symptoms, selected COVID-19 signs (as self-measured using the provided thermometer and pulse oximeter), responses to questions related to QOL measures, health care use measures, and concomitant medications taken in the previous 24 hours. Wellness visits by telephone will be conducted between days 1 and 14 to follow up on patient's health status and to ascertain compliance with KB109 and completion of questions. On day 14, all patients will undergo a telemedicine visit where the following will be conducted: abbreviated physical examination, assessment of safety and other protocol-specified measures of health, and an evaluation of whether follow-up treatment is recommended owing to a progression of COVID-19 symptoms. If feasible, blood samples for clinical chemistries, biomarkers and serological measure of immunity, and nasal/oropharyngeal swabs for quantitative viral load assessments will be collected. Beginning on day 15, patients in both groups will enter the follow-up period (days 15-35) where COVID-19 signs, symptoms, and health care use indices will be collected. Wellness visits by telephone will be conducted on days 21, 28, and 35 to follow-up on the patient's health status. On day 35, all patients will undergo a telemedicine visit where the same information as the day 14 telemedicine visit will be collected, including any blood samples. MAIN OUTCOMES: The primary outcome for the K031 and K032 studies is to evaluate the safety of KB109 in addition to SSC compared with SSC alone in outpatients with mild to moderate COVID-19 by assessing the number of patients experiencing KB109-related treatment-emergent adverse events (TEAEs) during the study. K031 will also evaluate duration of symptoms among outpatients with mild to moderate COVID-19. This will be as an assessment made during the intake and/or follow-up periods of the following: • Time to resolution of the 13 overall and the 8 cardinal COVID-19-related symptoms from day 1 until the day at which the composite score of the 13 overall and 8 cardinal COVID-19-related symptoms becomes 0 or 1 and remains at 0 or 1 for the rest of the intake period and for the follow-up period • Proportion of patients with a reduction from baseline in each of the 13 overall COVID-19-related symptoms • Proportion of patients in whom symptoms (present at baseline) become absent for each of the 13 overall COVID-19-related symptoms • Change from baseline in the overall composite score of the 13 overall COVID-19-related symptoms and the 8 cardinal COVID-19-related symptoms • Time to resolution of fever (defined as from day 1 until the day at which a patient's daily maximum temperature achieves and remains below 100.4°F without antipyretic medication) • Proportion of patients with oxygen saturation <95% and <98% on days 14 and 35 • Measures collected from the health care provider wellness visits • Proportion of patients experiencing hospital admissions (all cause and COVID-19-related) • Health care use K032 will evaluate the effect of KB109 in addition to SSC compared with SSC alone on the gut microbiota structure and function in outpatients with mild to moderate COVID-19. Before days 1, 14, and 35, microbiota structure (eg, magnitude of change in gut microbiome structure, composition of gut microbiome) will be analysed by methods such as nucleic acid sequencing and gut microbiome function will be analysed via levels of stool inflammatory biomarkers (eg, lipocalin) and gut microbiome metabolites (eg, SCFA). The health of outpatients with mild to moderate COVID-19 will be evaluated during the intake and follow- up periods by: measures of QOL; measures collected from the healthcare provider wellness visits; the proportion of patients experiencing hospital admissions; health care use, the proportions of patients with oxygen saturation <95% and <98%, and the proportionof patients with temperature below 100.4 °F without an anti-pyretic medication. Potential exploratory outcome measures may include: changes from baseline (day 1) in laboratory measures, specific biomarkers of infection, serology, inflammation (eg, D-dimer, lipocalin, cytokines, IgM/IgG sero-conversion, and neutralization assays), and viral load in outpatients with mild to moderate COVID-19 in the presence and absence of KB109. RANDOMISATION: All patients deemed eligible for the studies will be randomized in a 1:1 ratio to KB109 in addition to SSC or SSC alone group using an interactive response technology system. Randomization will be stratified by study site/center, age groups (≥18-<45 years, ≥45-<65 years, ≥65 years), and comorbidity status (yes, no). BLINDING (MASKING): These studies are open-label; therefore, no blinding is necessary. NUMBERS TO BE RANDOMISED (SAMPLE SIZE): K031 will enroll approximately 350 to 400 (175-200 patients per group) whereas K032 will enroll approximately 50 patients (25 per group). STUDY STATUS: K031 protocol version 4, December 9, 2020; recruitment started in August, 2020, and the study is estimated to be completed in March 2021. This study is active and enrollment was completed in January, 2021. K032 protocol version 2, June 30, 2020; recruitment is estimated to start in July, 2020. This study is recruiting and the study is estimated to be completed in March 2021. STUDY REGISTRATION: K031 is registered with the US National Library of Medicine, Identifier NCT04414124 as of June 4, 2020. K032 is registered with the US National Library of Medicine, Identifier NCT04486482 as of July 24, 2020. FULL PROTOCOL: The full protocols are attached as additional files (Additional files 1 and 2), accessible from the ClinicalTrials.gov website. In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this letter serves as a summary of the key elements of the full protocols. The study protocols have been reported in accordance with the Standard Protocol Items: Recommendations for Clinical Interventional Trials (SPIRIT) guidelines (Additional files 3 and 4).

The microbiota-mediated dietary and nutritional interventions for COVID-19.

Worldwide, scientists are looking for specific treatment for COVID-19. Apart from the antiviral approach, the interventions to support healthy immune responses to the virus are feasible through diet, nutrition, and lifestyle approaches. This narrative review explores the recent studies on dietary, nutritional, and lifestyle interventions that influence the microbiota-mediated immunomodulatory effects against viral infections. Cumulative studies reported that the airway microbiota and SARS-CoV-2 leverage each other and determine the pathogen-microbiota-host responses. Cigarette smoking can disrupt microbiota abundance. The composition and diversification of intestinal microbiota influence the airway microbiota and the innate and adaptive immunity, which require supports from the balance of macro- and micronutrients from the diet. Colorful vegetables supplied fermentable prebiotics and anti-inflammatory, antioxidant phytonutrients. Fermented foods and beverages support intestinal microbiota. In sensitive individuals, the avoidance of the high immunoreactive food antigens contributes to antiviral immunity. This review suggests associations between airway and intestinal microbiota, antiviral host immunity, and the influences of dietary, nutritional, and lifestyle interventions to prevent the clinical course toward severe COVID-19.

Peptide substrate screening for the diagnosis of SARS-CoV-2 using fluorescence resonance energy transfer (FRET) assay.

The novel corona (SARS-CoV-2) virus causes a global pandemic, which motivates researchers to develop reliable and effective methods for screening and detection of SARS-CoV-2. Though there are several methods available for the diagnosis of SARS-CoV-2 such as RT-PCR and ELSIA, nevertheless, these methods are time-consuming and may not apply at the point of care. In this study, we have developed a specific, sensitive, quantitative and fast detection method for SARS-CoV-2 by fluorescence resonance energy transfer (FRET) assay. The total extracellular protease proteolytic activity from the virus has been used as the biomarker. The specific peptide sequences from the library of 115 dipeptides were identified via changes in the fluorescence signal. The fluorogenic dipeptide substrates have the fluorophore and a quencher at the N- and the C- terminals, respectively. When the protease hydrolyzes the peptide bond between the two specific amino acids, it leads to a significant increase in the fluorescence signals. The specific fluorogenic peptide (H-d) produces a high fluorescence signal. A calibration plot was obtained from the changes in the fluorescence intensity against the different concentrations of the viral protease. The lowest limit of detection of this method was 9.7 ± 3 pfu/mL. The cross-reactivity of the SARS-CoV-2-specific peptide was tested against the MERS-CoV which does not affect the fluorescence signal. A significant change in the fluorescence signal with patient samples indicates that this FRET-based assay might be applied for the diagnosis of SARS-CoV-2 patients. Graphical abstract.

Resolvin D1 and D2 reduce SARS-CoV-2-induced inflammatory responses in cystic fibrosis macrophages.

An excessive, non-resolving inflammatory response underlies severe COVID-19 that may have fatal outcomes. Therefore, the investigation of endogenous pathways leading to resolution of inflammation is of interest to uncover strategies for mitigating inflammation in people with SARS-CoV-2 infection. This becomes particularly urgent in individuals with preexisting pathologies characterized by chronic respiratory inflammation and prone to bacterial infection, such as cystic fibrosis (CF). Here, we analyzed the immune responses to SARS-CoV-2 virion spike 1 glycoprotein (S1) of macrophages (MΦ) from volunteers with and without CF and tested the efficacy of resolvins (Rv) D1 and D2 in regulating the inflammatory and antimicrobial functions of MΦ exposed to S1. S1 significantly increased chemokine release, including interleukin (IL)-8, in CF and non-CF MΦ, while it enhanced IL-6 and tumor necrosis factor (TNF)-α in non-CF MΦ, but not in CF cells. S1 also triggered the biosynthesis of RvD1 and modulated microRNAs miR-16, miR-29a, and miR-103, known to control the inflammatory responses. RvD1 and RvD2 treatment abated S1-induced inflammatory responses in CF and non-CF MΦ, significantly reducing the release of select chemokines and cytokines including IL-8 and TNF-α. RvD1 and RvD2 both restored the expression of miR-16 and miR-29a, while selectively increasing miR-223 and miR-125a, which are involved in NF-κB activation and MΦ inflammatory polarization. During Pseudomonas aeruginosa infection, S1 stimulated the MΦ phagocytic activity that was further enhanced by RvD1 and RvD2. These results provide a map of molecular responses to SARS-CoV-2 in MΦ, key determinants of COVID-19-related inflammation, unveiling some peculiarity in the response of cells from individuals with CF. They also demonstrate beneficial, regulatory actions of RvD1 and RvD2 on SARS-CoV-2-induced inflammation.

Epidemiology and Mycology of Candidaemia in non-oncological medical intensive care unit patients in a tertiary center in the United States: Overall analysis and comparison between non-COVID-19 and COVID-19 cases.

The epidemiology and mycology of invasive candidiasis in the ICU is well-described in certain types of critically ill patients but not in others. One population that has been scarcely studied is non-neutropenic patients admitted specifically to medical ICUs. Even less is known about the broader category of medical ICU patients without active oncological disease. This group constitutes a very large share of the patients requiring critical care across the globe, especially in the era of the SARS-CoV-2 pandemic. We analysed medical ICU candidaemia episodes that occurred in non-oncological patients in our tertiary academic centre in the United States from May 2014 to October 2020 to determine the incidence and species distribution of the associated isolates. We then separately considered non-COVID-19 and COVID-19 cases and compared their characteristics. In the non-COVID-19 group, there were 38 cases for an incidence of 1.1% and rate of 11/1000 admissions. In the COVID-19 group, there were 12 cases for an incidence of 5.1% and rate of 51/1000 admissions. In the entire sample, as well as separately in the non-COVID-19 and COVID-19 groups,Candida albicans accounted for a minority of isolates. Compared to non-COVID-19 patients with candidaemia, COVID-19 patients had lower ICU admission SOFA score but longer ICU length of stay and central venous catheter dwell time at candidaemia detection. This study provides valuable insight into the incidence and species distribution of candidaemia cases occurring in non-oncological critically ill patients and identifies informative differences between non-COVID-19 and COVID-19 patients.

Limited Utility of Procalcitonin in Identifying Community-Associated Bacterial Infections in Patients Presenting with Coronavirus Disease 2019.

The role of procalcitonin in identifying community-associated bacterial infections among patients with coronavirus disease 2019 is not yet established. In 2,443 patients of whom 148 had bacterial coinfections, mean procalcitonin levels were significantly higher with any bacterial infection (13.16 ± 51.19 ng/ml; P = 0.0091) and with bacteremia (34.25 ± 85.01 ng/ml; P = 0.0125) than without infection (2.00 ± 15.26 ng/ml). Procalcitonin (cutoff, 0.25 or 0.50 ng/ml) did not reliably identify bacterial coinfections but may be useful in excluding bacterial infection.

Applicability of MuLBSTA scoring system as diagnostic and prognostic role in early warning of severe COVID-19.

To explore the applicability of MuLBSTA Score in COVID-19 patients, a retrospective analysis was performed on 330 cases of COVID-19 patients in Southeast Hospital of Xiaogan City, Hubei Province. The clinical characteristics of COVID-19 patients were described and multilobe infiltrate in CT, bacterial infection, lymphocyte count, smoke in history, history of hypertension, and age distribution in the population of mild and severe patients were analyzed. All included patients were scored according to the MuLBSTA early warning scoring system and its efficacy in early warning of severe symptoms was analyzed. CT feature of infiltration changes on multiple lobes, the absolute value of lymphocyte count of less than 0.8 × 109, accompanied by bacterial infection, history of smoking, history of hypertension, and an age of greater than 60 years old were all statistically significant factors in patients with severe COVID-19. ROC curve analysis indicated that the sensitivity, specificity and accuracy of the early warning system were 0.651, 0.954 and 0.93, respectively. The MuLBSTA Score has a good early warning effect on severe COVID-19 patients.

Association between different screening strategies for SARS-CoV-2 and deaths and severe disease in Italy.

BACKGROUND: The WHO recommends testing any suspected person with Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2), in order to limit the spread of the epidemic. In Italy, some Regions opted for extensive testing, whereas others limited tests to selected subjects. To assess the influence of different strategies, we examined the incidence of death and severe cases in Italy. METHODS: Data on new cases of SARS-CoV-2, number of tests, deaths and admissions to Intensive Care Units (ICU) were retrieved in each Italian Region, from 24 February to 18 March 2020. As an index of different screening strategies, the number of tests/positive test results (P/T) ratio as of 7 March 2020, was considered. The cumulative number of deaths and of new severe cases, between March 23 and 25 was recorded. The association of those two outcomes with the number of P/T ratio was assessed using linear regression models. RESULTS: In the interval between March 23 and 25, recorded deaths (*million inhabitants) were 14 (3-54), whereas severe cases were 31 (10-112). Both the number of deaths and that of severe cases showed a significant correlation (R2 .57 and .41, with P < .01) with the P/T ratio. Deaths and severe cases were associated with higher mean personal income and lower density of General Practioners (GPs). The association of P/T with severe cases and deaths retained statistical significance after adjusting for mean personal income (R2 .30 and .41, respectively; both P = .04) and GPs density (R2 .21 and .19, respectively; both P = .03). CONCLUSIONS: A more aggressive screening strategy for SARS-Cov-2, was associated with lower rates of death and severe disease in Regions of Italy.