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1.
JMIR Form Res ; 6(11): e41914, 2022 Nov 04.
Article in English | MEDLINE | ID: covidwho-2099006

ABSTRACT

BACKGROUND: Despite continuing efforts to improve the inclusion of underserved groups in clinical research, gaps in diversity remain. Participation of special populations is especially important when facing problems of unprecedented complexity such as the COVID-19 pandemic. A better understanding of factors associated with the immune response in diverse populations would advance future preventive and curative approaches. OBJECTIVE: The objective of this study was to investigate the factors potentially responsible for adverse events following COVID-19 immunization. The study population included adults from rural areas, transitional countries, and those with medically understudied conditions, across a broad age range. METHODS: The study evolved from peer support networks developed during the COVID-19 pandemic. Participants were recruited digitally through online neighborhood and health communities. Some of the participants volunteered as study investigators assisting with offline recruitment and safety monitoring. Individuals who consented to participate were asked to share their vaccination experiences either using constantly evolving web-based surveys or via one-on-one communication. Inferential statistical analysis to estimate differences between study groups was performed using parametric and nonparametric tests. RESULTS: Of 1430 participants who shared their vaccination experiences, 648 had outcome measures at their 1.5-year follow-up. Significant differences were found between age groups, types of vaccine adverse events (VAEs), incidences of breakthrough infections, and health conditions linked to the microbiome. Pairwise comparisons showed that VAEs interfering with daily activities were significantly higher in both younger (18-59 years) and older age groups (80-100 years, P<.001) than in the 60-79-year age group. Short-term VAEs were associated with lower incidence of breakthrough COVID-19 infections relative to those who reported either minimal or long-term adverse events (P<.001). A genetic origin was suggested for some adverse reactions. CONCLUSIONS: The findings of this study demonstrate that vaccine adverse reactions in older individuals are being overlooked, and the incidence of VAEs impairing immunity may be higher than previously perceived. Better preventive measures are needed for all those at risk for life-threatening and long-term adverse events due to vaccination. Supportive community-based studies focusing on these populations could add important data to the current body of knowledge. Further and more comprehensive studies should follow. TRIAL REGISTRATION: ClinicalTrials.gov NCT04832932; https://clinicaltrials.gov/ct2/show/NCT04832932. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.1101/2021.06.28.21256779.

2.
Adv Sci (Weinh) ; : e2203707, 2022 Oct 26.
Article in English | MEDLINE | ID: covidwho-2084977

ABSTRACT

The emergence of the coronavirus disease 2019 pandemic has dramatically increased the global prevalence of depression. Unfortunately, antidepressant drugs benefit only a small minority of patients. Thus, there is an urgent need to develop new interventions. Accumulating evidence supports a causal relationship between gut microbiota dysbiosis and depression. To advance microbiota-based diagnostics and therapeutics of depression, a comprehensive overview of microbial alterations in depression is presented to identify effector microbial biomarkers. This procedure generated 215 bacterial taxa from humans and 312 from animal models. Compared to controls, depression shows significant differences in ß-diversity, but no changes in microbial richness and diversity. Additionally, species-specific microbial changes are identified like increased Eggerthella in humans and decreased Acetatifactor in rodent models. Moreover, a disrupted microbiome balance and functional changes, characterized by an enrichment of pro-inflammatory bacteria (e.g., Desulfovibrio and Escherichia/Shigella) and depletion of anti-inflammatory butyrate-producing bacteria (e.g., Bifidobacterium and Faecalibacterium) are consistently shared across species. Confounding effects of geographical region, depression type, and intestinal segments are also investigated. Ultimately, a total of 178 species and subspecies probiotics are identified to alleviate the depressive phenotypes. Current findings provide a foundation for developing microbiota-based diagnostics and therapeutics and advancing microbiota-oriented precision medicine for depression.

3.
Front Pediatr ; 10: 941800, 2022.
Article in English | MEDLINE | ID: covidwho-2080210

ABSTRACT

Gestational diabetes mellitus (GDM), or any degree of glucose intolerance recognized for the first time during pregnancy, is one of the diseases that most frequently aggravates the course of gestation. Missed or late diagnosis and inadequate treatment are associated with high maternal and fetal morbidity, with possible short- and long-term repercussions. Estimates on the prevalence of GDM are alarming and increasing by about 30% in the last 10-20 years. In addition, there is the negative influence of the SARS-CoV-2 emergency on the glycemic control of pregnant women, making the matter increasingly topical. To date, knowledge on the metabolic maturation of newborns is still incomplete. However, in light of the considerable progress of the theory of "developmental origins of health and disease," the relevant role of the intrauterine environment cannot be overlooked. In fact, due to the high plasticity of the early stages of development, some detrimental metabolic alterations during fetal growth, including maternal hyperglycemia, are associated with a higher incidence of chronic diseases in adult life. In this context, metabolomic analysis which allows to obtain a detailed phenotypic portrait through the dynamic detection of all metabolites in cells, tissues and different biological fluids could be very useful for the early diagnosis and prevention of complications. Indeed, if the diagnostic timing is optimized through the identification of specific metabolites, the detailed understanding of the altered metabolic pathway could also allow better management and more careful monitoring, also from a nutritional profile, of the more fragile children. In this context, a further contribution derives from the analysis of the intestinal microbiota, the main responsible for the fecal metabolome, given its alteration in pregnancies complicated by GDM and the possibility of transmission to offspring. The purpose of this review is to analyze the available data regarding the alterations in the metabolomic profile and microbiota of the offspring of mothers with GDM in order to highlight future prospects for reducing GDM-related complications in children of mothers affected by this disorder.

4.
Diseases ; 10(4)2022 Oct 15.
Article in English | MEDLINE | ID: covidwho-2071293

ABSTRACT

Enteric viruses are commonly found obligate parasites in the gastrointestinal (GI) tract. These viruses usually follow a fecal-oral route of transmission and are characterized by their extraordinary stability as well as resistance in high-stress environments. Most of them cause similar symptoms including vomiting, diarrhea, and abdominal pain. In order to come in contract with mucosal surfaces, these viruses need to pass the three main lines of defense: mucus layer, innate immune defenses, and adaptive immune defenses. The following atypical gastrointestinal infections are discussed: SARS-CoV2, hantavirus, herpes simplex virus I, cytomegalovirus, and calicivirus. Dysbiosis represents any modification to the makeup of resident commensal communities from those found in healthy individuals and can cause a patient to become more susceptible to bacterial and viral infections. The interaction between bacteria, viruses, and host physiology is still not completely understood. However, with growing research on viral infections, dysbiosis, and new methods of detection, we are getting closer to understanding the nature of these viruses, their typical and atypical characteristics, long-term effects, and mechanisms of action in different organ systems.

5.
International Journal of Noncommunicable Diseases ; 6(5):47-54, 2021.
Article in English | Web of Science | ID: covidwho-2071981

ABSTRACT

In recent years, the various health benefits of Cyanobacteria microalgae - such as Arthrospira platensis, commonly called Spirulina, an edible blue-green algae - have attracted scientific attention including micro-level examinations of its bioactive components. As a whole food and nutritional supplement, it serves as a plant protein source, which has shown positive effects across a wide range of human health concerns, from malnutrition to metabolic syndrome. Spirulina bioactives, such as essential amino acids, phycocyanin, polysaccharides, carotenoids, and chlorophyll, and essential vitamins and trace minerals, are responsible for its holistic actions against oxidative stress and inflammation, and its antiviral, antibacterial, and immune-modulating effects. Various in vitro, in vivo, and ex vivo experiments have established Spirulina's mechanism of action and its effect on immunity as a proof of concept. The phenolic compounds and extracellular metabolites released from Spirulina whole food after digestion are postulated to strengthen the epithelial lining with antibacterial effects against pathogenic bacteria, adding to its prebiotic effect on the gut microbiota (like Bifidobacterium and Lactobacillus) due to its fiber content. In this study, the digestibility of Spirulina was assessed by the determination of free amino acids and peptide release during the each phase of digestion in a simulated static digestive model system. The hypothesis bridging poor gut health to low-level inflammation and metabolic syndrome, and the potential to address those issues with nutritional supplementation, such as with Spirulina, could also be beneficial in the long run to reduce comorbid illnesses, such as those associated with the currently prevailing coronavirus disease 2019 pandemic.

6.
Microb Pathog ; 173(Pt A): 105829, 2022 Oct 15.
Article in English | MEDLINE | ID: covidwho-2069489

ABSTRACT

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

7.
Przegl Epidemiol ; 76(2): 155-163, 2022.
Article in English | MEDLINE | ID: covidwho-2067619

ABSTRACT

There is an interaction between the bacteria and the host at the genetic, metabolic and immunological levels. The intestine is the largest immune organ in the human's body, and the microbes present in it influence the immune response. An imbalance in the type and the number of bacteria can affect human health. The study attempts to review the current reports on intestinal dysbiosis in the course of SARS-CoV-2 infection and the impact of the composition of the intestinal microbiome on the course and severity of COVID-19 disease.


Subject(s)
COVID-19 , Gastrointestinal Microbiome , Dysbiosis/microbiology , Humans , Poland , SARS-CoV-2
8.
American Journal of Transplantation ; 22(Supplement 3):736, 2022.
Article in English | EMBASE | ID: covidwho-2063513

ABSTRACT

Purpose: Kidney transplant recipients (KTR) commonly exhibit inadequate responses to 2-dose COVID-19 vaccination schedules and remain at increased risk of severe COVID-19. Gut dysbiosis is common among KTRs and has been associated with poor vaccine responses. We hypothesised that a dietary fibre supplement may correct dysbiosis and enhance responses to a third dose of COVID-19 vaccine in KTRs. Method(s): KTRs who had received 2 doses of a COVID-19 vaccine were recruited from 2 transplant programs in Australia. KTRs with an inadequate response (defined by anti-RBD <100U/mL) were randomised to receive inulin (fibre) or maltodextran (control), 10g dissolved in 200ml water twice daily for 4 weeks prior to, and 4 weeks after a 3rd vaccine, at which time vaccine response was measured by anti-RBD titre, vaccine-specific B and T cell responses, and changes in the gut microbiome. Patients and investigators were blinded to treatment assignment. COVID-19 infection was excluded by measurement of anti-nucleocapsid antigen. Result(s): Of 85 KTRs screened, 71 had baseline anti-RBD<100U/mL and were randomised to inulin (n=37) or control (n=34). Participants were 33% female, mean age 59 yrs (SD 11), with mean eGFR 56 ml/min/1.73m2 (SD 24.8), and were most commonly receiving tacrolimus, mycophenolate and prednisolone. All participants received a third dose of a mRNA COVID-19 vaccine after receiving a dietary supplement for 4 weeks. Week 8 assessment of vaccine response, supplement tolerability and change in microbiome are ongoing. Four participants tested positive for COVID-19 during the study. Conclusion(s): Gut dysbiosis is one potential contributor to the poor COVID-19 vaccine responses exhibited by KTRs. This trial will determine whether a simple dietary fibre supplement is well tolerated and effective in correcting gut dysbiosis and restoring vaccine responsiveness. Improved vaccine responses are urgently required to better protect KTRs from ongoing morbidity and mortality from COVID-19.

9.
The Lancet Gastroenterology and Hepatology ; 7(10):912, 2022.
Article in English | EMBASE | ID: covidwho-2062056
10.
Chest ; 162(4):A855, 2022.
Article in English | EMBASE | ID: covidwho-2060708

ABSTRACT

SESSION TITLE: COVID-19 Co-Infections SESSION TYPE: Rapid Fire Case Reports PRESENTED ON: 10/19/2022 12:45 pm - 1:45 pm INTRODUCTION: We present a case of Eggerthella bacteremia in a patient with COVID-19. CASE PRESENTATION: A 69-year-old woman presented to the emergency room with chief complaint of cough, dyspnea, and malaise. After testing positive with a home COVID-19 test three days earlier, she continued to have worsening respiratory status and was brought in via ambulance. She was found to be tachycardic and hypoxic, requiring high-flow oxygen to maintain saturation in the emergency department. Chest X-ray showed bilateral patchy opacities consistent with multifocal COVID-19 pneumonia, and she was admitted to the intensive care unit for acute hypoxic respiratory failure. COVID-19 drug therapy was initiated, including baricitinib, remdesivir and decadron. Shortly after hospitalization, she began to endorse worsening abdominal pain. Physical exam elicited tenderness to palpation of her right lower quadrant. Abdominal CT scan showed distal ileum fluid collection concerning for possible bowel perforation. She underwent exploratory laparotomy which confirmed perforation, and a small bowel resection with anastomosis was performed. Blood cultures were positive for gram-positive bacilli, which were further identified as Eggerthella species. She required mechanical ventilation for worsening respiratory function post-surgery but remained unresponsive on the ventilator. The patient was administered vancomycin but continued to decline and eventually expired. DISCUSSION: Eggerthella is an anaerobic, gram-positive bacilli present in the gut microflora. Eggerthella infection has most often been reported in intra-abdominal infections. However, cases of bacteremia infection remain sparse. Most infections have been associated with other gastrointestinal processes including Crohn's disease, ulcerative colitis, appendicitis, and diverticulitis abscesses. Our case involved a patient with no significant gastrointestinal history admitted for COVID-19 pneumonia infection on baricitinib complicated by bowel perforation and bacteremia. Bowel perforation is a known risk factor of baricitinib use, and these risks should be discussed with the patient before beginning therapy. Overall mortality for Eggerthella species infection remains high, with some estimates as high as 31%. Much remains unknown about the impact on gut microbiome by SARS-CoV-2, however, early research suggests a higher rate of fungal co-infection in patients with COVID-19. As the literature on COVID-19 expands, more and more unusual pathogens such as Eggerthella may be found to contribute to the morbidity and mortality of patients being treated for COVID-19. CONCLUSIONS: Unusual pathogens such as Eggerthella may complicate a patient's hospital course while undergoing treatment for COVID-19. Reference #1: Alejandra Ugarte-Torres, Mark R Gillrie, Thomas P Griener, Deirdre L Church, Eggerthella lenta Bloodstream Infections Are Associated With Increased Mortality Following Empiric Piperacillin-Tazobactam (TZP) Monotherapy: A Population-based Cohort Study, Clinical Infectious Diseases, Volume 67, Issue 2, 15 July 2018. Reference #2: Gardiner BJ, Tai AY, Kotsanas D, et al. Clinical and microbiological characteristics of Eggerthella lenta bacteremia. J Clin Microbiol. 2015. Reference #3: Lau SK, Woo PC, Fung AM, Chan K-M, Woo GK, Yuen K-Y. Anaerobic, non-sporulating, gram-positive bacilli bacteraemia characterized by 16s rrna gene sequencing. Journal of medical microbiology. 2004. DISCLOSURES: No relevant relationships by Kristin Davis No relevant relationships by Charles Peng

11.
SSRN; 2022.
Preprint in English | SSRN | ID: ppcovidwho-344362

ABSTRACT

Background: COVID-19 could develop severe respiratory symptoms in certain infected patients, especially in the patients with immune disorders. Microbiome acting an important immunological modulator in the human gut could contribute to the immune responses impacting the progression of COVID-19. Methods: This Mendelian randomization study was performed to determine the potential causal relationship between intestinal bacteria and COVID-19. Using summary statistics from the COVID-19 Host Genetics Initiative Program, >30000 COVID-19 patients and >1 million controls were involved. Single nucleotide polymorphisms (SNPs) strongly associated with the abundance of intestinal bacteria in gut were utilized to infer whether intestinal bacteria are causal factor of COVID-19 associated phenotypes including infection, hospitalization, and severe COVID-19. In addition, colocalization and pathway analyses were performed to explore the potential mechanism of intestinal bacteria affecting COVID-19. Results: We found that the abundance of Ruminococcus torques was a risk factor causing hospitalization and severe COVID-19 (1.25×10-4 [OR=1.86, 95%CI:1.36-2.56] and 7.0×10-4 [OR=6.66, 95%CI:2.23-19.94], respectively). Ruminococcus torques abundance was colocalized with severe COVID-19 (PP.H4=0.77), but not with COVID-19 hospitalization (PP.H4=0.18). In addition, Ruminococcus torques also colocalized with the colon expression of permeability related protein RASIP1 (PP.H4=0.95). Moreover, our data suggested that the Ruminococcus torques were strong associated with autoimmune diseases. The proteins regulated by rs35866622 (the instrument variable of Ruminococcus torques) were enriched in immune-related pathways. Conclusions: Our study implies that elevated Ruminococcus torques abundance in the gut could increase the risk of the development of severe COVID-19. Funding: This research was supported by the National Key Research and Development Program of China (No. 2021YFA1301203), Hunan Provincial Natural Science Foundation of China (2021JJ31074, 2019JJ50854), Chinese National Science Foundation (No.81803583), Open Fund Project of Hunan Universities Innovation Platform (18K006), and the Project Program of National Clinical Research Center for Geriatric Disorders (Xiangya Hospital, Grant No. 2020LNJJ06). Declaration of Interest: The authors declare no conflict of interest Ethical Approval: The study was approved by the ethics committee of Institute of Clinical Pharmacology, Central South University.

12.
Drug Development and Delivery ; 22(6):67-76, 2022.
Article in English | EMBASE | ID: covidwho-2058315
13.
Mikrobiolohichnyi Zhurnal ; 84(1):17-23, 2022.
Article in English | Scopus | ID: covidwho-2056527

ABSTRACT

The appointment of antibacterial agents for the treatment of pneumonia that develops with COVID-19 is one of the treatment regimens. Antibacterial agents are prescribed only in the case of the presence of confirmed bacterial co-infec-tion but can be appointed empirically. This approach promotes the development of antibiotic resistance of opportunistic and saprophytic microflora of almost all habitats, including the oropharynx, which can lead to dysbiosis with activation of fungal flora. The aim of the study was to analyze the composition of the oropharyngeal microbiome of patients with viral and bacterial pneumonia who took antibiotics, as well as the sensitivity of fungi of the genus Candida to antifungal drugs for effective treatment of the underlying disease. Methods. The results of the bacteriological examination of 113 patients treated with a diagnosis of COVID-19 were analyzed. Microbiological examination of oropharyngeal swabs was performed by the classical bacteriological method with dosed seeding of suspended material on differential diagnostic media (in particular Sabouraud agar was used for selection of fungi of the genus Candida) and genus identification by morphological, cultural, biochemical properties. Results. PCR tests were performed for all patients in the clinical trial to confirm the diagnosis of viral and bacterial pneumonia. According to the results of the bacteriological examination, fungi of the genus Candida were found in 52 (46.0%) patients with pneumonia associated with COVID-19. The analysis of prescriptions showed that only 14 (26.9%) patients were treated with one antibiotic, two antibiotics were prescribed to 31 (59.6%) patients, and three — to 7 (13.5%). In the structure of antibiotic therapy, the lion’s share were cephalosporins of the third generation (ceftriaxone, hepacef) — 33 (63.5%), and macrolides (azithromycin) — 16 (30.8%) patients. In the structure of the oropharyngeal microbiome, according to the results of the bacteriological research, fungi of the genus Candida significantly prevailed, which were found in 52 (46.0%), and in 29 patients (25.7%) S. pneumonia was found. The sensitivity of fungi of the genus Candida to antifungal agents was analyzed, and the maximum number of resistant strains was detected to nystatin and amphotericin — 38.5% and 26.9%, with only 8 (15.3%) fungi of the genus Candida sensitive to nystatin. Conclusions. All patients with viral-bacterial pneumonia associated with COVID-19 received antibiotic therapy with the lion’s share of third-generation cephalosporins (63.5%) and macrolides (30.8%). According to the results of the bacteriological examination of the oropharyngeal microbiome after antibiotic therapy, fungi of the genus Candida predominated (46.0%), followed by S. pneumoniae (25.7%). Isolated strains of fungi of the genus Candida showed resistance to nystatin (38.5%) and amphotericin (26.9%). Antifungal agents of the imidazole subgroup have shown high efficiency and a low percentage of resistant strains, which allows us to recommend them for the treatment of complications of COVID-19 caused by fungi of the genus Candida. © Publisher PH «Akademperiodyka» of the NAS of Ukraine, 2022. This is an open access article under the CC BY-NC-ND license (https://creativecommons.org/licenses/by-nc-nd/4.0/).

14.
Am J Respir Crit Care Med ; 206(7): 846-856, 2022 Oct 01.
Article in English | MEDLINE | ID: covidwho-2053497

ABSTRACT

Rationale: Bacterial lung microbiota are correlated with lung inflammation and acute respiratory distress syndrome (ARDS) and altered in severe coronavirus disease (COVID-19). However, the association between lung microbiota (including fungi) and resolution of ARDS in COVID-19 remains unclear. We hypothesized that increased lung bacterial and fungal burdens are related to nonresolving ARDS and mortality in COVID-19. Objectives: To determine the relation between lung microbiota and clinical outcomes of COVID-19-related ARDS. Methods: This observational cohort study enrolled mechanically ventilated patients with COVID-19. All patients had ARDS and underwent bronchoscopy with BAL. Lung microbiota were profiled using 16S rRNA gene sequencing and quantitative PCR targeting the 16S and 18S rRNA genes. Key features of lung microbiota (bacterial and fungal burden, α-diversity, and community composition) served as predictors. Our primary outcome was successful extubation adjudicated 60 days after intubation, analyzed using a competing risk regression model with mortality as competing risk. Measurements and Main Results: BAL samples of 114 unique patients with COVID-19 were analyzed. Patients with increased lung bacterial and fungal burden were less likely to be extubated (subdistribution hazard ratio, 0.64 [95% confidence interval, 0.42-0.97]; P = 0.034 and 0.59 [95% confidence interval, 0.42-0.83]; P = 0.0027 per log10 increase in bacterial and fungal burden, respectively) and had higher mortality (bacterial burden, P = 0.012; fungal burden, P = 0.0498). Lung microbiota composition was associated with successful extubation (P = 0.0045). Proinflammatory cytokines (e.g., tumor necrosis factor-α) were associated with the microbial burdens. Conclusions: Bacterial and fungal lung microbiota are related to nonresolving ARDS in COVID-19 and represent an important contributor to heterogeneity in COVID-19-related ARDS.


Subject(s)
COVID-19 , Microbiota , Respiratory Distress Syndrome , COVID-19/complications , Critical Illness , Humans , Lung/microbiology , Microbiota/genetics , RNA, Ribosomal, 16S/genetics , Respiration, Artificial , Tumor Necrosis Factor-alpha
15.
Microbiol Spectr ; 10(5): e0168222, 2022 Oct 26.
Article in English | MEDLINE | ID: covidwho-2053137

ABSTRACT

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.


Subject(s)
COVID-19 , Humans , Antiviral Agents/therapeutic use , COVID-19/drug therapy , COVID-19 Testing , Lactobacillus , Outpatients , Pandemics/prevention & control , Pharynx , SARS-CoV-2 , Treatment Outcome , Oral Sprays
16.
Indoor Air ; 32(9): e13107, 2022 09.
Article in English | MEDLINE | ID: covidwho-2052596

ABSTRACT

The aim of the study was to examine the effects of environmental factors including disinfection on airborne microbiome during the coronavirus disease 2019 pandemic, we evaluated indoor and outdoor air collected from 19 classrooms regularly disinfected. Extracted bacterial and fungal DNA samples were sequenced using the Illumina MiSeq™ platform. Using bacterial DNA copy number concentrations from qPCR analysis, multiple linear regressions including environmental factors as predictors were performed. Microbial diversity and community composition were evaluated. Classrooms disinfected with spray ≤1 week before sampling had lower bacterial DNA concentration (3116 DNA copies/m3 ) than those >1 week (5003 copies/m3 ) (p-values = 0.06). The bacterial DNA copy number concentration increased with temperature and was higher in classrooms in coastal than inland cities (p-values <0.01). Bacterial diversity in outdoor air was higher in coastal than inland cities while outdoor fungal diversity was higher in inland than coastal cities. These outdoor microbiomes affected classroom microbial diversity but bacterial community composition at the genus level in occupied classrooms were similar between coastal and inland cities. Our findings emphasize that environmental conditions including disinfection, climate, and school location are important factors in shaping classroom microbiota. Yet, further research is needed to understand the effects of modified microbiome by disinfection on occupants' health.


Subject(s)
Air Pollution, Indoor , COVID-19 , Microbiota , Air Pollution, Indoor/analysis , Bacteria , DNA, Bacterial , DNA, Fungal , Disinfection , Environmental Monitoring , Humans , Pandemics , Schools
17.
Open Forum Infect Dis ; 9(9): ofac448, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2051511

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may present risk to patients treated with donor-derived microbiome therapies when appropriate manufacturing controls and inactivation processes are lacking. We report that the manufacturing steps for SER-109, a purified investigational microbiome therapeutic developed to reduce risk of Clostridioides difficile recurrence, inactivate porcine epidemic diarrhea virus, a model coronavirus for SARS-CoV-2.

18.
Gut Microbes ; 14(1): 2128603, 2022.
Article in English | MEDLINE | ID: covidwho-2051074

ABSTRACT

Dysbiosis of gut microbiota is well-described in patients with coronavirus 2019 (COVID-19), but the dynamics of antimicrobial resistance genes (ARGs) reservoir, known as resistome, is less known. Here, we performed longitudinal fecal metagenomic profiling of 142 patients with COVID-19, characterized the dynamics of resistome from diagnosis to 6 months after viral clearance, and reported the impact of antibiotics or probiotics on the ARGs reservoir. Antibiotic-naive patients with COVID-19 showed increased abundance and types, and higher prevalence of ARGs compared with non-COVID-19 controls at baseline. Expansion in resistome was mainly driven by tetracycline, vancomycin, and multidrug-resistant genes and persisted for at least 6 months after clearance of SARS-CoV-2. Patients with expanded resistome exhibited increased prevalence of Klebsiella sp. and post-acute COVID-19 syndrome. Antibiotic treatment resulted in further increased abundance of ARGs whilst oral probiotics (synbiotic formula, SIM01) significantly reduced the ARGs reservoir in the gut microbiota of COVID-19 patients during the acute infection and recovery phase. Collectively, these findings shed new insights on the dynamic of ARGs reservoir in COVID-19 patients and the potential role of microbiota-directed therapies in reducing the burden of accumulated ARGs.


Subject(s)
COVID-19 , Gastrointestinal Microbiome , Probiotics , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , COVID-19/complications , COVID-19/drug therapy , Drug Resistance, Bacterial/genetics , Gastrointestinal Microbiome/genetics , Humans , Probiotics/therapeutic use , SARS-CoV-2/genetics , Tetracyclines , Vancomycin
19.
Crit Rev Food Sci Nutr ; : 1-21, 2022 Sep 26.
Article in English | MEDLINE | ID: covidwho-2050916

ABSTRACT

Celiac disease (CD) as a chronic gluten-sensitive intestinal condition, mainly affects genetically susceptible hosts. The primary determinants of CD have been identified as environmental and genetic variables. The development of CD is significantly influenced by environmental factors, including the gut microbiome. Therefore, gut microbiome re-programming-based therapies using probiotics, prebiotics, postbiotics, gluten-free diet, and fecal microbiota transplantation have shown promising results in the modification of the gut microbiome. Due to the importance and paucity of information regarding the CD pathophysiology, in this review, we have covered the association between CD development and gut microbiota, the effects of infectious agents, particularly the recent Covid-19 infection in CD patients, and the efficacy of potential therapeutic approaches in the CD have been discussed. Hence, scientific literature indicates that the diverse biological functions of the gut microbiota against immunomodulatory responses have made microbiome-based therapy an alternative therapeutic paradigm to ameliorate the symptoms of CD and quality of life. However, the exact potential of microbiota-based techniques that aims to quantitatively and qualitatively alter the gut microbiota to be used in the treatment and ameliorate the symptoms of CD will be determined with further research in the future.

20.
COVID-19: Tackling Global Pandemics through Scientific and Social Tools ; : 51-71, 2021.
Article in English | Scopus | ID: covidwho-2048795

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that presented in Wuhan, China in December of 2019. SARS-CoV-2-mediated coronavirus disease 2019 (COVID-19) is strongly associated with the rampant of infection with catastrophic morbidity. This pandemic has jiggled the society with its widespread social, psychologic, and economic distress. Society immunity or herd immunity is the most crucial and natural prophylactic vaccination interference against any infectious disease around the globe. It postulates protection at both the individual and population levels against pathogen-borne infections. The accomplishment of herd immunity is reliant upon the transmission efficiency of pathogens and the emerging natural immunity within a society. This is an exclusively pertinent mechanism to control any pandemic. The microbiome plays a crucial role in the coevolution of the body's immune cells, which are cardinal for bolstering a proficient vaccination process, ensuring herd immunity. The dynamics of interaction among microbiota, nutrients, and individual immunity determines the avidity of vaccines against several pathogens. Synchronization of microbial symbiosis preserves pathogen transmissibility and the engrossment of vaccination among different clusters based on the age and gender. Imbalance of nutrients refutes microbiome harmony, develops environmental enteropathy, and exacerbates immunity, which perturbs the efficacy of the vaccination process. Furthermore, discrepancies in the protective response of many vaccines in developing countries than developed countries are due to differences in healthy microbiota among the individuals in a particular cohort. We suggested that the rigorous pan-India oral poliovirus vaccination program for the past 30years has been finally capable of inducing herd immunity against poliovirus infection among societies, which may also inspire the commencement of natural heterologous immunity against SARS-CoV-2 infection. However, this anamnestic recall is somewhat counterintuitive, as antibody generation against original antigens of SARS-CoV-2 will be restrained due to original antigenic sin. © 2022 Elsevier Inc. All rights reserved.

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