Microbial co-infections in COVID-19: Associated microbiota and underlying mechanisms of pathogenesis

Microbial infection among SARS-COV-2-infected patients in a COVID-19-dedicated tertiary care hospital of Bangladesh: a cross-sectional study

Objectives. This study aimed to determine patterns of respiratory, blood-borne and uropathogenic microbial pathogens among SARS-CoV-2-infected patients in a COVID-19-(coronavirus disease 2019) dedicated tertiary care hospital in Dhaka, Bangladesh. Design.This was a cross-sectional study. Setting. In a COVID-19-dedicated tertiary care hospital in Dhaka, Bangladesh, conducted from March to June 2021. Participants. Hospitalized individuals with COVID-19 infection regardless of age or sex. Primary and secondary outcome measures. The percentage of co-infected COVID-19 patients and the characterization of the micro-organisms responsible for co-infection served as the primary outcome measures. Finding any associations between co-infection and age, co-infection and sex and co-infection and comorbidity was the secondary outcome variable. Interventions. Not applicable. Results.Out of 79 patients, 61 % were male, and the mean age was 49.53 years. Co-infection was seen in 7.7 % of patients, out of which 5.1 % of isolates were from urine samples, followed by 2.6 % from blood. Bacteria isolated from urine were Enterococcus (2.6 %), coagulase-negative Staphylococcus (CONS) (1.3 %) and Enterobacter spp. (1.3 %). Pseudomonas spp. was the only organism isolated from blood sample. Mixed growth was found in nasopharyngeal and throat swabs, with the predominant species being Staphylococcus aureus and Streptococcus spp. At the time of data collection, 55.7 % of patients had been given antimicrobials, and 30.4 % of patients had been given a single antimicrobial. HBsAg was positive in 1.3 % of patients and none were anti-hepatitis C or dengue NS1Ag positive. Conclusion. Microbial infection has been seen to be associated with SARS-CoV-2 infections and is of great value in prescribing antimicrobials and reducing fatal outcomes of hospitalized patients.

The "COVID effect" in culture-based clinical microbiology: Changes induced by COVID-19 pandemic in a Hungarian tertiary care center

BACKGROUND

The presence of bacterial and fungal coinfections plays an important role in the mortality of patients with coronavirus 2019 (COVID-19). We compared data from the 3 years before and 3 years after the COVID-19 pandemic outbreak to evaluate its effect on the traits of bacterial and fungal diseases.

METHODS

We retrospectively collected and analyzed data on positive respiratory tract samples (n = 13,133 samples from 7717 patients) and blood cultures (n = 23,652 from 9653 patients) between 2017 and 2022 from the Clinical Center of the University of Szeged, Hungary. We also evaluated antimicrobial susceptibility test results derived from 169,020 respiratory samples and 549,729 blood cultures to gain insight into changes in antimicrobial resistance.

RESULTS

The most common respiratory pathogen in the pre-COVID era was Pseudomonas aeruginosa, whereas Candida albicans was the most frequent during the pandemic. The number of respiratory isolates of Acinetobacter baumannii was also markedly increased. In blood cultures, Staphylococcus epidermidis, Escherichia coli, and S. aureus were dominant during the study period, and A. baumannii was widespread in blood cultures during the pandemic years. Resistance to ofloxacin, penicillin, piperacillin-tazobactam, ceftazidime, cefepime, imipenem, ceftolozane-tazobactam, and itraconazole increased significantly in the COVID era.

CONCLUSIONS

During the COVID-19 pandemic, there were changes in the prevalence of respiratory and blood culture pathogens at the Clinical Center of the University of Szeged. C. albicans became the predominant respiratory pathogen, and the number of A. baumannii isolates increased dramatically. Additionally, antimicrobial resistance notably increased during this period.

The characteristics of microbiome in the upper respiratory tract of COVID-19 patients

BACKGROUND

Co-infection with other pathogens in coronavirus disease 2019 (COVID-19) patients exacerbates disease severity and impacts patient prognosis. Clarifying the exact pathogens co-infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is premise of the precise treatment for COVID-19 patients.

METHODS

Sputum samples were collected from 17 patients in the COVID-19 positive group and 18 patients in the COVID-19 negative group. DNA extraction was performed to obtain the total DNA. Sequencing analysis using 16S and ITS rRNA gene was carried out to analyze the composition of bacterial and fungal communities. Meanwhile, all the samples were inoculated for culture.

RESULTS

We did not observe significant differences in bacterial composition between the COVID-19 positive and negative groups. However, a significantly higher abundance of Candida albicans was observed in the upper respiratory tract samples from the COVID-19 positive group compared to the COVID-19 negative group. Moreover, the Candida albicans strains isolated from COVID-19 positive group exhibited impaired secretion of aspartyl proteinases.

CONCLUSION

COVID-19 positive patients demonstrate a notable increase in the abundance of Candida albicans, along with a decrease in the levels of aspartyl proteinases, indicating the alteration of microbiota composition of upper respiratory tract.

Characteristics of Hospitalized COVID-19 Patients at Admission and Factors Associated with Clinical Severity in Low- and Middle-Income Countries: An Observational Study

Despite the numerous articles published on the clinical characteristics and outcomes of COVID-19 with regard to high-income countries, little is known about patients in low- and middle-income countries (LMIC) in this context. The objective of this observational, prospective, hospital-based multicentric study was to describe clinical features and outcomes of laboratory-confirmed COVID-19 patients hospitalized in each of the participating centers in Bangladesh, Guinea, Ivory Coast, Lebanon, Madagascar, and Mali during the first year of the pandemic (March 5, 2020 to May 4, 2021). The study outcome was the clinical severity of COVID-19, defined as hospitalization in intensive care unit or death. Multivariate logistic regression models were performed to identify independent variables associated with disease severity. Overall, 1,096 patients were included. The median age was 49.0 years, ranging from 38.0 in Mali to 63.0 years in Guinea. The overall clinical severity of COVID-19 was 12.3%, ranging from 6.4% in Mali to 18.8% in Guinea. In both groups of patients <60 and ≥60 years old, cardiovascular diseases (adjusted odds ratio [aOR]: 1.99; 95% CI: 1.13-3.50, P = 0.02; aOR: 2.47; 95% CI: 1.33-4.57, P = 0.004) were independently associated with clinical severity, whereas in patients <60 years, diabetes (aOR: 2.13; 95% CI: 1.11-4.10, P = 0.02) was also associated with clinical severity. Our findings suggest that COVID-19-related severity and death in LMICs are mainly driven by older age. However, the presence of chronic diseases can also increase the risk of severity especially in younger patients.

Virulent Klebsiella pneumoniae ST11 clone carrying blaKPC and blaNDM from patients with and without COVID-19 in Brazil

AIMS

Investigated and compared the occurrence of virulence genes fimH, mrkD, irp2, entB, cps, rmpA, and wabG, resistance genes blaKPC and blaNDM, and the genetic variability and clonal relationship of 29 Klebsiella pneumoniae clinical isolates of patients with and without COVID-19, from a hospital in Brazil.

METHODS AND RESULTS

All isolates were resistant to beta-lactams. The genes were investigated by PCR, and for molecular typing, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and MLST were used. The detection of blaNDM was greater (n = 23) when compared to that of blaKPC (n = 14). The virulence genes that most occurred were fimH, entB, cps, and wabG, which are responsible for adhesins, siderophore enterobactin, capsule, and lipopolysaccharides, respectively. Among the isolates, 21 distinct genetic profiles were found by ERIC-PCR, with multiclonal dissemination. Four isolates belonged to the ST11 clone.

CONCLUSIONS

The occurrence of the ST11 is worrying as it is a high-risk clone involved in the dissemination of virulent strains throughout the world.

Major alteration of Lung Microbiome and the Host Reaction in critically ill COVID-19 Patients with high viral load

Background

Patients with COVID-19 under invasive mechanical ventilation are at higher risk of developing ventilator-associated pneumonia (VAP), associated with increased healthcare costs, and unfavorable prognosis. The underlying mechanisms of this phenomenon have not been thoroughly dissected. Therefore, this study attempted to bridge this gap by performing a lung microbiota analysis and evaluating the host immune responses that could drive the development of VAP.

Materials and methods

In this prospective cohort study, mechanically ventilated patients with confirmed SARS-CoV-2 infection were enrolled. Nasal swabs (NS), endotracheal aspirates (ETA), and blood samples were collected initially within 12 hours of intubation and again at 72 hours post-intubation. Plasma samples underwent cytokine and metabolomic analyses, while NS and ETA samples were sequenced for lung microbiome examination. The cohort was categorized based on the development of VAP. Data analysis was conducted using RStudio version 4.3.1.

Results

In a study of 36 COVID-19 patients on mechanical ventilation, significant differences were found in the nasal and pulmonary microbiome, notably in Staphylococcus and Enterobacteriaceae, linked to VAP. Patients with VAP showed a higher SARS-CoV-2 viral load, elevated neutralizing antibodies, and reduced inflammatory cytokines, including IFN-δ, IL-1β, IL-12p70, IL-18, IL-6, TNF-α, and CCL4. Metabolomic analysis revealed changes in 22 metabolites in non-VAP patients and 27 in VAP patients, highlighting D-Maltose-Lactose, Histidinyl-Glycine, and various phosphatidylcholines, indicating a metabolic predisposition to VAP.

Conclusions

This study reveals a critical link between respiratory microbiome alterations and ventilator-associated pneumonia in COVID-19 patients, with elevated SARS-CoV-2 levels and metabolic changes, providing novel insights into the underlying mechanisms of VAP with potential management and prevention implications.

Aspergillus fumigatus secretes a protease(s) that displays in silico binding affinity towards the SARS-CoV-2 spike protein and mediates SARS-CoV-2 pseudovirion entry into HEK-293T cells

BACKGROUND

The novel coronavirus disease of 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Data from the COVID-19 clinical control case studies showed that this disease could also manifest in patients with underlying microbial infections such as aspergillosis. The current study aimed to determine if the Aspergillus (A.) fumigatus culture media (i.e., supernatant) possessed protease activity that was sufficient to activate the SARS-CoV-2 spike protein.

METHODS

The supernatant was first analysed for protease activity. Thereafter, it was assessed to determine if it possessed proteolytic activity to cleave a fluorogenic mimetic peptide of the SARS-CoV-2 spike protein that contained the S1/S2 site and a full-length spike protein contained in a SARS-CoV-2 pseudovirion. To complement this, a computer-based tool, HADDOCK, was used to predict if A. fumigatus alkaline protease 1 could bind to the SARS-CoV-2 spike protein.

RESULTS

We show that the supernatant possessed proteolytic activity, and analyses of the molecular docking parameters revealed that A. fumigatus alkaline protease 1 could bind to the spike protein. To confirm the in silico data, it was imperative to provide experimental evidence for enzymatic activity. Here, it was noted that the A. fumigatus supernatant cleaved the mimetic peptide as well as transduced the HEK-293T cells with SARS-CoV-2 pseudovirions.

CONCLUSION

These results suggest that A. fumigatus secretes a protease(s) that activates the SARS-CoV-2 spike protein. Importantly, should these two infectious agents co-occur, there is the potential for A. fumigatus to activate the SARS-CoV-2 spike protein, thus aggravating COVID-19 development.

Description of nasopharyngeal bacterial pathogens associated with different SARS-CoV-2 variants

The emergence of the coronavirus pandemic facilitated the acquisition of mutations in the SARS-CoV-2 genome, resulting in the appearance of new variants over the past three years. We previously identified several taxa associated with the clinical outcome of COVID-19 disease in a retrospective study involving 120 patients (infected patients and negative subjects). However, little is known about whether the different variants could influence variations in the composition of the nasopharyngeal microbiota. In this study, we used multiplex pathogen-specific PCR to analyse the presence of nasopharyngeal bacterial pathogens from 400 SARS-CoV-2 positive patients (equally distributed in the four SARS-CoV-2 variants studied: B.1.1.7 (Alpha), B.1 0.617.2 (Delta), B.1.160 (Marseille-4), and B.1.1.529 (omicron)). We then compared them to 400 patients who tested negative for all respiratory viruses tested in this study, including SARS-CoV-2. We first observed an enrichment of Staphylococcus aureus (P ≤ .05) and Corynebacterium propinquum (P ≤ .05) in COVID-19-positive patients, regardless of the variant, compared to negative subjects. We specifically highlighted a significantly higher frequency of S. aureus (P ≤ .0001), C. propinquum (P ≤ .0001), and Klebsiella pneumoniae (P ≤ .0001), in patients infected with the omicron variant, whereas that of Haemophilus influenzae was higher in patients infected with Marseille-4 (P ≤ .001) and Alpha (P ≤ .01) variants. Our results suggest that the nasopharyngeal bacterial pathogens have their own specificity according to the SARS-CoV-2 variant and independently of the season. Additional studies are needed to determine the role of these pathogens in the evolution of the clinical outcome of patients.

SARS-CoV-2 genetic variation and bacterial communities of naso-oropharyngeal samples in middle-aged and elderly COVID-19 patients in West Java, Indonesia

Objective

The number of COVID-19 cases in Indonesia reflects the disease severity and rapid dissemination. In response to the mounting threat, SARS-CoV-2 genomic surveillance and the investigation of naso-oropharyngeal bacterial communities in West Java were conducted, as dysbiosis of the upper respiratory tract microbiota might adversely affect the clinical condition of patients.

Methods

We utilized the Oxford Nanopore sequencing platform to analyze genetic variation of 43 samples of SARS-CoV-2 and 11 selected samples for 16S rRNA gene sequencing, using samples collected from May to August 2021.

Results

The prevalence of AY.23 (>82%) predominated among five virus lineages in the populations (AY.23, AY.24, AY.26, AY.42, B.1.1.7). The region in the SARS-CoV-2 genome found to have the highest number of mutations was the spike (S) protein (>20%). There was no association between SARS-CoV-2 lineages, mutation frequency, patient profile, and COVID-19 rapid spread-categorized cases. There was no association of bacterial relative abundance, alpha-beta diversity, and linear discriminant analysis effect size analysis with patient profile and rapid spread cases. MetagenomeSeq analysis showed eight differential abundance species in individual patient profiles, including Pseudomonas aeruginosa and Haemophilus parainfluenzae.

Conclusions

The data demonstrated relevant AY.23 dominance (the Delta variant) in West Java during that period supporting the importance of surveillance program in monitoring disease progression. The inconsistent results of the bacterial communities suggest that a complex multifactor process may contribute to the progression of bacterial-induced disease in each patient.

Investigation ways of causes needle sticks injuries, risk factors affecting on health and ways to preventive

Needle sticks injuries (NSIs) has caused many health concerns, including the widespread infection disease. Needle sticks injuries can have high threaten health human especially, all those who are in contact with health and medical centers. The purpose of this review study was the determination the effects of needle sticks injuries (NSIs) on health care worker and patents. In this a review study of literature studied conducted on international databases included Google Scholar, ISI/WOS (Web of Science), Springer, Scopus, Medline/PubMed. The literature signs a notable undesirable affect from potential needle sticks injuries related to ways to preventive and risks factors among patents and health care worker. The literature was shown needle stick injuries can cause with a variety of ways including needle recapping, non-standard safety boxes, thin gloves, and inadequate personal protective equipment. According to the result this study, needle stick injuries can transfer infectious disease (Human Immunodeficiency viruses [HIV], Hepatitis C virus [HCV]) and increase risk health on health care worker and patients. According to research related to the subject, the ways to prevent reduce needle sticks include personal protective equipment, holding retraining courses for medical staff in the direction to raise awareness can significantly reduce cases of needle sticks injuries. Further research using more sophisticated methodology is warranted.

Epidemiological investigation of lower respiratory tract infections during influenza A (H1N1) pdm09 virus pandemic based on targeted next-generation sequencing

Background

Co-infection has been a significant contributor to morbidity and mortality in previous influenza pandemics. However, the current influenza A (H1N1) pdm09 virus pandemic, as the first major outbreak following the SARS-CoV-2 pandemic, may differ epidemiologically. Further investigation is necessary to understand the specific features and impact of this influenza A pandemic. Study design: We conducted a retrospective cohort study at a Chinese hospital between January and April 2023, focusing on patients with lower respiratory tract infections. Pathogen detection employed targeted next-generation sequencing (tNGS) on bronchoalveolar lavage fluid (BALF) or sputum samples.

Results

This study enrolled 167 patients with lower respiratory tract infections, and the overall positivity rate detected through tNGS was around 80%. Among them, 40 patients had influenza A (H1N1) pdm09 virus infection, peaking in March. In these patients, 27.5% had sole infections, and 72.5% had co-infections, commonly with bacteria. The frequently detected pathogens were Aspergillus fumigatus, SARS-CoV-2, and Streptococcus pneumoniae. For non-influenza A virus-infected patients, the co-infection rate was 36.1%, with 42.3% having SARS-CoV-2. Patients with influenza A virus infection were younger, had more females and diabetes cases. Among them, those with sole infections were older, with less fever and asthma but more smoking history. Regarding prognosis, compared to sole influenza A virus infection, co-infected patients demonstrated higher 21-day recovery rates and a higher incidence of heart failure. However, they exhibited lower proportions of respiratory failure, acute kidney failure, septic shock, and hospital stays lasting more than 10 days. Interestingly, patients with non-influenza A virus infection had a significantly lower 21-day recovery rate. Correlation analysis indicated that the 21-day recovery rate was only associated with influenza A (H1N1) pdm09 virus.

Conclusion

During the current pandemic, the influenza A (H1N1) pdm09 virus may have been influenced by the SARS-CoV-2 pandemic and did not exhibit a strong pathogenicity. In fact, patients infected with influenza A virus showed better prognoses compared to those infected with other pathogens. Additionally, tNGS demonstrated excellent detection performance in this study and showed great potential, prompting clinical physicians to consider its use as an auxiliary diagnostic tool.

Mathematical Modeling of the Lethal Synergism of Coinfecting Pathogens in Respiratory Viral Infections: A Review

Influenza A virus (IAV) infections represent a substantial global health challenge and are often accompanied by coinfections involving secondary viruses or bacteria, resulting in increased morbidity and mortality. The clinical impact of coinfections remains poorly understood, with conflicting findings regarding fatality. Isolating the impact of each pathogen and mechanisms of pathogen synergy during coinfections is challenging and further complicated by host and pathogen variability and experimental conditions. Factors such as cytokine dysregulation, immune cell function alterations, mucociliary dysfunction, and changes to the respiratory tract epithelium have been identified as contributors to increased lethality. The relative significance of these factors depends on variables such as pathogen types, infection timing, sequence, and inoculum size. Mathematical biological modeling can play a pivotal role in shedding light on the mechanisms of coinfections. Mathematical modeling enables the quantification of aspects of the intra-host immune response that are difficult to assess experimentally. In this narrative review, we highlight important mechanisms of IAV coinfection with bacterial and viral pathogens and survey mathematical models of coinfection and the insights gained from them. We discuss current challenges and limitations facing coinfection modeling, as well as current trends and future directions toward a complete understanding of coinfection using mathematical modeling and computer simulation.

Case report of SARS-CoV-2 with secondary Clostridioides difficile infection

There has been an overuse of antibiotics in most patients suffering from COVID-19 which predisposes patients to hospital acquired C. difficile Infection (CDI). Also, COVID infection of the gastrointestinal tract also predisposes the patient to CDI. We here present a fatal case of SARS-CoV-2 coinfection with CDI.

The Impact of Viral and Bacterial Co-Infections and Home Antibiotic Treatment in SARS-CoV-2 Hospitalized Patients at the Policlinico Tor Vergata Hospital, Rome, Italy

Co-infections during COVID-19 may worsen patients' outcomes. This study reports the results of a screening assessing the presence of co-infections among patients hospitalized for SARS-CoV-2 infection in the Infectious Diseases-Ward of the Policlinico Tor Vergata Hospital, Rome, Italy, from 1 January to 31 December 2021. Data on hepatitis B and C virus, urinary antigens for legionella pneumophila and streptococcus pneumoniae, pharyngeal swab for respiratory viruses, QuantiFERON®-TB Gold Plus assay (QFT-P), blood cultures and pre-hospitalization antibiotic prescription were recorded. A total of 482 patients were included, 61% males, median age of 65 years (IQR 52-77), median Charlson comorbidity index of 4 (IQR 2-5). The mortality rate was 12.4%; 366 patients needed oxygen supply. In total, 151 patients (31.3%) received home antibiotics without any association with the outcome. No significant association between mortality and the positivity of viral hepatitis markers was found. Out of 442 patients, 125 had an indeterminate QFT-P, associated with increased mortality. SARS-CoV-2 was the only respiratory virus detected among 389 pharyngeal swabs; 15/428 patients were positive for S. pneumoniae; none for L. pneumophila. In total, 237 blood cultures were drawn within 48 h from hospital admission: 28 were positive and associated with increased mortality. In our cohort, bacterial and viral co-infections in COVID-19 hospitalized patients were rare and not associated with higher mortality.

COVID-19 alters human microbiomes: a meta-analysis

Introduction

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected a substantial portion of the world's population, and novel consequences of COVID-19 on the human body are continuously being uncovered. The human microbiome plays an essential role in host health and well-being, and multiple studies targeting specific populations have reported altered microbiomes in patients infected with SARS-CoV-2. Given the global scale and massive incidence of COVID on the global population, determining whether the effects of COVID-19 on the human microbiome are consistent and generalizable across populations is essential.

Methods

We performed a synthesis of human microbiome responses to COVID-19. We collected 16S rRNA gene amplicon sequence data from 11 studies sampling the oral and nasopharyngeal or gut microbiome of COVID-19-infected and uninfected subjects. Our synthesis included 1,159 respiratory (oral and nasopharyngeal) microbiome samples and 267 gut microbiome samples from patients in 11 cities across four countries.

Results

Our reanalyses revealed communitywide alterations in the respiratory and gut microbiomes across human populations. We found significant overall reductions in the gut microbial diversity of COVID-19-infected patients, but not in the respiratory microbiome. Furthermore, we found more consistent community shifts in the gut microbiomes of infected patients than in the respiratory microbiomes, although the microbiomes in both sites exhibited higher host-to-host variation in infected patients. In respiratory microbiomes, COVID-19 infection resulted in an increase in the relative abundance of potentially pathogenic bacteria, including Mycoplasma.

Discussion

Our findings shed light on the impact of COVID-19 on the human-associated microbiome across populations, and highlight the need for further research into the relationship between long-term effects of COVID-19 and altered microbiota.

Identification of Leading Compounds from Euphorbia neriifolia (Dudsor) Extracts as a Potential Inhibitor of SARS-CoV-2 ACE2-RBDS1 Receptor Complex: An Insight from Molecular Docking ADMET Profiling and MD-simulation Studies

Coronavirus disease-19 (COVID-19) are deadly and infectious disease that impacts individuals in a variety of ways. Scientists have stepped up their attempts to find an antiviral drug that targets the spike protein (S) of Angiotensin converting enzyme 2 (ACE2) (receptor protein) as a viable therapeutic target for coronavirus. The most recent study examines the potential antagonistic effects of 17 phytochemicals present in the plant extraction of Euphorbia neriifolia on the anti-SARS-CoV-2 ACE2 protein. Computational techniques like molecular docking, absorption, distribution, metabolism, excretion, and toxicity (ADMET) investigations, and molecular dynamics (MD) simulation analysis were used to investigate the actions of these phytochemicals. The results of molecular docking studies showed that the control ligand (2-acetamido-2-deoxy-β-D-glucopyranose) had a binding potential of -6.2 kcal/mol, but the binding potentials of delphin, β-amyrin, and tulipanin are greater at -10.4, 10.0, and -9.6 kcal/mol. To verify their drug-likeness, the discovered hits were put via Lipinski filters and ADMET analysis. According to MD simulations of the complex run for 100 numbers, delphin binds to the SARS-CoV-2 ACE2 receptor's active region with good stability. In root-mean-square deviation (RMSD) and root mean square fluctuation (RMSF) calculations, delphinan, β-amyrin, and tulipanin showed reduced variance with the receptor binding domain subunit 1(RBD S1) ACE2 protein complex. The solvent accessible surface area (SASA), radius of gyration (Rg), molecular surface area (MolSA), and polar surface area (PSA) validation results for these three compounds were likewise encouraging. The convenient binding energies across the 100 numbers binding period were discovered by using molecular mechanics of generalized born and surface (MM/GBSA) to estimate the ligand-binding free energies to the protein receptor. All things considered, the information points to a greater likelihood of chemicals found in Euphorbia neriifolia binding to the SARS-CoV-2 ACE2 active site. To determine these lead compounds' anti-SARS-CoV-2 potential, in vitro and in vivo studies should be conducted.

How to cite this article

Islam MN, Pramanik MEA, Hossain MA, et al. Identification of Leading Compounds from Euphorbia Neriifolia (Dudsor) Extracts as a Potential Inhibitor of SARS-CoV-2 ACE2-RBDS1 Receptor Complex: An Insight from Molecular Docking ADMET Profiling and MD-simulation Studies. Euroasian J Hepato-Gastroenterol 2023;13(2):89-107.

Fungal-Bacterial Co-Infections and Super-Infections among Hospitalized COVID-19 Patients: A Systematic Review

This study systematically reviewed fungal-bacterial co-infections and super-infections among hospitalized COVID-19 patients. A PRISMA systematic search was conducted. On September 2022, Medline, PubMed, Google Scholar, PsychINFO, Wiley Online Library, NATURE, and CINAHL databases were searched for all relevant articles published in English. All articles that exclusively reported the presence of fungal-bacterial co-infections and super-infections among hospitalized COVID-19 patients were included. Seven databases produced 6937 articles as a result of the literature search. Twenty-four articles met the inclusion criteria and were included in the final analysis. The total number of samples across the studies was 10,834, with a total of 1243 (11.5%) patients admitted to the intensive care unit (ICU). Of these patients, 535 underwent mechanical ventilation (4.9%), 2386 (22.0%) were male, and 597 (5.5%) died. Furthermore, hospitalized COVID-19 patients have a somewhat high rate (23.5%) of fungal-bacterial co-infections and super-infections. Moreover, for SARS-CoV-2 patients who have a chest X-ray that suggests a bacterial infection, who require immediate ICU admission, or who have a seriously immunocompromised condition, empiric antibiotic therapy should be taken into consideration. Additionally, the prevalence of co-infections and super-infections among hospitalized COVID-19 patients may have an impact on diagnosis and treatment. It is crucial to check for fungal and bacterial co-infections and super-infections in COVID-19 patients.

Dysbiosis of oropharyngeal microbiome and antibiotic resistance in hospitalized COVID-19 patients

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is ongoing and multiple studies have elucidated its pathogenesis, however, the related- microbiome imbalance caused by SARS-CoV-2 is still not clear. In this study, we have comprehensively compared the microbiome composition and associated function alterations in the oropharyngeal swabs of healthy controls and coronavirus disease 2019 (COVID-19) patients with moderate or severe symptoms by metatranscriptomic sequencing. We did observe a reduced microbiome alpha-diversity but significant enrichment of opportunistic microorganisms in patients with COVID-19 compared with healthy controls, and the microbial homeostasis was rebuilt following the recovery of COVID-19 patients. Correspondingly, less functional genes in multiple biological processes and weakened metabolic pathways such as carbohydrate metabolism, energy metabolism were also observed in COVID-19 patients. We only found higher relative abundance of limited genera such as Lachnoanaerobaculum between severe patients and moderate patients while no worthy-noting microbiome diversity and function alteration were observed. Finally, we noticed that the co-occurrence of antibiotic resistance and virulence was closely related to the microbiome alteration caused by SRAS-CoV-2. Overall, our findings demonstrate that microbial dysbiosis may enhance the pathogenesis of SARS-CoV-2 and the antibiotics treatment should be critically considered.

Changes in the Protein Profile in Staphylococcal Strains from Patients Infected with the SARS-CoV-2 Virus

Staphylococcus aureus strains are particularly often isolated from patients with SARS-CoV-2 infection. The aim of the current research was to determine whether the SARS-CoV-2 virus infection affects the protein profile of S. aureus. Bacteria were isolated from the forty swabs collected from the patients in the hospitals of the Pomeranian region. MALDI-TOF MS spectra were obtained using a Microflex LT instrument. Twenty-nine peaks were identified. The peak (2,430) is described here for the first time and was unique for the isolates from patients infected with the SARS-CoV-2 virus. These results support the hypothesis of bacterial adaptation to the conditions caused by viral infection.

From Co-Infections to Autoimmune Disease via Hyperactivated Innate Immunity: COVID-19 Autoimmune Coagulopathies, Autoimmune Myocarditis and Multisystem Inflammatory Syndrome in Children

Neutrophilia and the production of neutrophil extracellular traps (NETs) are two of many measures of increased inflammation in severe COVID-19 that also accompany its autoimmune complications, including coagulopathies, myocarditis and multisystem inflammatory syndrome in children (MIS-C). This paper integrates currently disparate measures of innate hyperactivation in severe COVID-19 and its autoimmune complications, and relates these to SARS-CoV-2 activation of innate immunity. Aggregated data include activation of Toll-like receptors (TLRs), nucleotide-binding oligomerization domain (NOD) receptors, NOD leucine-rich repeat and pyrin-domain-containing receptors (NLRPs), retinoic acid-inducible gene I (RIG-I) and melanoma-differentiation-associated gene 5 (MDA-5). SARS-CoV-2 mainly activates the virus-associated innate receptors TLR3, TLR7, TLR8, NLRP3, RIG-1 and MDA-5. Severe COVID-19, however, is characterized by additional activation of TLR1, TLR2, TLR4, TLR5, TLR6, NOD1 and NOD2, which are primarily responsive to bacterial antigens. The innate activation patterns in autoimmune coagulopathies, myocarditis and Kawasaki disease, or MIS-C, mimic those of severe COVID-19 rather than SARS-CoV-2 alone suggesting that autoimmunity follows combined SARS-CoV-2-bacterial infections. Viral and bacterial receptors are known to synergize to produce the increased inflammation required to support autoimmune disease pathology. Additional studies demonstrate that anti-bacterial antibodies are also required to account for known autoantigen targets in COVID-19 autoimmune complications.

Eliminating Potential Effects of Other Infections During Selection of Nonhuman Primates for COVID-19 Research

The study of nonhuman primates (NHP) can provide significant insights into our understanding numerous infectious agents. The etiological agent of COVID-19, SARS-CoV-2 virus, first emerged in 2019 and has so far been responsible for the deaths of over 4 million people globally. In the frenzied search to understand its pathogenesis and immunology and to find measures for prevention and control of this pandemic disease, NHP, particularly macaques, are the preferred model because they manifest similar clinical signs and immunologic features as humans. However, possible latent, subclinical, and opportunistic infections not previously detected in animals participating in a study may obscure experimental results and confound data interpretations in testing treatments and vaccine studies for COVID-19. Certain pathophysiologic changes that occur with SARS-CoV-2 virus infection are similar to those of simian pathogens. The current review discusses numerous coinfections of COVID-19 with other diseases and describes possible outcomes and mechanisms in COVID-19 studies of NHP that have coinfections. Due to the urgency triggered by the pandemic, screening that is more rigorous than usual is necessary to limit background noise and maximize the reliability of data from NHP COVID-19 studies. Screening for influenza virus, selected respiratory bacteria, and regional endemic pathogens such as vector-borne agents, together with the animal's individual exposure history, should be the main considerations in selecting a NHP for a COVID-19 study. In addition, because NHP are susceptible to the SARS-CoV-2 virus, management and surveillance measures should be established to prevent transmission to healthy animals from infected colony animals and husbandry staff. This review presents compiled data on the use of NHP in COVID-19 studies, emphasizing the need to create the most reliable NHP model for those studies by extensive screening for other pathogens.

Transcriptome analysis reveals increased abundance and diversity of opportunistic fungal pathogens in nasopharyngeal tract of COVID-19 patients

We previously reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiomes (bacteria, archaea and commensal respiratory viruses) with inclusion of pathobionts. This study aimed to assess the possible changes in the abundance and diversity of resident mycobiome in the nasopharyngeal tract (NT) of humans due to SARS-CoV-2 infections. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNA-sequencing followed by taxonomic profiling of mycobiome. Our analyses indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of fungi in the NT with inclusion of a high proportion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct mycobiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where S. cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species. Likewise, Recovered humans NT samples were predominated by Aspergillus penicillioides (36.64%), A. keveii (23.36%), A. oryzae (10.05%) and A. pseudoglaucus (4.42%). Conversely, Nannochloropsis oceanica (47.93%), Saccharomyces pastorianus (34.42%), and S. cerevisiae (2.80%) were the top abundant fungal species in Healthy controls nasal swabs. Importantly, 16% commensal fungal species found in the Healthy controls were not detected in either COVID-19 patients or when they were cured from COVID-19 (Recovered). We also detected several altered metabolic pathways correlated with the dysbiosis of fungal mycobiota in COVID-19 patients. Our results suggest that SARS-CoV-2 infection causes significant dysbiosis of mycobiome and related metabolic functions possibly play a determining role in the progression of SARS-CoV-2 pathogenesis. These findings might be helpful for developing mycobiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients.

Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors

The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease and death. Understanding the risk factors of severe COVID-19 is relevant both in the clinical setting and at the epidemiological level. Here, we provide an overview of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes. The factors considered in detail include the age and frailty, genetic polymorphisms, biological sex (and pregnancy), co- and superinfections, non-communicable comorbidities, immunological history, microbiota, and lifestyle of the patient; viral genetic variation and infecting dose; socioeconomic factors; and air pollution. For each category, we compile (sometimes conflicting) evidence for the association of the factor with COVID-19 outcomes (including the strength of the effect) and outline possible action mechanisms. We also discuss the complex interactions between the various risk factors.

SARS-CoV-2 Related Viral Respiratory Co-Infections: A Narrative Review

Background

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the new coronavirus originating from Wuhan, China, responsible for the illness known as coronavirus disease 2019 (COVID-19). Early experience and the recent literature have shown that co-infection of SARS-CoV-2 with another respiratory virus might occur. Similar symptoms of acute respiratory infections (ARIs) and COVID-19 represent a challenge for diagnostic and therapeutic efficacy and may modify COVID-19 outcomes.

Materials and Methods

We reviewed the literature on the epidemic pattern and major learning points on important aspects of SARS-CoV-2-related viral respiratory co-infections during the COVID-19 pandemic. Databases such as PubMed, Scopus, Science Direct, and Google Scholar were used to conduct a comprehensive search.

Results

The circulation of respiratory viruses changed as the COVID-19 epidemic continues. Phenomena like viral interference, resource competition, and differences in virus-host range might explain why simultaneous viral respiratory infections have seemed to vanish with the spread of SARS-CoV-2.

Conclusion

Key research to be conducted during this pandemic should include the simultaneous screening of other respiratory pathogens with many available commercial platforms for transmission containment and appropriate clinical management.

Therapeutic potential of kaempferol on Streptococcus pneumoniae infection

Co-infections with pathogens and secondary bacterial infections play significant roles during the pandemic coronavirus disease 2019 (COVID-19) pathogenetic process, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Notably, co-infections with Streptococcus pneumoniae (S. pneumoniae), as a major Gram-positive pathogen causing pneumonia or meningitis, severely threaten the diagnosis, therapy, and prognosis of COVID-19 worldwide. Accumulating evidences have emerged indicating that S. pneumoniae evolves multiple virulence factors, including pneumolysin (PLY) and sortase A (SrtA), which have been extensively explored as alternative anti-infection targets. In our study, natural flavonoid kaempferol was identified as a potential candidate drug for infection therapeutics via anti-virulence mechanisms. We found that kaempferol could interfere with the pore-forming activity of PLY by engaging with catalytic active sites and consequently inhibit PLY-mediated cytotoxicity. Additionally, exposed to kaempferol significantly reduced the SrtA peptidase activity by occupying the active sites of SrtA. Further, the biofilms formation and bacterial adhesion to the host cells could be significantly thwarted by kaempferol incubation. In vivo infection model by S. pneumoniae highlighted that kaempferol oral administration exhibited notable treatment benefits, as evidenced by decreased bacterial burden, suggesting that kaempferol has tremendous potential to attenuate S. pneumoniae pathogenicity. Scientifically, our study implies that kaempferol is a promising therapeutic option by targeting bacterial virulence factors.

The Effects of Propolis on Viral Respiratory Diseases

Propolis remains an interesting source of natural chemical compounds that show, among others, antibacterial, antifungal, antiviral, antioxidative and anti-inflammatory activities. Due to the growing incidence of respiratory tract infections caused by various pathogenic viruses, complementary methods of prevention and therapy supporting pharmacotherapy are constantly being sought out. The properties of propolis may be important in the prevention and treatment of respiratory tract diseases caused by viruses such as severe acute respiratory syndrome coronavirus 2, influenza viruses, the parainfluenza virus and rhinoviruses. One of the main challenges in recent years has been severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing COVID-19. Recently, an increasing number of studies are focusing on the activity of various propolis preparations against SARS-CoV-2 as an adjuvant treatment for this infection. Propolis has shown a few key mechanisms of anti-SARS-CoV-2 action such as: the inhibition of the interaction of the S1 spike protein and ACE-2 protein; decreasing the replication of viruses by diminishing the synthesis of RNA transcripts in cells; decreasing the particles of coronaviruses. The anti-viral effect is observed not only with extracts but also with the single biologically active compounds found in propolis (e.g., apigenin, caffeic acid, chrysin, kaempferol, quercetin). Moreover, propolis is effective in the treatment of hyperglycemia, which increases the risk of SARS-CoV-2 infections. The aim of the literature review was to summarize recent studies from the PubMed database evaluating the antiviral activity of propolis extracts in terms of prevention and the therapy of respiratory tract diseases (in vitro, in vivo, clinical trials). Based upon this review, it was found that in recent years studies have focused mainly on the assessment of the effectiveness of propolis and its chemical components against COVID-19. Propolis exerts wide-spectrum antimicrobial activities; thus, propolis extracts can be an effective option in the prevention and treatment of co-infections associated with diseases of the respiratory tract.

The Dynamics of the Neutrophil-to-Lymphocyte and Platelet-to-Lymphocyte Ratios Predict Progression to Septic Shock and Death in Patients with Prolonged Intensive Care Unit Stay

Background and objectives: The prognoses of patients experiencing a prolonged stay in the intensive care unit (ICU) are often significantly altered by hospital-acquired infections (HAIs), the early detection of which might be cumbersome. The aim of this study was to investigate the roles of the neutrophil-to-lymphocyte (NLR), derived-NRL (d-NLR), platelet-to-lymphocyte (PLR), and lymphocyte-to-C-reactive protein (LCR) ratios in predicting the progression to septic shock and death. Materials and Methods: A retrospective analysis of a consecutive series of ninety COVID-19 patients with prolonged hospitalization (exceeding 15 days) admitted to the ICU was conducted. The prevalence of culture-proven HAIs throughout their hospital stays was documented. NLR, dNLR, PLR, and LCR were recorded on admission, day 7, and day 14 to assess their discriminative prowess for detecting further progression to septic shock or death. Results: The prevalence of HAIs was 76.6%, 50% of patients met the criteria for septic shock, and 50% died. The median time to the first positive culture was 13.5 days and 20.5 days for developing septic shock. Mechanical ventilation was a key contributing factor to HAI, septic shock, and mortality. On admission and day 7 NLR, dNLR, PLR, and LCR values had no prognostic relevance for events occurring late during hospitalization. However, day-14 NLR, dNLR, and PLR were independent predictors for progression to septic shock and mortality and have shown good discriminative capabilities. The AUCs for septic shock were 0.762, 0.764, and 0.716, while the values for predicting in-hospital death were 0.782, 0.778, and 0.758, respectively. Conclusions: NLR, dNLR, and PLR are quick, easy-to-use, cheap, effective biomarkers for the detection of a more severe disease course, of the late development of HAIs, and of the risk of death in critically ill patients requiring a prolonged ICU stay.

Neutrophil extracellular traps: Modulation mechanisms by pathogens

Neutrophils, as innate effector cells, play an essential role in the containment and elimination of pathogens. Among the main neutrophil mechanisms use for these processes is the release of neutrophil extracellular traps (NETs), which consist of decondensed DNA decorated with various cytoplasmic proteins. NETs' principal role is the trapping and elimination of infectious agents; therefore, the formation of NETs is regulated by bacteria, fungi, parasites, and viruses through different mechanisms: the presence of virulence factors (adhered or secreted), microbial load, size of the microorganism, and even due to other immune cells activation (mainly platelets). This review summarizes the significant aspects that contribute to NETs modulation by pathogens and their components, and the effect NETs have on these pathogens as a cellular defense mechanism.

Nasopharyngeal microbiome of COVID-19 patients revealed a distinct bacterial profile in deceased and recovered individuals

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.

The impact of infection with COVID-19 on the respiratory microbiome: A narrative review

Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has affected millions of individuals with various implications. Consistent with the crucial role of the microbiome in determining health and disease in humans, various studies have investigated the gut and respiratory microbiome effect on the COVID-19. Microbiota dysbiosis might support the entry, replication, and establishment of SARS-CoV-2 infection by modulating various mechanisms. One of the main mechanisms that the modulation of respiratory microbiota composition during the COVID-19 infection affects the magnitude of the disease is changes in innate and acquired immune responses, including inflammatory markers and cytokines and B- and T-cells. The diversity of respiratory microbiota in COVID-19 patients is controversial; some studies reported low microbial diversity, while others found high diversity, suggesting the role of respiratory microbiota in this disease. Modulating microbiota diversity and profile by supplementations and nutrients can be applied prophylactic and therapeutic in combating COVID-19. Here, we discussed the lung microbiome dysbiosis during various lung diseases and its interaction with immune cells, focusing on COVID-19.

Global Coinfections with Bacteria, Fungi, and Respiratory Viruses in Children with SARS-CoV-2: A Systematic Review and Meta-Analysis

Background: Coinfection with bacteria, fungi, and respiratory viruses has been described as a factor associated with more severe clinical outcomes in children with COVID-19. Such coinfections in children with COVID-19 have been reported to increase morbidity and mortality. Objectives: To identify the type and proportion of coinfections with SARS-CoV-2 and bacteria, fungi, and/or respiratory viruses, and investigate the severity of COVID-19 in children. Methods: For this systematic review and meta-analysis, we searched ProQuest, Medline, Embase, PubMed, CINAHL, Wiley online library, Scopus, and Nature through the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for studies on the incidence of COVID-19 in children with bacterial, fungal, and/or respiratory coinfections, published from 1 December 2019 to 1 October 2022, with English language restriction. Results: Of the 169 papers that were identified, 130 articles were included in the systematic review (57 cohort, 52 case report, and 21 case series studies) and 34 articles (23 cohort, eight case series, and three case report studies) were included in the meta-analysis. Of the 17,588 COVID-19 children who were tested for co-pathogens, bacterial, fungal, and/or respiratory viral coinfections were reported (n = 1633, 9.3%). The median patient age ranged from 1.4 months to 144 months across studies. There was an increased male predominance in pediatric COVID-19 patients diagnosed with bacterial, fungal, and/or viral coinfections in most of the studies (male gender: n = 204, 59.1% compared to female gender: n = 141, 40.9%). The majority of the cases belonged to White (Caucasian) (n = 441, 53.3%), Asian (n = 205, 24.8%), Indian (n = 71, 8.6%), and Black (n = 51, 6.2%) ethnicities. The overall pooled proportions of children with laboratory-confirmed COVID-19 who had bacterial, fungal, and respiratory viral coinfections were 4.73% (95% CI 3.86 to 5.60, n = 445, 34 studies, I2 85%, p < 0.01), 0.98% (95% CI 0.13 to 1.83, n = 17, six studies, I2 49%, p < 0.08), and 5.41% (95% CI 4.48 to 6.34, n = 441, 32 studies, I2 87%, p < 0.01), respectively. Children with COVID-19 in the ICU had higher coinfections compared to ICU and non-ICU patients, as follows: respiratory viral (6.61%, 95% CI 5.06−8.17, I2 = 0% versus 5.31%, 95% CI 4.31−6.30, I2 = 88%) and fungal (1.72%, 95% CI 0.45−2.99, I2 = 0% versus 0.62%, 95% CI 0.00−1.55, I2 = 54%); however, COVID-19 children admitted to the ICU had a lower bacterial coinfection compared to the COVID-19 children in the ICU and non-ICU group (3.02%, 95% CI 1.70−4.34, I2 = 0% versus 4.91%, 95% CI 3.97−5.84, I2 = 87%). The most common identified virus and bacterium in children with COVID-19 were RSV (n = 342, 31.4%) and Mycoplasma pneumonia (n = 120, 23.1%). Conclusion: Children with COVID-19 seem to have distinctly lower rates of bacterial, fungal, and/or respiratory viral coinfections than adults. RSV and Mycoplasma pneumonia were the most common identified virus and bacterium in children infected with SARS-CoV-2. Knowledge of bacterial, fungal, and/or respiratory viral confections has potential diagnostic and treatment implications in COVID-19 children.

Therapeutic and palliative role of a Unani herbal decoction in COVID-19 and similar respiratory viral illnesses: Phytochemical & pharmacological perspective

ETHNOPHARMACOLOGICAL RELEVANCE

Outbreaks of respiratory viral infections like Severe Acute Respiratory Syndrome, Middle-East Respiratory Syndrome, and Coronavirus Disease-2019 have been a regular occurrence in the past 100 years. A significant proportion of the morbidity and mortality in influenza is attributed to the co-morbidities and complications induced by the disease, involving the vital organs and physiological functions. In this context, traditional medicines offer effective protective, palliative, and therapeutic benefits, as observed in several studies on various types of influenza, including COVID-19. The Unani herbal decoction comprising of 'Unnāb (Ziziphus jujuba Mill. fruit), Sapistān (Cordia dichotoma G. Forst. fruit), and Behīdāna (Cydonia oblonga Mill. seed) was originally prescribed by Hakim Ajmal Khan (1868-1927 AD) for various respiratory ailments as a bronchodilator, anti-inflammatory, and for clearing the respiratory tract. During COVID-19, the decoction was prescribed by the Ministry of Ayurveda, Yoga, Unani, Siddha, and Homeopathy (AYUSH), Government of India, for mild patients in home isolation, and also as a self-care drink for healthy people. Preliminary studies are of the view that the decoction could reduce COVID-19 incidence and prevent severe disease in the population where it was administered.

AIMS OF THE STUDY

We intend to review the pharmacological activity of the Unani decoction ingredients, i.e., Z. jujuba, C. dichotoma, and C. oblonga, in context with respiratory viral infections and their co-morbidities, to develop an understanding of its action mechanism.

METHODOLOGY

We reviewed Unani classical textbooks for information on the therapeutic activity of the decoction ingredients. Scientific studies published in English from the year 2000 onwards on leading scientific websites (PubMed, MEDLINE, Scopus, and Springer) were searched for information regarding the efficacy of the drugs in influenza and its common complications. Non-English language articles, or those published prior to 2000, and those which included plant parts other than those traditionally included in the decoction were excluded.

OBSERVATIONS

A wide range of therapeutic and palliative effects have been observed in the three herbs included in the Unani decoction, including anti-viral, anti-bacterial, immuno-modulatory, anti-inflammatory, hepato-, and nephroprotective, anti-atherosclerotic, anti-tussive, broncho-dilatory, and regulation of gut microbiota. Together, these effects can help to mitigate and prevent most of the complications caused as a result of respiratory viral infections.

CONCLUSION

The combined effects of ingredients in this Unani herbal decoction can potentially help to mitigate most of the pathological changes and complications caused by influenza viruses. With further clinical research, the decoction may be potentially utilized as a prophylactic and therapeutic against viral influenza.

Legionella pneumophila Cas2 Promotes the Expression of Small Heat Shock Protein C2 That Is Required for Thermal Tolerance and Optimal Intracellular Infection

Previously, we demonstrated that Cas2 encoded within the CRISPR-Cas locus of Legionella pneumophila strain 130b promotes the ability of the Legionella pathogen to infect amoebal hosts. Given that L. pneumophila Cas2 has RNase activity, we posited that the cytoplasmic protein is regulating the expression of another Legionella gene(s) that fosters intracellular infection. Proteomics revealed 10 proteins at diminished levels in the cas2 mutant, and reverse transcription-quantitative (qRT-PCR) confirmed the reduced expression of a gene encoding putative small heat shock protein C2 (HspC2), among several others. As predicted, the gene was expressed more highly at 37°C to 50°C than that at 30°C, and an hspC2 mutant, but not its complemented derivative, displayed ~100-fold reduced CFU following heat shock at 55°C. Compatible with the effect of Cas2 on hspC2 expression, strains lacking Cas2 also had impaired thermal tolerance. The hspC2 mutant, like the cas2 mutant before it, was greatly impaired for infection of Acanthamoeba castellanii, a frequent host for legionellae in waters. HspC2 and Cas2 were not required for entry into these host cells but promoted the replicative phase of intracellular infection. Finally, the hspC2 mutant exhibited an additional defect during the infection of macrophages, which are the primary host for legionellae during lung infection. In summary, hspC2 is upregulated by the presence of Cas2, and HspC2 uniquely promotes both L. pneumophila extracellular survival at high temperatures and infection of amoebal and human host cells. To our knowledge, these findings also represent the first genetic proof linking Cas2 to thermotolerance, expanding the repertoire of noncanonical functions associated with CRISPR-Cas proteins.

Antiviral Activity of Ficus rubiginosa Leaf Extracts against HSV-1, HCoV-229E and PV-1

Ficus rubiginosa plant extract showed antimicrobial activity, but no evidence concerning its antiviral properties was reported. The antiviral activity of the methanolic extract (MeOH) and its n-hexane (H) and ethyl acetate (EA) fractions against Herpes simplex virus-1 (HSV-1), Human coronavirus (HCoV) -229E, and Poliovirus-1 (PV-1) was investigated in the different phases of viral infection in the VERO CCL-81 cell line. To confirm the antiviral efficacy, a qPCR was conducted. The recorded cytotoxic concentration 50% was 513.1, 298.6, and 56.45 µg/mL for MeOH, H, and EA, respectively, assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay after 72 h of treatment. The Ficus rubiginosa leaf extract inhibited the replication of HSV-1 in the early stages of infection, showing a complete inhibition up to 0.62, 0.31, and 1.25 µg/mL. Against HCoV-229E, a total inhibition up to 1.25 µg/mL for MeOH and H as well as 5 µg/mL for EA was observed. Otherwise, no activity was recorded against PV-1. The leaf extract could act directly on the viral envelope, destructuring the lipid membrane and/or directly blocking the enriched proteins on the viral surface. The verified gene inhibition suggested that the treatments with M, H, and EA impaired HSV-1 and HCoV-229E replication, with a greater antiviral efficiency against HSV-1 compared to HCoV-229E, possibly due to a greater affinity of Ficus rubiginosa towards membrane glycoproteins and/or the different lipid envelopes.

Detection of Intestinal Dysbiosis in Post-COVID-19 Patients One to Eight Months after Acute Disease Resolution

The intestinal microbiota plays an important role in the immune response against viral infections, modulating both innate and adaptive immune responses. The cytokine storm is associated with COVID-19 severity, and the patient's immune status is influenced by the intestinal microbiota in a gut-lung bidirectional interaction. In this study, we evaluate the intestinal microbiota of Brazilian patients in different post-COVID-19 periods, and correlate this with clinical data and the antibiotic therapy used during the acute phase. DNA extracted from stool samples was sequenced and total anti-SARS-CoV-2 antibodies and C-reactive protein were quantified. Compared with controls, there were significant differences in the microbiota diversity in post-COVID-19 patients, suggesting an intestinal dysbiosis even several months after acute disease resolution. Additionally, we detected some genera possibly associated with the post-COVID-19 dysbiosis, including Desulfovibrio, Haemophillus, Dialister, and Prevotella, in addition to decreased beneficial microbes, associated with antibiotic-induced dysbiosis, such as Bifidobacterium and Akkermansia. Therefore, our hypothesis is that dysbiosis and the indiscriminate use of antibiotics during the pandemic may be associated with post-COVID-19 clinical manifestations. In our study, 39% (n = 58) of patients reported symptoms, including fatigue, dyspnea, myalgia, alopecia, anxiety, memory loss, and depression. These data suggest that microbiota modulation may represent a target for recovery from acute COVID-19 and a therapeutic approach for post-COVID-19 sequelae.

Differential gene expression profiling reveals potential biomarkers and pharmacological compounds against SARS-CoV-2: Insights from machine learning and bioinformatics approaches

The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has created an urgent global situation. Therefore, it is necessary to identify the differentially expressed genes (DEGs) in COVID-19 patients to understand disease pathogenesis and the genetic factor(s) responsible for inter-individual variability and disease comorbidities. The pandemic continues to spread worldwide, despite intense efforts to develop multiple vaccines and therapeutic options against COVID-19. However, the precise role of SARS-CoV-2 in the pathophysiology of the nasopharyngeal tract (NT) is still unfathomable. This study utilized machine learning approaches to analyze 22 RNA-seq data from COVID-19 patients (n = 8), recovered individuals (n = 7), and healthy individuals (n = 7) to find disease-related differentially expressed genes (DEGs). We compared dysregulated DEGs to detect critical pathways and gene ontology (GO) connected to COVID-19 comorbidities. We found 1960 and 153 DEG signatures in COVID-19 patients and recovered individuals compared to healthy controls. In COVID-19 patients, the DEG–miRNA, and DEG–transcription factors (TFs) interactions network analysis revealed that E2F1, MAX, EGR1, YY1, and SRF were the highly expressed TFs, whereas hsa-miR-19b, hsa-miR-495, hsa-miR-340, hsa-miR-101, and hsa-miR-19a were the overexpressed miRNAs. Three chemical agents (Valproic Acid, Alfatoxin B1, and Cyclosporine) were abundant in COVID-19 patients and recovered individuals. Mental retardation, mental deficit, intellectual disability, muscle hypotonia, micrognathism, and cleft palate were the significant diseases associated with COVID-19 by sharing DEGs. Finally, the detected DEGs mediated by TFs and miRNA expression indicated that SARS-CoV-2 infection might contribute to various comorbidities. Our results provide the common DEGs between COVID-19 patients and recovered humans, which suggests some crucial insights into the complex interplay between COVID-19 progression and the recovery stage, and offer some suggestions on therapeutic target identification in COVID-19 caused by the SARS-CoV-2.

Easy Fabrication of a Polymeric Transparent Sheet to Combat Microbial Infection

Surges in infectious diseases and their transmission in households and commercial and healthcare settings have increased the use of polymeric materials as protective covers. Despite ongoing efforts, conventional polymeric materials still pose the threat of surface-associated transmission of pathogens due to the fact that they lack antimicrobial properties. Here, we have developed an easy-to-fabricate polymeric sheet [quaternary polymeric transparent sheet (QPTS)] that shows an excellent antimicrobial property and is also transparent in nature, increasing its practical applications in a wide range of surfaces. The sheet was fabricated by combining cationic amphiphilic water-soluble polyethylenimine derivative (QPEINH-C₆) and poly(vinyl alcohol) (PVA). The optimum composition (QPTS-3) exhibited a complete reduction of bacterial and fungal infection (∼3-4 log reduction) within 15 min. QPTS-3 also exhibited activity against antibiotic-insusceptible metabolically inactive bacterial cells. The sheet prevented the growth of MRSA biofilm even after 72 h of incubation, which was confirmed through electron microscopy on the QPTS sheet. Most importantly, ∼99.9% of the influenza viral load was reduced completely within 30 min of exposure of the sheet. Apart from the antimicrobial property, the sheet successfully retained its transparency (∼88%) and maintained a significant mechanical strength (∼15 N), highlighting its potential applications in commercial and healthcare settings.

Evaluation of Bi-Lateral Co-Infections and Antibiotic Resistance Rates among COVID-19 Patients in Lahore, Pakistan

Background and Objective: Bacterial infections are among the major complications of many viral respiratory tract illnesses, such as influenza and coronavirus disease-2019 (COVID-19). These bacterial co-infections are associated with an increase in morbidity and mortality rates. The current observational study was conducted at a tertiary care hospital in Lahore, Pakistan among COVID-19 patients with the status of oxygen dependency to see the prevalence of bacterial co-infections and their antibiotic susceptibility patterns. Materials and Methods: A total of 1251 clinical samples were collected from already diagnosed COVID-19 patients and tested for bacterial identification (cultures) and susceptibility testing (disk diffusion and minimum inhibitory concentration) using gold standard diagnostic methods. Results: From the total collected samples, 234 were found positive for different bacterial isolates. The most common isolated bacteria were Escherichia coli (E. coli) (n = 62) and Acinetobacter baumannii (A. baumannii) (n = 47). The E. coli isolates have shown the highest resistance to amoxicillin and ampicillin, while in the case of A. baumannii, the highest resistance was noted against tetracycline. The prevalence of methicillin resistant Staphylococcus aureus (MRSA) was 14.9%, carbapenem resistant Enterobacteriaceae (CRE) was 4.5%, and vancomycin resistant Enterococcus (VRE) was 3.96%. Conclusions: The results of the current study conclude that empiric antimicrobial treatment in critically ill COVID-19 patients may be considered if properly managed within institutional or national level antibiotic stewardship programs, because it may play a protective role in the case of bacterial co-infections, especially when a patient has other AMR risk factors, such as hospital admission within the previous six months.

The Severity of the Co-infection of Mycoplasma pneumoniae in COVID-19 Patients

Background and objective

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that causes coronavirus disease 2019 (COVID-19) infection, with symptoms ranging from mild upper respiratory illness to multisystem organ failure, and even death. Since its discovery in December 2019, the SARS-CoV-2 virus has led to a global pandemic, rapidly spreading to countries around the world, with millions of reported deaths to date. As researchers around the world continue to analyze and interpret the data gathered regarding the novel virus, it is evident that its co-infection with various bacterial pathogens is associated with a worse overall prognosis. One such bacterial pathogen, Mycoplasma pneumoniae (M. pneumoniae), has been associated with an increase in inpatient mortality, length of hospital stay, and need for mechanical ventilation. The aim of this study was to evaluate the characteristics and outcomes of patients co-infected with SARS-CoV-2 and M. pneumoniae. We sought to determine if this co-infection led to increased incidence of ventilatory support, intensive care unit (ICU) stay, and mortality.

Materials and Methods

A multi-center retrospective study was conducted involving patients aged 18 years and older. We compared the incidence of in-hospital mortality, ICU stay, and mechanical ventilation support between COVID-19-positive patients with and without M. pneumoniae co-infection. Based on the collected data, a binary logistic regression model was implemented to assess the correlation between mortality and ventilatory support, while linear regression was used to study the length of stay (LOS) independent variable.

Results

A total of 1,208 patients with a positive SARS-CoV-2 test were identified. Among them, 604 (50%) had an M. pneumoniae co-infection. LOS (95% CI for the coefficient estimate [0.86, 1.05], p<0.001), need for mechanical ventilation (95% CI for the odds ratio [2.60, 6.02], p<0.001), and inpatient mortality (95% CI for the odds ratio [1.43, 2.97], p<0.001) among those co-infected were significantly higher compared to COVID-19 patients without concomitant M. pneumoniae infection.

Conclusion

COVID-19 with a concomitant M. pneumoniae infection was found to have worse outcomes and overall prognosis when compared to individuals with independent disease states. Based on retrospective data gathered from a large multicenter database, the rates of mortality, ventilatory support, and length of hospital stay were significantly worse in patients with a co-infection of SARS-CoV-2 and M. pneumoniae.

COVID-19 Clinical Profiles and Fatality Rates in Hospitalized Patients Reveal Case Aggravation and Selective Co-Infection by Limited Gram-Negative Bacteria

Bacterial co-infections may aggravate COVID-19 disease, and therefore being cognizant of other pathogens is imperative. We studied the types, frequency, antibiogram, case fatality rates (CFR), and clinical profiles of co-infecting-pathogens in 301 COVID-19 patients. Co-infection was 36% (n = 109), while CFR was 31.2% compared to 9.9% in non-co-infected patients (z-value = 3.1). Four bacterial species dominated, namely, multidrug-resistant Klebsiella pneumoniae (37%, n = 48), extremely drug-resistant Acinetobacter baumannii (26%, n = 34), multidrug-resistant Eschericia. coli (18.6%, n = 24), and extremely drug-resistant Pseudomonas aeruginosa (8.5%, n = 11), in addition to other bacterial species (9.3%, n = 12). Increased co-infection of K. pneumoniae and A. baumannii was associated with increased death rates of 29% (n = 14) and 32% (n = 11), respectively. Klebsiella pneumoniae was equally frequent in respiratory and urinary tract infections (UTI), while E. coli mostly caused UTI (67%), and A. baumannii and P. aeruginosa dominated respiratory infections (38% and 45%, respectively). Co-infections correlated with advance in age: seniors ≥ 50 years (71%), young adults 21–49 years (25.6%), and children 0–20 years (3%). These findings have significant clinical implications in the successful COVID-19 therapies, particularly in geriatric management. Future studies would reveal insights into the potential selective mechanism(s) of Gram-negative bacterial co-infection in COVID-19 patients.

An easy-to-use antimicrobial hydrogel effectively kills bacteria, fungi, and influenza virus

Various drug resistant pathogens such as bacteria, fungi and viruses enter a host through different routes, which can lead to health-related problems and even fatalities. Propagation of these infectious microbes majorly occurs through the mucosal openings or upon topical contact. To curb their transmission or to cure infections associated with these pathogens, herein we describe the development of an antimicrobial hydrogel, based on a water soluble quaternary lipophilic polyethyleneimine derivative (QPEINH-C₆). The cationic polymer QPEINH-C₆ exhibited antibacterial activity against drug-resistant Gram-positive bacteria (MIC = 10-62 μg mL^-1) and Gram-negative bacteria (MIC = 117-123 μg mL^-1). The derivative showed killing of human pathogenic fungi (MIC = 58-67 μg mL^-1), including their clinical isolates. The rapid bactericidal and fungicidal nature were confirmed from the fast inactivation kinetics of bacterial cells (methicillin resistant S. aureus and vancomycin resistant S. aureus) within 3-6 hours and C. albicans within 1 h with ∼5-6 log reduction in the microbial burden. This antibacterial and antifungal cationic polymer was then used to construct an antimicrobial shear-thinning hydrogel (Bacfuvir), through non-covalent crosslinking with biocompatible gellan and polyvinyl alcohol (PVA). This hydrogel displayed ∼5-7 log reduction of numerous multidrug-resistant bacteria and their stationary phase cells which are insusceptible to conventional antibiotics. In addition, >99.9 % viable bacterial burden was reduced from preformed biofilm matrices of drug-resistant bacteria. Alongside, fluconazole-resistant C. albicans strains were killed completely within 15-60 min upon exposure to Bacfuvir gel. Most importantly, MRSA and C. albicans cells were reduced (3-4 log) in polymicrobial biofilms after hydrogel treatment. The hydrogel exhibited 99.9 % reduction of influenza viruses in a rapid manner. Due to the biocompatibility of Bacfuvir gel on topical application in a murine model and easy administration owing to its shear-thinning behaviour, this hydrogel can markedly contribute to mitigating drug-resistant bacterial, fungal and viral infections in healthcare settings.

Acinetobacter baumannii Isolates from COVID-19 Patients in a Hospital Intensive Care Unit: Molecular Typing and Risk Factors

Infections caused by Acinetobacter baumannii represent a major concern for intensive care unit (ICU) patients. However, the epidemiology of these infections among COVID-19 patients has not been fully explored. The aims of this study were (i) to characterize the clonal spread of A. baumannii among COVID-19 patients admitted to the ICU of the Umberto I hospital of Rome during the first year of the pandemic and (ii) to identify risk factors for its acquisition. Isolates were analysed by pulsed-field gel electrophoresis, and a multivariable regression model was constructed. Adjusted odds ratios (aORs) and 95% confidence intervals (CIs) were calculated. Overall, 193 patients were included, and 102 strains were analysed. All isolates had highly antibiotic-resistant profiles and derived from two genotypes. The cumulative incidence of A. baumannii acquisition (colonization or infection) was 36.8%. Patients with A. baumannii had higher mortality and length of stay. Multivariable analysis showed that previous carbapenem use was the only risk factor associated with A. baumannii acquisition (aOR: 4.15, 95% CI: 1.78–9.64). We documented substantial A. baumannii infections and colonization and high levels of clonal transmission. Given the limited treatment options, effective prevention and containment strategies to limit the spread of A. baumannii should be implemented.

SARS-CoV-2-Legionella Co-Infections: A Systematic Review and Meta-Analysis (2020-2021)

Legionnaires' Disease (LD) is a severe, sometimes fatal interstitial pneumonia due to Legionella pneumophila. Since the inception of the SARS-CoV-2 pandemic, some contradictory reports about the effects of lockdown measures on its epidemiology have been published, but no summary evidence has been collected to date. Therefore, we searched two different databases (PubMed and EMBASE) focusing on studies that reported the occurrence of LD among SARS-CoV-2 cases. Data were extracted using a standardized assessment form, and the results of such analyses were systematically reported, summarized, and compared. We identified a total of 38 articles, including 27 observational studies (either prospective or retrospective ones), 10 case reports, and 1 case series. Overall, data on 10,936 SARS-CoV-2 cases were included in the analyses. Of them, 5035 (46.0%) were tested for Legionella either through urinary antigen test or PCR, with 18 positive cases (0.4%). A pooled prevalence of 0.288% (95% Confidence Interval (95% CI) 0.129-0.641), was eventually calculated. Moreover, detailed data on 19 co-infections LD + SARS-CoV-2 were obtained (males: 84.2%; mean age: 61.9 years, range 35 to 83; 78.9% with 1 or more underlying comorbidities), including 16 (84.2%) admissions to the ICU, with a Case Fatality Ratio of 26.3%. In summary, our analyses suggest that the occurrence of SARS-CoV-2-Legionella infections may represent a relatively rare but not irrelevant event, and incident cases are characterized by a dismal prognosis.

Does the Fetus Limit Antibiotic Treatment in Pregnant Patients with COVID-19?

During pregnancy, there is a state of immune tolerance that predisposes them to viral infection, causing maternal-fetal vulnerability to the adverse effects of COVID-19. Bacterial coinfections significantly increase the mortality rate for COVID-19. However, it is known that all drugs, including antibiotics, will enter the fetal circulation in a variable degree despite the role of the placenta as a protective barrier and can cause teratogenesis or other malformations depending on the timing of exposure to the drug. Also, it is important to consider the impact of the indiscriminate use of antibiotics during pregnancy can alter both the maternal and fetal-neonatal microbiota, generating future repercussions in both. In the present study, the literature for treating bacterial coinfections in pregnant women with COVID-19 is reviewed. In turn, we present the findings in 50 pregnant women hospitalized diagnosed with SARS-CoV-2 without previous treatment with antibiotics; moreover, a bacteriological culture of sample types was performed. Seven pregnant women had coinfection with Staphylococcus haemolyticus, Staphylococcus epidermidis, Streptococcus agalactiae, Escherichia coli ESBL +, biotype 1 and 2, Acinetobacter jahnsonii, Enterococcus faecium, and Clostridium difficile. When performing the antibiogram, resistance to multiple drugs was found, such as macrolides, aminoglycosides, sulfa, dihydrofolate reductase inhibitors, beta-lactams, etc. The purpose of this study was to generate more scientific evidence on the better use of antibiotics in these patients. Because of this, it is important to perform an antibiogram to prevent abuse of empirical antibiotic treatment with antibiotics in pregnant women diagnosed with SARS-CoV-2.

Dysbiosis of Oral and Gut Microbiomes in SARS-CoV-2 Infected Patients in Bangladesh: Elucidating the Role of Opportunistic Gut Microbes

Coronavirus disease-2019 (COVID-19) is an infectious disease caused by SARS-CoV-2 virus. The microbes inhabiting the oral cavity and gut might play crucial roles in maintaining a favorable gut environment, and their relationship with SARS-CoV-2 infection susceptibility and severity is yet to be fully explored. This study investigates the diversity and species richness of gut and oral microbiota of patients with COVID-19, and their possible implications toward the severity of the patient's illness and clinical outcomes. Seventy-four (n = 74) clinical samples (gut and oral) were collected from 22 hospitalized patients with COVID-19 with various clinical conditions and 15 apparently healthy people (served as controls). This amplicon-based metagenomic sequencing study yielded 1,866,306 paired-end reads that were mapped to 21 phyla and 231 classified genera of bacteria. Alpha and beta diversity analyses revealed a distinct dysbiosis of the gut and oral microbial communities in patients with COVID-19, compared to healthy controls. We report that SARS-CoV-2 infection significantly reduced richness and evenness in the gut and oral microbiomes despite showing higher unique operational taxonomic units in the gut. The gut samples of the patients with COVID-19 included 46 opportunistic bacterial genera. Escherichia, Shigella, and Bacteroides were detected as the signature genera in the gut of patients with COVID-19 with diarrhea, whereas a relatively higher abundance of Streptococcus was found in patients with COVID-19 having breathing difficulties and sore throat (BDST). The patients with COVID-19 had a significantly lower abundance of Prevotella in the oral cavity, compared to healthy controls and patients with COVID-19 without diabetes, respectively. The altered metabolic pathways, including a reduction in biosynthesis capabilities of the gut and oral microbial consortia after SARS-CoV-2 infection, were also observed. The present study may, therefore, shed light on interactions of SARS-CoV-2 with resilient oral and gut microbes which might contribute toward developing microbiome-based diagnostics and therapeutics for this deadly pandemic disease.

Immunomodulatory Potential of Non-Classical HLA-G in Infections including COVID-19 and Parasitic Diseases

Human Leukocyte Antigen-G (HLA-G), a polymorphic non-classical HLA (HLA-Ib) with immune-regulatory properties in cancers and infectious diseases, presents both membrane-bound and soluble (sHLA-G) isoforms. Polymorphism has implications in host responses to pathogen infections and in pathogenesis. Differential expression patterns of HLA-G/sHLA-G or its polymorphism seem to be related to different pathological conditions, potentially acting as a disease progression biomarker. Pathogen antigens might be involved in the regulation of both membrane-bound and sHLA-G levels and impact immune responses during co-infections. The upregulation of HLA-G in viral and bacterial infections induce tolerance to infection. Recently, sHLA-G was found useful to identify the prognosis of Coronavirus disease 2019 (COVID-19) among patients and it was observed that the high levels of sHLA-G are associated with worse prognosis. The use of pathogens, such as Plasmodium falciparum, as immune modulators for other infections could be extended for the modulation of membrane-bound HLA-G in COVID-19-infected tissues. Overall, such information might open new avenues concerning the effect of some pathogens such as parasites in decreasing the expression level of HLA-G to restrict pathogenesis in some infections or to influence the immune responses after vaccination among others.

SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts

The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. This study characterizes the effects of SARS-CoV-2 infection on human nasopharyngeal microbiomes and their relevant metabolic functions. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 patients = 8, recovered humans = 7, and healthy people = 7) were collected, and underwent to RNAseq-based metagenomic investigation. Our RNAseq data mapped to 2281 bacterial species (including 1477, 919 and 676 in healthy, COVID-19 and recovered metagenomes, respectively) indicating a distinct microbiome dysbiosis. The COVID-19 and recovered samples included 67% and 77% opportunistic bacterial species, respectively compared to healthy controls. Notably, 79% commensal bacterial species found in healthy controls were not detected in COVID-19 and recovered people. Similar dysbiosis was also found in viral and archaeal fraction of the nasopharyngeal microbiomes. We also detected several altered metabolic pathways and functional genes in the progression and pathophysiology of COVID-19. The nasopharyngeal microbiome dysbiosis and their genomic features determined by our RNAseq analyses shed light on early interactions of SARS-CoV-2 with the nasopharyngeal resident microbiota that might be helpful for developing microbiome-based diagnostics and therapeutics for this novel pandemic disease.