Molecular pathogenesis of secondary bacterial infection associated to viral infections including SARS-CoV-2

Assessment of upper respiratory and gut bacterial microbiomes during COVID-19 infection in adults: potential aerodigestive transmission

SARS-CoV-2 is the viral pathogen responsible for COVID-19. Although morbidity and mortality frequently occur as a result of lung disease, the gastrointestinal (GI) tract is recognized as a primary location for SARS-CoV-2. Connections and interactions between the microbiome of the gut and respiratory system have been linked with viral infections via what has been referred to as the 'gut-lung axis' with potential aerodigestive communication in health and disease. This research explored the relationship between the microbiomes of the upper respiratory and GI tracts in patients with COVID-19 and examined Extraesophageal reflux (EOR), a mechanism which could contribute to dysregulated communication between the GI and respiratory tract (as identified in COVID-19). 97 patients with a laboratory diagnosis of COVID-19 infection, and 50 age-matched controls were recruited and stool, saliva and sputum were obtained from each participant. ELISA Pepsin tests and Reflux Symptom Index scores (RSI) were conducted for EOR assessment. DNA sequencing of the V4 region of the 16 S rRNA gene was performed for microbiome analysis. No differences were observed between the fecal microbiome's alpha and Shannon diversity indices; however, a distinct microbial composition was observed in COVID-19 patients (when compared to the controls). The respiratory microbiota from individuals with COVID-19 demonstrated a statistically significant reduction in Shannon diversity and bacterial richness alongside an overall reduction in the prevalence of organisms from a typical healthy respiratory microbiome. Furthermore, the bacterial richness of the stool and sputum samples was significantly lower among COVID-19 patients admitted to ICU. A significantly higher RSI score and salivary pepsin level were detected among those with COVID-19. The data indicates that COVID-19 is associated with a dysregulation of both the gut and lung microbiome with a more marked perturbation in the lung, particularly among COVID-19 patients who had been admitted to the ICU. The presence of increased RSI scores, combined with elevated levels of Pepsin, suggests that increased micro-aspiration may occur, which is consistent with of under-recognized interactions between the GI and lung microbiomes in COVID-19 patients and requires additional study. Such studies would benefit from the insights provided by biological samples which reflect the continuum of the aerodigestive tract.

Diagnostic and prognostic values of NSCLC patients with or without obstructive pneumonia after sleeve lobectomy

Objective

We aimed to identify the diagnostic value of next-generation sequencing (NGS) of bronchoalveolar lavage fluid (BALF) from patients with non-small-cell lung cancer (NSCLC).

Methods

Forty patients who were initially diagnosed with pulmonary nodules were enrolled. Frozen section histology was used to identify the NSCLC cell types. NGS of collected BALF samples was used for microbial identification. We compared the bacterial and viral distributions in BALF samples from patients with NSCLC with and without obstructive pneumonia as well as their NSCLC drainage times following surgery.

Results

Of the 29 patients with NSCLC, eight had obstructive pneumonia. Streptococcus pneumoniae, Streptococcus pseudopneumoniae, and Haemophilus parainfluenzae were the top three bacteria present in almost 50% of patients, both with and without obstructive pneumonia. The viral detection rate was higher in the BALF of patients with NSCLC who did not have obstructive pneumonia. However, in patients with NSCLC and drain times of >5 days, the human herpes virus type 7 detection rate was higher following surgery than it was in patients with NSCLC who had drain times of ≤5 days.

Conclusion

Viral imbalance in NSCLC is closely related to the occurrence of obstructive pneumonia and postoperative drainage time.

Protective effect of interferon type I on barrier function of human airway epithelium during rhinovirus infections in vitro

The airway epithelium provides a crucial barrier against infection with respiratory pathogens. This barrier can be impaired following viral infection, paving the way for bacterial superinfections. Type I interferons (IFNs) are important antiviral mediators, and inhaled formulations of these glycoproteins are considered a potential approach for the treatment of respiratory viral infections. To investigate if type I IFNs can also protect against virus-induced epithelial barrier dysfunction, differentiated primary bronchial epithelial cells were pre-treated with IFN-β1a and subsequently infected with human rhinovirus (HRV) for 24 to 72h. Moreover, to functionally assess the effects of IFN-β1a pre-treatment on barrier integrity, we conducted co-infection experiments, in which cells were initially infected with HRV, and superinfected with Streptococcus pneumoniae 24 to 72 h later. In untreated cells, HRV infection significantly damaged ZO-1 positive tight junctions and cilia, and transiently increased permeability, whereas the barrier of cultures pre-treated with IFN-β1a remained intact. In co-infection experiments, bacteria were able to penetrate deeper into the cell layers of HRV-infected cultures than into those of uninfected cells. IFN-β1a pre-treatment abrogated virus-induced damage to the epithelial barrier. Taken together, these data demonstrate a beneficial effect of IFN-β in protecting epithelial barrier function in addition to its antiviral effects.

Potential activity of nanomaterials to combat SARS-CoV-2 and mucormycosis ‎coinfection‎

INTRODUCTION

Mucormycosis, popularly known as the black fungus, has become a worldwide concern in the continuing COVID-19 pandemic, causing increased morbidity and death in immunocompromised people. Due to multi-drug resistance and the limited number of antifungals, surgical interventions, ‎including the excision of infected tissue, remain a standard treatment option‎. Surgical treatment usually results in the loss of organs or their function, long-term intensive care, and a significant risk of reinfection during the procedure. A comprehensive approach is needed to treat the disease, and nanomaterials can be a powerful alternative therapeutic approach.

AREAS COVERED

We searched PubMed, Scopus, and Google Scholar with the keywords 'emerging role of nanomaterials,' and 'combating COVID-19-related mucormycosis,' and reviewed the related research paper. Antifungal nanomaterials and their delivery can significantly impact the treatment of COVID-19-related fungal infections like mucormycosis. However, the therapeutic options for mucormycosis are limited and drug resistance is also reported.

EXPERT OPINION

The current review encompasses a detailed overview of the recent developments in antifungal/antiviral nanomaterials and the properties of these therapeutic nanomaterials that may contribute to formulating an efficient strategy against invasive mucormycosis. Further extensive research is needed to develop nano-based therapeutics for the management of mucormycosis-viral coinfection with a definitive end-point.

Alteration of the Gut-Lung Axis After Severe COVID-19 Infection and Modulation Through Probiotics: A Randomized, Controlled Pilot Study

BACKGROUND

The gut-lung axis could be a potential therapeutic target for improving post-acute COVID-19 symptoms, and probiotics have been proposed as possible modulators.

AIM

We conducted a pilot study to understand alterations in the gut-lung axis and to explore the effects of a probiotic in post-acute COVID-19 disease.

METHODS

We included patients after severe COVID-19 disease (sCOV, n = 21) in a randomized, placebo-controlled trial to test the effect of a probiotic (Pro-Vi 5, Institute Allergosan, Graz, Austria) in a six-month intervention and used patients after mild disease (mCOV, n = 10) as controls, to compare the intestinal microbiome, metabolome, and patient-reported outcomes and biomarkers along the gut-lung axis at baseline and throughout probiotic intervention.

RESULTS

Compared to mCOV patients, sCOV patients showed lower microbial richness, which was significantly improved by probiotic intervention. A reorganization of Ruminococcaceae and Lachnospiraceae taxa was observed in sCOV patients but remained unaffected by the intervention. Serum metabolome showed a dysregulation of lipoproteins in accordance with higher BMI and comorbidities in sCOV patients. HDL and LDL fractions/components were temporarily decreased in the probiotic group. Stool metabolome was altered at baseline in sCOV patients and an increase in L-DOPA after 3 months and butyrate after 6 months of intervention could be observed. Probiotics partially improved reduced quality of life and modulated altered immune responses in sCOV patients. Increased intestinal permeability at baseline remained unaffected.

CONCLUSION

The study provides evidence of long-term alterations of the gut-lung axis after severe COVID-19 infection and suggests that probiotics can modulate the biomarkers of the gut-lung axis.

Dual Antimicrobial Activity of HTCC and Its Nanoparticles: A Synergistic Approach for Antibacterial and Antiviral Applications Through Combined In Silico and In Vitro Studies

N-(2-hydroxyl) propyl-3-trimethyl ammonium chitosan chloride (HTCC), a quaternized chitosan derivative, has been shown to exhibit a broad spectrum of antimicrobial activity, especially against bacteria and enveloped viruses. Despite this, molecular docking studies showing its atomic-level mechanisms against these microorganisms are scarce. Here, for the first time, we employed molecular docking analyses to investigate the potential antibacterial activity of HTCC against Staphylococcus aureus and its antiviral activity against human immunodeficiency virus 1 (HIV-1). According to the findings, HTCC exhibited promising antibacterial activity with high binding affinities; however, it had limited antiviral activity. To validate these theoretical outcomes, experimental studies were conducted. Different derivatives of HTCC were synthesized and characterized using NMR, XRD, FTIR, and DLS. The in vitro assays validated the potent antibacterial efficacy of HTCC against S. aureus, whereas the antiviral studies did not show good antiviral activity. However, our research also revealed a promising avenue for further exploration of the antimicrobial activity of HTCC nanoparticles (NPs), since, thus far, no studies have been conducted to show the antiviral activity of HTCC NPs against HIV-1. The nanosized HTCC exhibited superior antiviral performance compared to the parent polymers, with complete (100%) inhibition of HIV-1 viral activity at the highest tested concentration (0.33 mg/mL).

Inhibition of neutrophil swarming by type I interferon promotes intracellular bacterial evasion

Listeria monocytogenes (LM) possesses the ability to breach multiple barriers and elicit intricate immune responses. However, there remains a lack of explicit understanding regarding how LM evades innate immune surveillance within the body. Here, we utilized liver intravital imaging to elucidate the dynamic process of LM during infection in the liver. We discovered that LM can rapidly escape from Kupffer cells (KCs) through listeriolysin O (LLO) and proliferate within hepatocytes. Upon LM exposure to the hepatic sinusoids, neutrophils rapidly aggregate at the site of infection. Subsequently, LM can induce type I interferon (IFN-I) production primarily in the spleen, which acts systemically on neutrophils to hamper their swarming by deactivating the ERK pathway, thus evading neutrophil-mediated eradication. Furthermore, our findings suggest that virus-induced IFN-I suppresses neutrophil swarming, and COVID-19 patients exhibit impaired neutrophil aggregation function. In conclusion, our findings provide compelling evidence demonstrating that intracellular bacteria represented by LM can hijack host defense mechanisms against viral infections to evade immune surveillance. Additionally, impaired neutrophil swarming caused by IFN-I is one of the significant factors contributing to the increased susceptibility to bacterial infections following viral infections.

Host immunomodulation strategies to combat pandemic-associated antimicrobial-resistant secondary bacterial infections

The incidence of secondary bacterial infections has increased in recent decades owing to various viral pandemics. These infections further increase the morbidity and mortality rates associated with viral infections and remain a significant challenge in clinical practice. Intensive antibiotic therapy has mitigated the threat of such infections; however, overuse and misuse of antibiotics have resulted in poor outcomes, such as inducing the emergence of bacterial populations with antimicrobial resistance (AMR) and reducing the therapeutic options for this crisis. Several antibiotic substitutes have been suggested and employed; however, they have certain limitations and novel alternatives are urgently required. This review highlights host immunomodulation as a promising strategy against secondary bacterial infections to overcome AMR. The definition and risk factors of secondary bacterial infections, features and limitations of currently available therapeutic strategies, host immune responses, and future perspectives for treating such infections are discussed.

Consequences of the COVID-19 Pandemic on the Incidence, Management and Outcomes of Staphylococcus aureus Bacteraemia: Experience in a Spanish Hospital

This work aims to assess the impact of the COVID-19 pandemic on the mortality and incidence of complications in patients with bacteraemia due to Staphylococcus aureus (BSA). All episodes of BSA at the Costa del Sol University Hospital (Marbella, Spain) were recorded during the acute phase of the COVID-19 pandemic (March 2020-March 2022) and compared with those in a previous period (February 2018-February 2020). Demographic, clinical and prognostic variables were recorded. The outcomes were measured as 14- and 30-day mortality and the incidence of complications/death. Mortality during the pandemic was 28.7% at 14 days and 35% at 30 days, while in the pre-pandemic group, it was 18.9% and 23.3%, respectively. For overall complications/deaths, the incidence rate was higher in the pandemic group, with 42.7%. No significant differences were observed between groups. Seventeen patients with COVID-19 were identified, with mortality rates of 64.7% and 70.6% at 14 and 30 days. Multivariate analysis established the presence of sepsis at diagnosis as a predictor of mortality, but not BSA, during the pandemic phase. In conclusion, BSA is a disease with high mortality, which was slightly higher during the pandemic phase. No differences were found in adherence to the bundle in our centre.

A prospective longitudinal study assessing the impact of rhinovirus and bacterial infections in acute exacerbations of chronic rhinosinusitis

BACKGROUND

Acute exacerbations of chronic rhinosinusitis (AECRS) are thought to arise from common viral infections progressing to secondary bacterial infections. However, the pathophysiology of AECRS remains poorly understood due to a lack of prospective longitudinal studies.

METHODS

We conducted a one-year prospective longitudinal study involving chronic rhinosinusitis (CRS) adults. At baseline, we assessed subjective symptom scores using a validated upper respiratory infection questionnaire (WURSS), sinonasal outcome testing scores (SNOT-22), and endoscopic scores (modified Lund-Kennedy score). Every 2 weeks, we contacted subjects to collect WURSS and SNOT-22 scores. If WURSS scores were ≥1 and SNOT-22 scores were ≥ 8.9 compared with baseline, subjects underwent an AECRS assessment. We identified rhinovirus (RV) incidence through viral nasal brushings at each visit and bacterial infection through bacterial swabs if mucus scores were ≥1.

RESULTS

Thiry-five of 80 CRS subjects reported at least one AECRS episode during the year, predominantly occurring in the fall and winter seasons. RV infections were detected in 8 of 35 cases, bacterial infections in 17 of 35, and co-occurring infections in 7 of 35. All subjects with AECRS visits exhibited significantly higher endoscopic scores compared with baseline. Subjects with co-occurring RV and bacterial infections demonstrated higher disease severity compared with those with either RV or bacterial infection, or no infection.

CONCLUSIONS

In a one-year prospective longitudinal study involving CRS adults, we identified significant risk factors for AECRS including seasonality and the presence of RV and bacterial infections. These data suggest a standard definition of AECRS and the need to target RV and bacterial infections if we are to help reduce disease severity.

Highly diverse sputum microbiota correlates with the disease severity in patients with community-acquired pneumonia: a longitudinal cohort study

BACKGROUND

Community-acquired pneumonia (CAP) is a common and serious condition that can be caused by a variety of pathogens. However, much remains unknown about how these pathogens interact with the lower respiratory commensals, and whether any correlation exists between the dysbiosis of the lower respiratory microbiota and disease severity and prognosis.

METHODS

We conducted a retrospective cohort study to investigate the composition and dynamics of sputum microbiota in patients diagnosed with CAP. In total, 917 sputum specimens were collected consecutively from 350 CAP inpatients enrolled in six hospitals following admission. The V3-V4 region of the 16 S rRNA gene was then sequenced.

RESULTS

The sputum microbiota in 71% of the samples were predominately composed of respiratory commensals. Conversely, 15% of the samples demonstrated dominance by five opportunistic pathogens. Additionally, 5% of the samples exhibited sterility, resembling the composition of negative controls. Compared to non-severe CAP patients, severe cases exhibited a more disrupted sputum microbiota, characterized by the highly dominant presence of potential pathogens, greater deviation from a healthy state, more significant alterations during hospitalization, and sparser bacterial interactions. The sputum microbiota on admission demonstrated a moderate prediction of disease severity (AUC = 0.74). Furthermore, different pathogenic infections were associated with specific microbiota alterations. Acinetobacter and Pseudomonas were more abundant in influenza A infections, with Acinetobacter was also enriched in Klebsiella pneumoniae infections.

CONCLUSION

Collectively, our study demonstrated that pneumonia may not consistently correlate with severe dysbiosis of the respiratory microbiota. Instead, the degree of microbiota dysbiosis was correlated with disease severity in CAP patients.

Precision nutrition to reset virus-induced human metabolic reprogramming and dysregulation (HMRD) in long-COVID

SARS-CoV-2, the etiological agent of COVID-19, is devoid of any metabolic capacity; therefore, it is critical for the viral pathogen to hijack host cellular metabolic machinery for its replication and propagation. This single-stranded RNA virus with a 29.9 kb genome encodes 14 open reading frames (ORFs) and initiates a plethora of virus-host protein-protein interactions in the human body. These extensive viral protein interactions with host-specific cellular targets could trigger severe human metabolic reprogramming/dysregulation (HMRD), a rewiring of sugar-, amino acid-, lipid-, and nucleotide-metabolism(s), as well as altered or impaired bioenergetics, immune dysfunction, and redox imbalance in the body. In the infectious process, the viral pathogen hijacks two major human receptors, angiotensin-converting enzyme (ACE)-2 and/or neuropilin (NRP)-1, for initial adhesion to cell surface; then utilizes two major host proteases, TMPRSS2 and/or furin, to gain cellular entry; and finally employs an endosomal enzyme, cathepsin L (CTSL) for fusogenic release of its viral genome. The virus-induced HMRD results in 5 possible infectious outcomes: asymptomatic, mild, moderate, severe to fatal episodes; while the symptomatic acute COVID-19 condition could manifest into 3 clinical phases: (i) hypoxia and hypoxemia (Warburg effect), (ii) hyperferritinemia ('cytokine storm'), and (iii) thrombocytosis (coagulopathy). The mean incubation period for COVID-19 onset was estimated to be 5.1 days, and most cases develop symptoms after 14 days. The mean viral clearance times were 24, 30, and 39 days for acute, severe, and ICU-admitted COVID-19 patients, respectively. However, about 25-70% of virus-free COVID-19 survivors continue to sustain virus-induced HMRD and exhibit a wide range of symptoms that are persistent, exacerbated, or new 'onset' clinical incidents, collectively termed as post-acute sequelae of COVID-19 (PASC) or long COVID. PASC patients experience several debilitating clinical condition(s) with >200 different and overlapping symptoms that may last for weeks to months. Chronic PASC is a cumulative outcome of at least 10 different HMRD-related pathophysiological mechanisms involving both virus-derived virulence factors and a multitude of innate host responses. Based on HMRD and virus-free clinical impairments of different human organs/systems, PASC patients can be categorized into 4 different clusters or sub-phenotypes: sub-phenotype-1 (33.8%) with cardiac and renal manifestations; sub-phenotype-2 (32.8%) with respiratory, sleep and anxiety disorders; sub-phenotype-3 (23.4%) with skeleto-muscular and nervous disorders; and sub-phenotype-4 (10.1%) with digestive and pulmonary dysfunctions. This narrative review elucidates the effects of viral hijack on host cellular machinery during SARS-CoV-2 infection, ensuing detrimental effect(s) of virus-induced HMRD on human metabolism, consequential symptomatic clinical implications, and damage to multiple organ systems; as well as chronic pathophysiological sequelae in virus-free PASC patients. We have also provided a few evidence-based, human randomized controlled trial (RCT)-tested, precision nutrients to reset HMRD for health recovery of PASC patients.

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.

Common Bacterial Infections during the 3-Month Period after SARS-CoV-2 Infection: A Retrospective Cohort Study

INTRODUCTION

Correlations between SARS-CoV-2 and bacterial infections have mainly been studied in hospitals, and these studies have shown that such interactions may be lethal for many. In the context of community flora, less is known of the trends and consequences of viral infections relative to subsequent bacterial infections.

PURPOSE

This study aims to explore the prevalence and characteristics of bacterial infections in the three months following SARS-CoV-2 infections, in a community, real-world setting.

METHODS

In this retrospective cohort study, we compared patients who completed a polymerase chain reaction (PCR) test or an antigen test for SARS-CoV-2 during January 2022, the peak of the Omicron wave, and examined bacterial infections following the test. We searched these cases for diagnoses of the following four bacterial infections for three months following the test: Group A Streptococcus (GAS) pharyngitis, pneumonia, cellulitis, and urinary tract infections (UTI).

RESULTS

During January 2022, 267,931 patients tested positive and 261,909 tested negative for SARS-CoV-2. Test-positive compared to test-negative patients were significantly younger (42.5 years old vs. 48.5 years old, p < 0.001), smoked less, and had fewer comorbidities (including ischemic heart disease, diabetes mellitus, hypertension, chronic obstructive pulmonary disease, and chronic renal failure). In the multivariable analysis, test-positive patients had an increased risk for GAS pharyngitis (adjusted odds ratio [aOR] = 1.25, 95% CI 1.14-1.38, p-value < 0.001) and pneumonia (aOR = 1.25, 95% CI 1.15-1.35, p-value < 0.001), a trend towards an increased prevalence of UTI (aOR = 1.05, 95% CI 0.99-1.12, p-value = 0.092), and lower risk for cellulitis (aOR = 0.92, 95% CI 0.86-0.99, p-value < 0.05).

CONCLUSIONS

A history of SARS-CoV-2 infection in the past three months increased susceptibility to respiratory tract bacterial infections and the prevalence of UTI.

Improving antibacterial ability of Ti-Cu thin films with co-sputtering method

Due to the resistance of some bacteria to antibiotics, research in the field of dealing with bacterial infections is necessary. A practical approach utilized in this study involves the preparation of an antibacterial thin film on the surfaces, which can effectively inhibit and reduce biofilm formation and bacterial adherence. In this study, we report the fabrication of bactericidal titanium (Ti) and copper (Cu) surfaces which involves a powerful co-sputtering method. This method provides a situation in which constituent elements are deposited simultaneously to control the composition of the thin film. Prepared samples were examined by energy-dispersive X-ray spectroscopy (EDX), scanning electron microscopy (SEM), X-ray diffraction (XRD), atomic force microscopy (AFM), and contact angle measurements. To evaluate antibacterial behavior, we used two bacterial strains Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus aureus (S. aureus). Antibacterial activity of the prepared sample was assessed by determining the number of colony-forming units per milliliter (CFU/ml) using a standard viable cell count assay. Results indicated that as the Cu concentration increased, the nanoscale surfaces became rougher, with roughness values rising from 11.85 to 49.65 nm, and the contact angle increased from 40 to 80 degrees, indicating a hydrophilic character. These factors play a significant role in the antibacterial properties of the surface. The Ti-Cu films displayed superior antibacterial ability, with a 99.9% reduction (equivalent to a 5-log reduction) in bacterial viability after 2 h compared to Ti alone against both bacterial strains. Field emission scanning electron microscopy (FE-SEM) images verified that both E. coli and S. aureus cells were physically deformed and damaged the bacterial cell ultrastructure was observed. These findings highlight that adding Cu to Ti can improve the antibacterial ability of the surface while inhibiting bacterial adherence. Therefore, the Ti14-Cu86 sample with the highest percentage of Cu had the best bactericidal rate. Investigation of toxicity of Cu-Ti thin films was conducted the using the MTT assay, which revealed their biocompatibility and absence of cytotoxicity, further confirming their potential as promising biomaterials for various applications.

Fungal Infections Are Not Associated with Increased Mortality in COVID-19 Patients Admitted to Intensive Care Unit (ICU)

Introduction

Fungal infection is a cause of increased morbidity and mortality in intensive care patients. Critically unwell patients are at increased risk of developing invasive fungal infections. COVID-19 patients in the intensive care unit (ICU) may be at a particularly high risk. The primary aim of this study was to establish the incidence of secondary fungal infections in patients admitted to the ICU with COVID-19. Secondary aims were to investigate factors that may contribute to an increased risk of fungal infections and to calculate the mortality between fungal and nonfungal groups.

Methods

We undertook a retrospective observational study in a tertiary ICU in Wales, United Kingdom. 174 patients admitted with COVID-19 infection from March 2020 until May 2021 were included. Data were collected through a retrospective review of patient's clinical notes and microbiology investigation results obtained from the online clinical portal.

Results

81/174 (47%) COVID-19 patients developed fungal infections, 93% of which were Candida species, including Candida albicans (88%), and 6% had an Aspergillus infection. Age and smoking history did not appear to be contributing factors. The nonfungal group had a significantly higher body mass index (33 ± 8 vs. 31 ± 7, p=0.01). The ICU length of stay (23 (1-116) vs. 8 (1-60), p < 0.001), hospital length of stay (30 (3-183) vs. 15 (1-174) ± 7, p < 0.001), steroid days (10 (1-116) vs. 4 (0-28), p=0.02), and ventilation days (18 (0-120) vs. 2 (0-55), p < 0.001) were significantly higher in the fungal group. The mortality rate in both groups was similar (51% vs. 52%). The Kaplan-Meier survival analysis showed that the fungal group survived more than the nonfungal group (log rank (Mantel-Cox), p < 0.001).

Conclusion

Secondary fungal infections are common in COVID-19 patients admitted to the ICU. Longer treatment with corticosteroids, increased length of hospital and ICU stay, and greater length of mechanical ventilation significantly increase the risk of fungal infections. Fungal infection, however, was not associated with an increase in mortality.

Impact of immunosuppressive regimen on ICU acquired pneumonia in critically ill COVID-19

BACKGROUND

Immunosuppressors (IS) such as Dexamethasone (DXM), Tocilizumab, and high-dose methylprednisolone boli (HDMB), are used in COVID-19-related acute respiratory distress syndrome (ARDS). This study aimed to determine whether COVID-19 ARDS-related combined IS therapy was associated with an increased incidence of ICU-acquired pneumonia (IAP).

METHODS

We retrospectively analyzed COVID-19-ARDS admitted to ICU from March 2020 to April 2022. Patients' and IAP characteristics were analyzed according to five IS regimens: No IS, DXM alone, DXM+HDMB, DXM+tocilizumab, and DXM+tocilizumab+HDMB. To investigate the role of IS on IAP incidence, we performed a multivariate logistic regression and built a propensity score. Ultimately, we used a conditional logistic regression after pairing on the propensity score.

RESULTS

The study included 496 COVID-19-ARDS. Regarding the IS therapy, 12.7% received no IS, 43% DXM alone, 21.6% DXM+HDMB, 15.5% DXM+tocilizumab and 5.4% DXM+tocilizumab+HDMB. 37% presented at least one IAP, and the IAP incidence was higher with DXM+HDMB (66.4%) compared to no IS (P<0.0001), DXM (P<0.0001) and DXM+tocilizumab (P<0.0001). HDMB and probabilistic antibiotherapy at admission were independent IAP predictors after adjustment on the propensity score (respectively OR:2.44; P<0.0001 and OR:2.85; P<0.001).

CONCLUSIONS

In critically ill COVID-19, HDMB significantly increases the risk of IAP whereas DXM alone, nor in combination with tocilizumab, did not.

Coinfection and superinfection in ICU critically ill patients with severe COVID-19 pneumonia and influenza pneumonia: are the pictures different?

Background

Similar to influenza, coinfections and superinfections are common and might result in poor prognosis. Our study aimed to compare the characteristics and risks of coinfections and superinfections in severe COVID-19 and influenza virus pneumonia.

Methods

The data of patients with COVID-19 and influenza admitted to the intensive care unit (ICU) were retrospectively analyzed. The primary outcome was to describe the prevalence and pathogenic distribution of coinfections/ICU-acquired superinfections in the study population. The secondary outcome was to evaluate the independent risk factors for coinfections/ICU-acquired superinfections at ICU admission. Multivariate analysis of survivors and non-survivors was performed to investigate whether coinfections/ICU-acquired superinfections was an independent prognostic factor.

Results

In the COVID-19 (n = 123) and influenza (n = 145) cohorts, the incidence of coinfections/ICU-acquired superinfections was 33.3%/43.9 and 35.2%/52.4%, respectively. The most common bacteria identified in coinfection cases were Enterococcus faecium, Pseudomonas aeruginosa, and Acinetobacter baumannii (COVID-19 cohort) and A. baumannii, P. aeruginosa, and Klebsiella pneumoniae (influenza cohort). A significant higher proportion of coinfection events was sustained by Aspergillus spp. [(22/123, 17.9% in COVID-19) and (18/145, 12.4% in influenza)]. The COVID-19 group had more cases of ICU-acquired A. baumannii, Corynebacterium striatum and K. pneumoniae. A. baumannii, P. aeruginosa, and K. pneumoniae were the three most prevalent pathogens in the influenza cases with ICU-acquired superinfections. Patients with APACHE II ≥18, CD8+ T cells ≤90/μL, and 50 < age ≤ 70 years were more susceptible to coinfections; while those with CD8+ T cells ≤90/μL, CRP ≥120 mg/L, IL-8 ≥ 20 pg./mL, blood glucose ≥10 mmol/L, hypertension, and smoking might had a higher risk of ICU-acquired superinfections in the COVID-19 group. ICU-acquired superinfection, corticosteroid administration for COVID-19 treatment before ICU admission, and SOFA score ≥ 7 were independent prognostic factors in patients with COVID-19.

Conclusion

Patients with COVID-19 or influenza had a high incidence of coinfections and ICU-acquired superinfections. The represent agents of coinfection in ICU patients were different from those in the general ward. These high-risk patients should be closely monitored and empirically treated with effective antibiotics according to the pathogen.

Roles and Mechanisms of NLRP3 in Influenza Viral Infection

Pathogenic viral infection represents a major challenge to human health. Due to the vast mucosal surface of respiratory tract exposed to the environment, host defense against influenza viruses has perpetually been a considerable challenge. Inflammasomes serve as vital components of the host innate immune system and play a crucial role in responding to viral infections. To cope with influenza viral infection, the host employs inflammasomes and symbiotic microbiota to confer effective protection at the mucosal surface in the lungs. This review article aims to summarize the current findings on the function of NACHT, LRR and PYD domains-containing protein 3 (NLRP3) in host response to influenza viral infection involving various mechanisms including the gut-lung crosstalk.

Epidemiology of COVID-19-Associated Mucormycosis

Purpose of the Review

To describe the epidemiology and risk factors for Coronavirus disease-19 (COVID-19)-associated mucormycosis (CAM) based on current published literature.

Recent Findings

COVID-19 is associated with an increased risk of secondary infections. Mucormycosis is an uncommon invasive fungal infection that typically affects people with immunocompromising conditions and uncontrolled diabetes. Treatment of mucormycosis is challenging and is associated with high mortality even with standard care. During the second wave of the COVID 19 pandemic, an abnormally high number of CAM cases were seen particularly in India. Several case series have attempted to describe the risk factors for CAM.

Summary

A common risk profile identified for CAM includes uncontrolled diabetes and treatment with steroids. COVID-19-induced immune dysregulation as well as some unique pandemic specific risk factors may have played a role.

Complicated Acute Pericarditis and Peripheral Venous Catheter-Related Bloodstream Infection Caused by Methicillin-Resistant Staphylococcus aureus after Influenza B Virus Infection: A Case Report

Background

In this study, we report the case of a 14-month-old female patient transferred from another hospital to our hospital with a 9-day history of fever and worsening dyspnea. Case Report. The patient tested positive for influenza type B virus 7 days before being transferred to our hospital but was never treated. The physical examination performed at presentation revealed redness and swelling of the skin at the site of the peripheral venous catheter insertion performed at the previous hospital. Her electrocardiogram revealed ST segment elevations in leads II, III, aVF, and V2-V6. An emergent transthoracic echocardiogram revealed pericardial effusion. As ventricular dysfunction due to pericardial effusion was not present, pericardiocentesis was not performed. Furthermore, blood culture revealed methicillin-resistant Staphylococcus aureus (MRSA). Thus, a diagnosis of acute pericarditis complicated with sepsis and peripheral venous catheter-related bloodstream infection (PVC-BSI) due to MRSA was made. Frequent bedside ultrasound examinations were performed to evaluate the outcomes of the treatment. After administering vancomycin, aspirin, and colchicine, the patient's general condition stabilized.

Conclusions

In children, it is crucial to identify the causative organism and provide appropriate targeted therapy to prevent worsening of the condition and mortality due to acute pericarditis. Moreover, it is important to carefully monitor the clinical course for the progression of acute pericarditis to cardiac tamponade and evaluate the treatment outcomes.

Epidural Abscesses as a Complication of Interleukin-6 Inhibitor and Dexamethasone Treatment in a Patient with COVID-19 Pneumonia: A Case Report

A 66-year-old female patient was hospitalized with severe COVID-19 pneumonia, which led to hypoxia requiring oxygen support with high-flow nasal cannulae. She received anti-inflammatory treatment with a 10-day dexamethasone 6 mg PO course and a single infusion of IL-6 monoclonal antibody tocilizumab 640 mg IV. Treatment led to gradual reduction of oxygen support. However, on Day 10, she was found to have Staphylococcus aureus bacteremia with epidural, psoas, and paravertebral abscesses as the source. Targeted history taking revealed a dental procedure for periodontitis 4 weeks prior to hospitalization as the probable source. She received an 11-week antibiotic treatment, which led to resolution of the abscesses. This case report highlights the importance of individual infection risk assessment before the initiation of immunosuppressive treatment for COVID-19 pneumonia.

The conceptualization of acute bronchitis in general practice - a fuzzy problem with consequences? A qualitative study in primary care

BACKGROUND

Acute bronchitis is one of the most frequent diagnoses in primary care. Scientifically, it is conceptualized as a viral infection. Still, general practitioners (GPs) often prescribe antibiotics for acute bronchitis. The explanation for this discrepancy may lie in a different conceptualization of acute bronchitis. Therefore, we wanted to know, how GPs conceptualize acute bronchitis, and how they differentiate it from common cold and pneumonia. Furthermore, we tried to find out the GPs' reasons for prescribing antibiotics in those cases.

METHODS

To answer our study questions, we conducted a qualitative study with GPs in Bavaria, Germany, by using semi-structured guided interviews. The analysis of the data was conducted using the documentary method according to Ralf Bohnsack. The transcripts were subdivided into categories. Analyzing each part by reflective interpretation, first manually, secondly with the help of RQDA, we extracted the most representative citations and main messages from the interviews.

RESULTS

The term acute bronchitis seems to be applied when there is neither certainty of the diagnosis common cold, nor of pneumonia. It seems it bridges the gap of uncertainty between supposedly harmless clinical pictures (common cold/viral), to the more serious ones (pneumonia/bacterial). The conceptual transitions between common cold and acute bronchitis on the one side, and acute bronchitis and pneumonia on the other are fluid. The diagnosis acute bronchitis cannot solve the problem of uncertainty but seems to be a label to overcome it by offering a way to include different factors such as severity of symptoms, presumed signs of bacterial secondary infection, comorbidities, and presumed expectations of patients. It seems to solve the pathophysiologic riddle of bacterial or viral and of decision making in prescribing antibiotics.

CONCLUSION

Acute bronchitis as an "intermediate category" proved difficult to define for the GPs. Applying this diagnosis leaves GPs in abeyance of prescribing an antibiotic or not. As a consequence of this uncertainty in pathophysiologic reasoning (viral or bacterial) other clinical and social factors tip the balance towards antibiotic prescribing. Teaching physicians to better think in probabilities of outcomes instead of pathophysiologic reasoning and to deal with uncertainty might help reducing antibiotic overprescribing.

A Tale of Two Pandemics: Antimicrobial Resistance Patterns of Enterococcus spp. in COVID-19 Era

Although the COVID-19 pandemic has held the spotlight over the past years, the antimicrobial resistance (AMR) phenomenon continues to develop in an alarming manner. The lack of strict antibiotic regulation added to the overuse of antimicrobials fueled the AMR pandemic. This paper aims to analyze and identify the impact of the COVID-19 pandemic on antibiotic resistance patterns of Enterococcus spp. The study was designed as a retrospective observational study. Enterococcus spp. infections data were collected from one academic hospital in Cluj-Napoca, Romania over 18 months. A statistical analysis was performed to compare antibiotic resistance phenotypes identified. We recorded an increase in the isolation rates of Enterococcus spp. strains, from 26 isolates (26.53%) during Period A (November 2020-April 2021) to 42 strains (42.85%) during Period C (November 2021-April 2022). The number of strains with resistance to vancomycin increased from 8 during Period A to 17 during Period C. Of the total 36 strains with resistance to vancomycin, 25 were identified as E. faecium. SARS-CoV-2 patients (n = 29) proved to be at risk to develop an E. faecium co-infection (n = 18). We observed that strains with resistance to ampicillin (n = 20) and vancomycin (n = 15) are more often isolated from these patients. All changes identified in our study are to be considered in the light of COVID-19 pandemic, highlighting the threatening AMR phenomenon in Romania. Further studies should be performed to quantify the worldwide effects of these pandemics.

Dissecting Platelet's Role in Viral Infection: A Double-Edged Effector of the Immune System

Platelets play a major role in the processes of primary hemostasis and pathological inflammation-induced thrombosis. In the mid-2000s, several studies expanded the role of these particular cells, placing them in the "immune continuum" and thus changing the understanding of their function in both innate and adaptive immune responses. Among the many receptors they express on their surface, platelets express Toll-Like Receptors (TLRs), key receptors in the inflammatory cell-cell reaction and in the interaction between innate and adaptive immunity. In response to an infectious stimulus, platelets will become differentially activated. Platelet activation is variable depending on whether platelets are activated by a hemostatic or pathogen stimulus. This review highlights the role that platelets play in platelet modulation count and adaptative immune response during viral infection.

Constructing a self-healing injectable SABA/Borax/PDA@AgNPs hydrogel for synergistic low-temperature photothermal antibacterial therapy

Infections caused by bacteria are one of the biggest challenges humans face around the world. Photothermal therapy (PTT) has been regarded as a promising strategy in combating pathogenic infection, however the high temperatures (55-65 °C) required during a single PTT process can induce injury to healthy tissues nearby. Combination therapy could overcome this problem by reducing the photothermal temperature. Here, we developed a self-healing and injectable hydrogel to realize low-temperature PTT (LT-PTT, ≤45 °C) for antisepsis with high-efficiency. The hybrid hydrogel is prepared by incorporating borax into a mixture of 3-aminophenylboronic acid grafted sodium alginate and nano-silver decorated polydopamine nanoparticles. Our results showed that the SABA/Borax/PDA@AgNPs hydrogel possesses satisfactory mechanical properties and self-healing capacity, and as a result, it can repair itself after being damaged mechanically, retaining its integrality and recovering its initial functionalities. Furthermore, through utilizing the photothermal property of polydopamine nanoparticles and broad-spectrum antibacterial activity of nano-silver, the hybrid hydrogel achieves excellent LT-PTT for sterilization both in vitro as well as in an in vivo mice skin wound model with no distinct injury to normal tissues. Overall, our prepared hydrogel is expected to be an excellent candidate for treating bacterial infections.

Preventing Respiratory Viral Diseases with Antimicrobial Peptide Master Regulators in the Lung Airway Habitat

The vast surface area of the respiratory system acts as an initial site of contact for microbes and foreign particles. The whole respiratory epithelium is covered with a thin layer of the airway and alveolar secretions. Respiratory secretions contain host defense peptides (HDPs), such as defensins and cathelicidins, which are the best-studied antimicrobial components expressed in the respiratory tract. HDPs have an important role in the human body's initial line of defense against pathogenic microbes. Epithelial and immunological cells produce HDPs in the surface fluids of the lungs, which act as endogenous antibiotics in the respiratory tract. The production and action of these antimicrobial peptides (AMPs) are critical in the host's defense against respiratory infections. In this study, we have described all the HDPs secreted in the respiratory tract as well as how their expression is regulated during respiratory disorders. We focused on the transcriptional expression and regulation mechanisms of respiratory tract HDPs. Understanding how HDPs are controlled throughout infections might provide an alternative to relying on the host's innate immunity to combat respiratory viral infections.

Microbiome analysis revealing microbial interactions and secondary bacterial infections in COVID-19 patients comorbidly affected by Type 2 diabetes

The mortality of coronavirus disease 2019 (COVID-19) disease is very high among the elderly or individuals having comorbidities such as obesity, cardiovascular diseases, lung infections, hypertension, and/or diabetes. Our study characterizes the metagenomic features in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-infected patients with or without type 2 diabetes, to identify the microbial interactions associated with its fatal consequences.This study compared the baseline nasopharyngeal microbiome of SARS-CoV-2-infected diabetic and nondiabetic patients with controls adjusted for age and gender. The metagenomics based on next-generation sequencing was performed using Ion GeneStudio S5 Series and the data were analyzed by the Vegan-package in R. All three groups possessed significant bacterial diversity and dissimilarity indexes (p < 0.05). Spearman's correlation coefficient network analysis illustrated 183 significant positive correlations and 13 negative correlations of pathogenic bacteria (r = 0.6-1.0, p < 0.05), and 109 positive correlations between normal flora and probiotic bacteria (r > 0.6, p < 0.05). The SARS-CoV-2 diabetic group exhibited a significant increase in pathogens and secondary infection-causing bacteria (p < 0.05) with a simultaneous decrease of normal flora (p < 0.05). The dysbiosis of the bacterial community might be linked with severe consequences of COVID-19-infected diabetic patients, although a few probiotic strains inhibited numerous pathogens in the same pathological niches. This study suggested that the promotion of normal flora and probiotics through dietary supplementation and excessive inflammation reduction by preventing secondary infections might lead to a better outcome for those comorbid patients.

Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections

This study was conducted to investigate oropharyngeal microbiota alterations during the progression of coronavirus disease 2019 (COVID-19) by analyzing these alterations during the infection and clearance processes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnosis of COVID-19 was confirmed by using positive SARS-CoV-2 quantitative reverse transcription polymerase chain reaction (RT-qPCR). The alterations in abundance, diversity, and potential function of the oropharyngeal microbiome were identified using metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 47 patients with COVID-19 (within a week after diagnosis and within two months after recovery from COVID-19) and 40 healthy individuals. As a result, in the infection process of SARS-CoV-2, compared to the healthy individuals, the relative abundances of Prevotella, Aspergillus, and Epstein-Barr virus were elevated; the alpha diversity was decreased; the beta diversity was disordered; the relative abundance of Gram-negative bacteria was increased; and the relative abundance of Gram-positive bacteria was decreased. After the clearance of SARS-CoV-2, compared to the healthy individuals and patients with COVID-19, the above disordered alterations persisted in the patients who had recovered from COVID-19 and did not return to the normal level observed in the healthy individuals. Additionally, the expressions of several antibiotic resistance genes (especially multi-drug resistance, glycopeptide, and tetracycline) in the patients with COVID-19 were higher than those in the healthy individuals. After SARS-CoV-2 was cleared, the expressions of these genes in the patients who had recovered from COVID-19 were lower than those in the patients with COVID-19, and they were different from those in the healthy individuals. In conclusion, our findings provide evidence that potential secondary infections with oropharyngeal bacteria, fungi, and viruses in patients who have recovered from COVID-19 should not be ignored; this evidence also highlights the clinical significance of the oropharyngeal microbiome in the early prevention of potential secondary infections of COVID-19 and suggests that it is imperative to choose appropriate antibiotics for subsequent bacterial secondary infection in patients with COVID-19.

Prevalence and Mechanisms of Mucus Accumulation in COVID-19 Lung Disease

Rationale: The incidence and sites of mucus accumulation and molecular regulation of mucin gene expression in coronavirus (COVID-19) lung disease have not been reported. Objectives: To characterize the incidence of mucus accumulation and the mechanisms mediating mucin hypersecretion in COVID-19 lung disease. Methods: Airway mucus and mucins were evaluated in COVID-19 autopsy lungs by Alcian blue and periodic acid-Schiff staining, immunohistochemical staining, RNA in situ hybridization, and spatial transcriptional profiling. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected human bronchial epithelial (HBE) cultures were used to investigate mechanisms of SARS-CoV-2-induced mucin expression and synthesis and test candidate countermeasures. Measurements and Main Results: MUC5B and variably MUC5AC RNA concentrations were increased throughout all airway regions of COVID-19 autopsy lungs, notably in the subacute/chronic disease phase after SARS-CoV-2 clearance. In the distal lung, MUC5B-dominated mucus plugging was observed in 90% of subjects with COVID-19 in both morphologically identified bronchioles and microcysts, and MUC5B accumulated in damaged alveolar spaces. SARS-CoV-2-infected HBE cultures exhibited peak titers 3 days after inoculation, whereas induction of MUC5B/MUC5AC peaked 7-14 days after inoculation. SARS-CoV-2 infection of HBE cultures induced expression of epidermal growth factor receptor (EGFR) ligands and inflammatory cytokines (e.g., IL-1α/β) associated with mucin gene regulation. Inhibiting EGFR/IL-1R pathways or administration of dexamethasone reduced SARS-CoV-2-induced mucin expression. Conclusions: SARS-CoV-2 infection is associated with a high prevalence of distal airspace mucus accumulation and increased MUC5B expression in COVID-19 autopsy lungs. HBE culture studies identified roles for EGFR and IL-1R signaling in mucin gene regulation after SARS-CoV-2 infection. These data suggest that time-sensitive mucolytic agents, specific pathway inhibitors, or corticosteroid administration may be therapeutic for COVID-19 lung disease.

Coronavirus disease 2019 (COVID-19) associated bacterial coinfection: Incidence, diagnosis and treatment

Coronavirus disease 2019 (COVID-19) emerged as a pandemic that spread rapidly around the world, causing nearly 500 billion infections and more than 6 million deaths to date. During the first wave of the pandemic, empirical antibiotics was prescribed in over 70% of hospitalized COVID-19 patients. However, research now shows a low incidence rate of bacterial coinfection in hospitalized COVID-19 patients, between 2.5% and 5.1%. The rate of secondary infections was 3.7% in overall, but can be as high as 41.9% in the intensive care units. Over-prescription of antibiotics to treat COVID-19 patients fueled the ongoing antimicrobial resistance globally. Diagnosis of bacterial coinfection is challenging due to indistinguishable clinical presentations with overlapping lower respiratory tract symptoms such as fever, cough and dyspnea. Other diagnostic methods include conventional culture, diagnostic syndromic testing, serology test and biomarkers. COVID-19 patients with bacterial coinfection or secondary infection have a higher in-hospital mortality and longer length of stay, timely and appropriate antibiotic use aided by accurate diagnosis is crucial to improve patient outcome and prevent antimicrobial resistance.

Platelet in thrombo-inflammation: Unraveling new therapeutic targets

In the broad range of human diseases, thrombo-inflammation appears as a clinical manifestation. Clinically, it is well characterized in context of superficial thrombophlebitis that is recognized as thrombosis and inflammation of superficial veins. However, it is more hazardous when developed in the microvasculature of injured/inflamed/infected tissues and organs. Several diseases like sepsis and ischemia-reperfusion can cause formation of microvascular thrombosis subsequently leading to thrombo-inflammation. Thrombo-inflammation can also occur in cases of antiphospholipid syndrome, preeclampsia, sickle cell disease, bacterial and viral infection. One of the major contributors to thrombo-inflammation is the loss of normal anti-thrombotic and anti-inflammatory potential of the endothelial cells of vasculature. This manifest itself in the form of dysregulation of the coagulation pathway and complement system, pathologic platelet activation, and increased recruitment of leukocyte within the microvasculature. The role of platelets in hemostasis and formation of thrombi under pathologic and non-pathologic conditions is well established. Platelets are anucleate cells known for their essential role in primary hemostasis and the coagulation pathway. In recent years, studies provide strong evidence for the critical involvement of platelets in inflammatory processes like acute ischemic stroke, and viral infections like Coronavirus disease 2019 (COVID-19). This has encouraged the researchers to investigate the contribution of platelets in the pathology of various thrombo-inflammatory diseases. The inhibition of platelet surface receptors or their intracellular signaling which mediate initial platelet activation and adhesion might prove to be suitable targets in thrombo-inflammatory disorders. Thus, the present review summarizes the concept and mechanism of platelet signaling and briefly discuss their role in sterile and non-sterile thrombo-inflammation, with the emphasis on role of platelets in COVID-19 induced thrombo-inflammation. The aim of this review is to summarize the recent developments in deciphering the role of the platelets in thrombo-inflammation and discuss their potential as pharmaceutical targets.

Emerging Bacterial Pathogens in the COVID-19 Era: Chryseobacterium gleum—A Case in Point

Introduction In the ongoing severe acute respiratory syndrome coronavirus 2 pandemic, a long hospital stay and empirical broad-spectrum antibiotics make the patients prone to acquire nosocomial infections especially with unconventional organisms, and Chryseobacterium gleum is one such rare nosocomial pathogen.

Methods The given study is a case-series-based study conducted from September 2020 to April 2021 in which clinically suspected pneumonia patients who recovered from coronavirus disease 2019 (COVID-19) were included.

Results Seventeen C. gleum isolates were obtained in pure culture from the tracheal aspirates of nine COVID-19 patients (including repeat samples to rule out colonization) within a period of eight months (September 2020–April 2021). Our records showed that there has been an increase in the number of isolates of C. gleum obtained in respiratory samples in 2020. We also did a review of literature of all the cases of C. gleum pneumonia reported till now.

Conclusion To the best of our knowledge, this is the first study reporting the isolation of this rare pathogen from COVID-19 patients with clinical significance in a large cohort of patients. Therefore, it becomes important to consider this pathogen as a significant cause of respiratory infections, especially in patients recovered post COVID-19.

Gut as an Alternative Entry Route for SARS-CoV-2: Current Evidence and Uncertainties of Productive Enteric Infection in COVID-19

The gut has been proposed as a potential alternative entry route for SARS-CoV-2. This was mainly based on the high levels of SARS-CoV-2 receptor expressed in the gastrointestinal (GI) tract, the observations of GI disorders (such as diarrhea) in some COVID-19 patients and the detection of SARS-CoV-2 RNA in feces. However, the underlying mechanisms remain poorly understood. It has been proposed that SARS-CoV-2 can productively infect enterocytes, damaging the intestinal barrier and contributing to inflammatory response, which might lead to GI manifestations, including diarrhea. Here, we report a methodological approach to assess the evidence supporting the sequence of events driving SARS-CoV-2 enteric infection up to gut adverse outcomes. Exploring evidence permits to highlight knowledge gaps and current inconsistencies in the literature and to guide further research. Based on the current insights on SARS-CoV-2 intestinal infection and transmission, we then discuss the potential implication on clinical practice, including on long COVID. A better understanding of the GI implication in COVID-19 is still needed to improve disease management and could help identify innovative therapies or preventive actions targeting the GI tract.

Mechanisms Leading to Gut Dysbiosis in COVID-19: Current Evidence and Uncertainties Based on Adverse Outcome Pathways

Alteration in gut microbiota has been associated with COVID-19. However, the underlying mechanisms remain poorly understood. Here, we outlined three potential interconnected mechanistic pathways leading to gut dysbiosis as an adverse outcome following SARS-CoV-2 presence in the gastrointestinal tract. Evidence from the literature and current uncertainties are reported for each step of the different pathways. One pathway investigates evidence that intestinal infection by SARS-CoV-2 inducing intestinal inflammation alters the gut microbiota. Another pathway links the binding of viral S protein to angiotensin-converting enzyme 2 (ACE2) to the dysregulation of this receptor, essential in intestinal homeostasis-notably for amino acid metabolism-leading to gut dysbiosis. Additionally, SARS-CoV-2 could induce gut dysbiosis by infecting intestinal bacteria. Assessing current evidence within the Adverse Outcome Pathway framework justifies confidence in the proposed mechanisms to support disease management and permits the identification of inconsistencies and knowledge gaps to orient further research.

Invasiveness of Ventilation Therapy Is Associated to Prevalence of Secondary Bacterial and Fungal Infections in Critically Ill COVID-19 Patients

Superinfections are a fundamental critical care problem, and their significance in severe COVID-19 cases needs to be determined. This study analyzed data from the Lean European Open Survey on SARS-CoV-2-Infected Patients (LEOSS) cohort focusing on intensive care patients. A retrospective analysis of patient data from 840 cases of COVID-19 with critical courses demonstrated that co-infections were frequently present and were primarily of nosocomial origin. Furthermore, our analysis showed that invasive therapy procedures accompanied an increased risk for healthcare-associated infections. Non-ventilated ICU patients were rarely affected by secondary infections. The risk of infection, however, increased even when non-invasive ventilation was used. A further, significant increase in infection rates was seen with the use of invasive ventilation and even more so with extracorporeal membrane oxygenation (ECMO) therapy. The marked differences among ICU techniques used for the treatment of COVID-19-induced respiratory failure in terms of secondary infection risk profile should be taken into account for the optimal management of critically ill COVID-19 patients, as well as for adequate antimicrobial therapy.

Probiotics in the Management of Mental and Gastrointestinal Post-COVID Symptomes

Patients with “post-COVID” syndrome manifest with a variety of signs and symptoms that continue/develop after acute COVID-19. Among the most common are gastrointestinal (GI) and mental symptoms. The reason for symptom occurrence lies in the SARS-CoV-2 capability of binding to exact receptors, among other angiotensin converting enzyme 2 (ACE2) receptors in gastrointestinal lining and neuropilin-1 (NRP-1) in the nervous system, which leads to loss of gastrointestinal and blood-brain barriers integrity and function. The data are mounting that SARS-CoV-2 can trigger systemic inflammation and lead to disruption of gut-brain axis (GBA) and the development of disorders of gut brain interaction (DGBIs). Functional dyspepsia (FD) and irritable bowel syndrome (IBS) are the most common DGBIs syndromes. On the other hand, emotional disorders have also been demonstrated as DGBIs. Currently, there are no official recommendations or recommended procedures for the use of probiotics in patients with COVID-19. However, it can be assumed that many doctors, pharmacists, and patients will want to use a probiotic in the treatment of this disease. In such cases, strains with documented activity should be used. There is a constant need to plan and conduct new trials on the role of probiotics and verify their clinical efficacy for counteracting the negative consequences of COVID-19 pandemic. Quality control is another important but often neglected aspect in trials utilizing probiotics in various clinical entities. It determines the safety and efficacy of probiotics, which is of utmost importance in patients with post-acute COVID-19 syndrome.

Influenza Myopericarditis and Pericarditis: A Literature Review

Myopericarditis is a rare complication of influenza infection. The presentation may range from mild and frequently unrecognized, to fulminant and potentially complicated by cardiogenic and/or obstructive shock (tamponade), which is associated with high mortality. We performed a review of literature on all influenza pericarditis and myopericarditis cases according to PRISMA guidelines using the PubMed search engine of the Medline database. Seventy-five cases of influenza myopericarditis and isolated pericarditis were identified from 1951 to 2021. Influenza A was reported twice as often as influenza B; however, influenza type did not correlate with outcome. Men and elderly patients were more likely to have isolated pericarditis, while women and younger patients were more likely to have myopericarditis. All included patients had pericardial effusion, while 36% had tamponade. Tamponade was more common in those with isolated pericarditis (41.2%) than myopericarditis (13.8%). Cardiogenic shock was more common in patients with myopericarditis (64%), with an overall mortality rate of 14.7%. Nearly 88% of the recovered patients remained without long-term complications reported. Conclusion: Influenza A appears a more common cause of pericarditis and myopericarditis. Isolated pericarditis was more commonly associated with tamponade but without reported deaths, whereas myopericarditis was more commonly associated with cardiogenic shock and death (19%).

Secondary infections modify the overall course of hospitalized patients with COVID-19: a retrospective study from a network of hospitals across North India

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Secondary infections can complicate the course of 10% of hospitalized patients with coronavirus disease 2019.

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Elderly, diabetic and severely ill patients are at greatest risk of secondary infections.

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Length of hospital stay of patients with secondary infections was almost twice as long as that of patients without secondary infections.

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Patients with secondary infections had higher requirements for oxygen and intensive care unit care.

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The most common type of secondary infection was urinary tract infection, followed by bloodstream infection.

Objective

To gain better insight into the extent of secondary bacterial and fungal infections in hospitalized patients in India, and to assess how these alter the course of coronavirus disease 2019 (COVID-19) so that control measures can be suggested.

Methods

In this retrospective, multicentre study, the data of all patients who tested positive for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) on reverse transcriptase polymerase chain reaction (RT-PCR), admitted to hospital between March 2020 and July 2021, were accessed from the electronic health records of a network of 10 hospitals across five states in North India.

Results

Of 19,852 patients testing positive for SARS-CoV-2 on RT-PCR and admitted to the study hospitals during the study period, 1940 (9.8%) patients developed secondary infections (SIs). Patients with SIs were, on average, 8 years older than patients without SIs (median age 62.6 vs 54.3 years; P<0.001). The risk of SIs was significantly (P<0.001) associated with age, severity of disease at admission, diabetes, admission to the intensive care unit (ICU), and ventilator use. The most common site of infection was urine (41.7%), followed by blood (30.8%) and sputum/bronchoalveolar lavage/endotracheal fluid (24.8%); the least common was pus/wound discharge (2.6%). Gram-negative bacilli (GNB) were the most common organisms (63.2%), followed by Gram-positive cocci (GPC) (19.6%) and fungi (17.3%). Most patients with SIs were on multiple antimicrobials. The most commonly used antibiotics against GNB were beta-lactam/beta-lactamase inhibitors (76.9%), carbapenems (57.7%), cephalosporins (53.9%), and antibiotics against carbapenem-resistant Enterobacteriaceae (47.1%). Empirical use of antibiotics against GPC was seen in 58.9% of patients with SIs, and empirical use of antifungals was observed in 56.9% of patients with SIs. The average length of hospital stay for patients with SIs was almost twice as long as that of patients without SIs (median 13 vs 7 days). Overall mortality among patients with SIs (40.3%) was more than eight times higher than that among patients without SIs (4.6%). Only 1.2% of patients with SIs with mild COVID-19 at admission died, compared with 17.5% of those with moderate COVID-19 at admission and 58.5% of those with severe COVID-19 at admission (P<0.001). The mortality rate was highest in patients with bloodstream infections (49.8%), followed by those with hospital-acquired pneumonia (47.9%), urinary tract infections (29.4%), and skin and soft tissue infections (29.4%). The mortality rate in patients with diabetes with SIs was 45.2%, compared with 34.3% in those without diabetes (P<0.001).

Conclusions

SIs complicate the course of patients hospitalized with COVID-19. These patients tend to have a much longer hospital stay, a higher requirement for oxygen and ICU care, and a significantly higher mortality rate compared with those without SIs. The groups most vulnerable to SIs are patients with more severe COVID-19, elderly patients and patients with diabetes. Judicious empirical use of combination antimicrobials in these groups of vulnerable patients can save lives. It is desirable to have region- or country-specific guidelines for appropriate use of antibiotics and antifungals to prevent their overuse.

Neutrophil extracellular traps mediate severe lung injury induced by influenza A virus H1N1 in mice coinfected with Staphylococcus aureus

Influenza virus and bacterial infection contributed to massive morbidity and mortality. However, the underlying mechanisms were poorly understood. A coinfected model was generating by using sublethal doses of influenza A virus H1N1 A/FM/1/47(H1N1) and methicillin-resistant Staphylococcus aureus (MRSA). Further, the model was optimized to achieve the highest peak of mortality initiated by intranasal infection with 0.2LD₅₀ H1N1 and 0.16LD₅₀ MRSA at 3 days interval. Excessive neutrophil recruitment, accompanied by high levels of inflammatory cytokines and chemokines, and increased bacterial and viral load were observed in coinfected mice. Under the inflammatory environments triggered by H1N1 and MRSA, the excessive neutrophil recruitment led to the formation of neutrophil extracellular traps (NETs), associated with severe inflammation and vascular endothelial injury. Importantly, the severity of lung injury could be alleviated by treatment with DNase I or a selective neutrophil elastase inhibitor (NEi). Therefore, our data suggested that excessive neutrophil recruitment and NETs formation contributed to severe inflammation and acute lung injury in coinfected animals.

The Prevalence and Impact of Coinfection and Superinfection on the Severity and Outcome of COVID-19 Infection: An Updated Literature Review

Patients with viral illness are at higher risk of secondary infections—whether bacterial, viral, or parasitic—that usually lead to a worse prognosis. In the setting of Corona Virus Disease 2019 (COVID-19), the Severe Acute Respiratory Syndrome Coronavirus-type 2 (SARS-CoV-2) infection may be preceded by a prior microbial infection or has a concurrent or superinfection. Previous reports documented a significantly higher risk of microbial coinfection in SARS-CoV-2-positive patients. Initial results from the United States (U.S.) and Europe found a significantly higher risk of mortality and severe illness among hospitalized patients with SARS-CoV-2 and bacterial coinfection. However, later studies found contradictory results concerning the impact of coinfection on the outcomes of COVID-19. Thus, we conducted the present literature review to provide updated evidence regarding the prevalence of coinfection and superinfection amongst patients with SARS-CoV-2, possible mechanisms underlying the higher risk of coinfection and superinfection in SARS-CoV-2 patients, and the impact of coinfection and superinfection on the outcomes of patients with COVID-19.

SARS-CoV-2 Spike Protein and Mouse Coronavirus Inhibit Biofilm Formation by Streptococcus pneumoniae and Staphylococcus aureus

The presence of co-infections or superinfections with bacterial pathogens in COVID-19 patients is associated with poor outcomes, including increased morbidity and mortality. We hypothesized that SARS-CoV-2 and its components interact with the biofilms generated by commensal bacteria, which may contribute to co-infections. This study employed crystal violet staining and particle-tracking microrheology to characterize the formation of biofilms by Streptococcus pneumoniae and Staphylococcus aureus that commonly cause secondary bacterial pneumonia. Microrheology analyses suggested that these biofilms were inhomogeneous soft solids, consistent with their dynamic characteristics. Biofilm formation by both bacteria was significantly inhibited by co-incubation with recombinant SARS-CoV-2 spike S1 subunit and both S1 + S2 subunits, but not with S2 extracellular domain nor nucleocapsid protein. Addition of spike S1 and S2 antibodies to spike protein could partially restore bacterial biofilm production. Furthermore, biofilm formation in vitro was also compromised by live murine hepatitis virus, a related beta-coronavirus. Supporting data from LC-MS-based proteomics of spike-biofilm interactions revealed differential expression of proteins involved in quorum sensing and biofilm maturation, such as the AI-2E family transporter and LuxS, a key enzyme for AI-2 biosynthesis. Our findings suggest that these opportunistic pathogens may egress from biofilms to resume a more virulent planktonic lifestyle during coronavirus infections. The dispersion of pathogens from biofilms may culminate in potentially severe secondary infections with poor prognosis. Further detailed investigations are warranted to establish bacterial biofilms as risk factors for secondary pneumonia in COVID-19 patients.

Platelet-Mediated NET Release Amplifies Coagulopathy and Drives Lung Pathology During Severe Influenza Infection

The influenza A virus (IAV) causes a respiratory tract infection with approximately 10% of the population infected by the virus each year. Severe IAV infection is characterized by excessive inflammation and tissue pathology in the lungs. Platelet and neutrophil recruitment to the lung are involved in the pathogenesis of IAV, but the specific mechanisms involved have not been clarified. Using confocal intravital microscopy in a mouse model of IAV infection, we observed profound neutrophil recruitment, platelet aggregation, neutrophil extracellular trap (NET) production and thrombin activation within the lung microvasculature in vivo. Importantly, deficiency or antagonism of the protease-activated receptor 4 (PAR4) reduced platelet aggregation, NET production, and neutrophil recruitment. Critically, inhibition of thrombin or PAR4 protected mice from virus-induced lung tissue damage and edema. Together, these data imply thrombin-stimulated platelets play a critical role in the activation/recruitment of neutrophils, NET release and directly contribute to IAV pathogenesis in the lung.

Systemic toll-like receptor 9 agonist CpG oligodeoxynucleotides exacerbates aminoglycoside ototoxicity

The Toll-like receptor (TLR) signaling pathway is the key regulator of the innate immune system in response to systemic infection. Several studies have reported that the systemic TLR4 agonist lipopolysaccharide exacerbates aminoglycoside ototoxicity, but the influence of virus-associated TLR7 and TLR9 signaling cascades on the cochlea is unclear. The present study aimed to investigate the auditory effects of systemic TLR7 and TLR9 agonists during chronic kanamycin treatment. CBA/CaJ mice received the TLR7 agonist gardiquimod or TLR9 agonist CpG oligodeoxynucleotides (ODN) one day before kanamycin injection and on the 5th and 10th days during a 14-day course of kanamycin treatment. We observed that systemic gardiquimod or CpG ODN alone did not affect the baseline auditory brainstem response (ABR) threshold. Three weeks after kanamycin treatment, gardiquimod did not significantly change ABR threshold shifts, whereas CpG ODN significantly increased kanamycin-induced ABR threshold shifts. Furthermore, outer hair cell (OHC) evaluation revealed that CpG ODN reduced distortion product otoacoustic emission amplitudes and increased kanamycin-induced OHC loss. CpG ODN significantly elevated cochlear Irf-7, Tnf-α, Il-1, and Il-6 transcript levels. In addition, an increased number of Iba-1⁺ cells, which represented activated macrophages, was observed in the cochlea treated with CpG ODN. Our results indicated that systemic CpG ODN exacerbated kanamycin-induced ototoxicity and increased cochlear inflammation. This study implies that patients with underlying virus infection may experience more severe aminoglycoside-induced hearing loss if it occurs.

Repurposing carrimycin as an antiviral agent against human coronaviruses, including the currently pandemic SARS-CoV-2

COVID-19 pandemic caused by SARS-CoV-2 infection severely threatens global health and economic development. No effective antiviral drug is currently available to treat COVID-19 and any other human coronavirus infections. We report herein that a macrolide antibiotic, carrimycin, potently inhibited the cytopathic effects (CPE) and reduced the levels of viral protein and RNA in multiple cell types infected by human coronavirus 229E, OC43, and SARS-CoV-2. Time-of-addition and pseudotype virus infection studies indicated that carrimycin inhibited one or multiple post-entry replication events of human coronavirus infection. In support of this notion, metabolic labelling studies showed that carrimycin significantly inhibited the synthesis of viral RNA. Our studies thus strongly suggest that carrimycin is an antiviral agent against a broad-spectrum of human coronaviruses and its therapeutic efficacy to COVID-19 is currently under clinical investigation.

Co-infection with Legionella and SARS-CoV-2: a case report

INTRODUCTION

We report a case of COVID-19 with Legionella co-infection that was treated successfully.

CASE REPORT

A 73-year-old man presented to the hospital with symptoms of fatigue that continued for the next 5 days. The patient was receiving docetaxel and prednisolone chemotherapy for prostate cancer. Laboratory findings on admission showed positive urine Legionella antigen test and SARS-CoV-2 test. He was administered antiviral and antibacterial agents, and a corticosteroid. Pneumonia exacerbated on day 2 of hospitalization. The patient underwent tracheal intubation and began receiving multidisciplinary care. On day 8 of hospitalization, his oxygenation improved, and the patient was extubated. He discharged on day 27 of hospitalization.

CONCLUSIONS

The patient had a favorable outcome with early diagnosis and early treatment of both diseases. Patients with severe COVID-19 disease need to be evaluated for co-infection. Further, early diagnosis and early treatment of the microbial bacteria causing the co-infection are important.

Profiling of Oral Microbiota and Cytokines in COVID-19 Patients

The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been recently demonstrated in the sputum or saliva, suggesting how the shedding of viral RNA outlasts the end of symptoms. Recent data from transcriptome analysis show that the oral cavity mucosa harbors high levels of angiotensin-converting enzyme 2 (ACE2) and transmembrane protease, serine 2 (TMPRSS2), highlighting its role as a double-edged sword for SARS-CoV-2 body entrance or interpersonal transmission. Here, we studied the oral microbiota structure and inflammatory profile of 26 naive severe coronavirus disease 2019 (COVID-19) patients and 15 controls by 16S rRNA V2 automated targeted sequencing and magnetic bead-based multiplex immunoassays, respectively. A significant diminution in species richness was observed in COVID-19 patients, along with a marked difference in beta-diversity. Species such as Prevotella salivae and Veillonella infantium were distinctive for COVID-19 patients, while Neisseria perflava and Rothia mucilaginosa were predominant in controls. Interestingly, these two groups of oral species oppositely clustered within the bacterial network, defining two distinct Species Interacting Groups (SIGs). COVID-19-related pro-inflammatory cytokines were found in both oral and serum samples, along with a specific bacterial consortium able to counteract them. We introduced a new parameter, named CytoCOV, able to predict COVID-19 susceptibility for an unknown subject at 71% of power with an Area Under Curve (AUC) equal to 0.995. This pilot study evidenced a distinctive oral microbiota composition in COVID-19 subjects, with a definite structural network in relation to secreted cytokines. Our results would be usable in clinics against COVID-19, using bacterial consortia as biomarkers or to reduce local inflammation.

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

The novel coronavirus infectious disease-2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has traumatized the whole world with the ongoing devastating pandemic. A plethora of microbial domains including viruses (other than SARS-CoV-2), bacteria, archaea and fungi have evolved together, and interact in complex molecular pathogenesis along with SARS-CoV-2. However, the involvement of other microbial co-pathogens and underlying molecular mechanisms leading to extortionate ailment in critically ill COVID-19 patients has yet not been extensively reviewed. Although, the incidence of co-infections could be up to 94.2% in laboratory-confirmed COVID-19 cases, the fate of co-infections among SARS-CoV-2 infected hosts often depends on the balance between the host's protective immunity and immunopathology. Predominantly identified co-pathogens of SARS-CoV-2 are bacteria such as Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae, Acinetobacter baumannii, Legionella pneumophila and Clamydia pneumoniae followed by viruses including influenza, coronavirus, rhinovirus/enterovirus, parainfluenza, metapneumovirus, influenza B virus, and human immunodeficiency virus. The cross-talk between co-pathogens (especially lung microbiomes), SARS-CoV-2 and host is an important factor that ultimately increases the difficulty of diagnosis, treatment, and prognosis of COVID-19. Simultaneously, co-infecting microbiotas may use new strategies to escape host defense mechanisms by altering both innate and adaptive immune responses to further aggravate SARS-CoV-2 pathogenesis. Better understanding of co-infections in COVID-19 is critical for the effective patient management, treatment and containment of SARS-CoV-2. This review therefore necessitates the comprehensive investigation of commonly reported microbial co-pathogens amid COVID-19, their transmission pattern along with the possible mechanism of co-infections and outcomes. Thus, identifying the possible co-pathogens and their underlying molecular mechanisms during SARS-CoV-2 pathogenesis may shed light in developing diagnostics, appropriate curative and preventive interventions for suspected SARS-CoV-2 respiratory infections in the current pandemic.