Incidence of co-infections and superinfections in hospitalized patients with COVID-19: a retrospective cohort study

COVID-19 Pandemic and Upcoming Influenza Season-Does an Expert's Computed Tomography Assessment Differentially Identify COVID-19, Influenza and Pneumonias of Other Origin?

(1) Background: Time-consuming SARS-CoV-2 RT-PCR suffers from limited sensitivity in early infection stages whereas fast available chest CT can already raise COVID-19 suspicion. Nevertheless, radiologists' performance to differentiate COVID-19, especially from influenza pneumonia, is not sufficiently characterized. (2) Methods: A total of 201 pneumonia CTs were identified and divided into subgroups based on RT-PCR: 78 COVID-19 CTs, 65 influenza CTs and 62 Non-COVID-19-Non-influenza (NCNI) CTs. Three radiology experts (blinded from RT-PCR results) raised pathogen-specific suspicion (separately for COVID-19, influenza, bacterial pneumonia and fungal pneumonia) according to the following reading scores: 0-not typical/1-possible/2-highly suspected. Diagnostic performances were calculated with RT-PCR as a reference standard. Dependencies of radiologists' pathogen suspicion scores were characterized by Pearson's Chi2 Test for Independence. (3) Results: Depending on whether the intermediate reading score 1 was considered as positive or negative, radiologists correctly classified 83-85% (vs. NCNI)/79-82% (vs. influenza) of COVID-19 cases (sensitivity up to 94%). Contrarily, radiologists correctly classified only 52-56% (vs. NCNI)/50-60% (vs. COVID-19) of influenza cases. The COVID-19 scoring was more specific than the influenza scoring compared with suspected bacterial or fungal infection. (4) Conclusions: High-accuracy COVID-19 detection by CT might expedite patient management even during the upcoming influenza season.

Increased incidence of candidemia in a tertiary care hospital with the COVID-19 pandemic

Background

The incidence of candidemia in our hospital has been stable over an 18‐year period (1.3 episodes per 1000 admissions). Since March 2020, we have observed an increase in cases of candidemia.

Methods

In March 2020, the hospital was prepared to receive patients with COVID‐19, with cancellation of elective procedures, discharge of less sick patients and the activation of beds for COVID‐19. We compared the incidence of candidemia in 2 periods: from January 2019 to February 2020 (period 1) and from March to September 2020 (period 2).

Results

We diagnosed 41 episodes of candidemia, 16 in period 1 and 25 in period 2 (9 COVID‐19 patients). Compared with non‐COVID‐19 patients, COVID‐19 patients with candidemia were more likely to be under mechanical ventilation (100% vs. 34.4%, P < .001). The median number of monthly admissions in period 1 and 2 was 723 (interquartile range 655‐836) and 523 (interquartile range 389‐574), respectively. The incidence of candidemia (per 1000 admissions) was 1.54 in period 1 and 7.44 in period 2 (P < .001). In period 2, the incidence of candidemia (per 1000 admissions) was 4.76 if we consider only cases of candidemia in non‐COVID‐19 patients, 2.68 if we consider only cases of candidemia in COVID‐19 patients and 14.80 considering only admissions of patients with COVID‐19.

Conclusions

The increase in the incidence of candidemia in our hospital may be attributed to 2 factors: a reduction in the number of admissions (denominator) and the occurrence of candidemia in COVID‐19 patients.

Bacterial/fungal infection in hospitalized patients with COVID-19 in a tertiary hospital in the Community of Castilla y León, Spain

INTRODUCTION

Bacterial/fungal coinfection and superinfections contribute to the increased morbi-mortality of viral respiratory infections (RIs). The main objective of this study was to determine the incidence of these infections in hospitalized patients with COVID-19.

METHOD

Retrospective observational study of all patients admitted for COVID-19 and bacterial/fungal infections at the Hospital Clínico Universitario of Valladolid, Spain (March 1-May 31, 2020). Demographic, clinical and microbiological data were compared based on Intensive Care Unit (ICU) admission and predictors of mortality by were identified using multivariate logistic regression analyses.

RESULTS

Of the 712 COVID-19 patients, 113 (16%) presented bacterial/fungal coinfections or superinfections. Their median age was 73 years (IQR 57-89) and 59% were men. The profiles of ICU patients (44%) included male, SARS-CoV-2 pneumonia, leukocytosis, elevated inteleukin-6, with interferon β-1b and tocilizumab and superinfection (p < 0.05). Coinfections were diagnosed in 5% (39/712) patients. Most common pathogens of respiratory coinfection (18) were Streptococcus pneumoniae (6) and Staphylococcus aureus (6). Superinfections were detected in 11% (80/712) patients. Urinary (53) and RIs (39) constituted the majority of superinfections Acinetobacter baumannii multidrug-resistant was the main agent of IR and bacteremia. An outbreak of A. baumannii contributed to this result. Three patients were considered to have probable pulmonary aspergillosis. Mortality was higher in UCI patients (50 vs. 29%; p = 0.028). The predictive factors of mortality included being a male with various comorbidities, SARS-CoV-2 pneumonia, bacteremia and superinfections from A. baumannii.

CONCLUSION

The outbreak of A. baumannii was a determining factor in the increases of the incidence of infection and the morbi-mortality of ICU patients.

Covid-19-Associated Pulmonary Aspergillosis: The Other Side of the Coin

The immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a critical factor in the clinical presentation of COVID-19, which may range from asymptomatic to a fatal, multi-organ disease. A dysregulated immune response not only compromises the ability of the host to resolve the viral infection, but may also predispose the individual to secondary bacterial and fungal infections, a risk to which the current therapeutic immunomodulatory approaches significantly contribute. Among the secondary infections that may occur in COVID-19 patients, coronavirus-associated pulmonary aspergillosis (CAPA) is emerging as a potential cause of morbidity and mortality, although many aspects of the disease still remain unresolved. With this opinion, we present the current view of CAPA and discuss how the same mechanisms that underlie the dysregulated immune response in COVID-19 increase susceptibility to Aspergillus infection. Likewise, resorting to endogenous pathways of immunomodulation may not only restore immune homeostasis in COVID-19 patients, but also reduce the risk for aspergillosis. Therefore, CAPA represents the other side of the coin in COVID-19 and our advances in the understanding and treatment of the immune response in COVID-19 should represent the framework for the study of CAPA.

Peptide and peptide-based inhibitors of SARS-CoV-2 entry

To date, no effective vaccines or therapies are available against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pandemic agent of the coronavirus disease 2019 (COVID-19). Due to their safety, efficacy and specificity, peptide inhibitors hold great promise for the treatment of newly emerging viral pathogens. Based on the known structures of viral proteins and their cellular targets, antiviral peptides can be rationally designed and optimized. The resulting peptides may be highly specific for their respective targets and particular viral pathogens or exert broad antiviral activity. Here, we summarize the current status of peptides inhibiting SARS-CoV-2 entry and outline the strategies used to design peptides targeting the ACE2 receptor or the viral spike protein and its activating proteases furin, transmembrane serine protease 2 (TMPRSS2), or cathepsin L. In addition, we present approaches used against related viruses such as SARS-CoV-1 that might be implemented for inhibition of SARS-CoV-2 infection.

A multidisciplinary registry of patients with autoimmune and immune-mediated diseases with symptomatic COVID-19 from a single center

Background and aim

There is increasing interest regarding SARS-CoV-2 infection in patients with autoimmune and immune-mediated inflammatory diseases (AI/IMID) with some discrepancies in different cohorts about their risk and outcomes. The aim was to describe a multidisciplinary cohort of patients with AI/IMID and symptomatic SARS-CoV-2 infection in a single tertiary center and analyze sociodemographic, clinical, and therapeutic factors associated with poor outcomes.

Methods

A retrospective observational study was conducted from the 1st of March until May 29th, 2020 in a University tertiary hospital in Barcelona, Spain. Patients with an underlying AI/IMID and symptomatic SARS-CoV-2 infection were identified in our local SARS-CoV-2 infection database. Controls (2:1) were selected from the same database and matched by age and gender. The primary outcome was severe SARS-CoV-2 infection, which was a composite endpoint including admission to the intensive care unit (ICU), need for mechanical ventilation (MV), and/or death. Several covariates including age, sex, and comorbidities among others were combined into a multivariate model having severe SARS-CoV-2 as the dependent variable. Also, a sensitivity analysis was performed evaluating AID and IMID separately.

Results

The prevalence of symptomatic SARS-CoV-2 infection in a cohort of AI/IMID patients was 1.3%. Eighty-five patients with AI/IMID and symptomatic SARS-CoV-2 were identified, requiring hospitalization in 58 (68%) cases. A total of 175 patients admitted for SARS-CoV-2 (58 with AI/IMID and 117 matched-controls) were analyzed. In logistic regression analysis, a significant inverse association between AI/IMID group and severe SARS-CoV-2 (OR 0.28; 95% CI 0.12–0.61; p = 0.001), need of MV (OR 0.20; IC 95% 0.05–0.71; p = 0.014), and ICU admission (OR 0.25; IC 95% 0.10–0.62; p = 0.003) was found.

Conclusions

Patients with AI/IMID who require admission for SARS-CoV-2 infection have a lower risk of developing severe disease, including the need to stay in the ICU and MV.

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Patients with AI/IMID fwho required admission for SARS CoV2 infection have a lower risk of developing severe disease.

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Among patients with AID and IMID, there were no differences in terms of severity.

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According to the 7-category ordinal scale, maximum oxygen requirement was lower among AI/IMID group.

Potential implications of SARS-CoV-2 oral infection in the host microbiota

The oral cavity, as the entry point to the body, may play a critical role in the pathogenesis of SARS-CoV-2 infection that has caused a global outbreak of the coronavirus disease 2019 (COVID-19). Available data indicate that the oral cavity may be an active site of infection and an important reservoir of SARS-CoV-2. Considering that the oral surfaces are colonized by a diverse microbial community, it is likely that viruses have interactions with the host microbiota. Patients infected by SARS-CoV-2 may have alterations in the oral and gut microbiota, while oral species have been found in the lung of COVID-19 patients. Furthermore, interactions between the oral, lung, and gut microbiomes appear to occur dynamically whereby a dysbiotic oral microbial community could influence respiratory and gastrointestinal diseases. However, it is unclear whether SARS-CoV-2 infection can alter the local homeostasis of the resident microbiota, actively cause dysbiosis, or influence cross-body sites interactions. Here, we provide a conceptual framework on the potential impact of SARS-CoV-2 oral infection on the local and distant microbiomes across the respiratory and gastrointestinal tracts ('oral-tract axes'), which remains largely unexplored. Studies in this area could further elucidate the pathogenic mechanism of SARS-CoV-2 and the course of infection as well as the clinical symptoms of COVID-19 across different sites in the human host.

Random effects meta-analysis of COVID-19/S. aureus partnership in co-infection

Aim: To assess the hypothesis that coinfection with SARS-CoV-2 and S. aureus exacerbates morbidity and mortality among patients, the study aims to report the pooled burden of S. aureus co-infections in patients hospitalized with COVID-19. Methods: We searched electronic databases and the bibliographies of pertinent papers for articles. We considered studies in which the core result was the number of patients with bacterial (S. aureus) co-infection. We performed random effects meta-analysis (REM) because the studies included were sampled from a universe of different populations and high heterogeneity was anticipated. Using the Cochran's Q statistic, the observed dispersion (heterogeneity) among effect sizes was assessed. The percentage of total variability in the estimates of the effect size was calculated with the I2 index. To check for publication bias, the Egger weighted regression, Begg rank correlation and meta-funnel plot were used. We conducted meta-regression analysis to evaluate the variability between our outcomes and the covariates using computational options such as "methods of moments" and then "maximum likelihood" ratio. Results: We included 18 studies and retrieved data for 63,370 patients hospitalized with influenza-like illness, of which about 14,369 (22.67%) tested positive for COVID-19 by rRT-PCR. Of this number, 8,249 (57.4%) patient samples were analyzed. Bacterial, fungal and viral agents were detected in 3,038 (36.8%); S. aureus in 1,192 (39.2%). Five studies reported MRSA co-infection. Study quality ranged from 6 to 9 (median 7.1) on a JBI scale. From the meta-analysis, 33.1% patients were found to be coinfected (95%, CI 18.0 to 52.6%, Q=3473: df=17, I2=99·48%, p=0.00). The rate of S. aureus /COVID-19 co-infection was 25.6% (95% CI: 15.6 to 39.0, Q=783.4, df=17, I2=97.702%, p=0.003).The proportion of COVID-19/S. aureus co-infected patients with MRSA was 53.9% (95% CI, 24.5 to 80.9, n=66, 5 studies, Q=29.32, df=4, I2=86.369%, p=0.000). With the multivariate meta-regression model, study type (p=0.029), quality (p=0.000) and country (p=0.000) were significantly associated with heterogeneity. Conclusions: The pooled rates of S. aureus among COVID-19 patients documented in this study support the concern of clinicians about the presence of S. aureus in co-infections. Improved antibiotic stewardship can be accomplished through rapid diagnosis by longitudinal sampling of patients.

Increased circulating level of interleukin-6 and CD8+ T cell exhaustion are associated with progression of COVID-19

BACKGROUND

Coronavirus disease 2019 (COVID-19) is pandemic. It is critical to identify COVID-19 patients who are most likely to develop a severe disease. This study was designed to determine the clinical and epidemiological features of COVID-19 patients associated with the development of pneumonia and factors associated with disease progression.

METHODS

Seventy consecutive patients with etiologically confirmed COVID-19 admitted to PLA General Hospital in Beijing, China from December 27, 2019 to March 12, 2020 were enrolled in this study and followed-up to March 16, 2020. Differences in clinical and laboratory findings between COVID-19 patients with pneumonia and those without were determined by the χ2 test or the Fisher exact test (categorical variables) and independent group t test or Mann-Whitney U test (continuous variables). The Cox proportional hazard model and Generalized Estimating Equations were applied to evaluate factors that predicted the progression of COVID-19.

RESULTS

The mean incubation was 8.67 (95% confidence interval, 6.78-10.56) days. Mean duration from the first test severe acute respiratory syndrome coronavirus 2-positive to conversion was 11.38 (9.86-12.90) days. Compared to pneumonia-free patients, pneumonia patients were 16.5 years older and had higher frequencies of having hypertension, fever, and cough and higher circulating levels of neutrophil proportion, interleukin-6, low count (< 190/µl) of CD8+ T cells, and neutrophil/lymphocyte ratio. Thirteen patients deteriorated during hospitalization. Cox regression analysis indicated that older age and higher serum levels of interleukin-6, C-reactive protein, procalcitonin, and lactate at admission significantly predicted the progression of COVID-19. During hospitalization, circulating counts of T lymphocytes, CD4+ T cells, and CD8+ T cells were lower, whereas neutrophil proportion, neutrophil/lymphocyte ratio, and the circulating levels of interleukin-6, C-reactive protein, and procalcitonin were higher, in pneumonia patients than in pneumonia-free patients. CD8+ lymphocyte count in pneumonia patients did not recover when discharged.

CONCLUSIONS

Older age and higher levels of C-reactive protein, procalcitionin, interleukin-6, and lactate might predict COVID-19 progression. T lymphocyte, especially CD8+ cell-mediated immunity is critical in recovery of COVID-19. This study may help in predicting disease progression and designing immunotherapy for COVID-19.

A Retrospective Study of Coinfection of SARS-CoV-2 and Streptococcus pneumoniae in 11 Hospitalized Patients with Severe COVID-19 Pneumonia at a Single Center

Background

A lethal synergism between the influenza virus and Streptococcus pneumoniae has been identified. However, bacterial coinfection is considered relatively infrequent in hospitalized patients with COVID-19, and the co-prevalence of Streptococcus pneumoniae is low.

Material/Methods

We retrospectively analyzed the clinical characteristics and outcomes of patients subsequently admitted to AMITA Health Saint Francis Hospital between March 1 and June 30, 2020, with documented SARS-CoV-2 and S. pneumoniae coinfection.

Results

We identified 11 patients with S. pneumoniae coinfection. The median age was 77 years (interquartile range [IQR], 74–82 years), 45.5% (5/11) were males, 54.5% (6/11) were white, and 90.9% (10/11) were long-term care facility (LTCF) residents. The median length of stay was 7 days (IQR, 6–8 days). Among 11 patients, 4 were discharged in stable condition and 7 had died, resulting in an inpatient mortality rate of 64%.

Conclusions

At our center, 11 patients with COVID-19 pneumonia who had confirmed infection with SARS-CoV-2 were diagnosed with Streptococcus pneumoniae infection while in hospital. All patients had pneumonia confirmed on imaging and a nonspecific increase in markers of inflammation. The in-hospital mortality rate of 64% (7 patients) was higher in this group than in previous reports. This study highlights the importance of monitoring bacterial coinfection in patients with viral lung infection due to SARS-CoV-2.

Effectiveness of Streptococcus Pneumoniae Urinary Antigen Testing in Decreasing Mortality of COVID-19 Co-Infected Patients: A Clinical Investigation

Background and objectives: Streptococcus pneumoniae urinary antigen (u-Ag) testing has recently gained attention in the early diagnosis of severe and critical acute respiratory syndrome coronavirus-2/pneumococcal co-infection. The aim of this study is to assess the effectiveness of Streptococcus pneumoniae u-Ag testing in coronavirus disease 2019 (COVID-19) patients, in order to assess whether pneumococcal co-infection is associated with different mortality rate and hospital stay in these patients. Materials and Methods: Charts, protocols, mortality, and hospitalization data of a consecutive series of COVID-19 patients admitted to a tertiary hospital in northern Italy during COVID-19 outbreak were retrospectively reviewed. All patients underwent Streptococcus pneumoniae u-Ag testing to detect an underlying pneumococcal co-infection. Covid19+/u-Ag+ and Covid19+/u-Ag- patients were compared in terms of overall survival and length of hospital stay using chi-square test and survival analysis. Results: Out of 575 patients with documented pneumonia, 13% screened positive for the u-Ag test. All u-Ag+ patients underwent treatment with Ceftriaxone and Azithromycin or Levofloxacin. Lopinavir/Ritonavir or Darunavir/Cobicistat were added in 44 patients, and hydroxychloroquine and low-molecular-weight heparin (LMWH) in 47 and 33 patients, respectively. All u-Ag+ patients were hospitalized. Mortality was 15.4% and 25.9% in u-Ag+ and u-Ag- patients, respectively (p = 0.09). Survival analysis showed a better prognosis, albeit not significant, in u-Ag+ patients. Median hospital stay did not differ among groups (10 vs. 9 days, p = 0.71). Conclusions: The routine use of Streptococcus pneumoniae u-Ag testing helped to better target antibiotic therapy with a final trend of reduction in mortality of u-Ag+ COVID-19 patients having a concomitant pneumococcal infection. Randomized trials on larger cohorts are necessary in order to draw definitive conclusion.

Few bacterial co-infections but frequent empiric antibiotic use in the early phase of hospitalized patients with COVID-19: results from a multicentre retrospective cohort study in The Netherlands

BACKGROUND

Knowledge on bacterial co-infections in COVID-19 is crucial to use antibiotics appropriately. Therefore, we aimed to determine the incidence of bacterial co-infections, antibiotic use and application of antimicrobial stewardship principles in hospitalized patients with COVID-19.

METHODS

We performed a retrospective observational study in four hospitals (1 university, 2 non-university teaching, 1 non-teaching hospital) in the Netherlands from March to May 2020 including consecutive patients with PCR-confirmed COVID-19. Data on first microbiological investigations obtained at the discretion of the physician and antibiotic use in the first week of hospital admission were collected.

RESULTS

Twelve (1.2%) of the 925 patients included had a documented bacterial co-infection (75.0% pneumonia) within the first week. Microbiological testing was performed in 749 (81%) patients: sputum cultures in 105 (11.4%), blood cultures in 711 (76.9%), pneumococcal urinary antigen testing in 202 (21.8%), and Legionella urinary antigen testing in 199 (21.5%) patients, with clear variation between hospitals. On presentation 556 (60.1%; range 33.3-73.4%) patients received antibiotics for a median duration of 2 days (IQR 1-4). Intravenous to oral switch was performed in 41 of 413 (9.9%) patients who received intravenous treatment >48 h. Mean adherence to the local guideline on empiric antibiotic therapy on day 1 was on average 60.3% (range 45.3%-74.7%).

CONCLUSIONS

On presentation to the hospital bacterial co-infections are rare, while empiric antibiotic use is abundant. This implies that in patients with COVID-19 empiric antibiotic should be withheld. This has the potential to dramatically reduce the current overuse of antibiotics in the COVID-19 pandemic.

Comorbidities and the COVID-19 pandemic dynamics in Africa

The debate around the COVID‐19 response in Africa has mostly focused on effects and implications of public health measures, in light of the socio‐economic peculiarities of the continent. However, there has been limited exploration of the impact of differences in epidemiology of key comorbidities, and related healthcare factors, on the course and parameters of the pandemic. We summarise what is known about (a) the pathophysiological processes underlying the interaction of coinfections and comorbidities in shaping prognosis of COVID‐19 patients, (b) the epidemiology of key coinfections and comorbidities, and the state of related healthcare infrastructure that might shape the course of the pandemic, and (c) implications of (a) and (b) for pandemic management and post‐pandemic priorities. There is a critical need to generate empirical data on clinical profiles and the predictors of morbidity and mortality from COVID‐19. Improved protocols for acute febrile illness and access to diagnostic facilities, not just for SARS‐CoV‐2 but also other viral infections, are of urgent importance. The role of malaria, HIV/TB and chronic malnutrition on pandemic dynamics should be further investigated. Although chronic non‐communicable diseases account for a relatively lighter burden, they have a significant effect on COVID‐19 prognosis, and the fragility of care delivery systems implies that adjustments to clinical procedures and re‐organisation of care delivery that have been useful in other regions are unlikely to be feasible. Africa is a large region with local variations in factors that can shape pandemic dynamics. A one‐size‐fits‐all response is not optimal, but there are broad lessons relating to differences in epidemiology and healthcare delivery factors, that should be considered as part of a regional COVID‐19 response framework.

COVID-19-Associated Candidiasis (CAC): An Underestimated Complication in the Absence of Immunological Predispositions?

The recent global pandemic of COVID-19 has predisposed a relatively high number of patients to acute respiratory distress syndrome (ARDS), which carries a risk of developing super-infections. Candida species are major constituents of the human mycobiome and the main cause of invasive fungal infections, with a high mortality rate. Invasive yeast infections (IYIs) are increasingly recognized as s complication of severe COVID-19. Despite the marked immune dysregulation in COVID-19, no prominent defects have been reported in immune cells that are critically required for immunity to Candida. This suggests that relevant clinical factors, including prolonged ICU stays, central venous catheters, and broad-spectrum antibiotic use, may be key factors causing COVID-19 patients to develop IYIs. Although data on the comparative performance of diagnostic tools are often lacking in COVID-19 patients, a combination of serological and molecular techniques may present a promising option for the identification of IYIs. Clinical awareness and screening are needed, as IYIs are difficult to diagnose, particularly in the setting of severe COVID-19. Echinocandins and azoles are the primary antifungal used to treat IYIs, yet the therapeutic failures exerted by multidrug-resistant Candida spp. such as C. auris and C. glabrata call for the development of new antifungal drugs with novel mechanisms of action.