Co-infections in people with COVID-19: a systematic review and meta-analysis

Multidimensional Evaluation of All-Cause Mortality Risk and Survival Analysis for Hospitalized Patients with COVID-19

Background: Coronavirus disease 2019 (COVID-19) has caused over 3.8 million deaths globally. Up to date, the number of death in 2021 is more than that in 2020 globally. Here, we aimed to compare clinical characteristics of deceased patients and recovered patients, and analyze the risk factors of death to help reduce mortality of COVID-19. Methods: In this retrospective study, a total of 2719 COVID-19 patients were enrolled, including 109 deceased patients and 2610 recovered patients. Medical records of all patients were collected between February 4, 2020, and April 7, 2020. Clinical characteristics, laboratory indices, treatments, and deep-learning system- assessed lung lesion volumes were analyzed. The effect of different medications on survival time of fatal cases was also investigated. Results: The deceased patients were older (73 years versus 60 years) and had a male predominance. Nausea (10.1% versus 4.1%) and dyspnea (54.1% versus 39.2%) were more common in deceased patients. The proportion of patients with comorbidities in deceased patients was significantly higher than those in recovered patients. The median times from hospital admission to outcome in deceased patients and recovered patients were 9 days and 13 days, respectively. Patients with severe or critical COVID-19 were more frequent in deceased group. Leukocytosis (11.35×10⁹/L versus 5.60×10⁹/L) and lymphocytopenia (0.52×10⁹/L versus 1.58×10⁹/L) were shown in patients who died. The level of prothrombin time, activated partial prothrombin time, D-dimer, aspartate aminotransferase, alanine aminotransferase, urea, creatinine, creatine kinase, glucose, brain natriuretic peptide, and inflammatory indicators were significantly higher in deceased patients than in recovered patients. The volumes of ground-glass, consolidation, total lesions and total lung in all patients were quantified. Complications were more common in deceased patients than in recovered patients; respiratory failure (57.8%), septic shock (36.7%), and acute respiratory distress syndrome (26.6%) were the most common complications in patients who died. Many treatments were more frequent in deceased patients, such as antibiotic therapy (88.1% versus 53.7%), glucocorticoid treatment (70.6% versus 11.0%), intravenous immunoglobin treatment (36.6% versus 4.9%), invasive mechanical ventilation (62.3% versus 3.8%). Antivirals, antibiotics, traditional Chinese medicines and glucocorticoid treatment may significantly increase the survival time of fatal cases. Quantitative computed tomography imaging results were correlated with biochemical markers. Conclusions: Most patients with fatal outcomes were more likely to have common comorbidities. The leading causes of death were respiratory failure and multiple organ dysfunction syndrome. Acute respiratory distress syndrome, respiratory failure and septic shock were the most common serious complications. Antivirals, antibiotics, traditional Chinese medicines, and glucocorticoid treatment may prolong the survival time of deceased patients with COVID-19.

Use of procalcitonin for antibiotic stewardship in patients with COVID-19: A quality improvement project in a district general hospital

Antibiotic stewardship during the COVID-19 pandemic is an important part of a comprehensive strategy to improve patient outcomes and reduce long-term adverse effects secondary to rising antibiotic resistance. This report describes a quality improvement project which incorporates the use of procalcitonin (PCT) testing to rationalise antibiotic prescribing in patients with suspected or confirmed COVID-19 at Chesterfield Royal Hospital. Data were collected from 118 patients with a total of 127 PCT levels checked over a period of 20 days. Each PCT level was correlated with the subsequent antibiotic outcome as well as the result of the COVID-19 PCR swab. Results indicate that antibiotics were either never started or were stopped within 48 hours in 72% of COVID-confirmed cases with a PCT less than 0.25 μg/L. Our findings suggest that procalcitonin testing, when used in combination with thorough clinical assessment, is a safe, simple and sustainable way of reducing antibiotic use in COVID-19.

Retrospective review analysis of COVID-19 patients co-infected with Mycoplasma pneumoniae

Introduction

Coronavirus disease 2019 (COVID-19) is an extremely infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The outbreak of this virus has resulted in significant morbidity and mortality throughout the world. We have seen an unprecedented spread of this virus, leading to extreme pressure on health-care services. Mycoplasma pneumoniae causes atypical bacterial pneumonia and is known to co-infect patients with viral pneumonias.

Methods

In this retrospective study, patients' data of 580 inpatients with confirmed SARS-CoV-2 infection were reviewed retrospectively over a 3-month period which included the the first peak of COVID-19 infections in the UK.

Results

Eight patients with COVID-19 and M. pneumoniae coinfection were identified - four males and four females. All patients were Caucasian, with an age range of 44-89 years. 37.5% of patients were hypertensive, whereas 25% had Type 2 diabetes mellitus. Dyspnea, cough, and pyrexia were found to be very common in these patients. Majority of the patients had abnormal C-reactive protein, lymphopenia, neutrophilia along with bilateral consolidation, and ground-glass opacities. Two patients required admission to intensive care, both of whom unfortunately died along with one patient receiving ward based care.

Conclusion

Our confirmed the presence of co-infection with M. pneumoniae and describes the clinical features, investigation results, clinical course, and outcomes for these patients. Further research is needed to review the role of procalcitonin in excluding bacterial co-infection and to assess the impact of co-infection of patients with COVID-19 on morbidity and mortality.

Rationale for azithromycin in COVID-19: an overview of existing evidence

Azithromycin has rapidly been adopted as a repurposed drug for the treatment of COVID-19, despite the lack of high-quality evidence. In this review, we critically appraise the current pharmacological, preclinical and clinical data of azithromycin for treating COVID-19. Interest in azithromycin has been fuelled by favourable treatment outcomes in other viral pneumonias, a documented antiviral effect on SARS-CoV-2 in vitro and uncontrolled case series early in the pandemic. Its antiviral effects presumably result from interfering with receptor mediated binding, viral lysosomal escape, intracellular cell-signalling pathways and enhancing type I and III interferon expression. Its immunomodulatory effects may mitigate excessive inflammation and benefit tissue repair. Currently, in vivo reports on azithromycin in COVID-19 are conflicting and do not endorse its widespread use outside of clinical trials. They are, however, mostly retrospective and therefore inherently biased. The effect size of azithromycin may depend on when it is started. Also, extended follow-up is needed to assess benefits in the recovery phase. Safety data warrant monitoring of drug-drug interactions and subsequent cardiac adverse events, especially with hydroxychloroquine. More prospective data of large randomised controlled studies are expected and much-needed. Uniform reporting of results should be strongly encouraged to facilitate data pooling with the many ongoing initiatives.

Prevalence of Bloodstream Infections and their Etiology in COVID-19 Patients Admitted in a Tertiary Care Hospital in Jaipur

Background

World is in grip of coronavirus disease-2019 (COVID-19) pandemic right now. Majority of studies center around its epidemiological and clinical characteristics. Information regarding secondary bacterial infections is limited. This retrospective observational study was done to determine the prevalence and characteristics of bloodstream infections in COVID-19 patients admitted in a tertiary care center in Jaipur.

Materials and methods

All blood cultures received from COVID-19 positive patients admitted in designated COVID care ICUs and wards were included in the study. A predesigned pretested questionnaire was used to collect relevant data. Blood cultures were done using BD BACTEC™ FX40, and identification and antimicrobial susceptibility testing of isolates were done by VITEK® 2 COMPACT.

Results

One thousand five hundred seventy-eight (1578) COVID-19 positive patients were admitted in center during 5-month study period from whom 158 blood cultures were received. Out of these, 15 (9.4%) were positive. Median age of patients with positive blood culture was 54 years and included 10 males and 5 females. Ten (67%) patients needed intensive care in ICU. Significant correlation of blood culture positivity was found with parameters like ICU admission, presence of an indwelling device, underlying comorbidity, raised biochemical markers, and adverse clinical outcome.

Conclusions

Incidence of bloodstream infections is low for COVID-19 patients. Antibiotic prophylaxis needs to be used with caution, and prompt discontinuation should be done based on clinical judgment.

How to cite this article

Rajni E, Garg VK, Bacchani D, Sharma R, Vohra R, Mamoria V, et al. Prevalence of Bloodstream Infections and their Etiology in COVID-19 Patients Admitted in a Tertiary Care Hospital in Jaipur. Indian J Crit Care Med 2021;25(4):369-373.

Hydroxychloroquine can potentially interfere with immune function in COVID-19 patients: Mechanisms and insights

The recent global pandemic due to COVID-19 is caused by a type of coronavirus, SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2). Despite rigorous efforts worldwide to control the spread and human to human transmission of this virus, incidence and death due to COVID-19 continue to rise. Several drugs have been tested for treatment of COVID-19, including hydroxychloroquine. While a number of studies have shown that hydroxychloroquine can prolong QT interval, potentially increasing risk of ventricular arrhythmias and Torsade de Pointes, its effects on immune cell function have not been extensively examined. In the current review, an overview of coronaviruses, viral entry and pathogenicity, immunity upon coronavirus infection, and current therapy options for COVID-19 are briefly discussed. Further based on preclinical studies, we provide evidences that i) hydroxychloroquine impairs autophagy, which leads to accumulation of damaged/oxidized cytoplasmic constituents and interferes with cellular homeostasis, ii) this impaired autophagy in part reduces antigen processing and presentation to immune cells and iii) inhibition of endosome-lysosome system acidification by hydroxychloroquine not only impairs the phagocytosis process, but also potentially alters pulmonary surfactant in the lungs. Therefore, it is likely that hydroxychloroquine treatment may in fact impair host immunity in response to SARS-CoV-2, especially in elderly patients or those with co-morbidities. Further, this review provides a rationale for developing and selecting antiviral drugs and includes a brief review of traditional strategies combined with new drugs to combat COVID-19.

Seasonal influenza vaccination coverage and its association with COVID-19 in Saudi Arabia

Coronavirus Disease 2019 (COVID-19) pandemic is still on-going worldwide. The available information regarding the seasonal influenza vaccine (SIV) coverage during the COVID-19 pandemic and its impact on SARS-CoV-2 spread are limited. Moreover, it is argued that SIV may or may not lessen the COVID-19 severity. No previous studies have been revealed SIV coverage among COVID-19 patients and its association with COVID-19 spread and severity, especially in Saudi Arabia. Hence, this study aimed to estimate the influenza vaccine uptake in confirmed COVID-19 patients and investigate its impact on COVID-19 spread and severity. Accordingly, 1734 COVID-19 confirmed patients were included from three government hospitals in Saudi Arabia (SA). The data were collected electronically through a newly formed, self-administrated questionnaire. Among those patients, 335 were covered with SIV (19.31%), and the coverage rate of females and males was 23.4% and 15.8%, respectively. Severe COVID-19 cases were less in vaccinated patients than in non-vaccinated (2.69% vs. 3.5%, respectively). Additionally, the results showed a significant decrease in getting infected by SARS-CoV-2 after receiving SIV (P = 0.022). Even with the tremendous efforts to promote SIV uptake among the general population and high-risk groups, the SIV coverage in SA is not optimal yet. Nevertheless, there is a significant decrease in the probability of getting infected with SARS-CoV-2 after receiving SIV. Such findings with the continuous progression of the COVID-19 pandemic call for a novel approach regarding vaccination policies to increase SIV and COVID-19 vaccine uptake.

Timing of Invasive Mechanical Ventilation and Mortality among Patients with Severe COVID-19-associated Acute Respiratory Distress Syndrome

Background

Severe acute respiratory distress syndrome associated with coronavirus disease-2019 (COVID-19) (CARDS) pneumonitis presents a clinical challenge as regards to the timing of intubation and ambiguity of outcome. There is a lack of clear consensus on when to switch patients from trials of noninvasive therapies to invasive mechanical ventilation. We investigated the effect of the timing of intubation from the time of admission on the clinical outcome of CARDS.

Aim and objective

The aim and objective was to analyze the effect of timing of intubation early (within 48 hours of admission to critical care unit) versus delayed (after 48 hours of admission to critical care unit) on mortality in severe CARDS patients.

Materials and methods

A retrospective observational study performed in a 28-bedded COVID-19 intensive care unit of a tertiary care hospital in Pune, India. All patients admitted between April 1, 2020, and October 15, 2020, with confirmed COVID-19 (RT-PCR positive) requiring mechanical ventilation were included in the study.

Results

The primary outcome was in-hospital mortality. Among 2,230 patients that were admitted to the hospital, 525 required critical care (23.5%), invasive mechanical ventilation was needed in 162 patients and 147 (28%) of critical care admission were included in the study cohort after exclusion. Seventy-five patients (51%) were intubated within 48 hours of critical care admission (early group) and 72 (48.9%) were intubated after 48 hours of critical care admission (delayed group). With regards to the total of 147 included patients; male patients were 74.1% with a median age of 59 years (interquartile range, 51-68 years). Diabetes (44.9%) and hypertension (43.5%) were the most common comorbidities. Higher admission acute physiology and chronic health evaluation II scores and lower absolute lymphocyte count were observed in patients intubated within 48 hours. The early intubated group had a mortality of 60% whereas the same was observed as 77.7% in delayed intubation group, and this difference was statistically significant (p = 0.02).

Conclusion

Current study concludes that early intubation is associated with improved survival rates in severe CARDS patients.

How to cite this article

Zirpe KG, Tiwari AM, Gurav SK, Deshmukh AM, Suryawanshi PB, Wankhede PP, et al. Timing of Invasive Mechanical Ventilation and Mortality among Patients with Severe COVID-19-associated Acute Respiratory Distress Syndrome. Indian J Crit Care Med 2021;25(5):493-498.

Effectiveness of mid-regional pro-adrenomedullin (MR-proADM) as prognostic marker in COVID-19 critically ill patients: An observational prospective study

OBJECTIVE

To test the effectiveness of mid-regional pro-adrenomedullin (MR-proADM) in comparison to C-reactive protein (CRP), procalcitonin (PCT), D-dimer, lactate dehydrogenase (LDH) in predicting mortality in COVID-19-ICU-patients.

METHODS

All consecutive COVID-19 adult patients admitted between March and June 2020 to the ICU of a referral, university hospital in Northern-Italy were enrolled. MR-proADM and routine laboratory test were measured within 48 hours from ICU admission, on day 3, 7 and 14. Survival curves difference with MR-proADM cut-off set to 1.8 nmol/L were tested using log-rank test. Predictive ability was compared using area under the curve and 95% confidence interval of different receiver-operating characteristics curves.

RESULTS

57 patients were enrolled. ICU and overall mortality were 54.4%. At admission, lymphocytopenia was present in 86% of patients; increased D-dimer and CRP levels were found in 84.2% and 87.7% of patients respectively, while PCT values > 0.5 μg/L were observed in 47.4% of patients. MR-proADM, CRP and LDH were significantly different between surviving and non-surviving patients and over time, while PCT, D-dimer and NT-pro-BNP did not show any difference between the groups and over time; lymphocytes were different between surviving and non-surviving patients only. MR-proADM was higher in dying patients (2.65±2.33vs1.18±0.47, p<0.001) and a higher mortality characterized patients with MR-proADM >1.8 nmol/L (p = 0.016). The logistic regression model adjusted for age, gender, cardiovascular disease, diabetes mellitus and PCT values confirmed an odds ratio = 10.3 [95%CI:1.9-53.6] (p = 0.006) for MR-proADM >1.8 nmol/L and = 22.2 [95%CI:1.6-316.9] (p = 0.022) for cardiovascular disease. Overall, MR-proADM had the best predictive ability (AUC = 0.85 [95%CI:0.78-0.90]).

CONCLUSIONS

In COVID-19 ICU-patients, MR-proADM seems to have constantly higher values in non-survivor patients and predict mortality more precisely than other biomarkers. Repeated MR-proADM measurement may support a rapid and effective decision-making. Further studies are needed to better explain the mechanisms responsible of the increase in MR-proADM in COVID-19 patients.

A Direct Rapid Phenotypic Antimicrobial Susceptibility Test Enables Early Selection of Optimal Antibiotics to Treat Bacteremia in COVID-19 Patients

Background

Co-infection with bacteria and severe acute respiratory syndrome coronavirus 2 may result in greater use of healthcare resources and a poor prognosis. Therefore, early selection and use of optimal antibiotics are essential. The direct rapid antibiotic susceptibility test (dRAST) can detect antibiotic resistance within 6 h of a Gram smear result. This study aimed to assess the effectiveness of dRAST for improving early selection of appropriate antibiotics for coronavirus disease 2019 (COVID-19) patients with bacteremia.

Materials and Methods

This retrospective study included 96 blood culture-positive COVID-19 patients. Bacterial isolates and antimicrobial resistance profiles of each case were evaluated. Cases were divided into two groups based on whether they underwent conventional antibiotic susceptibility test (AST) or dRAST. The time to optimal targeted treatment for the two groups was investigated and compared. In addition, we examined the proportion of cases for which appropriate antibiotics were selected and broad spectrum antibiotics were administered at 72 h from blood sample collection.

Results

The mean time to optimal targeted antibiotic treatment was shorter for the dRAST group [55.7; standard deviation (SD), 28.7 vs. 92.3; SD, 51.1 h; P = 0.041]. The proportion of cases receiving optimal targeted antibiotics 72 h after blood collection for culture was higher [6/10 (60.0%) vs. 10/25 (40.0%)] and the percentage receiving broad spectrum antibiotics at 72 h was lower [6/10 (60.0%) vs. 19/25 (76.0%)] in the dRAST group than in the conventional AST group. In terms of microbiology profile, the contamination rate was high (35.5%) and multidrug-resistant strains were common (63.2%) in COVID-19 patients with bacteremia.

Conclusion

Application of dRAST for selection of antibiotics to treat bacteremia in COVID-19 patients may enable earlier and optimal treatment. The high incidence of contamination and resistant organisms in blood cultures from COVID-19 patients suggest that dRAST may speed up appropriate targeted treatment.

Superadded Coinfections and Antibiotic Resistance in the Context of COVID-19: Where do We Stand?

Purpose of review

Poor outcomes in the current coronavirus disease 2019 (COVID-19) pandemic have been attributed to superadded bacterial coinfections. The World Health Organization has reported overzealous usage of broad-spectrum antibiotics during this current pandemic raising concerns of increasing antimicrobial resistance? Therefore, the knowledge of coinfection and the common pathogens during these challenging times is essential for antibiotic stewardship practices.

Recent findings

The incidence of reported superimposed bacterial and viral coinfections in COVID-19 patients is around 0.04 to 17%. However, more than 70% of patients have received broad-spectrum antibiotics. The presence of a simultaneous coinfection can be suspected in patients with neutrophilic lymphocytosis and elevated procalcitonin in the setting of COVID-19. Multiplex polymerase chain reaction (PCR) panels, with its short turnaround time, aid in the definitive diagnosis of possible coinfection. Acinetobacter baumanii, Mycoplasma pneumonia, influenza virus, Aspergillus, Candida, etc., are commonly implicated pathogens.

Summary

Rapid characterization of coinfection and avoidance of overzealous use of broad-spectrum antibiotics in COVID-19 patients are the key to prevent antibiotic resistance during this pandemic.

How to cite this article

Kayarat B, Khanna P, Sarkar S. Superadded Coinfections and Antibiotic Resistance in the Context of COVID-19: Where do We Stand? Indian J Crit Care Med 2021;25(6):699–703.

Prevalence of Co-infection at the Time of Hospital Admission in COVID-19 Patients, A Multicenter Study

BACKGROUND

Bacterial infections may complicate viral pneumonias. Recent reports suggest that bacterial co-infection at time of presentation is uncommon in coronavirus disease 2019 (COVID-19); however, estimates were based on microbiology tests alone. We sought to develop and apply consensus definitions, incorporating clinical criteria to better understand the rate of co-infections and antibiotic use in COVID-19.

METHODS

A total of 1016 adult patients admitted to 5 hospitals in the Johns Hopkins Health System between March 1, 2020, and May 31, 2020, with COVID-19 were evaluated. Adjudication of co-infection using definitions developed by a multidisciplinary team for this study was performed. Both respiratory and common nonrespiratory co-infections were assessed. The definition of bacterial community-acquired pneumonia (bCAP) included proven (clinical, laboratory, and radiographic criteria plus microbiologic diagnosis), probable (clinical, laboratory, and radiographic criteria without microbiologic diagnosis), and possible (not all clinical, laboratory, and radiographic criteria met) categories. Clinical characteristics and antimicrobial use were assessed in the context of the consensus definitions.

RESULTS

Bacterial respiratory co-infections were infrequent (1.2%); 1 patient had proven bCAP, and 11 (1.1%) had probable bCAP. Two patients (0.2%) had viral respiratory co-infections. Although 69% of patients received antibiotics for pneumonia, the majority were stopped within 48 hours in patients with possible or no evidence of bCAP. The most common nonrespiratory infection was urinary tract infection (present in 3% of the cohort).

CONCLUSIONS

Using multidisciplinary consensus definitions, proven or probable bCAP was uncommon in adults hospitalized due to COVID-19, as were other nonrespiratory bacterial infections. Empiric antibiotic use was high, highlighting the need to enhance antibiotic stewardship in the treatment of viral pneumonias.

COVID-19 Clinical Phenotypes: Presentation and Temporal Progression of Disease in a Cohort of Hospitalized Adults in Georgia, United States

BACKGROUND

The epidemiological features and outcomes of hospitalized adults with coronavirus disease 2019 (COVID-19) have been described; however, the temporal progression and medical complications of disease among hospitalized patients require further study. Detailed descriptions of the natural history of COVID-19 among hospitalized patients are paramount to optimize health care resource utilization, and the detection of different clinical phenotypes may allow tailored clinical management strategies.

METHODS

This was a retrospective cohort study of 305 adult patients hospitalized with COVID-19 in 8 academic and community hospitals. Patient characteristics included demographics, comorbidities, medication use, medical complications, intensive care utilization, and longitudinal vital sign and laboratory test values. We examined laboratory and vital sign trends by mortality status and length of stay. To identify clinical phenotypes, we calculated Gower's dissimilarity matrix between each patient's clinical characteristics and clustered similar patients using the partitioning around medoids algorithm.

RESULTS

One phenotype of 6 identified was characterized by high mortality (49%), older age, male sex, elevated inflammatory markers, high prevalence of cardiovascular disease, and shock. Patients with this severe phenotype had significantly elevated peak C-reactive protein creatinine, D-dimer, and white blood cell count and lower minimum lymphocyte count compared with other phenotypes (P < .01, all comparisons).

CONCLUSIONS

Among a cohort of hospitalized adults, we identified a severe phenotype of COVID-19 based on the characteristics of its clinical course and poor prognosis. These findings need to be validated in other cohorts, as improved understanding of clinical phenotypes and risk factors for their development could help inform prognosis and tailored clinical management for COVID-19.

A Systematic Review of Systematic Reviews on the COVID-19 Pandemic

COVID-19 a systemic inflammation involving multiple organs, affecting all age groups, with high mortality rate, severe adverse outcomes, and high economic burden need to be described. A systematic review of systematic reviews conducted. We searched PubMed, OVID Medline, Cochrane library, COVID-19 resource centers of N Engl. J Med, AHA, and LITCOVID. Certainty of evidences was evaluated by GRADE approach. Meta-analysis according to random effects model was conducted. Seventy-one eligible systematic reviews are included in the study. A total of 86.5% of them had high quality, and 13.5% had medium quality. Meta-analysis results are presented in tabular format, and the remaining results are presented in narration fashion. COVID-19 involves blood vessels, lung, heart, nervous system, liver, gastrointestinal system, kidney, eyes, and other organs and infects adult and children, neonates, pregnant women, and elderly, transmitted via air born and droplet. Comorbidities associated with COVID-19 are HTN 20.7%, CVD 9.6%, DM 9.55%, respiratory diseases 7%, and 9% of cigarette smoking. Prognostic factors for mortality among COVID-19 cases are acute cardiac injury, diagnosed CVD, DM, respiratory disease, and HTN. Prognostic factors for disease severity are CVD and HTN. Prognostic factors for disease progression were fever, shortness of breath, and smoking. There is no specific antiviral treatment. Preventive measures including physical distancing of 2 m and more, using PPE, avoiding social gatherings, quarantine, and isolation have been recommended. Encouraging telemedicine, online training, and homeschooling are highly recommended. Vaccine is approaching, and concerns exist about vaccine with a high efficacy. Modification of CVD and cardiometabolic risk became the cornerstone for sustainable control of pandemic.

Impact of the healthcare potential in the European countries on infections and mortality caused by Covid-19

The COVID-19 outbreak posed several challenges to healthcare professionals in treating patients: limiting the spread of infection; develop appropriate short-term strategies; and formulating long-term plans. Each of the affected countries had specific capacities before the outbreak began. This potential may have helped reduce the spread of the disease and should help reduce its impact. This paper uses the VMCM method to determine the capacity of health services in European countries. It allowed for a ranking of countries in terms of this potential. This allows the capacity of the health service to be related to the number of infected and deceased people. The purpose of this article is to examine the relationship of infections and mortality on COVID-19 to health care capacity.

Fecal microbiota transplantation for COVID-19; a potential emerging treatment strategy

At the end of 2019, an emerging outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that first reported from Wuhan, China. The first manifestations of patients infected with SARS-CoV-2 was flu-like symptoms, while other type of manifestations, especially gastrointestinal manifestations were discovered recently. As of June 2020, there is no specific drug or treatment strategy for COVID-19, a disease caused by SARS-CoV-2, so different combination of antiviral drugs is currently being used. Gut microbiota mostly consists of four phyla, including Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. The interaction between gut microbiota and immune system through releasing some cytokines such as IL-1β, IL-2, IL-10, TNF-α, and IFN-γ that play roles in the severity of COVID-19. In this article, a new potential treatment for COVID-19 by fecal microbiota transplantation (FMT) is described. FMT revealed promising results in different diseases, especially recurrent clostridium difficile infection, and it might reduce length of hospital admission and severity of the disease by modification of gut microbiota composition.

Impact of COVID-19 in patients with concurrent co-infections: A systematic review and meta-analyses

The burden and impact of secondary superadded infections in critically ill coronavirus disease 2019 (COVID-19) patients is widely acknowledged. However, there is a dearth of information regarding the impact of COVID-19 in patients with tuberculosis, HIV, chronic hepatitis, and other concurrent infections. This review was conducted to evaluate the consequence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in patients with concurrent co-infections based on the publications reported to date. An extensive comprehensive screening was conducted using electronic databases up to 3rd September 2020 after obtaining registration with PROSPERO (CRD420202064800). The observational studies or interventional studies in English, evaluating the impact of SARS-CoV-2 in patients with concurrent infections are included for the meta-analyses. Our search retrieved 20 studies, with a total of 205,702 patients. Patients with tuberculosis (RR = 2.10; 95% CI, 1.75-2.51; I²  = 0%), influenza (RR = 2.04; 95% CI, 0.15-28.25, I²  = 99%) have an increased risk of mortality during a co-infection with SARS-CoV-2. No significant impact is found in people living with HIV (RR = 0.99; 95% CI, 0.82-1.19; I²  = 30%), Chronic hepatitis (RR = 1.15; 95% CI, 0.73-1.81; I²  = 10%). Several countries (Brazil, Paraguay, Argentina, Peru, Colombia, and Singapore) are on the verge of a dengue co epidemic (cumulative 878,496 and 5,028,380 cases of dengue and COVID-19 respectively). The impact of COVID-19 in patients of concurrent infections with either tuberculosis or influenza is detrimental. The clinical outcomes of COVID-19 in HIV or chronic hepatitis patients are comparable to COVID-19 patients without these concurrent infections.

Exacerbation of antimicrobial resistance: another casualty of the COVID-19 pandemic?

Introduction: The widespread use of antimicrobial drugs during the ongoing coronavirus disease 2019 (COVID-19) pandemic and the likely emergence of antibiotic-resistant microorganisms is a global health concern. Even before the COVID-19 pandemic, several antimicrobial drugs have lost their efficacy and are no longer useful to treat life-threatening infections. Since the exacerbation of antimicrobial resistance is likely to be another casualty of the COVID-19 pandemic, there is a pressing need to develop innovative strategies to minimize the risk of antimicrobial resistance.Areas covered: Focusing on the COVID-19 pandemic, I have briefly summarized the current knowledge and challenges in our understanding of antimicrobial resistance, emphasizing quorum sensing and quorum quenching. Our understanding of bacterial communication by quorum sensing to acquire virulence has paved the way to reduce bacterial pathogenicity through quorum quenching. Availability of clinically viable quorum quenching agents would likely to diminish bacterial virulence to create a microenvironment for the host phagocytic cells to reduce bacterial infection.Expert opinion: Future studies that aim to generate clinically useful quorum quenching agents need to be considered. An important benefit of such agents may be a diminished risk of antimicrobial resistance.

Metagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19

Broad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs (n = 45). mNGS identified all viruses detected by routine clinical testing (influenza A [n = 3], human metapneumovirus [n = 2], and human coronavirus OC43 [n = 2], and human coronavirus HKU1 [n = 1]). mNGS also identified both coinfections (1, 2.2%) and alternative viral infections (4, 13.3%) that were not detected by routine clinical workup (respiratory syncytial virus [n = 3], human metapneumovirus [n = 1], and human coronavirus NL63 [n = 1]). Among SARS-CoV-2 RT-PCR-positive PUIs, lower cycle threshold (C_T ) values correlated with greater SARS-CoV-2 read recovery by mNGS (R ², 0.65; P < 0.001). Our results suggest that current broad-spectrum molecular testing algorithms identify most respiratory viral infections among SARS-CoV-2 PUIs, when available and implemented consistently.

Bacterial co-infections and antibiotic resistance in patients with COVID-19

Background: Bacterial co-infections are frequently identified in viral respiratory infections and are significant reasons for morbidity and mortality. Information on the prevalence of bacterial co-infection in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is lacking. The purpose of this study was to determine the prevalence of bacterial infections and antibiotic resistance in patients with coronavirus disease (COVID-19). Methods: In a cross-sectional study, blood culture (BC) and endotracheal aspirate (ETA) were obtained from COVID-19 patients (RT-PCR positive for SARS-CoV-2). The bacterial isolates were confirmed by the standard microbiological methods. Antibiotic resistance was determined using the disk diffusion method. Results: Among these 340 patients with COVID-19, a total of 43 (12.46%) patients had secondary bacterial infections. The most common bacteria isolated through ETA and BC included Klebsiella species 11 (25.59%), methicillin-sensitive Staphylococcus aureus (MSSA) 9 (20.93%), Escherichia coli 7 (16.28%), methicillin-resistant Staph ylo coccus aureus (MRSA) 6 (13.95%), Enterobacter species 5 (11.63%), Streptococcus pneumoniae 1 (2.32%), and Pseudomonas aeruginosa 4 (9.30%). The results showed that Enterobacteriaceae isolates from COVID-19 patients had the highest resistance to cotrimoxazole (74%), piperacillin (67.5%), ceftazidime (47.5%), and cefepime (42.5%). All isolates were susceptible to amikacin (100%). S. aureus isolates were susceptible to vancomycin (100%) and the rates of resistance to oxacillin, erythromycin and clindamycin were over (90%). P. aeruginosa was susceptible (90%) to imipenem. Conclusions: Bacterial co-infection is relatively infrequent in hospitalized COVID-19 patients. According to the results, one of the causes of death of these patients could be a secondary infections.

Antimicrobial Resistance as a Hidden Menace Lurking Behind the COVID-19 Outbreak: The Global Impacts of Too Much Hygiene on AMR

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new coronavirus that was recently discovered in 2019. While the world is working hard to overcome and control the coronavirus disease 2019 (COVID-19) pandemic, it is also crucial to be prepared for the great impacts of this outbreak on the development of antimicrobial resistance (AMR). It is predicted that inappropriate and too much use of antibiotics, biocides, and disinfectants during this pandemic may raise disastrous effects on antibiotic stewardship programs and AMR control all around the world. Furthermore, the use of certain antibiotics alone or in combination with antiviral agents or other medications for the treatment of secondary bacterial infections among COVID-19 patients may be regarded as a major factor that negatively affects host immune response by disrupting mitochondrial function and activity. Herein, we suggest that the current management strategies to control AMR and prioritize antibiotic stewardship schemes should be extremely highlighted in relation to the COVID-19 outbreak. The rising concerns about excessive use of antimicrobials and biocides and taking too much hygiene also need to be addressed during this pandemic due to their impacts on AMR, public health, and the environment.

Antibiotic usage and stewardship in patients with COVID-19: too much antibiotic in uncharted waters?

Background

Antimicrobial usage and stewardship programmes during COVID-19 have been poorly studied. Prescribing practice varies despite national guidelines, and there is concern that stewardship principles have suffered.

Aim

To analyse antibiotic prescriptions during the COVID-19 pandemic at a teaching hospital and to propose improved approaches to stewardship.

Methods

We reviewed COVID-19 admissions to medical wards and intensive care units (ICUs) in a London teaching hospital to assess initial antibiotic usage and evidence of bacterial co-infection, and to determine if our current antibiotic guidelines were adhered to.

Findings

Data from 130 inpatients (76% medical and 24% ICU) were obtained. On admission, 90% were treated with antibiotics. No microbiological samples taken on admission provided definitive evidence of respiratory co-infection. In 13% of cases, antibiotics were escalated, usually without supporting clinical, radiological or laboratory evidence. In 16% of cases, antibiotics were stopped or de-escalated within 72 h. Blood results and chest radiographs were characteristic of COVID-19 in 20% of ward patients and 42% of ICU patients. Overall mortality was 25% at 14 days - similar to rates described for the UK as a whole.

Conclusion

The majority of patients received antibiotics despite limited evidence of co-infection. Most patients received narrower spectrum antibiotics than recommended by NICE. As understanding of the natural history of COVID-19 infections progresses, stewardship programmes will need to evolve; however, at this point, we feel that a more restrictive antibiotic prescribing approach is warranted. We propose strategies for effective stewardship and estimate the effect this may have on antibiotic consumption.

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.

Bacterial co-infection and secondary infection in patients with COVID-19: a living rapid review and meta-analysis

BACKGROUND

Bacterial co-pathogens are commonly identified in viral respiratory infections and are important causes of morbidity and mortality. The prevalence of bacterial infection in patients infected with SARS-CoV-2 is not well understood.

AIMS

To determine the prevalence of bacterial co-infection (at presentation) and secondary infection (after presentation) in patients with COVID-19.

SOURCES

We performed a systematic search of MEDLINE, OVID Epub and EMBASE databases for English language literature from 2019 to April 16, 2020. Studies were included if they (a) evaluated patients with confirmed COVID-19 and (b) reported the prevalence of acute bacterial infection.

CONTENT

Data were extracted by a single reviewer and cross-checked by a second reviewer. The main outcome was the proportion of COVID-19 patients with an acute bacterial infection. Any bacteria detected from non-respiratory-tract or non-bloodstream sources were excluded. Of 1308 studies screened, 24 were eligible and included in the rapid review representing 3338 patients with COVID-19 evaluated for acute bacterial infection. In the meta-analysis, bacterial co-infection (estimated on presentation) was identified in 3.5% of patients (95%CI 0.4-6.7%) and secondary bacterial infection in 14.3% of patients (95%CI 9.6-18.9%). The overall proportion of COVID-19 patients with bacterial infection was 6.9% (95%CI 4.3-9.5%). Bacterial infection was more common in critically ill patients (8.1%, 95%CI 2.3-13.8%). The majority of patients with COVID-19 received antibiotics (71.9%, 95%CI 56.1 to 87.7%).

IMPLICATIONS

Bacterial co-infection is relatively infrequent in hospitalized patients with COVID-19. The majority of these patients may not require empirical antibacterial treatment.

Update on COVID-19: A teleconference with the Paediatric Virology Study Group (Review)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is transmitted to humans mainly via contact and droplet transmission and its entry into cells is mediated by the efficient binding of the spike (S) viral protein with the angiotensin converting enzyme-2 (ACE2) receptors. Although acute respiratory distress syndrome (ARDS) caused by SARS-CoV-2 fulfills the criteria of the Berlin definition, in a considerable proportion of patients with COVID-19, there is a dissociation between their relatively well-preserved lung mechanics and the severity of hypoxaemia. The extent of pneumococcal related morbidity and mortality is largely unknown. Respiratory comorbidities that increase the risk of severe disease and mortality due to SARS-CoV-2 include chronic obstructive pulmonary disease, asthma, bronchiectasis and fibrotic interstitial lung diseases, regardless of aetiology. Pneumococcal and seasonal influenza vaccinations are useful in preventing a substantial burden of mortality in high-risk populations, while general quarantine and social distancing can reduce the infiltration of the virus within the community. To date, several therapeutic agents have been studied or are currently examined, such as hydroxychloroquine, chloroquine, ritonavir/lopinavir, remdesivir, colchicines and interleukin-6 inhibitors. However, the usage of most of these into clinical practice was not based on randomised clinical trials and their results should be viewed with extreme caution; remdesivir seems to be the more promising option. Rigorous efforts are under way for the development of a safe and successful vaccine against SARS-CoV-2.

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.

COVID-19 pneumonia: the great radiological mimicker

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread worldwide since December 2019. Although the reference diagnostic test is a real-time reverse transcription-polymerase chain reaction (RT-PCR), chest-computed tomography (CT) has been frequently used in diagnosis because of the low sensitivity rates of RT-PCR. CT findings of COVID-19 are well described in the literature and include predominantly peripheral, bilateral ground-glass opacities (GGOs), combination of GGOs with consolidations, and/or septal thickening creating a "crazy-paving" pattern. Longitudinal changes of typical CT findings and less reported findings (air bronchograms, CT halo sign, and reverse halo sign) may mimic a wide range of lung pathologies radiologically. Moreover, accompanying and underlying lung abnormalities may interfere with the CT findings of COVID-19 pneumonia. The diseases that COVID-19 pneumonia may mimic can be broadly classified as infectious or non-infectious diseases (pulmonary edema, hemorrhage, neoplasms, organizing pneumonia, pulmonary alveolar proteinosis, sarcoidosis, pulmonary infarction, interstitial lung diseases, and aspiration pneumonia). We summarize the imaging findings of COVID-19 and the aforementioned lung pathologies that COVID-19 pneumonia may mimic. We also discuss the features that may aid in the differential diagnosis, as the disease continues to spread and will be one of our main differential diagnoses some time more.

Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients

Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens. In contrast to targeted methods, mNGS also provides valuable information on the composition of the microbiome and might uncover coinfections that may associate with disease progression and impact prognosis. To evaluate the use of mNGS for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or other infecting pathogens, we applied direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing. Nasopharyngeal (NP) swab specimens from 50 patients under investigation for CoV disease 2019 (COVID-19) were sequenced, and the data were analyzed by the CosmosID bioinformatics platform. Further, we characterized coinfections and the microbiome associated with a four-point severity index. SARS-CoV-2 was identified in 77.5% (31/40) of samples positive by RT-PCR, correlating with lower cycle threshold (Ct) values and fewer days from symptom onset. At the time of sampling, possible bacterial or viral coinfections were detected in 12.5% of SARS-CoV-2-positive specimens. A decrease in microbial diversity was observed among COVID-19-confirmed patients (Shannon diversity index, P = 0.0082; Chao richness estimate, P = 0.0097; Simpson diversity index, P = 0.018), and differences in microbial communities were linked to disease severity (P = 0.022). Furthermore, statistically significant shifts in the microbiome were identified among SARS-CoV-2-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae (P = 0.028) and a reduction in the abundance of Corynebacterium accolens (P = 0.025) were observed. Our study corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages rather than the severity of COVID-19. Further, we demonstrate that SARS-CoV-2 causes a significant change in the respiratory microbiome. This work illustrates the utility of mNGS for the detection of SARS-CoV-2, for diagnosing coinfections without viral target enrichment or amplification, and for the analysis of the respiratory microbiome.IMPORTANCE SARS-CoV-2 has presented a rapidly accelerating global public health crisis. The ability to detect and analyze viral RNA from minimally invasive patient specimens is critical to the public health response. Metagenomic next-generation sequencing (mNGS) offers an opportunity to detect SARS-CoV-2 from nasopharyngeal (NP) swabs. This approach also provides information on the composition of the respiratory microbiome and its relationship to coinfections or the presence of other organisms that may impact SARS-CoV-2 disease progression and prognosis. Here, using direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing of NP swab specimens from 50 patients under investigation for COVID-19, we detected SARS-CoV-2 sequences by applying the CosmosID bioinformatics platform. Further, we characterized coinfections and detected a decrease in the diversity of the microbiomes in these patients. Statistically significant shifts in the microbiome were identified among COVID-19-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae and a reduction in the abundance of Corynebacterium accolens were observed. Our study also corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages of disease rather than with severity of disease. This work illustrates the utility of mNGS for the detection and analysis of SARS-CoV-2 from NP swabs without viral target enrichment or amplification and for the analysis of the respiratory microbiome.

Pleural diseases and COVID-19: ubi fumus, ibi ignis

More than 45 000 articles in the PubMed database and around 3200 studies registered in ClinicalTrials.gov, of which greater than half are clinical trials, are the result of ongoing and relentless research into the global pandemic nature of an acute respiratory disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which made its initial appearance in December 2019 in China. As of 28 August 2020, the total confirmed cases of coronavirus disease 2019 (COVID-19) surpasses 24.5 million, with more than 830 000 global deaths [1]. An estimated 40% to 45% of persons infected with SARS-CoV-2 will remain asymptomatic, but they can transmit the virus to others for an extended period, perhaps longer than 14 days [2]. The primary presentation of symptomatic infection is that of an influenza-like illness or viral pneumonia, with about 20% of these patients developing severe or critical manifestations [3].

There is both direct and circumstantial evidence that SARS-CoV-2 is responsible for the generation of pleural effusions and secondary spontaneous pneumothorax/pneumomediastinumhttps://bit.ly/3gZqA7Z

Tropical peatlands and their conservation are important in the context of COVID-19 and potential future (zoonotic) disease pandemics

The COVID-19 pandemic has caused global disruption, with the emergence of this and other pandemics having been linked to habitat encroachment and/or wildlife exploitation. High impacts of COVID-19 are apparent in some countries with large tropical peatland areas, some of which are relatively poorly resourced to tackle disease pandemics. Despite this, no previous investigation has considered tropical peatlands in the context of emerging infectious diseases (EIDs). Here, we review: (i) the potential for future EIDs arising from tropical peatlands; (ii) potential threats to tropical peatland conservation and local communities from COVID-19; and (iii) potential steps to help mitigate these risks. We find that high biodiversity in tropical peat-swamp forests, including presence of many potential vertebrate and invertebrate vectors, combined, in places, with high levels of habitat disruption and wildlife harvesting represent suitable conditions for potential zoonotic EID (re-)emergence. Although impossible to predict precisely, we identify numerous potential threats to tropical peatland conservation and local communities from the COVID-19 pandemic. This includes impacts on public health, with the potential for haze pollution from peatland fires to increase COVID-19 susceptibility a noted concern; and on local economies, livelihoods and food security, where impacts will likely be greater in remote communities with limited/no medical facilities that depend heavily on external trade. Research, training, education, conservation and restoration activities are also being affected, particularly those involving physical groupings and international travel, some of which may result in increased habitat encroachment, wildlife harvesting or fire, and may therefore precipitate longer-term negative impacts, including those relating to disease pandemics. We conclude that sustainable management of tropical peatlands and their wildlife is important for mitigating impacts of the COVID-19 pandemic, and reducing the potential for future zoonotic EID emergence and severity, thus strengthening arguments for their conservation and restoration. To support this, we list seven specific recommendations relating to sustainable management of tropical peatlands in the context of COVID-19/disease pandemics, plus mitigating the current impacts of COVID-19 and reducing potential future zoonotic EID risk in these localities. Our discussion and many of the issues raised should also be relevant for non-tropical peatland areas and in relation to other (pandemic-related) sudden socio-economic shocks that may occur in future.

Fundus Lesions in Patients Hospitalized With COVID-19 Infection in Mumbai, India: A Retrospective Review

Background and objective

Coronavirus disease 2019 (COVID-19) is a viral infection that has grown to be a global pandemic, and it is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The ocular involvement in COVID-19, both in the anterior and posterior segments, is increasingly being recognized by ophthalmologists. We report the fundus photographic and systemic findings in 25 patients without recent-onset visual symptoms who were hospitalized with COVID-19.

Methods

Patients with COVID-19 infection who were admitted to an isolation ward/ICU in Mumbai, India during June-August 2020 underwent a comprehensive clinical and systemic evaluation. We performed a fundus evaluation using a handheld fundus camera during their admission period. We conducted a retrospective case record review and extracted demographic characteristics, laboratory findings, and fundus photographs from each case record.

Results

We screened 25 non-consecutive patients, and they included 20 (80%) men and five (20%) women, with ages ranging from 31 to 79 years (mean: 56.3 years). Systemically, the spectrum of severity on admission varied from mild to moderate to severely ill. The majority of the patients had no complaints of recent visual loss. An analysis of fundus photographs of 50 eyes of 25 patients revealed no evidence of fundus lesions in as many as 48 photographs. Two photographs of two eyes of patients showed incidental lesions.

Conclusions

We found no evidence of vascular, inflammatory, or thromboembolic disease that could be linked to COVID-19 infection in any of the images we studied; however, fundus examination may be utilized in patients with co-infection.

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.

Is the Frequency of Candidemia Increasing in COVID-19 Patients Receiving Corticosteroids?

Corticosteroids have potent anti-inflammatory and immunosuppressive effects. Recently, these medications have gained importance in the treatment of severe COVID-19. Here we present data demonstrating a marked (10-fold) increase in frequency of candidemia in hospitalized patients with COVID-19 receiving corticosteroids in Brazil. Overall mortality was 72.7%, despite antifungal therapy. Physicians should be aware of the potential risk for candidemia among severely ill COVID-19 patients receiving high-doses of corticosteroids.

Staphylococcus aureus Bacteremia in Patients Infected With COVID-19: A Case Series

Background

Previous viral pandemics have shown that secondary bacterial infections result in higher morbidity and mortality, with Staphylococcus aureus being the primary causative pathogen. The impact of secondary S. aureus bacteremia on mortality in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains unknown.

Methods

This was a retrospective observational case series of patients with coronavirus disease 2019 (COVID-19) who developed secondary S. aureus bacteremia across 2 New York City hospitals. The primary end point was to describe 14-day and 30-day hospital mortality rates of patients with COVID-19 and S. aureus bacteremia. Secondary end points included predictors of 14-day and 30-day hospital mortality in patients with COVID-19 and S. aureus bacteremia.

Results

A total of 42 patients hospitalized for COVID-19 with secondary S. aureus bacteremia were identified. Of these patients, 23 (54.8%) and 28 (66.7%) died at 14 days and 30 days, respectively, from their first positive blood culture. Multivariate analysis identified hospital-onset bacteremia (≥4 days from date of admission) and age as significant predictors of 14-day hospital mortality and Pitt bacteremia score as a significant predictor of 30-day hospital mortality (odds ratio [OR], 11.9; 95% CI, 2.03-114.7; P = .01; OR, 1.10; 95% CI, 1.03-1.20; P = .02; and OR, 1.56; 95% CI, 1.19-2.18; P = .003, respectively).

Conclusions

Bacteremia with S. aureus is associated with high mortality rates in patients hospitalized with COVID-19. Further investigation is warranted to understand the impact of COVID-19 and secondary S. aureus bacteremia.

The clinical value of minimal invasive autopsy in COVID-19 patients

BACKGROUND

Minimally invasive autopsy (MIA) is a validated and safe method to establish the cause of death (COD), mainly in low-resource settings. However, the additional clinical value of MIA in Coronavirus disease (COVID-19) patients in a high-resource setting is unknown. The objective was to assess if and how MIA changed clinical COD and contributing diagnoses in deceased COVID-19 patients.

METHODS AND FINDINGS

A prospective observational cohort from April to May 2020 in a 981-bed teaching hospital in the epicenter of the COVID-19 pandemic in Belgium was established. Patients who died with either PCR-confirmed or radiologically confirmed COVID-19 infection were consecutively included. MIA consisted of whole-body CT and CT-guided Tru-Cut® biopsies. Diagnostic modalities were clinical chart review, radiology, microbiology, and histopathology which were assessed by two independent experts per modality. MIA COD and contributing diagnoses were established during a multi-disciplinary meeting. Clinical COD (CCOD) and contributing diagnosis were abstracted from the discharge letter. The main outcomes were alterations in CCOD and contributing diagnoses after MIA, and the contribution of each diagnostic modality. We included 18 patients, of which 7 after intensive care unit hospitalization. MIA led to an alteration in 15/18 (83%) patients. The CCOD was altered in 5/18 (28%) patients. MIA found a new COD (1/5), a more specific COD (1/5), a less certain COD (1/5), or a contributing diagnosis to be the COD (2/5). Contributing diagnoses were altered in 14/18 (78%) patients: 9 new diagnoses, 5 diagnoses dismissed, 3 made more specific, and 2 made less certain. Overall, histopathology contributed in 14/15 (93%) patients with alterations, radiology and microbiology each in 6/15 (40%), and clinical review in 3/15 (20%). Histopathology was deemed the most important modality in 10 patients, radiology in two patients, and microbiology in one patient.

CONCLUSION

MIA, especially histological examination, can add valuable new clinical information regarding the cause of death in COVID-19 patients, even in a high-resource setting with wide access to premortem diagnostic modalities. MIA may provide important clinical insights and should be applied in the current ongoing pandemic.

TRIAL REGISTRATION

Clinicaltrials.gov identifier: NCT04366882.

COVID-19: A Rural US Emergency Department Perspective

Several aspects led to the poor control of the coronavirus disease 2019 (COVID-19) outbreak in the US from a rural emergency department (ED) perspective. These include US residents’ attitude towards political involvement in health and civil rights; lack of enough testing kits and rapid test results, or not available at all; and personal protective equipment (PPE) shortages. These obstacles related to medical supplies and resources, and lack of coordinated approach to the pandemic in the US, are important information for retrospective disaster research to understand study limitations, extrapolate accurate and valid data, and for other countries to understand how and why the US had higher numbers of COVID-19 cases and deaths compared to other countries.

Clinical characteristics and antibiotics treatment in suspected bacterial infection patients with COVID-19

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Secondary bacterial infection induced negative clinical outcomes.

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Empirical use of antibiotics had no more benefits for patients with COVID-19.

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Detailed antimicrobial policies and guidelines should be applied and promoted.

Coronavirus disease 2019 (COVID-19) pandemic has brought challenges to health and social care systems. However, the empirical use of antibiotics is still confusing. Presently, a total of 1123 patients with COVID-19 admitted to Renmin Hospital of Wuhan University was included in this retrospective cohort study. The clinical features, complications and outcomes were compared between the suspected bacterial infection and the no evidence of bacterial infection. The risk factors of mortality and the incidence of acute organ injury were analyzed. As a result, 473 patients were selected to suspected bacterial infection (SI) group based on higher white blood cell count and procalcitonin or bacterial pneumonia on chest radiography. 650 patients were selected to the no evidence of bacterial infection (NI) group. The SI group had more severely ill patients (70.2% vs. 39.8%), more death (20.5% vs. 2.2%), and more acute organ injury (40.2% vs. 11.2%). Antibiotics were found associated with improved mortality and an increased risk for acute organ injury in hospitalized patients with COVID-19. Intravenous moxifloxacin and meropenem increased the death rate in patients with suspected bacterial infection, while oral antibiotics reduced mortality in this group. Moreover, penicillin and meropenem treatments were associated with increased mortality of the patients with no evidence of bacterial infection. In conclusion, patients with suspected bacterial infection were more likely to have negative clinical outcomes than those without bacterial infection. Empirical use of antibiotics may not have the expected benefits.

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.

Similar Clinical Course and Significance of Circulating Innate and Adaptive Immune Cell Counts in STEMI and COVID-19

This study aimed to assess the time course of circulating neutrophil and lymphocyte counts and their ratio (NLR) in ST-segment elevation myocardial infarction (STEMI) and coronavirus disease (COVID)-19 and explore their associations with clinical events and structural damage. Circulating neutrophil, lymphocyte and NLR were sequentially measured in 659 patients admitted for STEMI and in 103 COVID-19 patients. The dynamics detected in STEMI (within a few hours) were replicated in COVID-19 (within a few days). In both entities patients with events and with severe structural damage displayed higher neutrophil and lower lymphocyte counts. In both scenarios, higher maximum neutrophil and lower minimum lymphocyte counts were associated with more events and more severe organ damage. NLR was higher in STEMI and COVID-19 patients with the worst clinical and structural outcomes. A canonical deregulation of the immune response occurs in STEMI and COVID-19 patients. Boosted circulating innate (neutrophilia) and depressed circulating adaptive immunity (lymphopenia) is associated with more events and severe organ damage. A greater understanding of these critical illnesses is pivotal to explore novel alternative therapies.

Changes in antimicrobial utilization during the coronavirus disease 2019 (COVID-19) pandemic after implementation of a multispecialty clinical guidance team

Objective:

Evaluate changes in antimicrobial use during COVID-19 and after implementation of a multispecialty COVID-19 clinical guidance team compared to pre–COVID-19 antimicrobial use.

Design:

Retrospective observational study.

Setting:

Tertiary-care academic medical center.

Participants:

Internal medicine and medical intensive care unit (MICU) provider teams and hospitalized COVID-19 patients.

Methods:

Difference-in-differences analyses of antibiotic days of therapy per 1,000 patient days present (DOT) for internal medicine and MICU teams treating COVID-19 patients versus teams that did not were performed for 3 periods: before COVID-19, initial COVID-19 period, and after implementation of a multispecialty COVID-19 clinical guidance team which included daily, patient-specific antimicrobial stewardship recommendations. Patient characteristics associated with antibiotic DOT were evaluated using multivariable Poisson regression.

Results:

In the initial COVID-19 period, compared to the pre–COVID-19 period, internal medicine and MICU teams increased weekly antimicrobial use by 145.3 DOT (95% CI, 35.1–255.5) and 204.0 DOT (95% CI, −16.9 to 424.8), respectively, compared to non–COVID-19 teams. In the intervention period, internal medicine and MICU COVID-19 teams both had significant weekly decreases of 362.3 DOT (95% CI, −443.3 to −281.2) and 226.3 DOT (95% CI, −381.2 to –71.3). Of 131 patients hospitalized with COVID-19, 86 (65.6%) received antibiotics; no specific patient factors were significantly associated with an expected change in antibiotic days.

Conclusions:

Antimicrobial use initially increased for COVID-19 patient care teams compared to pre–COVID-19 levels but significantly decreased after implementation of a multispecialty clinical guidance team, which may be an effective strategy to reduce unnecessary antimicrobial use.

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.

A COVID-19 Case Complicated by Candida dubliniensis and Klebsiella pneumoniae-Carbapenem-Resistant Enterobacteriaceae

There has been increasing evidence of co-infections with coronavirus disease 2019 (COVID-19) pneumonia, which increases the severity of the disease. Organisms such as Klebsiella pneumoniae and Streptococcus pneumoniae have been previously isolated. We present a case of a COVID-19 patient treated with baricitinib and dexamethasone who later developed Klebsiella pneumoniae-carbapenem-resistant Enterobacteriaceae (CRE) and Candida dubliniensis bloodstream infections, treated with meropenem/vaborbactam and micafungin, respectively. These infections are exceedingly rare and are mostly reported in immunosuppressed patients. The finding of these bloodstream infections raises concerns on the cause of immunosuppression in this patient infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) treated with baricitinib and dexamethasone. There has been no report so far of COVID-19 associated with these co-infections.