Recommendations for antibacterial therapy in adults with COVID-19 - an evidence based guideline

A COVID-19 first evaluation clinic at a university hospital in Turkey

BACKGROUND

We aimed to analyze the usefulness of such a reserved area for the admission of the patients' symptoms suggesting COVID-19 and compare the demographic and clinical characteristics of the patients with COVID-19 and without COVID-19 who were admitted to C1 during the first month of the COVID-19 outbreak in our hospital.

METHODS

A new area was set up in Hacettepe University Adult Hospital to limit the contact of COVID-19 suspicious patients with other patients, which was named as COVID-19 First Evaluation Outpatient Clinic (C1). C1 had eight isolation rooms and two sampling rooms for SARS-CoV-2 polymerase-chain-reaction (PCR). All rooms were negative-pressurized. Patients who had symptoms that were compatible with COVID-19 were referred to C1 from pretriage areas. All staff received training for the appropriate use of personal protective equipment and were visited daily by the Infection Prevention and Control team.

RESULTS

One hundred and ninety-eight (29.4%) of 673 patients who were admitted to C1were diagnosed with COVID-19 between March 20, 2020, and April 19, 2020. SARS-CoV-2 PCR was positive in 142 out of 673 patients. Chest computerized tomography (CT) was performed in 421 patients and COVID-19 was diagnosed in 56 of them based on CT findings despite negative PCR. Four hundred and ninety-three patients were tested for other viral and bacterial infections with multiplex real-time reverse-transcriptase PCR (RTPCR). Blood tests that included complete blood count, renal and liver functions, d-dimer levels, ferritin, C- reactive protein, and procalcitonin were performed in 593 patients. Only one out of 44 healthcare workers who worked at C1 was infected by SARS-CoV-2.

DISCUSSION

Early diagnosis of infected patients and ensuring adequate isolation are very important to control the spread of COVID-19. The purpose of setting up the COVID-19 first evaluation outpatient clinic was to prevent the overcrowding of ER due to mild or moderate infections, ensure appropriate distancing and isolation, and enable emergency services to serve for real emergencies. A wellplanned outpatient care area and teamwork including internal medicine, microbiology, and radiology specialists under the supervision of infectious diseases specialists allowed adequate management of the mild-to-moderate patients with suspicion of COVID-19.

International alliance and AGREE-ment of 71 clinical practice guidelines on the management of critical care patients with COVID-19: a living systematic review

OBJECTIVE

We aimed to systematically identify and critically assess the clinical practice guidelines (CPGs) for the management of critically ill patients with COVID-19 with the AGREE II instrument.

STUDY DESIGN AND SETTING

We searched Medline, CINAHL, EMBASE, CNKI, CBM, WanFang, and grey literature from November 2019 - November 2020. We did not apply language restrictions. One reviewer independently screened the retrieved titles and abstracts, and a second reviewer confirmed the decisions. Full texts were assessed independently and in duplicate. Disagreements were resolved by consensus. We included any guideline that provided recommendations on the management of critically ill patients with COVID-19. Data extraction was performed independently and in duplicate by two reviewers. We descriptively summarized CPGs characteristics. We assessed the quality with the AGREE II instrument and we summarized relevant therapeutic interventions.

RESULTS

We retrieved 3,907 records and 71 CPGs were included. Means (Standard Deviations) of the scores for the 6 domains of the AGREE II instrument were 65%(SD19.56%), 39%(SD19.64%), 27%(SD19.48%), 70%(SD15.74%), 26%(SD18.49%), 42%(SD34.91) for the scope and purpose, stakeholder involvement, rigor of development, clarity of presentation, applicability, editorial independence domains, respectively. Most of the CPGs showed a low overall quality (less than 40%).

CONCLUSION

Future CPGs for COVID-19 need to rely, for their development, on standard evidence-based methods and tools.

Antibiotic Therapy in the Treatment of COVID-19 Pneumonia: Who and When?

Background: COVID-19 imposes challenges in antibiotic decision-making due to similarities between bacterial pneumonia and moderate to severe COVID-19. We evaluated the effects of antibiotic therapy on the clinical outcomes of COVID-19 pneumonia patients and diagnostic accuracy of key inflammatory markers to inform antibiotic decision-making. Methods: An observational cohort study was conducted in patients hospitalised with COVID-19 at the National Centre for Infectious Diseases and Tan Tock Seng Hospital, Singapore, from January to April 2020. Patients were defined as receiving empiric antibiotic treatment for COVID-19 if started within 3 days of diagnosis. Results: Of 717 patients included, 86 (12.0%) were treated with antibiotics and 26 (3.6%) had documented bacterial infections. Among 278 patients with COVID-19 pneumonia, those treated with antibiotics had more diarrhoea (26, 34.7% vs. 24, 11.8%, p < 0.01), while subsequent admissions to the intensive care unit were not lower (6, 8.0% vs. 10, 4.9% p = 0.384). Antibiotic treatment was not independently associated with lower 30-day (adjusted odds ratio, aOR 19.528, 95% confidence interval, CI 1.039–367.021) or in-hospital mortality (aOR 3.870, 95% CI 0.433–34.625) rates after adjusting for age, co-morbidities and severity of COVID-19 illness. Compared to white cell count and procalcitonin level, the C-reactive protein level had the best diagnostic accuracy for documented bacterial infections (area under the curve, AUC of 0.822). However, the sensitivity and specificity were less than 90%. Conclusion: Empiric antibiotic use in those presenting with COVID-19 pneumonia did not prevent deterioration or mortality. More studies are needed to evaluate strategies to diagnose bacterial co-infections in these patients.

Spread of hypervirulent multidrug-resistant ST147 Klebsiella pneumoniae in patients with severe COVID-19: an observational study from Italy, 2020-21

Objectives

To report an outbreak of hypervirulent Klebsiella pneumoniae (hvKp) in COVID-19 patients.

Methods

Prospective, observational study including consecutive COVID-19 patients with hvKp infections admitted to the University Hospital of Pisa (Italy). Clinical data and outcome of patients were collected. All patients were followed-up to 30 days from the diagnosis of infection. Mortality within 30 days of the diagnosis of hvKp infection was reported. The hypermucoviscous phenotype was determined by the ‘string test’. Molecular typing was performed on three strains collected during different periods of the outbreak. The strains underwent whole genome sequencing using the Illumina MiSeq instrument. The complete circular assemblies were also obtained for the chromosome and a large plasmid using the Unicycler tool.

Results

From November 2020 to March 2021, hvKp has been isolated from 36 COVID-19 patients: 29/36 (80.6%) had infections (15 bloodstream infections, 8 ventilator-associated pneumonias and 6 complicated urinary tract infections), while 7/36 (19.4%) had colonization (3 urine, 2 rectal and 2 skin). The isolates belonged to ST147 and their plasmid carried three replicons of the IncFIB (Mar), IncR and IncHI1B types and several resistance genes, including the rmpADC genes encoding enhancers of capsular synthesis. The hvKp isolates displayed an ESBL phenotype, with resistance to piperacillin/tazobactam and ceftolozane/tazobactam and susceptibility only to meropenem and ceftazidime/avibactam. The majority of patients were treated with meropenem alone or in combination with fosfomycin. Thirty-day mortality was 48.3% (14/29).

Conclusions

ST147 ESBL-producing hvKp is associated with high mortality in COVID-19 patients. Strict microbiological surveillance and infection control measures are needed in this population.

Candida Pneumonia with Lung Abscess as a Complication of Severe COVID-19 Pneumonia

A South Asian male patient in his mid-forties presented with symptoms of severe 2019-nCoV (COVID-19) and recent brain infarction. Subsequently, he was found to have evidence of sepsis, underlying undetected diabetes mellitus (DM) and oral candida mucositis, possibly leading to the rare occurrence of direct spread to the lung, manifesting as a necrotizing candida lung abscess. We describe the diagnosis, clinical course, and management of the unique complication in this case that occurred during his admission, hospitalization, and eventual successful discharge from the hospital. This case highlights the importance of early identification and treatment of suspected COVID-19 infection based on clinical and radiological assessments before the confirmation of COVID-19 by real-time polymerase chain reaction (rtPCR) test result, especially in patients with hyperglycemia. It also indicates the complications that can occur due to COVID-19 such as arteriovenous manifestations and the rare occurrence of pulmonary candida lung abscess. Early detection and prompt management by interdisciplinary teams in the emergency room, followed by close monitoring of complications in the intensive care unit (ICU), can lead to successful outcomes in severe/critical COVID-19 infection.

Pattern of medication utilization in hospitalized patients with COVID-19 in three District Headquarters Hospitals in the Punjab province of Pakistan

Purpose

In Pakistan, a wide range of repurposed drugs are recommended to manage hospitalized patients with COVID-19. Therefore, the current study was conducted to evaluate the pattern of utilization of repurposed drugs and other potential therapeutic options among hospitalized patients with COVID-19 in Pakistan.

Methods

This retrospective, multicenter, descriptive study enrolled consecutive hospitalized patients with COVID-19 who were admitted between March 1, 2021, and April 30, 2021, from three District Headquarter Hospitals in the Punjab province of Pakistan. We described patient and clinical characteristics and medications, stratified by COVID-19 severity during hospitalization: mild, moderate, and severe. In addition, an analytical study of drug utilization was conducted.

Findings

A total of 444 hospitalized patients with COVID-19 were included. Remdesvir, corticosteroids, antibiotics, and antithrombotics were administered to 45.0%, 93.9%, 84.9%, and 60.1% of patients, respectively. Specifically, dexamethasone was the most commonly used corticosteroid among the included patients (n = 405; 91.2%), irrespective of their clinical severity. Only 60.1% of patients hospitalized with COVID-19 in our cohort received antithrombotic therapy, and the prevalence of use was especially low (27.8%) in patients with mild illness. Of 444 patientsscreened, 399 (89.9%) patients had been discharged, and 45 patients (10.1%) died.

Implications

We provided an important glimpse into the utilization patterns of several medications of interest for the treatment of COVID-19 in Pakistan, which had not been entirely evidence-based, especially concerning systemic corticosteroids and antibiotics.

Non-typhoidal Salmonella Bacteremia in COVID-19 with Recrudescence of Fever After Corticosteroid Discontinuation: A case report

•

Secondary bacterial infections occur in COVID-19 patients treated with corticosteroid.

•

Rebound phenomenon is observed after the cessation of steroid treatment.

•

Non-typhoidal Salmonella bacteremia is associated with immunosuppressive conditions.

•

Blood cultures distinguish between secondary infections and rebound phenomena.

It is challenging for clinicians to determine the cause of occurrence of fever in COVID-19 patients after corticosteroid discontinuation. Blood cultures help us distinguish between secondary infections and rebound phenomena. We report a case of non-typhoidal Salmonella bacteremia in a 34-year-old male COVID-19 patient who developed fever after discontinuing corticosteroids.

Improving management and antimicrobial stewardship for bacterial and fungal infections in hospitalized patients with COVID-19

SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) infection is being one of the most significant challenges of health care systems worldwide. Bacterial and fungal infections in hospitalized patients with coronavirus disease 2019 (COVID-19) are uncommon but consumption of antibiotics and antifungals has increased dramatically during the ongoing pandemic resulting in increased selective pressure for global antimicrobial resistance. Nosocomial bacterial superinfections appear to be more frequent than community-acquired coinfections, particularly among patients admitted to the intensive care unit (ICU) and those receiving immunosuppressive treatment. Fungal infections associated with COVID-19 might be missed or misdiagnosed. Existing and new antimicrobial stewardship (AMS) programmes can be utilized directly in COVID-19 pandemic and are urgently needed to contain the high rates of misdiagnosis and antimicrobial prescription. The aim of this review is to describe the role of bacterial and fungal infections and possible strategies of AMS to use in daily practice for optimal management of COVID-19.

Increased Use of Antibiotics in the Intensive Care Unit During Coronavirus Disease (COVID-19) Pandemic in a Brazilian Hospital

Background: Microbial drug resistance is one of the biggest public health problems. Antibiotic consumption is an essential factor for the emergence and spread of multiresistant bacteria. Therefore, we aimed to analyze the antibiotics consumption in the Intensive Care Unit (ICU), identifying trends in the antibiotics use profile and microbiological isolates throughout the COVID-19 pandemic. Methods: We performed this retrospective observational study in intensive care units of a Brazilian tertiary hospital from January 2019 to December 2020. The primary outcome was antimicrobial consumption in the ICU, measured by defined daily doses (DDDs) per 100 bed-days. As a secondary outcome, bacterial infections (microbiological isolates) were calculated in the same fashion. Outcomes trends were analyzed using Joinpoint regression models, considering constant variance (homoscedasticity) and first-order autocorrelation assumptions. A monthly percent change (MPC) was estimated for each analyzed segment. Results: Seven thousand and nine hundred fifty-three patients had data available on prescribed and received medications and were included in the analyses. Overall, the use of antibiotics increased over time in the ICU. The reserve group (World Health Organization Classification) had an increasing trend (MPC = 7.24) from February to April 2020. The azithromycin consumption (J01FA) increased rapidly, with a MPC of 5.21 from January to April 2020. Polymyxin B showed a relevant increase from March to June 2020 (MPC = 6.93). The peak of the antibiotic consumption of Reserve group did not overlap with the peak of the pathogenic agents they are intended to treat. Conclusion: Overall antimicrobial consumption in ICU has increased in the context of the COVID-19 pandemic. The peaks in the antimicrobial's use were not associated with the rise of the pathogenic agents they intended to treat, indicating an empirical use, which is especially concerning in the context of treating multidrug-resistant (MDR) infections. This fact may contribute to the depletion of the therapeutic arsenal for MDR treatment.

Recent Updates in Experimental Research and Clinical Evaluation on Drugs for COVID-19 Treatment

Since the outbreak of corona virus disease 2019 (COVID-19) in Wuhan (China) in December 2019, the epidemic has rapidly spread to many countries around the world, posing a huge threat to global public health. In response to the pandemic, a number of clinical studies have been initiated to evaluate the effect of various treatments against COVID-19, combining medical strategies and clinical trial data from around the globe. Herein, we summarize the clinical evaluation about the drugs mentioned in this review for COVID-19 treatment. This review discusses the recent data regarding the efficacy of various treatments in COVID-19 patients, to control and prevent the outbreak.

Detection of bacteria via multiplex PCR in respiratory samples of critically ill COVID-19 patients with suspected HAP/VAP in the ICU

Background

Critically ill Coronavirus disease 2019 (COVID-19) patients have high rates of bacterial superinfection. Multiplex polymerase chain reaction panels may be able to provide useful information about the incidence and spectrum of bacteria causing superinfections.

Methods

In this retrospective observational study we included all COVID-19 positive patients admitted to our intensive care unit with suspected hospital-acquired pneumonia/ventilator-associated pneumonia (HAP/VAP) in whom the BioFire® Pneumonia Panel (PP) was performed from tracheal aspirate or bronchoalveolar lavage fluid for diagnostic purposes. The aim of our study was to analyze the spectrum of pathogens detected with the PP.

Results

In this study 60 patients with a median age of 62.5 years were included. Suspected VAP was the most frequent (48/60, 80%) indication for performing the PP. Tracheal aspirate was the predominant sample type (50/60, 83.3%).

The PP led to a negative, monomicrobial and polymicrobial result in 36.7%, 35% and 28.3% of the patients, respectively. The three most detected bacteria were Staphylococcus aureus (13/60, 21.7%), Klebsiella pneumoniae (12/60, 20%) and Haemophilus influenzae (9/60, 15%). Neither atypical bacteria nor resistance genes were detected.

Microbiological culture of respiratory specimens was performed in 36 (60%) patients concomitantly. The PP and microbiological culture yielded a non-concordant, partial concordant and completely concordant result in 13.9% (5/36), 30.6% (11/36) and 55.6% (20/36) of the analyzed samples, respectively.

Conclusion

In critically ill COVID-19 patients with suspected HAP/VAP results of the PP and microbiological culture methods were largely consistent. In our cohort, S. aureus and K. pneumoniae were the most frequently detected organisms. A higher diagnostic yield may be achieved if both methods are combined.

Predictors and microbiology of respiratory and bloodstream bacterial infection in patients with COVID-19: living rapid review update and meta-regression

Background

The prevalence of bacterial infection in patients with COVID-19 is low, however, empiric antibiotic use is high. Risk stratification may be needed to minimize unnecessary empiric antibiotic use.

Objective

To identify risk factors and microbiology associated with respiratory and bloodstream bacterial infection in patients with COVID-19.

Data sources

We searched MEDLINE, OVID Epub and EMBASE for published literature up to 5 February 2021.

Study eligibility criteria

Studies including at least 50 patients with COVID-19 in any healthcare setting.

Methods

We used a validated ten-item risk of bias tool for disease prevalence. The main outcome of interest was the proportion of COVID-19 patients with bloodstream and/or respiratory bacterial co-infection and secondary infection. We performed meta-regression to identify study population factors associated with bacterial infection including healthcare setting, age, comorbidities and COVID-19 medication.

Results

Out of 33 345 studies screened, 171 were included in the final analysis. Bacterial infection data were available from 171 262 patients. The prevalence of co-infection was 5.1% (95% CI 3.6–7.1%) and secondary infection was 13.1% (95% CI 9.8–17.2%). There was a higher odds of bacterial infection in studies with a higher proportion of patients in the intensive care unit (ICU) (adjusted OR 18.8, 95% CI 6.5–54.8). Female sex was associated with a lower odds of secondary infection (adjusted OR 0.73, 95% CI 0.55–0.97) but not co-infection (adjusted OR 1.05, 95% CI 0.80–1.37). The most common organisms isolated included Staphylococcus aureus, coagulase-negative staphylococci and Klebsiella species.

Conclusions

While the odds of respiratory and bloodstream bacterial infection are low in patients with COVID-19, meta-regression revealed potential risk factors for infection, including ICU setting and mechanical ventilation. The risk for secondary infection is substantially greater than the risk for co-infection in patients with COVID-19. Understanding predictors of co-infection and secondary infection may help to support improved antibiotic stewardship in patients with COVID-19.

Clinical practice in COVID-19: The most frequently asked questions to infectious diseases specialists

Since the emergence of the disease caused by the severe respiratory syndrome coronavirus 2 (SARS-CoV-2) - COVID-19 - in late December 2019, a vast number of publications on the subject appeared in peer-reviewed journals and preprints. Despite the significant amount of available information, infectious disease physicians are requested to solve questions from colleagues, patients, and relatives on a daily basis. Here, we aim to describe the evidence supporting the answers for frequently asked questions, based on a literature review. We created a web-based questionnaire which was distributed to a group of 70 infectious disease specialists and medical residents, asking what questions and issues they most frequently faced. The 10 most frequent questions guided the topics for a narrative review. We provide evidence and consensus-based information on subjects such as infection and transmission, isolation, management of COVID-19 confirmed cases, reinfection, clinical-therapeutic management, vaccination, and antibodies post-infection/vaccination. Correctly clarifying doubts and providing clear information to physicians, patients, and family members helps to better manage COVID-19 in the community and the hospital settings.

Identification of Coinfections by Viral and Bacterial Pathogens in COVID-19 Hospitalized Patients in Peru: Molecular Diagnosis and Clinical Characteristics

The impact of respiratory coinfections in COVID-19 is still not well understood despite the growing evidence that consider coinfections greater than expected. A total of 295 patients older than 18 years of age, hospitalized with a confirmed diagnosis of moderate/severe pneumonia due to SARS-CoV-2 infection (according to definitions established by the Ministry of Health of Peru) were enrolled during the study period. A coinfection with one or more respiratory pathogens was detected in 154 (52.2%) patients at hospital admission. The most common coinfections were Mycoplasma pneumoniae (28.1%), Chlamydia pneumoniae (8.8%) and with both bacteria (11.5%); followed by Adenovirus (1.7%), Mycoplasma pneumoniae/Adenovirus (0.7%), Chlamydia pneumoniae/Adenovirus (0.7%), RSV-B/Chlamydia pneumoniae (0.3%) and Mycoplasma pneumoniae/Chlamydia pneumoniae/Adenovirus (0.3%). Expectoration was less frequent in coinfected individuals compared to non-coinfected (5.8% vs. 12.8%). Sepsis was more frequent among coinfected patients than non-coinfected individuals (33.1% vs. 20.6%) and 41% of the patients who received macrolides empirically were PCR-positive for Mycoplasma pneumoniae and Chlamydia pneumoniae.

COVID-19, congenital heart disease, and pregnancy: dramatic conjunction-case report

Background 

Epidemiological data from the COVID-19 pandemic report that patients with pre-existing cardiovascular disease have worse outcomes and higher mortality, and that pregnant women should be considered at high risk.

Case summary 

A 25-year-old pregnant woman on the waiting list for a heart transplant, with a history of complete atrioventricular canal surgery, mitral mechanical prosthetic implant (St Jude-27), and cardiac resynchronization therapy (Boston Scientific) was hospitalized at 30 weeks of gestation for treatment of heart failure. After 7 days of hospitalization, she had a positive RT–PCR test for severe acute respiratory syndrome coronavirus 2 with progressive worsening of her clinical condition and acute foetal distress. Hence emergency caesarean section was performed. After the birth, the patient required mechanical ventilation, progressing to multiple organ system failures. Conventional inotropic drugs, antibiotics, and mechanical ventilation for 30 days in the intensive care unit provided significant clinical, haemodynamic, and respiratory improvement. However, on the 37th day, she suddenly experienced respiratory failure, gastrointestinal and airway bleeding, culminating in death.

Discussion 

Progressive physiological changes during pregnancy cause cardiovascular complications in women with severe heart disease and higher susceptibility to viral infection and severe pneumonia. COVID-19 is known to incite an intense inflammatory and prothrombotic response with clinical expression of severe acute respiratory syndrome, heart failure, and thromboembolic events. The overlap of these COVID-19 events with those of pregnancy in this woman with underlying heart disease contributed to an unfortunate outcome and maternal death.

COVID-19 Advanced Care

The coronavirus disease 2019 (COVID-19) pandemic, related to the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a worldwide sudden and substantial burden in public health due to an enormous increase in hospitalizations for pneumonia with the multiorgan disease. Treatment for individuals with COVID-19 includes best practices for supportive management of acute hypoxic respiratory failure. Emerging data indicate that dexamethasone therapy reduces 28-day mortality in patients requiring supplemental oxygen compared with usual care, and ongoing trials are testing the efficacy of antiviral therapies, immune modulators and anticoagulants in the prevention of disease progression and complications, while monoclonal antibodies and hyperimmune globulin may provide additional preventive strategies. Consensus suggestions can standardize care, thereby improving outcomes and facilitating future research. This review discusses current evidence regarding the pharmacotherapy of COVID-19.

Clostridioides difficile and Vancomycin-Resistant Enterococci in COVID-19 Patients with Severe Pneumonia

Broad-spectrum antibiotics administered to patients with severe COVID-19 pneumonia pose a risk of infection caused by Clostridioides difficile. This risk is reduced mainly by strict hygiene measures and early de-escalation of antibiotic therapy. Recently, oral vancomycin prophylaxis (OVP) has also been discussed. This retrospective study aimed to assess the prevalence of C. difficile in critical COVID-19 patients staying in an intensive care unit of a tertiary hospital department of anesthesiology, resuscitation, and intensive care from November 2020 to May 2021 and the rates of vancomycin-resistant enterococci (VRE) after the introduction of OVP and to compare the data with those from controls in the pre-pandemic period (November 2018 to May 2019). During the COVID-19 pandemic, there was a significant increase in toxigenic C. difficile rates to 12.4% of patients, as compared with 1.6% in controls. The peak rates were noted in February 2021 (25% of patients), immediately followed by initiation of OVP, changes to hygiene precautions, and more rapid de-escalation of antibiotic therapy. Subsequently, toxigenic C. difficile detection rates started to fall. There was a nonsignificant increase in VRE detected in non-gastrointestinal tract samples to 8.9% in the COVID-19 group, as compared to 5.3% in the control group. Molecular analysis confirmed mainly clonal spread of VRE.

Impact of SARS-CoV-2 Epidemic on Antimicrobial Resistance: A Literature Review

Antimicrobial resistance is an urgent threat to public health and global development; in this scenario, the SARS-CoV2 pandemic has caused a major disruption of healthcare systems and practices. A narrative review was conducted on articles focusing on the impact of COVID-19 on multidrug-resistant gram-negative, gram-positive bacteria, and fungi. We found that, worldwide, multiple studies reported an unexpected high incidence of infections due to methicillin-resistant S. aureus, carbapenem-resistant A. baumannii, carbapenem-resistant Enterobacteriaceae, and C. auris among COVID-19 patients admitted to the intensive care unit. In this setting, inappropriate antimicrobial exposure, environmental contamination, and discontinuation of infection control measures may have driven selection and diffusion of drug-resistant pathogens.

Impact of the COVID-19 pandemic on the surveillance, prevention and control of antimicrobial resistance: a global survey

OBJECTIVES

The COVID-19 pandemic has had a substantial impact on health systems. The WHO Antimicrobial Resistance (AMR) Surveillance and Quality Assessment Collaborating Centres Network conducted a survey to assess the effects of COVID-19 on AMR surveillance, prevention and control.

METHODS

From October to December 2020, WHO Global Antimicrobial Resistance and Use Surveillance System (GLASS) national focal points completed a questionnaire, including Likert scales and open-ended questions. Data were descriptively analysed, income/regional differences were assessed and free-text questions were thematically analysed.

RESULTS

Seventy-three countries across income levels participated. During the COVID-19 pandemic, 67% reported limited ability to work with AMR partnerships; decreases in funding were frequently reported by low- and middle-income countries (LMICs; P < 0.01). Reduced availability of nursing, medical and public health staff for AMR was reported by 71%, 69% and 64%, respectively, whereas 67% reported stable cleaning staff availability. The majority (58%) reported reduced reagents/consumables, particularly LMICs (P < 0.01). Decreased numbers of cultures, elective procedures, chronically ill admissions and outpatients and increased ICU admissions reported could bias AMR data. Reported overall infection prevention and control (IPC) improvement could decrease AMR rates, whereas increases in selected inappropriate IPC practices and antimicrobial prescribing could increase rates. Most did not yet have complete data on changing AMR rates due to COVID-19.

CONCLUSIONS

This was the first survey to explore the global impact of COVID-19 on AMR among GLASS countries. Responses highlight important actions to help ensure that AMR remains a global health priority, including engaging with GLASS to facilitate reliable AMR surveillance data, seizing the opportunity to develop more sustainable IPC programmes, promoting integrated antibiotic stewardship guidance, leveraging increased laboratory capabilities and other system-strengthening efforts.

All-cause mortality and disease progression in SARS-CoV-2-infected patients with or without antibiotic therapy: an analysis of the LEOSS cohort

Purpose

Reported antibiotic use in coronavirus disease 2019 (COVID-19) is far higher than the actual rate of reported bacterial co- and superinfection. A better understanding of antibiotic therapy in COVID-19 is necessary.

Methods

6457 SARS-CoV-2-infected cases, documented from March 18, 2020, until February 16, 2021, in the LEOSS cohort were analyzed. As primary endpoint, the correlation between any antibiotic treatment and all-cause mortality/progression to the next more advanced phase of disease was calculated for adult patients in the complicated phase of disease and procalcitonin (PCT) ≤ 0.5 ng/ml. The analysis took the confounders gender, age, and comorbidities into account.

Results

Three thousand, six hundred twenty-seven cases matched all inclusion criteria for analyses. For the primary endpoint, antibiotic treatment was not correlated with lower all-cause mortality or progression to the next more advanced (critical) phase (n = 996) (both p > 0.05). For the secondary endpoints, patients in the uncomplicated phase (n = 1195), regardless of PCT level, had no lower all-cause mortality and did not progress less to the next more advanced (complicated) phase when treated with antibiotics (p > 0.05). Patients in the complicated phase with PCT > 0.5 ng/ml and antibiotic treatment (n = 286) had a significantly increased all-cause mortality (p = 0.029) but no significantly different probability of progression to the critical phase (p > 0.05).

Conclusion

In this cohort, antibiotics in SARS-CoV-2-infected patients were not associated with positive effects on all-cause mortality or disease progression. Additional studies are needed. Advice of local antibiotic stewardship- (ABS-) teams and local educational campaigns should be sought to improve rational antibiotic use in COVID-19 patients.

Ten things you need to know about intensive care unit management of mechanically ventilated patients with COVID-19

Introduction: The ongoing pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has posed important challenges for clinicians and health-care systems worldwide.Areas covered: The aim of this manuscript is to provide brief guidance for intensive care unit management of mechanically ventilated patients with COVID-19 based on the literature and our direct experience with this population. PubMed, EBSCO, and the Cochrane Library were searched up until 15th of January 2021 for relevant literature.Expert opinion: Initially, the respiratory management of COVID-19 relied on the general therapeutic principles for acute respiratory distress syndrome; however, recent findings have suggested that the pathophysiology of hypoxemia in patients with COVID-19 presents specific features and changes over time. Several therapies, including antiviral and anti-inflammatory agents, have been proposed recently. The optimal intensive care unit management of patients with COVID-19 remains unclear; therefore, ongoing and future clinical trials are warranted to clarify the optimal strategies to adopt in this cohort of patients.

Variation in therapeutic strategies for the management of severe COVID-19 in India: A nationwide cross-sectional survey

AIM

During the pandemic of coronavirus disease 2019 (COVID-19), the physicians are using various off-label therapeutics to manage COVID-19. We undertook a cross-sectional survey to study the current variation in therapeutic strategies for managing severe COVID-19 in India.

METHODS

From January 4 to January 18, 2021, an online cross-sectional survey was conducted among physicians involved in the management of severe COVID-19. The survey had three sections: 1. Antiviral agents, 2. Immunomodulators, and 3. Adjuvant therapies.

RESULTS

1055 respondents (from 24 states and five union territories), of which 64.2% were consultants, 54.3% working in private hospitals, and 39.1% were from critical care medicine completed the survey. Remdesivir (95.2%), antithrombotics (94.2%), corticosteroids (90.3%), vitamins (89.7%) and empirical antibiotics (85.6%) were the commonly used therapeutics. Ivermectin (33%), convalescent plasma (28.6%) and favipiravir (17.6%) were other antiviral agents used. Methylprednisolone (50.2%) and dexamethasone (44.1%) were preferred corticosteroids and at a dose equivalent of 8 mg of dexamethasone phosphate (70.2%). There was significant variation among physicians from different medical specialities in the use of favipiravir, corticosteroids, empirical antibiotics and vitamins.

CONCLUSION

There is a considerable variation in the physicians' choice of therapeutic strategies for the management of severe COVID-19 in India, as compared with the available evidence.

Antibiotic Prescriptions Targeting Bacterial Respiratory Infections in Admitted Patients with COVID-19: A Prospective Observational Study

Introduction

Although bacterial co- and superinfections are rarely present in patients with COVID-19, overall antibiotic prescribing in admitted patients is high. In order to counter antibiotic overprescribing, antibiotic stewardship teams need reliable data concerning antibiotic prescribing in admitted patients with COVID-19.

Methods

In this prospective observational cohort study, we performed a quantitative and qualitative evaluation of antibiotic prescriptions in patients admitted to the COVID-19 ward of a 721-bed Belgian university hospital between 1 May and 2 November 2020. Data on demographics, clinical and microbiological parameters and antibiotic consumption were collected. Defined daily doses (DDD) were calculated for antibiotics prescribed in the context of a (presumed) bacterial respiratory tract infection and converted into two indicators: DDD/admission and DDD/100 hospital bed days. A team of infectious disease specialists performed an appropriateness evaluation for every prescription. A driver analysis was performed to identify factors increasing the odds of an antibiotic prescription in patients with a confirmed COVID-19 diagnosis.

Results

Of 403 eligible participants with a suspected COVID-19 infection, 281 were included. In 13.8% of the 203 admissions with a COVID-19 confirmed diagnosis, antibiotics were initiated for a (presumed) bacterial respiratory tract co-/superinfection (0.86 DDD/admission; 8.92 DDD/100 bed days; 39.4% were scored as ‘appropriate’). Five drivers of antibiotic prescribing were identified: history of cerebrovascular disease, high neutrophil/lymphocyte ratio in male patients, age, elevated ferritin levels and the collection of respiratory samples for bacteriological analysis.

Conclusion

In the studied population, the antibiotic consumption for a (presumed) bacterial respiratory tract co-/superinfection was low. In particular, the small total number of DDDs in patients with confirmed COVID-19 diagnosis suggests thoughtful antibiotic use. However, antibiotic stewardship programmes remain crucial to counter unnecessary and inappropriate antibiotic use in hospitalized patients with COVID-19.

Trial Registration

The study is registered at ClinicalTrials.gov (NCT04544072).

Supplementary Information

The online version contains supplementary material available at 10.1007/s40121-021-00535-2.

Sars-Cov-2 Infection in Patients on Long-Term Treatment with Macrolides in Spain: A National Cross-Sectional Study

The aim of this study was to know the prevalence and severity of COVID-19 in patients treated with long-term macrolides and to describe the factors associated with worse outcomes. A cross-sectional study was conducted in Primary Care setting. Patients with macrolides dispensed continuously from 1 October 2019 to 31 March 2020, were considered. Main outcome: diagnosis of coronavirus disease-19 (COVID-19). Secondary outcomes: symptoms, severity, characteristics of patients, comorbidities, concomitant treatments. A total of 3057 patients met the inclusion criteria. Median age: 73 (64–81) years; 55% were men; 62% smokers/ex-smokers; 56% obese/overweight. Overall, 95% of patients had chronic respiratory diseases and four comorbidities as a median. Prevalence of COVID-19: 4.8%. This was in accordance with official data during the first wave of the pandemic. The most common symptoms were respiratory: shortness of breath, cough, and pneumonia. Additionally, 53% percent of patients had mild/moderate symptoms, 28% required hospital admission, and 19% died with COVID-19. The percentage of patients hospitalized and deaths were 2.6 and 5.8 times higher, respectively, in the COVID-19 group (p < 0.001). There was no evidence of a beneficial effect of long-term courses of macrolides in preventing SARS-CoV-2 infection or the progression to worse outcomes in old patients with underlying chronic respiratory diseases and a high burden of comorbidity.

Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study

BACKGROUND

Microbiological characterisation of co-infections and secondary infections in patients with COVID-19 is lacking, and antimicrobial use is high. We aimed to describe microbiologically confirmed co-infections and secondary infections, and antimicrobial use, in patients admitted to hospital with COVID-19.

METHODS

The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK (CCP-UK) study is an ongoing, prospective cohort study recruiting inpatients from 260 hospitals in England, Scotland, and Wales, conducted by the ISARIC Coronavirus Clinical Characterisation Consortium. Patients with a confirmed or clinician-defined high likelihood of SARS-CoV-2 infection were eligible for inclusion in the ISARIC WHO CCP-UK study. For this specific study, we excluded patients with a recorded negative SARS-CoV-2 test result and those without a recorded outcome at 28 days after admission. Demographic, clinical, laboratory, therapeutic, and outcome data were collected using a prespecified case report form. Organisms considered clinically insignificant were excluded.

FINDINGS

We analysed data from 48 902 patients admitted to hospital between Feb 6 and June 8, 2020. The median patient age was 74 years (IQR 59-84) and 20 786 (42·6%) of 48 765 patients were female. Microbiological investigations were recorded for 8649 (17·7%) of 48 902 patients, with clinically significant COVID-19-related respiratory or bloodstream culture results recorded for 1107 patients. 762 (70·6%) of 1080 infections were secondary, occurring more than 2 days after hospital admission. Staphylococcus aureus and Haemophilus influenzae were the most common pathogens causing respiratory co-infections (diagnosed ≤2 days after admission), with Enterobacteriaceae and S aureus most common in secondary respiratory infections. Bloodstream infections were most frequently caused by Escherichia coli and S aureus. Among patients with available data, 13 390 (37·0%) of 36 145 had received antimicrobials in the community for this illness episode before hospital admission and 39 258 (85·2%) of 46 061 patients with inpatient antimicrobial data received one or more antimicrobials at some point during their admission (highest for patients in critical care). We identified frequent use of broad-spectrum agents and use of carbapenems rather than carbapenem-sparing alternatives.

INTERPRETATION

In patients admitted to hospital with COVID-19, microbiologically confirmed bacterial infections are rare, and more likely to be secondary infections. Gram-negative organisms and S aureus are the predominant pathogens. The frequency and nature of antimicrobial use are concerning, but tractable targets for stewardship interventions exist.

FUNDING

National Institute for Health Research (NIHR), UK Medical Research Council, Wellcome Trust, UK Department for International Development, Bill & Melinda Gates Foundation, EU Platform for European Preparedness Against (Re-)emerging Epidemics, NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, and NIHR HPRU in Respiratory Infections at Imperial College London.

Impact of Pneumococcal Urinary Antigen Testing in COVID-19 Patients: Outcomes from the San Matteo COVID-19 Registry (SMACORE)

Despite low rates of bacterial co-infections, most COVID-19 patients receive antibiotic therapy. We hypothesized that patients with positive pneumococcal urinary antigens (PUAs) would benefit from antibiotic therapy in terms of clinical outcomes (death, ICU admission, and length of stay). The San Matteo COVID-19 Registry (SMACORE) prospectively enrolls patients admitted for COVID-19 pneumonia at IRCCS Policlinico San Matteo, Pavia. We retrospectively extracted the data of patients tested for PUA from October to December 2020. Demographic, clinical, and laboratory data were recorded. Of 469 patients, 42 tested positive for PUA (8.95%), while 427 (91.05%) tested negative. A positive PUA result had no significant impact on death (HR 0.53 CI [0.22-1.28] p-value 0.16) or ICU admission (HR 0.8; CI [0.25-2.54] p-value 0.70) in the Cox regression model, nor on length of stay in linear regression (estimate 1.71; SE 2.37; p-value 0.47). After adjusting for age, we found no significant correlation between urinary antigen positivity and variations in the WHO ordinal scale and laboratory markers at admission and after 14 days. We found that a positive PUA result was not frequent and had no impact on clinical outcomes or clinical improvement. Our results did not support the routine use of PUA tests to select COVID-19 patients who will benefit from antibiotic therapy.

Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation

The microbial populations in the gut microbiome have recently been associated with COVID-19 disease severity. However, a causal impact of the gut microbiome on COVID-19 patient health has not been established. Here we provide evidence that gut microbiome dysbiosis is associated with translocation of bacteria into the blood during COVID-19, causing life-threatening secondary infections. Antibiotics and other treatments during COVID-19 can potentially confound microbiome associations. We therefore first demonstrate that the gut microbiome is directly affected by SARS-CoV-2 infection in a dose-dependent manner in a mouse model, causally linking viral infection and gut microbiome dysbiosis. Comparison with stool samples collected from 101 COVID-19 patients at two different clinical sites also revealed substantial gut microbiome dysbiosis, paralleling our observations in the animal model. Specifically, we observed blooms of opportunistic pathogenic bacterial genera known to include antimicrobial-resistant species in hospitalized COVID-19 patients. Analysis of blood culture results testing for secondary microbial bloodstream infections with paired microbiome data obtained from these patients suggest that bacteria translocate from the gut into the systemic circulation of COVID-19 patients. These results are consistent with a direct role for gut microbiome dysbiosis in enabling dangerous secondary infections during COVID-19.

Diagnostic yield of bacteriological tests and predictors of severe outcome in adult patients with COVID-19 presenting to the emergency department

BACKGROUND

Guidelines recommend maximal efforts to obtain blood and sputum cultures in patients with COVID-19, as bacterial coinfection is associated with worse outcomes. The aim of this study was to evaluate the yield of bacteriological tests, including blood and sputum cultures, and the association of multiple biomarkers and the Pneumonia Severity Index (PSI) with clinical and microbiological outcomes in patients with COVID-19 presenting to the emergency department (ED).

METHODS

This is a substudy of a large observational cohort study (PredictED study). The PredictED included adult patients from whom a blood culture was drawn at the ED of Haga Teaching Hospital, The Netherlands. For this substudy, all patients who tested positive for SARS-CoV-2 by PCR in March and April 2020 were included. The primary outcome was the incidence of bacterial coinfection. We used logistic regression analysis for associations of procalcitonin, C reactive protein (CRP), ferritin, lymphocyte count and PSI score with a severe disease course, defined as intensive care unit admission and/or 30-day mortality. The area under the receiver operating characteristics curve (AUC) quantified the discriminatory performance.

RESULTS

We included 142 SARS-CoV-2 positive patients. On presentation, the median duration of symptoms was 8 days. 41 (29%) patients had a severe disease course and 24 (17%) died within 30 days. The incidence of bacterial coinfection was 2/142 (1.4%). None of the blood cultures showed pathogen growth while 6.3% was contaminated. The AUCs for predicting severe disease were 0.76 (95% CI 0.68 to 0.84), 0.70 (0.61 to 0.79), 0.62 (0.51 to 0.74), 0.62 (0.51 to 0.72) and 0.72 (0.63 to 0.81) for procalcitonin, CRP, ferritin, lymphocyte count and PSI score, respectively.

CONCLUSION

Blood cultures appear to have limited value while procalcitonin and the PSI appear to be promising tools in helping physicians identify patients at risk for severe disease course in COVID-19 at presentation to the ED.

Penicillin Allergy Label Increases Risk of Worse Clinical Outcomes in COVID-19

BACKGROUND

Coronavirus disease-2019 (COVID-19) ranges from asymptomatic to severe. Several comorbidities are associated with worse clinical outcomes. Antibiotic use is common in COVID-19 and penicillin (PCN) allergy can affect antibiotic choice and may influence COVID-19 outcomes.

OBJECTIVE

To investigate the impact of PCN allergy label on COVID-19 outcomes.

METHODS

For this retrospective, cohort study, a Web-based tool for population cohort research, TriNetX, was used to identify adult COVID-19 patients with and without PCN allergy label. The two cohorts were matched using 1:1 propensity score matching for baseline demographics and conditions associated with risk for severe COVID-19. The 30-day risks for hospitalization, acute respiratory failure, intensive care unit requirement, mechanical ventilation requirement, and mortality were then compared between groups. Because bacterial infection can drive alternative antibiotic regimens, additional analyses focused on patients without bacterial infection.

RESULTS

After propensity score matching, each cohort consisted of 13,183 patients. COVID-19 patients with PCN allergy had higher risks for hospitalization (risk ratio [RR] = 1.46; 95% confidence interval [CI], 1.41-1.52) acute respiratory failure (RR = 1.25; 95% CI, 1.19-1.31), intensive care unit requirement (RR = 1.20; 95% CI, 1.08-1.34), and mechanical ventilation (RR = 1.17; 95% CI 1.03-1.32) compared with patients without PCN allergy; however, there was no mortality difference (RR = 1.09; 95% CI, 0.96-1.23). Although the bacterial infection risk was higher in PCN allergic COVID-19 patients, exclusion of patients with bacterial infections yielded similar results.

CONCLUSIONS

Penicillin allergic patients have higher risk for worse COVID-19 outcomes and should be considered for risk mitigation strategies.

Association between Early Antibiotic Therapy and In-Hospital Mortality among Older Patients with SARS-CoV-2 Pneumonia

Background

It is uncertain whether antibiotic therapy should be started in SARS CoV-2 pneumonia. We aimed to investigate the association between early antibiotic therapy and the risk of in-hospital mortality in older patients.

Methods

We performed a retrospective international cohort study (ANTIBIOVID) in five COVID-19 geriatric units in France and Switzerland. Among 1,357 consecutive patients aged 75 or more hospitalised and testing positive for SARS-CoV-2, 1072 had a radiologically confirmed pneumonia, of which 914 patients were still alive and hospitalized at 48 hours. To adjust for confounders, a propensity score for treatment was created, and stabilized inverse probability of treatment weighting (SIPTW) was applied. To assess the association between early antibiotic therapy and in-hospital 30-day mortality, SIPTW-adjusted Kaplan-Meier and Cox proportional hazards regression analyses were performed.

Results

Of the 914 patients with SARS-CoV-2 pneumonia, median age of 86, 428 (46.8%) received antibiotics in the first 48 hours after diagnosis. Among these patients, 147 (34.3%) died in hospital within one month vs 118 patients (24.3%) with no early antibiotic treatment. After SIPTW, early antibiotic treatment was not significantly associated with mortality (adjusted hazard ratio, 1.23; 95% CI, 0.92-1.63; P = .160). Microbiologically confirmed superinfections occurred rarely in both groups (bacterial pneumonia: 2.5% vs 1.5%, P = .220; blood stream infection: 8.2% vs 5.2%, P = .120; Clostridioides difficile colitis: 2.4% vs 1.0%, P = .222).

Conclusions

In a large multicentre cohort of older inpatients with SARS-CoV-2 pneumonia, early antibiotic treatment did not appear to be associated with an improved prognosis.

Application of an evidence-based, out-patient treatment strategy for COVID-19: Multidisciplinary medical practice principles to prevent severe disease

The COVID-19 pandemic has devastated individuals, families, and institutions throughout the world. Despite the breakneck speed of vaccine development, the human population remains at risk of further devastation. The decision to not become vaccinated, the protracted rollout of available vaccine, vaccine failure, mutational forms of the SARS virus, which may exhibit mounting resistance to our molecular strike at only one form of the viral family, and the rapid ability of the virus(es) to hitch a ride on our global transportation systems, means that we are will likely continue to confront an invisible, yet devastating foe. The enemy targets one of our human physiology's most important and vulnerable life-preserving body tissues, our broncho-alveolar gas exchange apparatus. Notwithstanding the fear and the fury of this microbe's potential to raise existential questions across the entire spectrum of human endeavor, the application of an early treatment intervention initiative may represent a crucial tool in our defensive strategy. This strategy is driven by evidence-based medical practice principles, those not likely to become antiquated, given the molecular diversity and mutational evolution of this very clever "world traveler".

Bacterial superinfection in adults with COVID-19 hospitalized in two clinics in Medellín-Colombia, 2020

COVID-19 represents high morbidity and mortality, its complications and lethality have increased due to bacterial superinfections. We aimed to determine the prevalence of bacterial superinfection in adults with COVID-19, hospitalized in two clinics in Medellín-Colombia during 2020, and its distribution according to sociodemographic and clinical conditions. A cross sectional study was made with 399 patients diagnosed with COVID-19 by RT-PCR. We determined the prevalence of bacterial superinfection and its factors associated with crude and adjusted prevalence ratios by a generalized linear model. The prevalence of superinfection was 49.6%, with 16 agents identified, the most frequent were Klebsiella (pneumoniae and oxytoca) and Staphylococcus aureus. In the multivariate adjustment, the variables with the strongest association with bacterial superinfection were lung disease, encephalopathy, mechanical ventilation, hospital stay, and steroid treatment. A high prevalence of bacterial superinfections, a high number of agents, and multiple associated factors were found. Among these stood out comorbidities, complications, days of hospitalization, mechanical ventilation, and steroid treatment. These results are vital to identifying priority clinical groups, improving the care of simultaneous infections with COVID-19 in people with the risk factors exposed in the population studied, and identifying bacteria of public health interest.

[COVID-19 in the Family Practice - Outpatient Treatment or Hospitalization?]

COVID-19 in the Family Practice - Outpatient Treatment or Hospitalization? Abstract. Switzerland has been severely affected by the COVID-19 pandemic. The clinical spectrum of this disease in terms of its clinical presentation and course is very broad. A correct initial evaluation in the practice or in the emergency department is important and includes history-taking and clinical examination as well as imaging and laboratory tests. Most patients with COVID-19 can be treated as outpatients. Hospitalization may be necessary in patients with a marked COVID-19 pneumonia or further complications, which occur primarily in the second or third phase of the disease. The dynamics of the disease must also be taken into consideration. In outpatients, symptomatic therapy is often sufficient, antibiotics and corticosteroids are not indicated.

Antimicrobial Use in COVID-19 Patients in the First Phase of the SARS-CoV-2 Pandemic: A Scoping Review

This scoping review provides new evidence on the prevalence and patterns of global antimicrobial use in the treatment of COVID-19 patients; identifies the most commonly used antibiotics and clinical scenarios associated with antibiotic prescribing in the first phase of the pandemic; and explores the impact of documented antibiotic prescribing on treatment outcomes in COVID-19 patients. The review complies with PRISMA guidelines for Scoping Reviews and the protocol is registered with the Open Science Framework. In the first six months of the pandemic, there was a similar mean antibiotic prescribing rate between patients with severe or critical illness (75.4%) and patients with mild or moderate illness (75.1%). The proportion of patients prescribed antibiotics without clinical justification was 51.5% vs. 41.9% for patients with mild or moderate illness and those with severe or critical illness. Comparison of patients who were provided antibiotics with a clinical justification with those who were given antibiotics without clinical justification showed lower mortality rates (9.5% vs. 13.1%), higher discharge rates (80.9% vs. 69.3%), and shorter length of hospital stay (9.3 days vs. 12.2 days). In the first 6 months of the pandemic, antibiotics were prescribed for COVID-19 patients regardless of severity of illness. A large proportion of antibiotic prescribing for mild and moderate COVID-19 patients did not have clinical evidence of a bacterial co-infection. Antibiotics may not be beneficial to COVID-19 patients without clinical evidence of a bacterial co-infection.

A 29-mRNA host response test from blood accurately distinguishes bacterial and viral infections among emergency department patients

BACKGROUND

Whether or not to administer antibiotics is a common and challenging clinical decision in patients with suspected infections presenting to the emergency department (ED). We prospectively validate InSep, a 29-mRNA blood-based host response test for the prediction of bacterial and viral infections.

METHODS

The PROMPT trial is a prospective, non-interventional, multi-center clinical study that enrolled 397 adult patients presenting to the ED with signs of acute infection and at least one vital sign change. The infection status was adjudicated using chart review (including a syndromic molecular respiratory panel, procalcitonin and C-reactive protein) by three infectious disease physicians blinded to InSep results. InSep (version BVN-2) was performed using PAXgene Blood RNA processed and quantified on NanoString nCounter SPRINT. InSep results (likelihood of bacterial and viral infection) were compared to the adjudicated infection status.

RESULTS

Subject mean age was 64 years, comorbidities were significant for diabetes (17.1%), chronic obstructive pulmonary disease (13.6%), and severe neurological disease (6.8%); 16.9% of subjects were immunocompromised. Infections were adjudicated as bacterial (14.1%), viral (11.3%) and noninfected (0.25%): 74.1% of subjects were adjudicated as indeterminate. InSep distinguished bacterial vs. viral/noninfected patients and viral vs. bacterial/noninfected patients using consensus adjudication with AUROCs of 0.94 (95% CI 0.90-0.99) and 0.90 (95% CI 0.83-0.96), respectively. AUROCs for bacterial vs. viral/noninfected patients were 0.88 (95% CI 0.79-0.96) for PCT, 0.80 (95% CI 0.72-89) for CRP and 0.78 (95% CI 0.69-0.87) for white blood cell counts (of note, the latter biomarkers were provided as part of clinical adjudication). To enable clinical actionability, InSep incorporates score cutoffs to allocate patients into interpretation bands. The Very Likely (rule in) InSep bacterial band showed a specificity of 98% compared to 94% for the corresponding PCT band (> 0.5 µg/L); the Very Unlikely (rule-out) band showed a sensitivity of 95% for InSep compared to 86% for PCT. For the detection of viral infections, InSep demonstrated a specificity of 93% for the Very Likely band (rule in) and a sensitivity of 96% for the Very Unlikely band (rule out).

CONCLUSIONS

InSep demonstrated high accuracy for predicting the presence of both bacterial and viral infections in ED patients with suspected acute infections or suspected sepsis. When translated into a rapid, point-of-care test, InSep will provide ED physicians with actionable results supporting early informed treatment decisions to improve patient outcomes while upholding antimicrobial stewardship. Registration number at Clinicaltrials.gov NCT03295825.

Extracorporeal Blood Purification in Moderate and Severe COVID-19 Patients: A Prospective Cohort Study

INTRODUCTION

Coronavirus disease 2019 (COVID-19) is characterized by hyperinflammation and coagulopathy. Severe cases often develop respiratory distress, requiring mechanical ventilation and with critical cases progressing to acute respiratory distress syndrome. Control of hyperinflammation has been proposed as a possible therapeutic avenue for COVID-19; extracorporeal blood purification (EBP) modalities offer an attractive mean to ameliorate maladaptive inflammation. With this work, we evaluated the longitudinal changes of systemic inflammatory markers in critically ill COVID-19 patients treated with blood purification using AN69ST (oXiris®) haemofilter.

METHODS

We performed a time-series analysis of 44 consecutive COVID-19 cases treated with the AN69ST (oXiris®) cytokine adsorbing haemofilter (CAH) according to local practice; we visualize longitudinal results of biochemical, inflammatory, blood gas, and vital sign parameters focussing on systemic levels of interleukin-6 (IL-6), C-reactive protein (CRP), and procalcitonin.

RESULTS

All patients were treated with ≥1 cycle extracorporeal continuous venovenous haemofiltration (CVVH) with CAH; of these, 30 severe patients received CVVH-CAH within 4-12 h of admission after recognizing a hyper-inflammatory state. Another 14 patients admitted with mild-to-moderate symptoms progressed to severe disease and were placed on EBP during hospitalization. The treatment was associated with a reduction of ferritin, CRP, fibrinogen, several inflammatory markers, and a resolution of numerous cytopenias. The observed mortality across the cohort was 36.3%.

CONCLUSION

EBP with CAH was associated with a decrease in CRP, and control of IL-6 and procalcitonin.

Rapid identification of bacteria from respiratory samples of patients hospitalized in intensive care units, with FilmArray Pneumonia Panel Plus

OBJECTIVES

This study aimed to evaluate the performance of FilmArray Pneumonia Panel Plus (FA-PP) for the detection of typical bacterial pathogens in respiratory samples from patients hospitalized in intensive care units (ICUs).

METHODS

FA-PP was implemented for clinical use in the microbiology laboratory in March 2020. A retrospective analysis on a consecutive cohort of adult patients hospitalized in ICUs between March 2020 and May 2020 was undertaken. The respiratory samples included sputum, blind bronchoalveolar lavage (BBAL) and protected specimen brush (PSB). Conventional culture and FA-PP were performed in parallel.

RESULTS

In total, 147 samples from 92 patients were analysed; 88% had coronavirus disease 2019 (COVID-19). At least one pathogen was detected in 46% (68/147) of samples by FA-PP and 39% (57/147) of samples by culture. The overall percentage agreement between FA-PP and culture results was 98% (93-100%). Bacteria with semi-quantitative FA-PP results ≥10⁵ copies/mL for PSB samples, ≥10⁶ copies/mL for BBAL samples and ≥10⁷ copies/mL for sputum samples reached clinically significant thresholds for growth in 90%, 100% and 91% of cultures, respectively. FA-PP detected resistance markers, including mecA/C, bla_CTX-M and bla_VIM. The median turnaround time was significantly shorter for FA-PP than for culture.

CONCLUSIONS

FA-PP may constitute a faster approach to the diagnosis of bacterial pneumonia in patients hospitalized in ICUs.

Antibiotic misuse and compliance with infection control measures during COVID-19 pandemic in community pharmacies in Egypt

BACKGROUND

Globally, antibiotics misuse by the public has been reported in the era of COVID-19, despite the discouraging instructions of the World Health Organization, especially for mild cases.

OBJECTIVE

Is to describe this antibiotic misuse and its contributing factors. Also, to measure the pharmacists' application of infection preventive practices during the pandemic.

METHODS

A cross-sectional study was conducted among randomly selected Egyptian community pharmacists (Center, East, Delta, and Upper Egypt) using a questionnaire and direct interviews from 1 to 30 August 2020. The questionnaire consisted of two parts, the first covered pharmacist's demographic data and their application of basic infection preventive practices (eg, wearing face masks, regular hand sanitization, etc), and the other part was related to antibiotic dispensing patterns. Data were descriptively analyzed and the impact of participant experience on the responses was evaluated using the χ² test.

RESULTS

From 480 randomly selected Egyptian community pharmacists, 413 (87%) consented to participate in the study. 86.7% of the participants were keen to wear face masks (n = 358) and 86.2% kept regular hand sanitization (n = 356); whereas, 46.9% (n = 194) maintained adequate antibiotic stock supply during the pandemic. Nearly 67% (n = 275) of the pharmacists reported that patients were more likely to be given antibiotics for showing any sign or symptom of COVID-19 infection, and 82% (n = 74 278) of the dispensed antibiotics were given upon physician recommendation. Azithromycin, Ceftriaxone, and Linezolid were the major antibiotics dispensed to COVID-19 presumptive patients Azithromycin was given to ~40% of presumptive patients showing only mild or moderate symptoms for 5-10 days. Additionally, antibiotic combinations were given to 74% (n = 62 479) of home-isolated patients for a maximum of 2 weeks.

CONCLUSIONS

Pharmacists applied suitable sanitation and infection control protocols. Meanwhile, antibiotics were dispensed heavily during this pandemic without proper clinical indication and for long durations supporting the idea of antibiotic misuse.

[Basic aspects of COVID-19 for management from primary care]

SARS-CoV-2 is transmitted from person to person by inhalation or contact with respiratory droplets and aerosols. The median incubation period is 5.1 days. Fever, dry cough, dyspnea and fatigue are the most common symptoms. Almost half of the cases are asymptomatic. The spectrum of disease varies from mild (81%) to critical (5%). Older age, male gender and comorbidities negatively impact on the severity and mortality of COVID-19. The diagnosis of acute COVID-19 is made with RT-PCR or antigenic detection tests. In hospital patients, remdesivir reduces recovery time. Oral steroids are recommended for severe or critical cases requiring oxygen therapy or mechanical ventilation. Thromboprophylaxis is recommended in all severe and non-severe cases with high thrombotic risk. Antibiotherapy is limited to cases of high suspicion of bacterial superinfection. Mild-moderate and severe cases after discharge from hospital should be clinically monitored for a minimum period of two weeks.

Antimicrobial consumption among hospitalized patients with COVID-19 in Pakistan

The discovery of different antimicrobial agents has revolutionized the treatment against a variety of infections for many decades, but the emergence of antimicrobial resistance require rigorous measures, even amid the coronavirus disease 2019 (COVID-19) pandemic. This retrospective study aimed to examine the consumption of antibiotics in patients with COVID-19 admitted into the five hospitals in the province of Punjab, Pakistan. We collected data on the consumption of antibiotics, classified using the World Health Organization (WHO) AWaRe (Access, Watch, and Reserve), within two months—August and September, 2020, and the corresponding months in 2019. Consumption of antibiotics was presented as daily define dose (DDD) per 100 occupied bed-days. Eight different classes of antibiotics were prescribed to patients with COVID-19 without culture tests being performed, with the prescribing of antibiotics of the Watch category was especially prevalent. The consumption of antibiotics was higher during the COVID-19 pandemic compared to the pre-pandemic period: the consumption of azithromycin increased from 11.5 DDDs per 100 occupied bed-days in 2019 to 17.0 DDDs per 100 occupied bed-days in 2020, while the consumption of ceftriaxone increased from 20.2 DDDs per 100 occupied bed-days in 2019 to 25.1 DDDs per 100 occupied bed-days in 2020. The current study revealed non-evidence-based utilization of antibiotics among patients with COVID-19 admitted into the hospitals in Pakistan. Evidently, the current COVID-19 pandemic is a public health threat of notable dimensions which has compromised the ongoing antimicrobial stewardship program, potentially leading to the emergence of antimicrobial resistance among pathogens.

Inappropriate antibiotic use in the COVID-19 era: Factors associated with inappropriate prescribing and secondary complications. Analysis of the registry SEMI-COVID

BACKGROUND

Most patients with COVID-19 receive antibiotics despite the fact that bacterial co-infections are rare. This can lead to increased complications, including antibacterial resistance. We aim to analyze risk factors for inappropriate antibiotic prescription in these patients and describe possible complications arising from their use.

METHODS

The SEMI-COVID-19 Registry is a multicenter, retrospective patient cohort. Patients with antibiotic were divided into two groups according to appropriate or inappropriate prescription, depending on whether the patient fulfill any criteria for its use. Comparison was made by means of multilevel logistic regression analysis. Possible complications of antibiotic use were also identified.

RESULTS

Out of 13,932 patients, 3047 (21.6%) were prescribed no antibiotics, 6116 (43.9%) were appropriately prescribed antibiotics, and 4769 (34.2%) were inappropriately prescribed antibiotics. The following were independent factors of inappropriate prescription: February-March 2020 admission (OR 1.54, 95%CI 1.18-2.00), age (OR 0.98, 95%CI 0.97-0.99), absence of comorbidity (OR 1.43, 95%CI 1.05-1.94), dry cough (OR 2.51, 95%CI 1.94-3.26), fever (OR 1.33, 95%CI 1.13-1.56), dyspnea (OR 1.31, 95%CI 1.04-1.69), flu-like symptoms (OR 2.70, 95%CI 1.75-4.17), and elevated C-reactive protein levels (OR 1.01 for each mg/L increase, 95% CI 1.00-1.01). Adverse drug reactions were more frequent in patients who received ANTIBIOTIC (4.9% vs 2.7%, p < .001).

CONCLUSION

The inappropriate use of antibiotics was very frequent in COVID-19 patients and entailed an increased risk of adverse reactions. It is crucial to define criteria for their use in these patients. Knowledge of the factors associated with inappropriate prescribing can be helpful.

The role of co-infections and secondary infections in patients with COVID-19

BACKGROUND

It has been recognised for a considerable time-period, that viral respiratory infections predispose patients to bacterial infections, and that these co-infections have a worse outcome than either infection on its own. However, it is still unclear what exact roles co-infections and/or superinfections play in patients with COVID-19 infection.

MAIN BODY

This was an extensive review of the current literature regarding co-infections and superinfections in patients with SARS-CoV-2 infection. The definitions used were those of the Centers for Disease Control and Prevention (US), which defines coinfection as one occurring concurrently with the initial infection, while superinfections are those infections that follow on a previous infection, especially when caused by microorganisms that are resistant, or have become resistant, to the antibiotics used earlier. Some researchers have envisioned three potential scenarios of bacterial/SARS-CoV-2 co-infection; namely, secondary SARS-CoV-2 infection following bacterial infection or colonisation, combined viral/bacterial pneumonia, or secondary bacterial superinfection following SARS-CoV-2. There are a myriad of published articles ranging from letters to the editor to systematic reviews and meta-analyses describing varying ranges of co-infection and/or superinfection in patients with COVID-19. The concomitant infections described included other respiratory viruses, bacteria, including mycobacteria, fungi, as well as other, more unusual, pathogens. However, as will be seen in this review, there is often not a clear distinction made in the literature as to what the authors are referring to, whether true concomitant/co-infections or superinfections. In addition, possible mechanisms of the interactions between viral infections, including SARS-CoV-2, and other infections, particularly bacterial infections are discussed further. Lastly, the impact of these co-infections and superinfections in the severity of COVID-19 infections and their outcome is also described.

CONCLUSION

The current review describes varying rates of co-infections and/or superinfections in patients with COVID-19 infections, although often a clear distinction between the two is not clear in the literature. When they occur, these infections appear to be associated with both severity of COVID-19 as well as poorer outcomes.

Undetected Causes of Death in Hospitalized Elderly with COVID-19: Lessons from Autopsy

Background: Mechanisms and causes of death in older patients with SARS-CoV-2 infection are still poorly understood. Methods: We conducted in a retrospective monocentric study, a clinical chart review and post-mortem examination of patients aged 75 years and older hospitalized in acute care and positive for SARS-CoV-2. Full body autopsy and correlation with clinical findings and suspected causes of death were done. Results: Autopsies were performed in 12 patients (median age 85 years; median of 4 comorbidities, mainly hypertension and cardiovascular disease). All cases showed exudative or proliferative phases of alveolar damage and/or a pattern of organizing pneumonia. Causes of death were concordant in 6 cases (50%), and undetected diagnoses were found in 6. Five patients died from hypoxemic respiratory failure due to coronavirus disease 2019 (COVID-19), five had another associated diagnosis and two died from alternative causes. Deaths that occurred in the second week were related to SARS-CoV-2 pneumonia whereas those occurring earlier were related mainly to heart failure and those occurring later to complications. Conclusions: Although COVID-19 hypoxemic respiratory failure was the most common cause of death, post-mortem pathological examination revealed that acute decompensation from chronic comorbidities during the first week of COVID-19 and complications in the third week contributed to mortality.

Antimicrobial Resistance Threats in the emerging COVID-19 pandemic: Where do we stand?

Antimicrobial resistance (AMR) continues to exert a substantial toll on the global health and world economy and is now expected to be hidden by COVID-19 for a while. The wrong consumption of antibiotics during the COVID-19 pandemic will raise disastrous effects on AMR management and antibiotic stewardship programs. This is related to the concerns extrapolated due to an increase in mortality rates in patients with bacterial coinfections. Importantly, the immune system of COVID-19 patients in regions with high AMR may be fighting on two fronts altogether, the virus and MDR bacteria. Current control policies to manage AMR and prioritization of antibiotic stewardship plans are mandatory during this pandemic. This review aims to discuss the rising concerns of the excess use of antibiotics in COVID-19 patients highlighting the role of bacterial coinfections in these patients. Types of prescribed antibiotics and the development of antibiotic resistance is addressed as well.

Therapeutic strategies for severe COVID-19: a position paper from the Italian Society of Infectious and Tropical Diseases (SIMIT)

SCOPE

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has become pandemic, reaching almost one million death worldwide. At present standard treatment for coronavirus disease 2019 (COVID-19) is not well defined because the evidence, either from randomized or observational studies, with conflicting results, has led to rapid changes in treatment guidelines. Our aim was to narratively summarize the available literature on the management of COVID-19 in order to combine current evidence and interpretation of the data by experts who are treating patients in the frontline setting.

METHODS

The panel conducted a detailed review of the literature and eventual press releases from randomized clinical trials for each possible available treatment. Inductive PubMed search waws performed for publications relevant to the topic, including all clinical trials conducted. The result was a flowchart with treatment indications for patients with COVID-19.

IMPLICATIONS

After 6 months of a pandemic situation and before a possible second coronavirus wave descends on Europe, it is important to evaluate which drugs proved to be effective while also considering that results from many randomized clinical trials are still awaited. Indeed, among treatments for COVID-19, only glucocorticoids have resulted in an association with a significant decrease in mortality in published randomized controlled trials. New therapeutic strategies are urgently needed.

Community-acquired bacteraemia in COVID-19 in comparison to influenza A and influenza B: a retrospective cohort study

Background

During the coronavirus disease 2019 (COVID-19) pandemic in the Netherlands it was noticed that very few blood cultures from COVID-19 patients turned positive with clinically relevant bacteria. This was particularly evident in comparison to the number of positive blood cultures during previous seasonal epidemics of influenza. This observation raised questions about the occurrence and causative microorganisms of bacteraemia in COVID-19 patients, especially in the perspective of the widely reported overuse of antibiotics and the rising rate of antibiotic resistance.

Methods

We conducted a retrospective cohort study on blood culture results in influenza A, influenza B and COVID-19 patients presenting to two hospitals in the Netherlands. Our main outcome consisted of the percentage of positive blood cultures. The percentage of clinically relevant blood cultures, isolated bacteria and 30-day all-cause mortality served as our secondary outcomes.

Results

A total of 1331 viral episodes were analysed in 1324 patients. There was no statistically significant difference (p = 0.47) in overall occurrence of blood culture positivity in COVID-19 patients (9.0, 95% CI 6.8–11.1) in comparison to influenza A (11.4, 95% CI 7.9–14.8) and influenza B patients (10.4, 95% CI 7.1–13.7,). After correcting for the high rate of contamination, the occurrence of clinically relevant bacteraemia in COVID-19 patients amounted to 1.0% (95% CI 0.3–1.8), which was statistically significantly lower (p = 0.04) compared to influenza A patients (4.0, 95% CI 1.9–6.1) and influenza B patients (3.0, 95% CI 1.2–4.9). The most frequently identified bacterial isolates in COVID-19 patients were Escherichia coli (n = 2) and Streptococcus pneumoniae (n = 2). The overall 30-day all-cause mortality for COVID-19 patients was 28.3% (95% CI 24.9–31.7), which was statistically significantly higher (p = <.001) when compared to patients with influenza A (7.1, 95% CI 4.3–9.9) and patients with influenza B (6.4, 95% CI 3.8–9.1).

Conclusions

We report a very low occurrence of community-acquired bacteraemia amongst COVID-19 patients in comparison to influenza patients. These results reinforce current clinical guidelines on antibiotic management in COVID-19, which only advise utilization of antibiotics when a bacterial co-infection is suspected.

The clinical impact of bacterial co-infection among moderate, severe and critically ill COVID-19 patients in the second referral hospital in Surabaya

Background: Data on the prevalence of bacterial co-infections among COVID-19 patients are limited, especially in our country, Indonesia. We aimed to assess the rate of bacterial co-infections in hospitalized COVID-19 patients and report the most common microorganisms involved and the antibiotic use in these patients.

Methods: This study is a retrospective cohort study,among COVID-19 adult patients admitted to Universitas Airlangga Hospital Surabaya from 14 March-30 September 2020. The bacterial infection is defined based on clinical assessment, laboratory parameters, and microbiology results.

Results: A total of 218 patients with moderate to critical illness and confirmed COVID-19 were included in this study. Bacterial infection was confirmed in 43 patients (19.7%). COVID-19 patients with bacterial infections had longer hospital length of stay (17.6 6.62 vs 13.317.12), a higher proportion of respiratory failure, intensive care treatment, and ventilator use. COVID-19 patients with bacterial infection had a worse prognosis than those without bacterial infection (p<0.04). The empirical antibiotic was given to 75.2% of the patients. Gram-negative bacteria were commonly found as causative agents in this study (n = 39; 70.37%).

Conclusion: COVID-19 patients with bacterial infection have a longer length of stay and worse outcomes. Healthcare-associated infections during intensive care treatment for COVID-19 patients must be carefully prevented.