Prevalence of opportunistic invasive aspergillosis in COVID-19 patients with severe pneumonia

Incidence and Temporal Dynamics of Combined Infections in SARS-CoV-2-Infected Patients With Risk Factors for Severe Complications

BACKGROUND

Coronavirus disease 2019 (COVID-19) is a newly emerged infectious disease that needs further clinical investigation. Characterizing the temporal pattern of combined infections in patients with COVID-19 may help clinicians understand the clinical nature of this disease and provide valuable diagnostic and therapeutic guidelines.

METHODS

We retrospectively analyzed COVID-19 patients isolated in four study hospitals in Korea for one year period from May 2021 to April 2022 when the delta and omicron variants were dominant. The temporal characteristics of combined infections based on specific diagnostic tests were analyzed.

RESULTS

A total of 16,967 COVID-19 patients were screened, 2,432 (14.3%) of whom underwent diagnostic microbiologic tests according to the clinical decision-making, 195 of whom had positive test results, and 0.55% (94/16,967) of whom were ultimately considered to have clinically meaningful combined infections. The median duration for the diagnosis of combined infections was 15 (interquartile range [IQR], 5-25) days after admission. The proportion of community-acquired coinfections (≤ 2 days after admission) was 11.7% (11/94), which included bacteremia (10/94, 10.63%) and tuberculosis (1/94, 1.06%). Combined infections after 2 days of admission were diagnosed at median 16 (IQR, 9-26) days, and included bacteremia (72.3%), fungemia (19.3%), cytomegalovirus (CMV) diseases (8.4%), Pneumocystis jerovecii pneumonia (PJP, 8.4%) and invasive pulmonary aspergillosis (IPA, 4.8%).

CONCLUSION

Among COVID-19 patients with risk factors for severe complications, 0.55% had laboratory-confirmed combined infections, which included community and nosocomial pathogens in addition to unusual pathogens such as CMV disease, PJP and IPA.

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

INTRODUCTION

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

AREAS COVERED

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

EXPERT OPINION

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

Outcomes of Patients with COVID-19 and Fungal Coinfections: A Systematic Review and Meta-Analysis Study

Background & Objective

Fungal co-infections increase the incidence and mortality of viral respiratory tract infections. This study systematically reviews and conducts a meta-analysis to evaluate the prevalence of COVID-19 patients with fungal coinfections. The aim is to provide a concise overview of the impact of these infections on patient outcomes especially association with risk of mortality, informing future research and optimizing patient management strategies.

Methods

To identify relevant studies on COVID-19 patients, we conducted a systematic search of databases from the beginning of the year until July 2023, including fungal co-infections, mortality, and sequelae. Eligibility criteria were developed using the PICO framework, and data extraction was carried out separately by two authors using standard techniques. Statistical analysis was performed using the correlation model and differences between studies were evaluated using the I2 test. R and RStudio were used for statistical analysis and visualization.

Results

We initially identified 6,764 studies, and after checking for equivalence and consistency, 41 studies were included in the final analysis. The overall COVID-19 odds ratio for people who died from fungal infections was 2.65, indicating that patients infected with both COVID-19 and fungal infections had a higher risk of death compared to patients with COVID-19 alone. Specifically, COVID-19-associated pulmonary aspergillosis (CAPA) has a higher odds ratio of 3.36, while COVID-19-associated candidiasis (CAC) has an odds ratio of 1.84, and both are much more associated with death. However, coinfection of the fungus with other fungal species did not show a significant difference in the risk of mortality.

Conclusion

This study identified CAPA and CAC as the most common infections acquired in healthcare settings. Fungal coinfections may be associated with an increased risk of death in COVID-19 patients.

Nanotherapeutics for the delivery of antifungal drugs

The treatment of fungal infections is challenging with high death rates reported among immunocompromised patients. The currently available antifungals suffer from poor bioavailability and solubility, pharmacokinetics, and drug resistance, with limited cellular uptake. The clinical pipeline of new antifungals is dry. The incorporation of antifungal drugs into polymer-based nanocarriers to form nanotherapeutics is a promising approach to enhance the therapeutic outcomes of the available antifungal drugs. This review summarizes different polymer-based nanotherapeutics strategies that have been explored for the delivery of antifungals, resulting in enhanced therapeutic outcomes, such as improved pharmacokinetics, targeted/sustained delivery, prolonged drug circulation, retention of the drugs at the localized site of action, and overcoming drug resistance when compared with the free antifungal drugs.

Prevalence of pharmaceuticals and personal care products, microplastics and co-infecting microbes in the post-COVID-19 era and its implications on antimicrobial resistance and potential endocrine disruptive effects

The COVID-19 (coronavirus disease 2019) pandemic's steady condition coupled with predominance of emerging contaminants in the environment and its synergistic implications in recent times has stoked interest in combating medical emergencies in this dynamic environment. In this context, high concentrations of pharmaceutical and personal care products (PPCPs), microplastics (MPs), antimicrobial resistance (AMR), and soaring coinfecting microbes, tied with potential endocrine disruptive (ED) are critical environmental concerns that requires a detailed documentation and analysis. During the pandemic, the identification, enumeration, and assessment of potential hazards of PPCPs and MPs and (used as anti-COVID-19 agents/applications) in aquatic habitats have been attempted globally. Albeit receding threats in the magnitude of COVID-19 infections, both these pollutants have still posed serious consequences to aquatic ecosystems and the very health and hygiene of the population in the vicinity. The surge in the contaminants post-COVID also renders them to be potent vectors to harbor and amplify AMR. Pertinently, the present work attempts to critically review such instances to understand the underlying mechanism, interactions swaying the current health of our environment during this post-COVID-19 era. During this juncture, although prevention of diseases, patient care, and self-hygiene have taken precedence, nevertheless antimicrobial stewardship (AMS) efforts have been overlooked. Unnecessary usage of PPCPs and plastics during the pandemic has resulted in increased emerging contaminants (i.e., active pharmaceutical ingredients and MPs) in various environmental matrices. It was also noticed that among COVID-19 patients, while the bacterial co-infection prevalence was 0.2-51%, the fungi, viral, protozoan and helminth were 0.3-49, 1-22, 2-15, 0.4-15% respectively, rendering them resistant to residual PPCPs. There are inevitable chances of ED effects from PPCPs and MPs applied previously, that could pose far-reaching health concerns. Furthermore, clinical and other experimental evidence for many newer compounds is very scarce and demands further research. Pro-active measures targeting effective waste management, evolved environmental policies aiding strict regulatory measures, and scientific research would be crucial in minimizing the impact and creating better preparedness towards such events among the masses fostering sustainability.

Risk factors and the value of microbiological examinations of COVID-19 associated pulmonary aspergillosis in critically ill patients in intensive care unit: the appropriate microbiological examinations are crucial for the timely diagnosis of CAPA

Introduction

During the Omicron pandemic in China, a significant proportion of patients with Coronavirus Disease 2019 (COVID-19) associated pulmonary aspergillosis (CAPA) necessitated admission to intensive care unit (ICU) and experienced a high mortality. To explore the clinical risk factors and the application/indication of microbiological examinations of CAPA in ICU for timely diagnosis are very important.

Methods

This prospective study included patients with COVID-19 admitted to ICU between December 1, 2022, and February 28, 2023. The clinical data of influenza-associated pulmonary aspergillosis (IAPA) patients from the past five consecutive influenza seasons (November 1, 2017, to March 31, 2022) were collected for comparison. The types of specimens and methods used for microbiological examinations were also recorded to explore the efficacy in early diagnosis.

Results

Among 123 COVID-19 patients, 36 (29.3%) were diagnosed with probable CAPA. CAPA patients were more immunosuppressed, in more serious condition, required more advanced respiratory support and had more other organ comorbidities. Solid organ transplantation, APACHEII score ≥20 points, 5 points ≤SOFA score <10 points were independent risk factors for CAPA. Qualified lower respiratory tract specimens were obtained from all patients, and 84/123 (68.3%) patients underwent bronchoscopy to obtain bronchoalveolar lavage fluid (BALF) specimens. All patients' lower respiratory tract specimens underwent fungal smear and culture; 79/123 (64.2%) and 69/123 (56.1%) patients underwent BALF galactomannan (GM) and serum GM detection, respectively; metagenomic next-generation sequencing (mNGS) of the BALF was performed in 62/123 (50.4%) patients. BALF GM had the highest diagnostic sensitivity (84.9%), the area under the curve of the mNGS were the highest (0.812).

Conclusion

The incidence of CAPA was extremely high in patients admitted to the ICU. CAPA diagnosis mainly depends on microbiological evidence owing to non-specific clinical manifestations, routine laboratory examinations, and CT findings. The bronchoscopy should be performed and the BALF should be obtained as soon as possible. BALF GM are the most suitable microbiological examinations for the diagnosis of CAPA. Due to the timely and accuracy result of mNGS, it could assist in early diagnosis and might be an option in critically ill CAPA patients.

Diagnosis of invasive pulmonary aspergillosis by lateral flow assay of galactomannan in bronchoalveolar lavage fluid: a meta-analysis of diagnostic performance

The performance of lateral flow assay (LFA) in diagnosing invasive pulmonary aspergillosis (IPA) has not been well demonstrated. To address this, we conducted a meta-analysis assessing the overall accuracy of LFA in diagnosing IPA using bronchoalveolar lavage fluid (BALF). Over a systematical search and assessment of bias risk, we calculated the pooled specificity, sensitivity, and area under the receiver operating curve (AUC) to assess the diagnostic performance. Our meta-analysis included 11 studies. The combined total sensitivity and specificity for diagnosing IPA were 0.78 (95% confidence interval (CI): 0.71, 0.83) and 0.87 (95% CI: 0.81, 0.91), respectively. The AUC was 0.86 (95% CI: 0.82, 0.89). Our results demonstrate that LFA using galactomannan in BALF exhibits high sensitivity and specificity for diagnosing IPA.

Respiratory co-infections in COVID-19-positive patients

BACKGROUND

Opportunistic respiratory infections may complicate critically ill patients with COVID-19. Early detection of co-infections helps to administrate the appropriate antimicrobial agent, to guard against patient deterioration. This study aimed at estimating co-infections in COVID-19-positive patients.

METHODS

Eighty-nine COVID-19-positive patients confirmed by SARS-COV-2 PCR were tested for post-COVID-19 lower respiratory tract co-infections through bacterial culture, fungal culture and galactomannan (GM) testing.

RESULTS

Fourteen patients showed positive coinfection with Klebsiella, nine with Acinetobacter, six with Pseudomonas and three with E. coli. As for fungal infections, nine showed coinfection with Aspergillus, two with Zygomycetes and four with Candida. Galactomannan was positive among one patient with Aspergillus coinfection, one with Zygomycetes coinfection and three with Candida, 13 samples with negative fungal culture were positive for GM. Ten samples showed positive fungal growth, however, GM test was negative.

CONCLUSION

In our study, SARS-COV-2 respiratory coinfections were mainly implicated by bacterial pathogens; most commonly Klebsiella species (spp.), Aspergillus spp. were the most common cause of fungal coinfections, GM test showed low positive predictive value for fungal infection. Respiratory coinfections may complicate SARS-COV-2 probably due to the prolonged intensive care units (ICU) hospitalization, extensive empiric antimicrobial therapy, steroid therapy, mechanical ventilation during the COVID-19 outbreak. Antimicrobial stewardship programs are required so that antibiotics are prescribed judiciously according to the culture results.

COVID-19-associated pulmonary aspergillosis in immunocompetent patients: a virtual patient cohort study

The opportunistic fungus Aspergillus fumigatus infects the lungs of immunocompromised hosts, including patients undergoing chemotherapy or organ transplantation. More recently however, immunocompetent patients with severe SARS-CoV2 have been reported to be affected by COVID-19 Associated Pulmonary Aspergillosis (CAPA), in the absence of the conventional risk factors for invasive aspergillosis. This paper explores the hypothesis that contributing causes are the destruction of the lung epithelium permitting colonization by opportunistic pathogens. At the same time, the exhaustion of the immune system, characterized by cytokine storms, apoptosis, and depletion of leukocytes may hinder the response to A. fumigatus infection. The combination of these factors may explain the onset of invasive aspergillosis in immunocompetent patients. We used a previously published computational model of the innate immune response to infection with Aspergillus fumigatus. Variation of model parameters was used to create a virtual patient population. A simulation study of this virtual patient population to test potential causes for co-infection in immunocompetent patients. The two most important factors determining the likelihood of CAPA were the inherent virulence of the fungus and the effectiveness of the neutrophil population, as measured by granule half-life and ability to kill fungal cells. Varying these parameters across the virtual patient population generated a realistic distribution of CAPA phenotypes observed in the literature. Computational models are an effective tool for hypothesis generation. Varying model parameters can be used to create a virtual patient population for identifying candidate mechanisms for phenomena observed in actual patient populations.

Recommendations and guidelines for the diagnosis and management of Coronavirus Disease-19 (COVID-19) associated bacterial and fungal infections in Taiwan

Coronavirus disease-19 (COVID-19) is an emerging infectious disease caused by SARS-CoV-2 that has rapidly evolved into a pandemic to cause over 600 million infections and more than 6.6 million deaths up to Nov 25, 2022. COVID-19 carries a high mortality rate in severe cases. Co-infections and secondary infections with other micro-organisms, such as bacterial and fungus, further increases the mortality and complicates the diagnosis and management of COVID-19. The current guideline provides guidance to physicians for the management and treatment of patients with COVID-19 associated bacterial and fungal infections, including COVID-19 associated bacterial infections (CABI), pulmonary aspergillosis (CAPA), candidiasis (CAC) and mucormycosis (CAM). Recommendations were drafted by the 7th Guidelines Recommendations for Evidence-based Antimicrobial agents use Taiwan (GREAT) working group after review of the current evidence, using the grading of recommendations assessment, development, and evaluation (GRADE) methodology. A nationwide expert panel reviewed the recommendations in March 2022, and the guideline was endorsed by the Infectious Diseases Society of Taiwan (IDST). This guideline includes the epidemiology, diagnostic methods and treatment recommendations for COVID-19 associated infections. The aim of this guideline is to provide guidance to physicians who are involved in the medical care for patients with COVID-19 during the ongoing COVID-19 pandemic.

Assessing and Reassessing the Association of Comorbidities and Coinfections in COVID-19 Patients

Coronavirus disease 2019 (COVID-19) has posed an enormous global health and economic burden. To date, 324 million confirmed cases and over 5.5 million deaths have been reported. Several studies have reported comorbidities and coinfections associated with complicated and serious COVID-19 infections. Data from retrospective, prospective, case series, and case reports from various geographical locations were assessed, which included ~ 2300 COVID-19 patients with varying comorbidities and coinfection. We report that Enterobacterales with Staphylococcus aureus was the most while Mycoplasma pneumoniae was the least prevalent coinfection in COVID-19 patients with a comorbidity. In this order, hypertension, diabetes, cardiovascular disease, and pulmonary disease were the prevalent comorbidities observed in COVID-19 patients. There was a statistically significant difference in the prevalent comorbidities observed in patients coinfected with Staphylococcus aureus and COVID-19 and a statistically non-significant difference in the prevalent comorbidities in patients coinfected with Mycoplasma pneumoniae and COVID-19 as compared to similar infections in non-COVID-19 coinfection. We report a significant difference in the prevalent comorbidities recorded in COVID-19 patients with varying coinfections and varying geographic study regions. Our study provides informative data on the prevalence of comorbidities and coinfections in COVID-19 patients to aid in evidence-based patient management and care.

COVID-19-associated pulmonary aspergillosis in immunocompetent patients: A virtual patient cohort study

Purpose

The opportunistic fungus Aspergillus fumigatus infects the lungs of immunocompromised hosts, including patients undergoing chemotherapy or organ transplantation. More recently however, immunocompetent patients with severe SARS-CoV2 have been reported to be affected by COVID-19 Associated Pulmonary Aspergillosis (CAPA), in the absence of the conventional risk factors for invasive aspergillosis. This paper explores the hypothesis that contributing causes are the destruction of the lung epithelium permitting colonization by opportunistic pathogens. At the same time, the exhaustion of the immune system, characterized by cytokine storms, apoptosis, and depletion of leukocytes may hinder the response to A. fumigatus infection. The combination of these factors may explain the onset of invasive aspergillosis in immunocompetent patients.

Methods

We used a previously published computational model of the innate immune response to infection with Aspergillus fumigatus . Variation of model parameters was used to create a virtual patient population. A simulation study of this virtual patient population to test potential causes for co-infection in immunocompetent patients.

Results

The two most important factors determining the likelihood of CAPA were the inherent virulence of the fungus and the effectiveness of the neutrophil population, as measured by granule half-life and ability to kill fungal cells. Varying these parameters across the virtual patient population generated a realistic distribution of CAPA phenotypes observed in the literature.

Conclusions

Computational models are an effective tool for hypothesis generation. Varying model parameters can be used to create a virtual patient population for identifying candidate mechanisms for phenomena observed in actual patient populations.

Off-label treatments as potential accelerators in the search for the ideal antifungal treatment of cryptococcosis

Cryptococcosis is an opportunistic mycosis that mainly affects immunosuppressed patients. The treatment is a combination of three antifungal agents: amphotericin B, 5-flucytosine and fluconazole. However, these drugs have many disadvantages, such as high nephrotoxicity, marketing bans in some countries and fungal resistance. One of the solutions to find possible new drugs is pharmacological repositioning. This work presents repositioned drugs as an alternative for new antifungal therapies for cryptococcosis. All the studies here were performed in vitro or in animal models, except for sertraline, which reached phase III in humans. There is still no pharmacological repositioning approval for cryptococcosis in humans, though this review shows the potential of repurposing as a rapid approach to finding new agents to treat cryptococcosis.

Specific Focus on Antifungal Peptides against Azole Resistant Aspergillus fumigatus: Current Status, Challenges, and Future Perspectives

The prevalence of fungal infections is increasing worldwide, especially that of aspergillosis, which previously only affected people with immunosuppression. Aspergillus fumigatus can cause allergic bronchopulmonary aspergillosis and endangers public health due to resistance to azole-type antimycotics such as fluconazole. Antifungal peptides are viable alternatives that combat infection by forming pores in membranes through electrostatic interactions with the phospholipids as well as cell death to peptides that inhibit protein synthesis and inhibit cell replication. Engineering antifungal peptides with nanotechnology can enhance the efficacy of these therapeutics at lower doses and reduce immune responses. This manuscript explains how antifungal peptides combat antifungal-resistant aspergillosis and also how rational peptide design with nanotechnology and artificial intelligence can engineer peptides to be a feasible antifungal alternative.

Aspergillus-SARS-CoV-2 Coinfection: What Is Known?

COVID-19-associated pulmonary aspergillosis (CAPA) has had a high incidence. In addition, it has been associated with prolonged hospital stays, as well as several predisposing risk factors, such as fungal factors (nosocomial organism, the size of the conidia, and the ability of the Aspergillus spp. of colonizing the respiratory tract), environmental factors (remodeling in hospitals, use of air conditioning and negative pressure in intensive care units), comorbidities, and immunosuppressive therapies. In addition to these factors, SARS-CoV-2 per se is associated with significant dysfunction of the patient's immune system, involving both innate and acquired immunity, with reduced CD4+ and CD8+ T cell counts and cytokine storm. Therefore, this review aims to identify the factors influencing the fungus so that coinfection with SARS-CoV-2 can occur. In addition, we analyze the predisposing factors in the fungus, host, and the immune response alteration due to the pathogenicity of SARS-CoV-2 that causes the development of CAPA.

The impact of mucormycosis (black fungus) on SARS-CoV-2-infected patients: at a glance

The emergence of various diseases during the COVID-19 pandemic made health workers more attentive, and one of the new pathogens is the black fungus (mucormycosis). As a result, millions of lives have already been lost. As a result of the mutation, the virus is constantly changing its traits, including the rate of disease transmission, virulence, pathogenesis, and clinical signs. A recent analysis revealed that some COVID-19 patients were also coinfected with a fungal disease called mucormycosis (black fungus). India has already categorized the COVID-19 patient black fungus outbreak as an epidemic. Only a few reports are observed in other countries. The immune system is weakened by COVID-19 medication, rendering it more prone to illnesses like black fungus (mucormycosis). COVID-19, which is caused by a B.1.617 strain of the SARS-CoV-2 virus, has been circulating in India since April 2021. Mucormycosis is a rare fungal infection induced by exposure to a fungus called mucormycete. The most typically implicated genera are Mucor rhyzuprhizopusdia and Cunninghamella. Mucormycosis is also known as zygomycosis. The main causes of infection are soil, dumping sites, ancient building walls, and other sources of infection (reservoir words "mucormycosis" and "zygomycosis" are occasionally interchanged). Zygomycota, on the other hand, has been identified as polyphyletic and is not currently included in fungal classification systems; also, zygomycosis includes Entomophthorales, but mucormycosis does not. This current review will be focused on the etiology and virulence factors of COVID-19/mucormycosis coinfections in COVID-19-associated mucormycosis patients, as well as their prevalence, diagnosis, and treatment.

Evaluation of environmental Mucorales contamination in and around the residence of COVID-19-associated mucormycosis patients

Introduction

Recently, India witnessed an unprecedented surge of coronavirus disease 2019 (COVID-19)-associated mucormycosis (CAM) cases. In addition to patient management issues, environmental Mucorales contamination possibly contributed to the outbreak. A recent study evaluated environment contamination by Mucorales in the hospital setting. However, a considerable number of CAM patients were never admitted to a hospital before the development of the disease. The present study, therefore, planned to evaluate Mucorales contamination of patients’ residences.

Methods

The residential environment of 25 patients with CAM living in north India was surveyed. Air samples were collected from indoor and immediate outdoor vicinity of the patients’ residence and cultured on Dichloran Rose–Bengal Chloramphenicol (DRBC) agar with benomyl for selective isolation of Mucorales. Surface swab samples were also collected from the air coolers fitted in those residences and cultured on DRBC agar. The isolates were identified by phenotypic and genotypic methods. Amplified fragment length polymorphism (AFLP) was employed to evaluate the genetic relatedness of the environmental and patients’ clinical isolates.

Results

The median spore count (mean ± SD, cfu/m3) of Mucorales in the air of patients’ bedrooms was significantly higher than in the air in other rooms in those residences (3.55 versus 1.5, p = 0.003) or the air collected directly from the front of the air cooler (p &lt; 0.0001). The Mucorales spore count in the environment did not correlate with either ventilation of the room or hygiene level of the patients’ residences. Rhizopus arrhizus was isolated from the environment of all patients’ residences (n = 25); other Mucorales species isolated were Cunninghamella bertholletiae (n = 14), Rhizopus microsporus (n = 6), Rhizopus delemar (n = 6), Syncephalastrum racemosum (n = 1), Lichtheimia corymbifera (n = 1), and Mucor racemosus (n = 1). Genetic relatedness was observed between 11 environmental isolates from the patients’ bedrooms and respective clinical isolates from patients.

Discussion

The study supported the view that the patients might have acquired Mucorales from the home environment during the post-COVID-19 convalescence period. Universal masking at home during patients’ convalescence period and environmental decontamination could minimize exposure in those susceptible patients.

Antifungal therapy in the management of fungal secondary infections in COVID-19 patients: A systematic review and meta-analysis

Objectives

The prevalence of fungal secondary infections among COVID-19 patients and efficacy of antifungal therapy used in such patients is still unknown. Hence, we conducted this study to find the prevalence of fungal secondary infections among COVID-19 patients and patient outcomes in terms of recovery or all-cause mortality following antifungal therapy (AFT) in such patients.

Methods

We performed a comprehensive literature search in PubMed^®, Scopus^®, Web of Sciences^™, The Cochrane Library, ClinicalTrial.gov, MedRxiv.org, bioRxiv.org, and Google scholar to identify the literature that used antifungal therapy for the management fungal secondary infections in COVID-19 patients. We included case reports, case series, prospective & retrospective studies, and clinical trials. Mantel Haenszel random-effect model was used for estimating pooled risk ratio for required outcomes.

Results

A total of 33 case reports, 3 case series, and 21 cohort studies were selected for final data extraction and analysis. The prevalence of fungal secondary infections among COVID-19 patients was 28.2%. Azoles were the most commonly (65.1%) prescribed AFT. Study shows that high survival frequency among patients using AFT, received combination AFT and AFT used for >28 days. The meta-analysis showed, no significant difference in all-cause mortality between patients who received AFT and without AFT (p = 0.17), between types of AFT (p = 0.85) and the duration of AFT (p = 0.67).

Conclusion

The prevalence of fungal secondary infections among COVID-19 patients was 28.2%. The survival frequency was high among patients who used AFT for fungal secondary infections, received combination AFT and AFT used for >28 days. However, meta-analysis results found that all-cause mortality in COVID-19 patients with fungal secondary infections is not significantly associated with type and duration of AFT, mostly due to presence of confounding factors such as small number of events, delay in diagnosis of fungal secondary infections, presence of other co-infections and multiple comorbidities.

Overview of COVID-19-Associated Invasive Fungal Infection

Purpose of Review

Invasive fungal infections are a complication of COVID-19 disease. This article reviews literature characterizing invasive fungal infections associated with COVID-19.

Recent Findings

Multiple invasive fungal infections including aspergillosis, candidiasis, pneumocystosis, other non-Aspergillus molds, and endemic fungi have been reported in patients with COVID-19. Risk factors for COVID-19-associated fungal disease include underlying lung disease, diabetes, steroid or immunomodulator use, leukopenia, and malignancy. COVID-19-associated pulmonary aspergillosis (CAPA) and COVID-19-associated mucormycosis (CAM) are the most common fungal infections described. However, there is variability in the reported incidences related to use of differing diagnostic algorithms.

Summary

Fungal pathogens are important cause of infection in patients with COVID-19, and the diagnostic strategies continue to evolve. Mortality in these patients is increased, and providers should operate with a high index of suspicion. Further studies will be required to elucidate the associations and pathogenesis of these diseases and best management and prevention strategies.

Monoclonal Antibodies and Invasive Aspergillosis: Diagnostic and Therapeutic Perspectives

Invasive aspergillosis (IA) is a life-threatening fungal disease that causes high morbidity and mortality in immunosuppressed patients. Early and accurate diagnosis and treatment of IA remain challenging. Given the broad range of non-specific clinical symptoms and the shortcomings of current diagnostic techniques, most patients are either diagnosed as "possible" or "probable" cases but not "proven". Moreover, because of the lack of sensitive and specific tests, many high-risk patients receive an empirical therapy or a prolonged treatment of high-priced antifungal agents, leading to unnecessary adverse effects and a high risk of drug resistance. More precise diagnostic techniques alongside a targeted antifungal treatment are fundamental requirements for reducing the morbidity and mortality of IA. Monoclonal antibodies (mAbs) with high specificity in targeting the corresponding antigen(s) may have the potential to improve diagnostic tests and form the basis for novel IA treatments. This review summarizes the up-to-date application of mAb-based approaches in assisting IA diagnosis and therapy.

Prevalence of COVID-19-Associated Pulmonary Aspergillosis: Critical Review and Conclusions

First reports of cases and case series of COVID-19-associated pulmonary aspergillosis (CAPA) emerged during the first months of the pandemic. Prevalence rates varied widely due to the fact that CAPA was, and still remains, challenging to diagnose in patients with COVID-19-associated acute respiratory failure (ARF). The clinical picture and radiological findings of CAPA are unspecific and can resemble those of severe COVID-19. Hence, mycological evidence became a key component in establishing a diagnosis. However, blood tests lack sensitivity in early treatable phases of CAPA and once positive, mortality has been shown to exceed 80% despite systemic antifungal therapy. The primarily airway invasive growth in non-neutropenic patients and the late occurrence of angioinvasion in the course of disease may mainly account for these diagnostic obstacles. Testing of bronchoalveolar lavage (BAL) is therefore crucial in the diagnostic process, but was rarely performed during the early phase of the pandemic, which potentially interfered with the accuracy of reported prevalence. Current guidelines recommend treatment of CAPA during its early airway invasive phase, which may result in some overtreatment (i.e., treatment in patients that may not develop angioinvasive infection) and adverse drug events, yet there is no viable alternative approach. Timely treatment of cases needs to be ensured for patients with mycological evidence of CAPA in the lower respiratory tract given the independent contribution of CAPA to devastating mortality rates of around 50% that have been shown in multiple studies. Here, we review the evolution of reported CAPA prevalence and the role of CAPA as an important opportunistic infection affecting COVID-19 patients in intensive care units (ICUs).

Usefulness of Sōna Aspergillus Galactomannan LFA with digital readout as diagnostic and as screening tool of COVID-19 associated pulmonary aspergillosis in critically ill patients. Data from a multicenter prospective study performed in Argentina

COVID-19 associated pulmonary aspergillosis (CAPA) incidence varies depending on the country. Serum galactomannan quantification is a promising diagnostic tool since samples are easy to obtain with low biosafety issues. A multicenter prospective study was performed to evaluate the CAPA incidence in Argentina and to assess the performance of the lateral flow assay with digital readout (Sōna Aspergillus LFA) as a CAPA diagnostic and screening tool. The correlation between the values obtained with Sōna Aspergillus LFA and Platelia® EIA was evaluated. In total, 578 serum samples were obtained from 185 critically ill COVID patients. CAPA screening was done weekly starting from the first week of ICU stay. Probable CAPA incidence in critically ill patients was 10.27% (19/185 patients when LFA was used as mycological criteria) and 9% (9/100 patients when EIA was used as mycological criteria). We found a very good correlation between the two evaluated galactomannan quantification methods (overall agreement of 92.16% with a Kappa statistic value of 0.721). CAPA diagnosis (>0.5 readouts in LFA) were done during the first week of ICU stay in 94.7% of the probable CAPA patients. The overall mortality was 36.21%. CAPA patients' mortality and length of ICU stay were not statistically different from for COVID (non-CAPA) patients (42.11% vs 33.13% and 29 vs 24 days, respectively). These indicators were lower than in other reports. LFA-IMMY with digital readout is a reliable tool for early diagnosis of CAPA using serum samples in critically ill COVID patients. It has a good agreement with Platelia® EIA.

Invasive aspergillosis in coronavirus disease 2019: a practical approach for clinicians

PURPOSE OF REVIEW

Invasive pulmonary aspergillosis (IPA) can affect patients with severe coronavirus disease 2019 (COVID-19), but many questions remain open about its very variable incidence across the world, the actual link between the viral infection and the fungal superinfection, the significance of Aspergillus recovery in a respiratory sample, and the management of such cases. This review addresses these questions and aims at providing some clues for the practical diagnostic and therapeutic approaches of COVID-19-associated pulmonary aspergillosis (CAPA) in a clinical perspective.

RECENT FINDINGS

Definitions have been proposed for possible/probable/proven CAPA, but distinction between colonization and invasive fungal infection is difficult and not possible in most cases in the absence of histopathological proof or positive galactomannan in serum. Most importantly, the recovery of an Aspergillus by a direct (culture, PCR) or indirect (galactomannan) test in a respiratory sample is an indicator of worse outcome, which justifies a screening for early detection and initiation of preemptive antifungal therapy in such cases.

SUMMARY

The COVID-19 pandemic has increased our awareness of IPA among ICU patients. Although current recommendations are mainly based on experts' opinions, prospective studies are needed to get more evidence-based support for the diagnostic approach and management of CAPA.

COVID-19 Associated Pulmonary Aspergillosis (CAPA): Hospital or Home Environment as a Source of Life-Threatening Aspergillus fumigatus Infection?

Most cases of invasive aspergillosis are caused by Aspergillus fumigatus, whose conidia are ubiquitous in the environment. Additionally, in indoor environments, such as houses or hospitals, conidia are frequently detected too. Hospital-acquired aspergillosis is usually associated with airborne fungal contamination of the hospital air, especially after building construction events. A. fumigatus strain typing can fulfill many needs both in clinical settings and otherwise. The high incidence of aspergillosis in COVID patients from our hospital, made us wonder if they were hospital-acquired aspergillosis. The purpose of this study was to evaluate whether the hospital environment was the source of aspergillosis infection in CAPA patients, admitted to the Hospital Universitario Central de Asturias, during the first and second wave of the COVID-19 pandemic, or whether it was community-acquired aspergillosis before admission. During 2020, sixty-nine A. fumigatus strains were collected for this study: 59 were clinical isolates from 28 COVID-19 patients, and 10 strains were environmentally isolated from seven hospital rooms and intensive care units. A diagnosis of pulmonary aspergillosis was based on the ECCM/ISHAM criteria. Strains were genotyped by PCR amplification and sequencing of a panel of four hypervariable tandem repeats within exons of surface protein coding genes (TRESPERG). A total of seven genotypes among the 10 environmental strains and 28 genotypes among the 59 clinical strains were identified. Genotyping revealed that only one environmental A. fumigatus from UCI 5 (box 54) isolated in October (30 October 2020) and one A. fumigatus isolated from a COVID-19 patient admitted in Pneumology (Room 532-B) in November (24 November 2020) had the same genotype, but there was a significant difference in time and location. There was also no relationship in time and location between similar A. fumigatus genotypes of patients. The global A. fumigatus, environmental and clinical isolates, showed a wide diversity of genotypes. To our knowledge, this is the first study monitoring and genotyping A. fumigatus isolates obtained from hospital air and COVID-19 patients, admitted with aspergillosis, during one year. Our work shows that patients do not acquire A. fumigatus in the hospital. This proves that COVID-associated aspergillosis in our hospital is not a nosocomial infection, but supports the hypothesis of “community aspergillosis” acquisition outside the hospital, having the home environment (pandemic period at home) as the main suspected focus of infection.

SARS-CoV-2 Associated Immune Dysregulation and COVID-Associated Pulmonary Aspergilliosis (CAPA): A Cautionary Tale

As the global SARS-CoV-2 pandemic continues to plague healthcare systems, it has become clear that opportunistic pathogens cause a considerable proportion of SARS-CoV-2-associated mortality and morbidity cases. Of these, Covid-Associated Pulmonary Aspergilliosis (CAPA) is a major concern with evidence that it occurs in the absence of traditional risk factors such as neutropenia and is diagnostically challenging for the attending physician. In this review, we focus on the immunopathology of SARS-CoV-2 and how this potentiates CAPA through dysregulation of local and systemic immunity as well as the unintended consequences of approved COVID treatments including corticosteroids and IL-6 inhibitors. Finally, we will consider how knowledge of the above may aid in the diagnosis of CAPA using current diagnostics and what treatment should be instituted in probable and confirmed cases.

Antimicrobial resistance (AMR) in COVID-19 patients: a systematic review and meta-analysis (November 2019-June 2021)

BACKGROUND

Pneumonia from SARS-CoV-2 is difficult to distinguish from other viral and bacterial etiologies. Broad-spectrum antimicrobials are frequently prescribed to patients hospitalized with COVID-19 which potentially acts as a catalyst for the development of antimicrobial resistance (AMR).

OBJECTIVES

We conducted a systematic review and meta-analysis during the first 18 months of the pandemic to quantify the prevalence and types of resistant co-infecting organisms in patients with COVID-19 and explore differences across hospital and geographic settings.

METHODS

We searched MEDLINE, Embase, Web of Science (BioSIS), and Scopus from November 1, 2019 to May 28, 2021 to identify relevant articles pertaining to resistant co-infections in patients with laboratory confirmed SARS-CoV-2. Patient- and study-level analyses were conducted. We calculated pooled prevalence estimates of co-infection with resistant bacterial or fungal organisms using random effects models. Stratified meta-analysis by hospital and geographic setting was also performed to elucidate any differences.

RESULTS

Of 1331 articles identified, 38 met inclusion criteria. A total of 1959 unique isolates were identified with 29% (569) resistant organisms identified. Co-infection with resistant bacterial or fungal organisms ranged from 0.2 to 100% among included studies. Pooled prevalence of co-infection with resistant bacterial and fungal organisms was 24% (95% CI 8-40%; n = 25 studies: I2 = 99%) and 0.3% (95% CI 0.1-0.6%; n = 8 studies: I2 = 78%), respectively. Among multi-drug resistant organisms, methicillin-resistant Staphylococcus aureus, carbapenem-resistant Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and multi-drug resistant Candida auris were most commonly reported. Stratified analyses found higher proportions of AMR outside of Europe and in ICU settings, though these results were not statistically significant. Patient-level analysis demonstrated > 50% (n = 58) mortality, whereby all but 6 patients were infected with a resistant organism.

CONCLUSIONS

During the first 18 months of the pandemic, AMR prevalence was high in COVID-19 patients and varied by hospital and geography although there was substantial heterogeneity. Given the variation in patient populations within these studies, clinical settings, practice patterns, and definitions of AMR, further research is warranted to quantify AMR in COVID-19 patients to improve surveillance programs, infection prevention and control practices and antimicrobial stewardship programs globally.

Opportunistic Infections in COVID-19: A Systematic Review and Meta-Analysis

The prevalence, incidence, and characteristics of bacterial infections in patients infected with severe acute respiratory syndrome coronavirus 2 are not well understood and have been raised as an important knowledge gap. Therefore, our study focused on the most common opportunistic infections/secondary infections/superinfections in coronavirus disease 2019 (COVID-19) patients.

This systematic review and meta-analysis was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses. Eligible studies were identified using PubMed/Medline since inception to June 25, 2021. Studies meeting the inclusion criteria were selected. Statistical analysis was conducted in Review Manager 5.4.1. A random-effect model was used when heterogeneity was seen to pool the studies, and the result was reported as inverse variance and the corresponding 95% confidence interval.

We screened 701 articles comprising 22 cohort studies which were included for analysis. The pooled prevalence of opportunistic infections/secondary infections/superinfections was 16% in COVID-19 patients. The highest prevalence of secondary infections was observed among viruses at 33%, followed by bacteria at 16%, fungi at 6%, and 25% among the miscellaneous group/wrong outcome.

Opportunistic infections are more prevalent in critically ill patients. The isolated pathogens included Epstein-Barr virus, Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii, Hemophilus influenza, and invasive pulmonary aspergillosis. Large-scale studies are required to better identify opportunistic/secondary/superinfections in COVID-19 patients.

Defining COVID-19 associated pulmonary aspergillosis: systematic review and meta-analysis

Background

Pulmonary aspergillosis may complicate coronavirus disease 2019 (COVID-19) and contribute to excess mortality in intensive care unit (ICU) patients. The disease is poorly understood, in part due to discordant definitions across studies.

Objectives

We sought to review the prevalence, diagnosis, treatment, and outcomes of COVID-19–associated pulmonary aspergillosis (CAPA) and compare research definitions.

Data sources

PubMed, Embase, Web of Science, and MedRxiv were searched from inception to October 12, 2021.

Study eligibility criteria

ICU cohort studies and CAPA case series including ≥3 patients were included.

Participants

Adult patients in ICUs with COVID-19.

Interventions

Patients were reclassified according to four research definitions. We assessed risk of bias with an adaptation of the Joanna Briggs Institute cohort checklist tool for systematic reviews.

Methods

We calculated CAPA prevalence using the Freeman-Tukey random effects method. Correlations between definitions were assessed with Spearman's rank test. Associations between antifungals and outcome were assessed with random effects meta-analysis.

Results

Fifty-one studies were included. Among 3297 COVID-19 patients in ICU cohort studies, 313 were diagnosed with CAPA (prevalence 10%; 95% CI 8%–13%). Two hundred seventy-seven patients had patient-level data allowing reclassification. Definitions had limited correlation with one another (ρ = 0.268–0.447; p < 0.001), with the exception of Koehler and Verweij (ρ = 0.893; p < 0.001); 33.9% of patients reported to have CAPA did not fulfill any research definitions. Patients were diagnosed after a median of 8 days (interquartile range 5–14) in ICUs. Tracheobronchitis occurred in 3% of patients examined with bronchoscopy. The mortality rate was high (59.2%). Applying CAPA research definitions did not strengthen the association between mould-active antifungals and survival.

Conclusions

The reported prevalence of CAPA is significant but may be exaggerated by nonstandard definitions.

Worldwide prevalence of fungal coinfections among COVID-19 patients: a comprehensive systematic review and meta-analysis

Microbial coinfections can increase the morbidity and mortality rates of viral respiratory diseases. Therefore, this study aimed to determine the pooled prevalence of fungal coinfections in coronavirus disease 2019 (COVID-19) patients. Web of Science, Medline, Scopus, and Embase were searched without language restrictions to identify the related research on COVID-19 patients with fungal coinfections from December 1, 2019, to December 30, 2020. A random-effects model was used for analysis. The sample size included 2,246 patients from 8 studies. The pooled prevalence of fungal coinfections was 12.60%. The frequency of fungal subtype coinfections was 3.71% for Aspergillus, 2.39% for Candida, and 0.39% for other. The World Health Organization’s Regional Office for Europe and Regional Office for Southeast Asia had the highest (23.28%) and lowest (4.53%) estimated prevalence of fungal coinfection, respectively. Our findings showed a high prevalence of fungal coinfections in COVID-19 cases, which is a likely contributor to mortality in COVID-19 patients. Early identification of fungal pathogens in the laboratory for COVID-19 patients can lead to timely treatment and prevention of further damage by this hidden infection.

The Harris’ hawk (Parabuteo unicinctus) as a source of pathogenic human yeasts: a potential risk to human health

Aim: Invasive human fungal infections have been a serious public health problem among immunocompromised patients. Wild bird species are related to the eco-epidemiology of some infectious diseases, mainly Cryptococcosis, Histoplasmosis, Aspergillosis, Chlamydiosis, Salmonellosis and allergic diseases. Falconry is the art of training predators for hunting. Nowadays, birds of prey are used as pets, which brings new sources of infections to humans. Materials & methods: We identified fungal pathogenic yeasts, Candida parapsilosis, Debaryomyces hansenii and Rhodotorula mucilaginosa. Conclusion: Study new environmental niches of human pathogens is vitally important to establish preventive actions with the purpose of minimizing the risks of human contamination. Our work describes yeast microbiota from the excreta of Parabuteo unicinctus as a potential hazard for human disease.

COVID-19-Associated Pulmonary Aspergillosis in a Tertiary Hospital

Our study aims to assess the prevalence of CAPA (COVID-19-associated pulmonary aspergillosis) and describe the associated risk factors and their impact on mortality. A prospective study was conducted. We included patients with COVID-19 disease who were admitted to the ICU with a diagnosis of respiratory failur. Mycological culture and other biomarkers (calcofluor staining, LFD, LFA, PCR, GM, and B-D-glucan) were performed. A total of 300 patients were included in the study. Thirty-five patients were diagnosed with CAPA (prevalence 11.7%). During admission, 57 patients died (19%), and, in the group of CAPA patients, mortality was 31.4%. In multivariate analysis, independent risk factors associated with CAPA diagnosis were age (OR: 1.05; 95% CI 1.01–1.09; p = 0.037), chronic lung disease (OR: 3.85; 95% CI 1.02–14.9; p = 0.049) and treatment with tocilizumab during admission (OR: 14.5; 95% 6.1–34.9; p = 0.001). Factors independently associated with mortality were age (OR: 1.06; 95% CI 1.01–1.11; p = 0.014) and CAPA diagnosis during admission (OR: 3.34; 95% CI 1.38–8.08; p = 0.007). CAPA is an infection that appears in many patients with COVID-19 disease. CAPA is associated with high mortality rates, which may be reduced by early diagnosis and initiation of appropriate antifungal therapy, so screening of COVID-19 ARDS (acute respiratory distress syndrome) patients for CAPA is essential.

Pathogenesis of Respiratory Viral and Fungal Coinfections

Individuals suffering from severe viral respiratory tract infections have recently emerged as "at risk" groups for developing invasive fungal infections. Influenza virus is one of the most common causes of acute lower respiratory tract infections worldwide. Fungal infections complicating influenza pneumonia are associated with increased disease severity and mortality, with invasive pulmonary aspergillosis being the most common manifestation. Strikingly, similar observations have been made during the current coronavirus disease 2019 (COVID-19) pandemic. The copathogenesis of respiratory viral and fungal coinfections is complex and involves a dynamic interplay between the host immune defenses and the virulence of the microbes involved that often results in failure to return to homeostasis. In this review, we discuss the main mechanisms underlying susceptibility to invasive fungal disease following respiratory viral infections. A comprehensive understanding of these interactions will aid the development of therapeutic modalities against newly identified targets to prevent and treat these emerging coinfections.

COVID-19-associated pulmonary aspergillosis in a tertiary care center in Shenzhen City

Objectives

The severe coronavirus disease 2019 (COVID-19) is characterized by acute respiratory distress syndrome (ARDS) and risk of fungal co-infection, pulmonary aspergillosis in particular. However, COVID-19 associated pulmonary aspergillosis (CAPA) cases remain limited due to the difficulty in diagnosis.

Methods

We describe presumptive invasive aspergillosis in eight patients diagnosed with COVID-19 in a single center in Shenzhen, China. Data collected include underlying conditions, mycological findings, immunodetection results, therapies and outcomes.

Results

Four of the eight patients had tested positive for Aspergillus by either culture or Next-generation sequencing analysis of sputum or bronchoalveolar lavage fluid (BALF), while the rest of patients had only positive results in antigen or antibody detection. Although all patients received antifungal therapies, six of these eight patients (66.7%) died.

Conclusion

Due to the high mortality rate of CAPA, clinical care in patients with CAPA deserves more attention.

Worldwide prevalence of microbial agents' coinfection among COVID-19 patients: A comprehensive updated systematic review and meta-analysis

BACKGROUND

To provide information about pathogens' coinfection prevalence with SARS-CoV-2 could be a real help to save patients' lives. This study aims to evaluate the pathogens' coinfection prevalence among COVID-19 patients.

METHOD

In order to find all of the relevant articles, we used systematic search approach. Research-based databases including PubMed, Web of Science, Embase, and Scopus, without language restrictions, were searched to identify the relevant bacterial, fungal, and viral coinfections among COVID-19 cases from December 1, 2019, to August 23, 2021. In order to dig deeper, other scientific repositories such as Medrxiv were probed.

RESULTS

A total of 13,023 studies were found through systematic search. After thorough analysis, only 64 studies with 61,547 patients were included in the study. The most common causative agents of coinfection among COVID-19 patients were bacteria (pooled prevalence: 20.97%; 95% CI: 15.95-26.46; I2 : 99.9%) and less frequent were virus coinfections (pooled prevalence: 12.58%; 95% CI: 7.31-18.96; I2 : 98.7%). The pooled prevalence of fungal coinfections was also 12.60% (95% CI: 7.84-17.36; I2 : 98.3%). Meta-regression analysis showed that the age sample size and WHO geographic region did not influenced heterogeneity.

CONCLUSION

We identified a high prevalence of pathogenic microorganism coinfection among COVID-19 patients. Because of this rate of coinfection empirical use of antibacterial, antifungal, and antiviral treatment are advisable specifically at the early stage of COVID-19 infection. We also suggest running simultaneously diagnostic tests to identify other microbiological agents' coinfection with SARS-CoV-2.

Trichosporon asahii Urinary Tract Infection in a Patient with Severe COVID-19

Trichosporon asahii is a yeast-like basidiomycete that is an emerging opportunistic infection in immunocompromised patients. Urinary tract infections due to T. asahii are rarely reported in the literature and typically seen only in immunocompromised patients. In addition to being immunocompromised, critically ill COVID-19 patients often have prolonged exposure to antibiotics, corticosteroids, and Foley catheters, which further increases their susceptibility to infection with T. asahii. There are limited case reports documenting successful treatment of T. asahii among hospitalized patients, particularly among COVID-19 patients, in the literature. Therefore, it is important that successful treatment regimens be reported. Here, we report a case of T. asahii urinary tract infection successfully treated with fluconazole and voriconazole in a 73-year-old male recovering from COVID-19. Urinary tract infections with T. asahii should be considered in persistently febrile COVID-19 patients with fungal urinary tract infections since prompt recognition and treatment can reduce the risk of disseminated disease and early mortality.

A Visual and Comprehensive Review on COVID-19-Associated Pulmonary Aspergillosis (CAPA)

Coronavirus disease 19 (COVID-19)-associated pulmonary aspergillosis (CAPA) is a severe fungal infection complicating critically ill COVID-19 patients. Numerous retrospective and prospective studies have been performed to get a better grasp on this lethal co-infection. We performed a qualitative review and summarized data from 48 studies in which 7047 patients had been included, of whom 820 had CAPA. The pooled incidence of proven, probable or putative CAPA was 15.1% among 2953 ICU-admitted COVID-19 patients included in 18 prospective studies. Incidences showed great variability due to multiple factors such as discrepancies in the rate and depth of the fungal work-up. The pathophysiology and risk factors for CAPA are ill-defined, but therapy with corticosteroids and anti-interleukin-6 therapy potentially confer the biggest risk. Sampling for mycological work-up using bronchoscopy is the cornerstone for diagnosis, as imaging is often aspecific. CAPA is associated with an increased mortality, but we do not have conclusive data whether therapy contributes to an increased survival in these patients. We conclude our review with a comparison between influenza-associated pulmonary aspergillosis (IAPA) and CAPA.

Coronavirus Disease 2019-Associated Invasive Fungal Infection

Coronavirus disease 2019 (COVID-19) can become complicated by secondary invasive fungal infections (IFIs), stemming primarily from severe lung damage and immunologic deficits associated with the virus or immunomodulatory therapy. Other risk factors include poorly controlled diabetes, structural lung disease and/or other comorbidities, and fungal colonization. Opportunistic IFI following severe respiratory viral illness has been increasingly recognized, most notably with severe influenza. There have been many reports of fungal infections associated with COVID-19, initially predominated by pulmonary aspergillosis, but with recent emergence of mucormycosis, candidiasis, and endemic mycoses. These infections can be challenging to diagnose and are associated with poor outcomes. The reported incidence of IFI has varied, often related to heterogeneity in patient populations, surveillance protocols, and definitions used for classification of fungal infections. Herein, we review IFI complicating COVID-19 and address knowledge gaps related to epidemiology, diagnosis, and management of COVID-19-associated fungal infections.

Medicines for Malaria Venture COVID Box: a source for repurposing drugs with antifungal activity against human pathogenic fungi

BACKGROUND

Treatment of mycoses is often ineffective, usually prolonged, and has some side effects. These facts highlight the importance of discovering new molecules to treat fungal infections.

OBJECTIVES

To search the Medicines for Malaria Venture COVID Box for drugs with antifungal activity.

METHODS

Fourteen human pathogenic fungi were tested against the 160 drugs of this collection at 1.0 µM concentration. We evaluated the ability of the drugs to impair fungal growth, their fungicidal nature, and morphological changes caused to cells.

FINDINGS

Thirty-four molecules (21.25%) presented antifungal activity. Seven are antifungal drugs and one is the agricultural fungicide cycloheximide. The other drugs with antifungal activity included antibiotics (n = 3), antimalarials (n = 4), antivirals (n = 2), antiparasitcs (n = 3), antitumor agents (n = 5), nervous system agents (n = 3), immunosuppressants (n = 3), antivomiting (n = 1), antiasthmatic (n = 1), and a genetic disorder agent (n = 1). Several of these drugs inhibited Histoplasma capsulatum and Paracoccidioides brasiliensis growth (15 and 20, respectively), while Fusarium solani was not affected by the drugs tested. Most drugs were fungistatic, but niclosamide presented fungicidal activity against the three dimorphic fungi tested. Cyclosporine affected morphology of Cryptococcus neoformans.

MAIN CONCLUSIONS

These drugs represent new alternatives to the development of more accessible and effective therapies to treat human fungal infections.

COVID-19-Associated Pulmonary Aspergillosis: A Single-Center Experience in Central Valley, California, January 2020-March 2021

Reports of coronavirus disease 2019 (COVID-19)-associated pulmonary aspergillosis (CAPA) have been widely published across the world since the onset of the pandemic with varying incidence rates. We retrospectively studied all patients with severe COVID-19 infection who were admitted to our tertiary care center′s intensive care units between January 2020 and March 2021, who also had respiratory cultures positive for Aspergillus species. Among a large cohort of 970 patients admitted to the ICU with severe COVID-19 infections during our study period, 48 patients had Aspergillus species growing in respiratory cultures. Based on the 2020 European Confederation of Medical Mycology and the International Society for Human and Animal Mycology (ECMM/ISHAM) consensus criteria, 2 patients in the study had proven CAPA, 9 had probable CAPA, and 37 had possible CAPA. The incidence of CAPA was 5%. The mean duration from a positive COVID-19 test to Aspergillus spp. being recovered from the respiratory cultures was 16 days, and more than half of the patients had preceding fever or worsening respiratory failure despite adequate support and management. Antifungals were given for treatment in 44% of the patients for a mean duration of 13 days. The overall mortality rate in our study population was extremely high with death occurring in 40/48 patients (83%).

Invasive Fungal Infections Complicating COVID-19: A Narrative Review

Invasive fungal infections (IFIs) can complicate the clinical course of COVID-19 and are associated with a significant increase in mortality, especially in critically ill patients admitted to an intensive care unit (ICU). This narrative review concerns 4099 cases of IFIs in 58,784 COVID-19 patients involved in 168 studies. COVID-19-associated invasive pulmonary aspergillosis (CAPA) is a diagnostic challenge because its non-specific clinical/imaging features and the fact that the proposed clinically diagnostic algorithms do not really apply to COVID-19 patients. Forty-seven observational studies and 41 case reports have described a total of 478 CAPA cases that were mainly diagnosed on the basis of cultured respiratory specimens and/or biomarkers/molecular biology, usually without histopathological confirmation. Candidemia is a widely described secondary infection in critically ill patients undergoing prolonged hospitalisation, and the case reports and observational studies of 401 cases indicate high crude mortality rates of 56.1% and 74.8%, respectively. COVID-19 patients are often characterised by the presence of known risk factors for candidemia such as in-dwelling vascular catheters, mechanical ventilation, and broad-spectrum antibiotics. We also describe 3185 cases of mucormycosis (including 1549 cases of rhino-orbital mucormycosis (48.6%)), for which the main risk factor is a history of poorly controlled diabetes mellitus (>76%). Its diagnosis involves a histopathological examination of tissue biopsies, and its treatment requires anti-fungal therapy combined with aggressive surgical resection/debridement, but crude mortality rates are again high: 50.8% in case reports and 16% in observational studies. The presence of other secondary IFIs usually diagnosed in severely immunocompromised patients show that SARS-CoV-2 is capable of stunning the host immune system: 20 cases of Pneumocystis jirovecii pneumonia, 5 cases of cryptococcosis, 4 cases of histoplasmosis, 1 case of coccidioides infection, 1 case of pulmonary infection due to Fusarium spp., and 1 case of pulmonary infection due to Scedosporium.

COVID-19-Associated Pulmonary Aspergillosis (CAPA)

Invasive Pulmonary Aspergillosis (IPA) has been recognized as a possible secondary infection complicating Coronavirus disease 2019 (COVID-19) and increasing mortality. The aim of this review was to report and summarize the available data in the literature concerning the incidence, pathophysiology, diagnosis, and treatment of COVID-19-Associated Pulmonary Aspergillosis (CAPA). Currently, the incidence of CAPA is unclear due to different definitions and diagnostic criteria used among the studies. It was estimated that approximately 8.6% (206/2383) of mechanically ventilated patients were diagnosed with either proven, probable, or putative CAPA. Classical host factors of invasive aspergillosis are rarely recognized in patients with CAPA, who are mainly immuno-competent presenting with comorbidities, while the role of steroids warrants further investigation. Direct epithelial injury and diffuse pulmonary micro thrombi in combination with immune dysregulation, hyper inflammatory response, and immunosuppressive treatment may be implicated. Discrimination between two forms of CAPA (e.g., tracheobronchial and parenchymal) is required, whereas radiological signs of aspergillosis are not typically evident in patients with severe COVID-19 pneumonia. In previous studies, the European Organization for Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG) criteria, a clinical algorithm to diagnose Invasive Pulmonary Aspergillosis in intensive care unit patients (AspICU algorithm), and influenza-associated pulmonary aspergillosis (IAPA) criteria were used for the diagnosis of proven/probable and putative CAPA, as well as the differentiation from colonization, which can be challenging. Aspergillus fumigatus is the most commonly isolated pathogen in respiratory cultures. Bronchoalveolar lavage (BAL) and serum galactomannan (GM), β-d-glucan (with limited specificity), polymerase chain reaction (PCR), and Aspergillus-specific lateral-flow device test can be included in the diagnostic work-up; however, these approaches are characterized by low sensitivity. Early treatment of CAPA is necessary, and 71.4% (135/189) of patients received antifungal therapy, mainly with voriconazole, isavuconazole, and liposomal amphotericin B . Given the high mortality rate among patients with Aspergillus infection, the administration of prophylactic treatment is debated. In conclusion, different diagnostic strategies are necessary to differentiate colonization from bronchial or parenchymal infection in intubated COVID-19 patients with Aspergillus spp. in their respiratory specimens vs. those not infected with severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). Following confirmation, voriconazole or isavuconazole should be used for the treatment of CAPA.

Comparing the clinical characteristics and outcomes of COVID-19-associate pulmonary aspergillosis (CAPA): a systematic review and meta-analysis

PURPOSE

Invasive pulmonary aspergillosis has been increasingly recognized in COVID-19 patients, termed COVID-19-associate pulmonary aspergillosis (CAPA). Our meta-analysis aims to assess the clinical characteristics and outcomes of patients diagnosed with CAPA compared to those without CAPA.

METHODS

We searched the Pubmed, Cochrane Library, SCOPUS, and Web of Science databases for studies published between January 1, 2020 and August 1, 2021, containing comparative data of patients diagnosed with CAPA and those without CAPA.

RESULTS

Eight cohort studies involving 729 critically ill COVID-19 patients with comparative data were included. CAPA patients were older (mean age 66.58 vs. 59.25 years; P = 0.007) and had underlying chronic obstructive pulmonary disease (COPD) (13.7 vs. 6.1%; OR 2.75; P = 0.05). No differences in gender, body mass index (BMI), and comorbidities of diabetes and cancer were observed. CAPA patients were more likely to receive long-term corticosteroid treatment (15.0 vs. 5.3%; OR 3.53; P = 0.03). CAPA patients had greater severity of illness based on sequential organ failure assessment (SOFA) score with a higher all-cause in-hospital mortality rate (42.6 vs. 26.5%; OR 3.39; P < 0.001) and earlier ICU admission from illness onset (mean 11.00 vs. 12.00 days; P = 0.003). ICU length of stay (LOS), invasive mechanical ventilation (IMV) duration, the requirement of inotropic support and renal replacement therapy were comparable between the two groups.

CONCLUSIONS

CAPA patients are typically older with underlying COPD and received long-term corticosteroid treatment. Furthermore, CAPA is associated with higher SOFA scores, mortality, and earlier onset of ICU admission from illness onset.

COVID-19-associated subacute invasive pulmonary aspergillosis

BACKGROUND

Though invasive pulmonary aspergillosis is a well known complication of COVID-19 pneumonia, indolent forms of aspergillosis have been rarely described.

METHODS

We prospectively collected the clinico-radio-microbiological data of 10 patients of subacute invasive pulmonary aspergillosis (SAIA), who presented to our hospital with recent history of COVID-19 pneumonia along with cavitary lung disease, positive IgG (against Aspergillus) with or without positive respiratory samples for Aspergillus spp.

RESULT

The mean age of presentation of SAIA was 50.7 ± 11.8 years. All the patients had recently recovered from severe COVID-19 illness with a mean duration of 29.2 ± 12 days from COVID-19 positivity. Cough was the predominant symptom seen in 8/10 (80%) patients followed by haemoptysis. 7/10 (70%) patients were known diabetic. While serum galactomannan was positive in 5/9 patients (55.5%), fungal culture was positive in 2/7 patients (28.5%) and polymerase chain reaction (PCR) for Aspergillus was positive in three patients. Eight (80%) patients presented with a single cavitary lesion; pseudoaneurysm of pulmonary artery was seen in two patients and post-COVID-19 changes were seen in all patients. All patients were treated with voriconazole, out of which four (40%) patients died during the follow-up period.

CONCLUSION

SAIA should be considered in the differential diagnosis of cavitating lung lesions in patients with recent history of COVID-19 in the background of steroid use with or without pre-existing diabetes.

Antifungal prophylaxis for prevention of COVID-19-associated pulmonary aspergillosis in critically ill patients: an observational study

BACKGROUND

Coronavirus disease 19 (COVID-19)-associated pulmonary aspergillosis (CAPA) emerged as important fungal complications in patients with COVID-19-associated severe acute respiratory failure (ARF). Whether mould active antifungal prophylaxis (MAFP) can prevent CAPA remains elusive so far.

METHODS

In this observational study, we included all consecutive patients admitted to intensive care units with COVID-19-associated ARF between September 1, 2020, and May 1, 2021. We compared patients with versus without antifungal prophylaxis with respect to CAPA incidence (primary outcome) and mortality (secondary outcome). Propensity score adjustment was performed to account for any imbalances in baseline characteristics. CAPA cases were classified according to European Confederation of Medical Mycology (ECMM)/International Society of Human and Animal Mycoses (ISHAM) consensus criteria.

RESULTS

We included 132 patients, of whom 75 (57%) received antifungal prophylaxis (98% posaconazole). Ten CAPA cases were diagnosed, after a median of 6 days following ICU admission. Of those, 9 CAPA cases were recorded in the non-prophylaxis group and one in the prophylaxis group, respectively. However, no difference in 30-day ICU mortality could be observed. Thirty-day CAPA incidence estimates were 1.4% (95% CI 0.2-9.7) in the MAFP group and 17.5% (95% CI 9.6-31.4) in the group without MAFP (p = 0.002). The respective subdistributional hazard ratio (sHR) for CAPA incidence comparing the MAFP versus no MAFP group was of 0.08 (95% CI 0.01-0.63; p = 0.017).

CONCLUSION

In ICU patients with COVID-19 ARF, antifungal prophylaxis was associated with significantly reduced CAPA incidence, but this did not translate into improved survival. Randomized controlled trials are warranted to evaluate the efficacy and safety of MAFP with respect to CAPA incidence and clinical outcomes.

Induced pluripotent stem cell-based disease modeling and prospective immune therapy for coronavirus disease 2019

The emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic poses a never before seen challenge to human health and the economy. Considering its clinical impact, with no streamlined therapeutic strategies in sight, it is crucial to understand the infection process of SARS-CoV-2. Our limited knowledge of the mechanisms underlying SARS-CoV-2 infection impedes the development of alternative therapeutics to address the pandemic. This aspect can be addressed by modeling SARS-CoV-2 infection in the human context to facilitate drug screening and discovery. Human induced pluripotent stem cell (iPSC)-derived lung epithelial cells and organoids recapitulating the features and functionality of the alveolar cell types can serve as an in vitro human model and screening platform for SARS-CoV-2. Recent studies suggest an immune system asynchrony leading to compromised function and a decreased proportion of specific immune cell types in coronavirus disease 2019 (COVID-19) patients. Replenishing these specific immune cells may serve as useful treatment modality against SARS-CoV-2 infection. Here the authors review protocols for deriving lung epithelial cells, alveolar organoids and specific immune cell types, such as T lymphocytes and natural killer cells, from iPSCs with the aim to aid investigators in making relevant in vitro models of SARS-CoV-2 along with the possibility derive immune cell types to treat COVID-19.

Fungal Infections in COVID-19 Intensive Care Patients

Opportunistic fungal infections increase morbidity and mortality in COVID-19 patients monitored in intensive care units (ICU). As patients' hospitalization days in the ICU and intubation period increase, opportunistic infections also increase, which prolongs hospital stay days and elevates costs. The study aimed to describe the profile of fungal infections and identify the risk factors associated with mortality in COVID-19 intensive care patients. The records of 627 patients hospitalized in ICU with the diagnosis of COVID-19 were investigated from electronic health records and hospitalization files. The demographic characteristics (age, gender), the number of ICU hospitalization days and mortality rates, APACHE II scores, accompanying diseases, antibiotic-steroid treatments taken during hospitalization, and microbiological results (blood, urine, tracheal aspirate samples) of the patients were recorded. Opportunistic fungal infection was detected in 32 patients (5.10%) of 627 patients monitored in ICU with a COVID-19 diagnosis. The average APACHE II score of the patients was 28 ± 6. While 25 of the patients (78.12%) died, seven (21.87%) were discharged from the ICU. Candida parapsilosis (43.7%) was the opportunistic fungal agent isolated from most blood samples taken from COVID-19 positive patients. The mortality rate of COVID-19 positive patients with candidemia was 80%. While two out of the three patients (66.6%) for whom fungi were grown from their tracheal aspirate died, one patient (33.3%) was transferred to the ward. Opportunistic fungal infections increase the mortality rate of COVID-19-positive patients. In addition to the risk factors that we cannot change, invasive procedures should be avoided, constant blood sugar regulation should be applied, and unnecessary antibiotics use should be avoided.

Mortality in critically ill patients with coronavirus disease 2019-associated pulmonary aspergillosis: A systematic review and meta-analysis

Reports of COVID-19 associated pulmonary aspergillosis (CAPA) are rising, but the associated mortality and factors affecting it are not well-characterised. We performed a systematic review including 20 peer-reviewed English language studies reporting mortality in CAPA published till 18 February 2021from PubMed, Ovid SP, Web of Science, Embase and CINHAL. The pooled mortality in CAPA was 51.2% (95% CI: 43.1-61.1, I2  = 38%). The leave one out sensitivity analysis and influential case diagnostics revealed one outlier and its exclusion resulted in a mortality estimate of 54% (95% CI: 45-62). Higher odds of mortality: 2.83 (95% CI: 1.8-4.5) were seen in CAPA compared to controls. No significant difference in various subgroups according to the country of study, the continent of study, income category of country and quality of the included study was seen. None of the host risk factors, mycological test results, therapy for COVID-19 and antifungal therapy affected mortality. Thus, patients with CAPA have a high probability of mortality and early diagnosis with prompt therapy must be ensured to optimally manage these patients. However, more prospective studies with global and multi-centre coordination may help to address CAPA in a better way.

Risk factors and outcome of pulmonary aspergillosis in critically ill coronavirus disease 2019 patients-a multinational observational study by the European Confederation of Medical Mycology

Objectives

Coronavirus disease 2019 (COVID-19) -associated pulmonary aspergillosis (CAPA) has emerged as a complication in critically ill COVID-19 patients. The objectives of this multinational study were to determine the prevalence of CAPA in patients with COVID-19 in intensive care units (ICU) and to investigate risk factors for CAPA as well as outcome.

Methods

The European Confederation of Medical Mycology (ECMM) conducted a multinational study including 20 centres from nine countries to assess epidemiology, risk factors and outcome of CAPA. CAPA was defined according to the 2020 ECMM/ISHAM consensus definitions.

Results

A total of 592 patients were included in this study, including 11 (1.9%) patients with histologically proven CAPA, 80 (13.5%) with probable CAPA, 18 (3%) with possible CAPA and 483 (81.6%) without CAPA. CAPA was diagnosed a median of 8 days (range 0–31 days) after ICU admission predominantly in older patients (adjusted hazard ratio (aHR) 1.04 per year; 95% CI 1.02–1.06) with any form of invasive respiratory support (HR 3.4; 95% CI 1.84–6.25) and receiving tocilizumab (HR 2.45; 95% CI 1.41–4.25). Median prevalence of CAPA per centre was 10.7% (range 1.7%–26.8%). CAPA was associated with significantly lower 90-day ICU survival rate (29% in patients with CAPA versus 57% in patients without CAPA; Mantel–Byar p < 0.001) and remained an independent negative prognostic variable after adjusting for other predictors of survival (HR 2.14; 95% CI 1.59–2.87, p ≤ 0.001).

Conclusion

Prevalence of CAPA varied between centres. CAPA was significantly more prevalent among older patients, patients receiving invasive ventilation and patients receiving tocilizumab, and was an independent strong predictor of ICU mortality.

Epidemiology of Systemic Mycoses in the COVID-19 Pandemic

The physiopathologic characteristics of COVID-19 (high levels of inflammatory cytokines and T-cell reduction) promote fungal colonization and infection, which can go unnoticed because the symptoms in both diseases are very similar. The objective of this work was to study the current epidemiology of systemic mycosis in COVID-19 times. A literature search on the subject (January 2020–February 2021) was performed in PubMed, Embase, Cochrane Library, and LILACS without language restrictions. Demographic data, etiological agent, risk factors, diagnostic methods, antifungal treatment, and fatality rate were considered. Eighty nine publications were found on co-infection by COVID-19 and pneumocystosis, candidiasis, aspergillosis, mucormycosis, coccidioidomycosis, or histoplasmosis. In general, the co-infections occurred in males over the age of 40 with immunosuppression caused by various conditions. Several species were identified in candidiasis and aspergillosis co-infections. For diagnosis, diverse methods were used, from microbiological to molecular. Most patients received antifungals; however, the fatality rates were 11–100%. The latter may result because the clinical picture is usually attributed exclusively to SARS-CoV-2, preventing a clinical suspicion for mycosis. Diagnostic tests also have limitations beginning with sampling. Therefore, in the remainder of the pandemic, these diagnostic limitations must be overcome to achieve a better patient prognosis.