Pulmonary Aspergillosis After Covid-19, A Case Report (preprint)

This study presents a 57-year-old male patient with COVID-19 who had had no lung disease before COVID-19 pneumonia. However, after COVID-19 pneumonia with sequels and treatments that include corticosteroids and IL-6 receptor antagonists, an invasive pulmonary aspergillus (IPA) cavity occurred immediately.

Impact of Aspergillus PCR on the Management of Invasive Aspergillosis: A Tertiary-care Hospital Experience during the COVID-19 Pandemic (preprint)

In this study, we investigated whether Aspergillus polymerase chain reaction (PCR) test had any effect on the management of invasive aspergillosis (IA) in routine patient management, retrospectively. A total of 293 Aspergillus PCR tests were performed in 235 patients between November 2020 and April 2022. One hundred and eighty-nine (80.4%) patients were hospitalized in the intensive care unit, and 142 (60.4%) were positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the day of Aspergillus PCR request. Only 21 (7.2%) samples were bronchoalveolar lavage (BAL) fluid; the remaining were non-bronchoscopic lavage (NBL) fluid (n = 156, 53.2%), and sputum (n = 116, 39.6%). Aspergillus PCR was positive in 35 (11.9%) samples. Twenty-six patients were diagnosed with IA (1 proven, 6 probable, 19 possible) according to the EORTC/MSG criteria, and nine SARS-CoV-2 infected patients with no host factor were diagnosed with coronavirus disease 2019 (COVID-19) associated pulmonary aspergillosis (8 probable, 1 possible) according to ECMM/ISHAM criteria when PCR testing was excluded. Although positive PCR result did not change the IA diagnostic category of any patient, substantial agreement was found between galactomannoprotein antigen and PCR tests in BAL fluid (87.5%) and moderate agreement in NBL fluid (81.8%), with Cohen's kappa values of 0.714 and 0.506, respectively (p < 0.05 for both). A total of 22 patients (62.9%) who met at least probable or possible IA criteria received antifungal treatment, whereas 32 patients who received antifungal treatment did not meet any of the consensus criteria for IA; 9 of them received treatment with a positive Aspergillus PCR result. In conclusion, we observed a limited impact of Aspergillus PCR on treatment decisions for IA in a period when bronchoscopy was avoided due to COVID-19 and PCR results were not readily available for a cost-effective and appropriate use of Aspergillus PCR, it might be beneficial to establish an institutional diagnostic algorithm.

Fungal pleural infection due to Microascus gracilis with pulmonary aspergillosis after COVID-19 pneumonia (preprint)

Background: Scopulariopsis/Microascus is a rare but devastating pathogen due to its intrinsic resistance to nearly all available antifungal agents. Microascus gracilis, an ascomycetous mould in the order Microascales, family Microascaceae, has recently emerged as a significant invasive pathogen causing opportunistic infections. Objectives and Methods: We present a case of pleural infection caused by M. gracilis with pulmonary aspergillosis in an immunocompromised man after COVID-19 pneumonia. To further understand the characteristics of the pathogen isolated from the patient, we identified the strain through mycological characteristics, matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MALDI-TOF MS) and internal transcribed spacer (ITS)-based sequencing, and performed in vitro drug susceptibility testing against common antifungal agents. Moreover, we assessed lymphocyte subsets and programmed cell death protein 1 (PD-1) expression in peripheral blood and pleural effusion to monitor the efficacy of therapy with thymosin-α-1 and intravenous immunoglobulin. Results: Filamentous fungi isolated from pleural fluid were identified as M. gracilis based on classical morphology, mass spectrometry and molecular biology methods. The susceptibility results in vitro revealed that multiple antifungal agents were inactive against the strain. Adjuvant immunomodulatory treatment successfully increased the levels of CD3+ T and CD4+ T cells while decreasing the levels of CD3+PD-1+ and CD4+PD-1+ T cells in both peripheral blood and pleural effusion. Conclusions: The immunocompromised host with opportunistic M. gracilis infection, rapid and accurate recognition through direct microscopic testing with calcofluor white and MOLDI-TOF MS, is the key to achieving a definite diagnosis, and a combination of antifungal therapy with immunomodulatory therapy is vital for improving survival.

Genomic epidemiology of European Aspergillus fumigatus causing COVID-19-associated pulmonary aspergillosis in Europe (preprint)

The opportunistic fungus Aspergillus fumigatus has been found to cause coinfections in patients with severe SARS-CoV-2 virus infection, leading to COVID-19-associated pulmonary aspergillosis (CAPA). The CAPA all-cause mortality rate is approximately 50% and may be complicated by azole-resistance. Genomic epidemiology can help shed light on the genetics of A. fumigatus causing CAPA including the prevalence of alleles that are associated with azole-resistance. Here, a population genomic analysis of 21 CAPA isolates from four European countries is presented. The CAPA isolates were compared with A. fumigatus from a wider population of 167 non-CAPA clinical isolates and 73 environmental isolates. Bioinformatic analysis and antifungal susceptibility testing were performed to quantify resistance and identify possible genetically-encoded azole-resistant mechanisms. Phylogenetic analysis of the 21 CAPA isolates showed a lack of genetic distinction from the wider A. fumigatus population, with isolates distributed within two distinct clades (A and B), with the majority of the CAPA isolates in clade B (71.4%). The prevalence of phenotypic azole-resistance in CAPA was 14.3% (n=3/21); all three CAPA isolates contained a known resistance-associated cyp51A polymorphism. CAPA isolates are drawn from the wider A. fumigatus population rather than forming a unique genetic background showing that COVID-19 patients are susceptible to the entire A. fumigatus population. However, the relatively high prevalence of azole-resistance alleles that we document poses a threat to treatment success rates, warranting enhanced detection and surveillance of A. fumigatus genotypes in these patients. Furthermore, potential changes to antifungal first-line treatment guidelines may be needed to improve patient outcomes.

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.

Autopsy Findings of Severe COVID-19 Pneumonia Combined with Pulmonary Aspergillosis, Pneumothorax, and Pulmonary Thromboembolisms.

BACKGROUND COVID-19-associated pulmonary aspergillosis (CAPA), acute respiratory distress syndrome (ARDS), pulmonary thromboembolism (PTE), and pneumothorax are complications in severe COVID-19 patients. CASE REPORT A 64-year-old Japanese man was diagnosed with COVID-19. His past medical history included uncontrolled diabetes mellitus. He had no vaccination for COVID-19. Despite oxygen inhalation, remdesivir, dexamethasone (6.6 mg per day), and baricitinib (4 mg per day for 12 days), the disease progressed. The patient was supported with mechanical ventilation. Dexamethasone was switched to methylprednisolone (1000 mg per day for 3 days, and then reduced by half every 3 days), and intravenous heparin was initiated. Voriconazole (800 mg on the first day and then 400 mg per day for 14 days) was also started because Aspergillus fumigatus was detected in intratracheal sputum. However, he died of respiratory failure. Pathological findings of autopsy showed: (1) diffuse alveolar damage in a wide area of the lungs, which is consistent with ARDS due to COVID-19 pneumonia, (2) PTEs in peripheral pulmonary arteries, (3) CAPA, and (4) pneumothorax induced by CAPA. These conditions were all active states, suggesting that the treatments were insufficient. CONCLUSIONS Autopsy revealed active findings of ARDS, PTEs, and CAPA in a severe COVID-19 patient despite heavy treatment for each condition. CAPA can be a cause of pneumothorax. It is not easy to improve these conditions simultaneously because their treatments can induce antagonizing biological actions. To prevent severe COVID-19, it is important to reduce risk factors, such as by vaccination and appropriate blood glucose control.

Assessing the safety profile of voriconazole use in suspected COVID-19-associated pulmonary aspergillosis-a two-centre observational study.

The decision to use voriconazole for suspected COVID-19-associated pulmonary aspergillosis (CAPA) is based on clinical judgement weighed against concerns about its potential toxicity. We assessed the safety profile of voriconazole for patients with suspected CAPA by conducting a retrospective study of patients across two intensive care units. We compared changes in any liver enzymes or bilirubin and any new or increasing corrected QT interval (QTc) prolongation following voriconazole use to patient baseline to indicate possible drug effect. In total, 48 patients with presumed CAPA treated with voriconazole were identified. Voriconazole therapy was administered for a median of 8 days (interquartile range [IQR] 5-22) and the median level was 1.86 mg/L (IQR 1.22-2.94). At baseline, 2% of patients had a hepatocellular injury profile, 54% had a cholestatic injury profile, and 21% had a mixed injury profile. There were no statistically significant changes in liver function tests over the first 7 days after voriconazole initiation. At day 28, there was a significant increase in alkaline phospahte only (81-122 U/L, P = 0.006), driven by changes in patients with baseline cholestatic injury. In contrast, patients with baseline hepatocellular or mixed injury had a significant decrease in alanine transaminase and aspartate transaminase. Baseline QTc was 437 ms and remained unchanged after 7 days of voriconazole therapy even after sensitivity analysis for concomitantly administered QT prolonging agents. Therefore, at the doses used in this study, we did not detect evidence of significant liver or cardiac toxicity related to voriconazole use. Such information can be used to assist clinicians in the decision to initiate such treatment.

Our study did not show significant voriconazole-related liver or cardiac side effects in a critically ill cohort of patients with suspected COVID-19-associated pulmonary aspergillosis. These findings may allay specific clinician concerns when commencing therapy for such patients.

Mycobiome analyses of critically ill COVID-19 patients suggests antifungal prophylaxis may be protective against A. fumigatus-associated mortality (preprint)

Rationale: Covid-associated pulmonary aspergillosis (CAPA) is a life-threatening complication in patients with severe COVID -19. Previously, acute respiratory distress syndrome in patients with COVID-19 has been associated with lung fungal dysbiosis, evidenced by reduced microbial diversity and Candida colonisation. Increased fungal burden in the lungs of critically ill COVID-19 patients is linked to prolonged mechanical ventilation and increased mortality. However, specific mycobiome signatures associated with severe COVID-19 in the context of survival and antifungal drug prophylaxis have not yet been determined and such knowledge could have an important impact on treatment. Objectives: To understand the composition of the respiratory mycobiome in critically ill COVID -19 patients with and without CAPA, the impact of antifungal use and its role in patient outcome. Methods: We performed a multi-national study of 39 COVID-19 patients in intensive care units (ICU) with and without CAPA. Respiratory mycobiome was profiled using ITS1 sequencing and Aspergillus fumigatus burden was further validated using qPCR. Fungal communities were investigated using alpha diversity, beta diversity, taxa prevalence and taxa abundances. Measurements and Main Results: Respiratory mycobiomes were dominated by Candida and Aspergillus. There was no significant association with corticosteroid use or CAPA diagnosis and respiratory fungal communities. Increased A. fumigatus burden was associated with mortality. The use of antifungals at ICU admission was associated with an absence of A. fumigatus. Conclusions: Our findings suggest that systemic antifungal treatment at ICU admission may be protective against A. fumigatus-associated mortality in CAPA.

Can bronchial secretion cultures identify the etiologic agent of COVID-19-associated pulmonary aspergillosis in ICU patients? Comparison with a species-specific Aspergillus PCR in serum.

Aspergillus spp. isolated from non-BAL cultures of coronavirus disease 2019 (COVID-19)-associated pulmonary aspergillosis (CAPA) patients may reflect colonization rather than infection. Sera (n = 181) from 49 adult ICU CAPA patients (24 probable and 25 possible CAPA) with bronchial secretions (BS) culture positive for Aspergillus spp. were collected and tested for Aspergillus DNA detection by species-specific real-time PCR. Overall, 30/49 (61%) patients were PCR positive. BS culture/serum PCR agreement was moderate (21/30; 70%). Based on serum PCR positive patients, all CAPAs were due to A. fumigatus (80%), A. flavus (10%), and A. terreus (10%). No A. niger/A. nidulans or mixed infections were found despite positive BS cultures.

Discordant results were observed between bronchial secretion cultures and species-specific serum PCR (30%) with A. fumigatus being by far the most common etiological agent of CAPA (80%). No A. niger/A. nidulans or mixed infections were found despite positive cultures.

Liposomal amphotericin B-the future.

Advances in medicine have led to a growing number of people with compromised or suppressed immune systems who are susceptible to invasive fungal infections. In particular, severe fungal infections are becoming increasingly common in ICUs, affecting people within and outside of traditional risk groups alike. This is exemplified by the emergence of severe viral pneumonia as a significant risk factor for invasive pulmonary aspergillosis, and the recognition of influenza-associated pulmonary aspergillosis and, more recently, COVID-19-associated pulmonary aspergillosis. The treatment landscape for haematological malignancies has changed considerably in recent years, and some recently introduced targeted agents, such as ibrutinib, are increasing the risk of invasive fungal infections. Consideration must also be given to the risk of drug-drug interactions between mould-active azoles and small-molecule kinase inhibitors. At the same time, infections caused by rare moulds and yeasts are increasing, and diagnosis continues to be challenging. There is growing concern about azole resistance among both moulds and yeasts, mandating continuous surveillance and personalized treatment strategies. It is anticipated that the epidemiology of fungal infections will continue to change and that new populations will be at risk. Early diagnosis and appropriate treatment remain the most important predictors of survival, and broad-spectrum antifungal agents will become increasingly important. Liposomal amphotericin B will remain an essential therapeutic agent in the armamentarium needed to manage future challenges, given its broad antifungal spectrum, low level of acquired resistance and limited potential for drug-drug interactions.

Targeting Sterylglucosidase A to Treat Aspergillus fumigatus Infections.

Invasive fungal infections are a leading cause of death in immunocompromised patients. Current therapies have several limitations, and innovative antifungal agents are critically needed. Previously, we identified the fungus-specific enzyme sterylglucosidase as essential for pathogenesis and virulence of Cryptococcus neoformans and Aspergillus fumigatus (Af) in murine models of mycoses. Here, we developed Af sterylglucosidase A (SglA) as a therapeutic target. We identified two selective inhibitors of SglA with distinct chemical scaffolds that bind in the active site of SglA. Both inhibitors induce sterylglucoside accumulation and delay filamentation in Af and increase survival in a murine model of pulmonary aspergillosis. Structure-activity relationship (SAR) studies identified a more potent derivative that enhances both in vitro phenotypes and in vivo survival. These findings support sterylglucosidase inhibition as a promising antifungal approach with broad-spectrum potential. IMPORTANCE Invasive fungal infections are a leading cause of death in immunocompromised patients. Aspergillus fumigatus is a fungus ubiquitously found in the environment that, upon inhalation, causes both acute and chronic illnesses in at-risk individuals. A. fumigatus is recognized as one of the critical fungal pathogens for which a substantive treatment breakthrough is urgently needed. Here, we studied a fungus-specific enzyme, sterylglucosidase A (SglA), as a therapeutic target. We identified selective inhibitors of SglA that induce accumulation of sterylglucosides and delay filamentation in A. fumigatus and increase survival in a murine model of pulmonary aspergillosis. We determined the structure of SglA, predicted the binding poses of these inhibitors through docking analysis, and identified a more efficacious derivative with a limited SAR study. These results open several exciting avenues for the research and development of a new class of antifungal agents targeting sterylglucosidases.

Optimal control for co-infection with COVID-19-Associated Pulmonary Aspergillosis in ICU patients with environmental contamination.

In this paper, we propose a mathematical model for COVID-19-Associated Pulmonary Aspergillosis (CAPA) co-infection, that enables the study of relationship between prevention and treatment. The next generation matrix is employed to find the reproduction number. We enhanced the co-infection model by incorporating time-dependent controls as interventions based on Pontryagin's maximum principle in obtaining the necessary conditions for optimal control. Finally, we perform numerical experiments with different control groups to assess the elimination of infection. In numerical results, transmission prevention control, treatment controls, and environmental disinfection control provide the best chance of preventing the spread of diseases more rapidly than any other combination of controls.

Superinfections in COVID-19 patients receiving extracorporeal membrane oxygenation support.

BACKGROUND: The risk of superinfections and associations with mortality among patients with corona virus disease 2019 (COVID-19) receiving veno-venous extracorporeal membrane oxygenation (VV-ECMO) is poorly elucidated. METHOD: We identified all patients with COVID-19 treated with VV-ECMO >24 h at Rigshospitalet, Denmark from March 2020 to December 2021. Data were obtained by review of medical files. Associations between superinfections and mortality were assessed by logistic regression analyses adjusted for sex and age. RESULTS: Fifty patients, median age 53 years (interquartile range [IQR] 45-59), 66% male, were included. Median time on VV-ECMO was 14.5 days (IQR 6.3-23.5), 42% were discharged from hospital alive. Bacteremia, ventilator associated pneumonia (VAP), invasive candidiasis, pulmonary aspergillosis, herpes simplex virus, and cytomegalovirus (CMV) were detected in 38%, 42%, 12%, 12%, 14%, and 20% of patients, respectively. No patients with pulmonary aspergillosis survived. CMV was associated with increased risk of death, odds ratio 12.6 (95% confidence interval 1.9-257, p = .05), whereas we found no associations between other superinfections and risk of death. CONCLUSION: Bacteremia and VAP are common but does not seem to affect mortality, whereas pulmonary aspergillosis and CMV are associated with poor prognosis among COVID-19 patients treated with VV-ECMO.

Pulmonary aspergillosis: diagnosis and treatment.

Aspergillus species are the most frequent cause of fungal infections of the lungs with a broad spectrum of clinical presentations including invasive pulmonary aspergillosis (IPA) and chronic pulmonary aspergillosis (CPA). IPA affects immunocompromised populations, which are increasing in number and diversity with the advent of novel anti-cancer therapies. Moreover, IPA has emerged as a complication of severe influenza and coronavirus disease 2019 in apparently immunocompetent hosts. CPA mainly affects patients with pre-existing lung lesions and is recognised increasingly frequently among patients with long-term survival following cure of tuberculosis or lung cancer. The diagnosis of pulmonary aspergillosis is complex as it relies on the presence of clinical, radiological and microbiological criteria, which differ according to the type of pulmonary aspergillosis (IPA or CPA) and the type of patient population. The management of pulmonary aspergillosis is complicated by the limited number of treatment options, drug interactions, adverse events and the emergence of antifungal resistance.

A 64-Year-Old Man Hospitalized for COVID-19 Pneumonia and Treated with Tocilizumab Who Developed Chronic Cavitary Pulmonary Aspergillosis.

BACKGROUND The management of (Coronavirus disease 2019) COVID-19 pneumonia is ever-evolving. Tocilizumab, a monoclonal antibody against interleukin-6 (IL-6) receptor, have known mortality benefit in severe COVID-19 pneumonia, but data are limited regarding safety. Attributable to the immunomodulatory nature of this medication, patients may be at risk for opportunistic infections, including chronic cavitary pulmonary aspergillosis (CPPA), a slowly progressive disease characterized pulmonary infiltrates and often a newly-formed cavity. However, current guidelines do not emphasize post-treatment surveillance of patients for opportunistic infections, including CPPA. CASE REPORT We present a particular case of a 64-year-old man treated for COVID-19 pneumonia with Tocilizumab and dexamethasone who developed cavitary pulmonary aspergillosis. He presented to the emergency department with hemoptysis, associated with worsening productive cough, shortness of breath, and weight loss. Computed tomography (CT) of the chest showed areas of focal consolidation and a cavitary lung lesion within the left upper lobe. Sputum culture was positive for Aspergillus niger. The patient received a long course of oral triazole therapy for CPPA, with clinical improvement. CT scan of the chest at 9 months showed that the Itraconazole therapy was effective in resolving the extensive airspace disease and decreasing the size of the upper-lobe cavity and fungal ball. CONCLUSIONS This article illustrates the possibility of a serious infection such as CCPA as an adverse effect of Tocilizumab treatment, especially with concurrent immunosuppressive therapy. Furthermore, this case highlights the importance of regular monitoring of patients who have received Tocilizumab therapy to ensure that early signs of opportunistic infections such as CPPA are detected and treated promptly to prevent permanent lung damage.

Effect of glucocorticoids on the development of COVID-19-associated pulmonary aspergillosis: a meta-analysis of 21 studies and 5174 patients (preprint)

Objective: COVID-19-associated pulmonary aspergillosis (CAPA) remains a high mortality mycotic infection throughout the pandemic, and glucocorticoids (GCs) may be its root cause. We aimed to evaluate the effect of systemic GC treatment on the development of CAPA. Methods: We systematically searched the PubMed, Google Scholar, Scopus, and Embase databases to collect eligible studies published until December 31, 2022. The pooled outcome of CAPA development was calculated as the log odds ratio (LOR) with 95% confidence intervals (CI) using a random effect model. Results: A total of 21 studies with 5174 patients were included. Of these, 20 studies with 4675 patients consisting of 2565 treated with GC but without other immunomodulators (GC group) and 2110 treated without GC and other immunomodulators (controls) were analyzed. The pooled LOR of CAPA development was higher for the GC group than for the control group (0.54; 95% CI: 0.22, 0.86; p<0.01). In the subgroups, the pooled LOR was higher for high-dose GC (0.90; 95% CI: 0.17, 1.62: p=0.01) and dexamethasone (0.71; 95% CI: 0.35, 1.07; p<0.01)-treated patients, but there was no significant difference for low-dose GC (0.41; 95% CI: -0.07, 0.89; p=0.09)- and non-dexamethasone GC (0.21; 95% CI: -0.36, 0.79; p=0.47)-treated patients versus controls. Conclusion: GC treatment increased the risk of CAPA development, and the risk was associated with the use of high-dose GC or dexamethasone therapy.