A national strategy to diagnose COVID-19 associated invasive fungal disease in the ICU

Aspergillus fumigatus escape mechanisms from its harsh survival environments

Aspergillus fumigatus is a ubiquitous pathogenic mold and causes several diseases, including mycotoxicosis, allergic reactions, and systemic diseases (invasive aspergillosis), with high mortality rates. In its ecological niche, the fungus has evolved and mastered many reply strategies to resist and survive against negative threats, including harsh environmental stress and deficiency of essential nutrients from natural environments, immunity responses and drug treatments in host, and competition from symbiotic microorganisms. Hence, treating A. fumigatus infection is a growing challenge. In this review, we summarized A. fumigatus reply strategies and escape mechanisms and clarified the main competitive or symbiotic relationships between A. fumigatus, viruses, bacteria, or fungi in host microecology. Additionally, we discussed the contemporary drug repertoire used to treat A. fumigatus and the latest evidence of potential resistance mechanisms. This review provides valuable knowledge which will stimulate further investigations and clinical applications for treating and preventing A. fumigatus infections. KEY POINTS: • Harsh living environment was a great challenge for A. fumigatus survival. • A. fumigatus has evolved multiple strategies to escape host immune responses. • A. fumigatus withstands antifungal drugs via intrinsic escape mechanisms.

COVID-19 vs. non-COVID-19 related nosocomial pneumonias: any differences in etiology, prevalence, and mortality?

PURPOSE OF REVIEW

This review explores the similarities and differences between coronavirus disease 2019 (COVID-19)-related and non-COVID-related nosocomial pneumonia, particularly hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP). It critically assesses the etiology, prevalence, and mortality among hospitalized patients, emphasizing the burden of these infections during the period before and after the severe acute respiratory syndrome coronavirus 2 pandemic.

RECENT FINDINGS

Recent studies highlight an increase in nosocomial infections during the COVID-19 pandemic, with a significant rise in cases involving severe bacterial and fungal superinfections among mechanically ventilated patients. These infections include a higher incidence of multidrug-resistant organisms (MDROs), complicating treatment and recovery. Notably, COVID-19 patients have shown a higher prevalence of VAP than those with influenza or other respiratory viruses, influenced by extended mechanical ventilation and immunosuppressive treatments like corticosteroids.

SUMMARY

The findings suggest that COVID-19 has exacerbated the frequency and severity of nosocomial infections, particularly VAP. These complications not only extend hospital stays and increase healthcare costs but also lead to higher morbidity and mortality rates. Understanding these patterns is crucial for developing targeted preventive and therapeutic strategies to manage and mitigate nosocomial infections during regular or pandemic care.

Prevalence and prognostic relevance of invasive fungal disease during veno-arterial ECMO: A retrospective single-center study

PURPOSE

To assess the prevalence and relevance of invasive fungal disease (IFD) during veno-arterial (V-A) extracorporeal membrane oxygenation (ECMO).

METHODS

Retrospective analysis from January 2013 to November 2023 of adult V-A ECMO cases at a German University Hospital. Parameters relating to IFD, demographics, length of stay (LoS), days on ECMO and mechanical ventilation, prognostic scores and survival were assessed. Multivariable logistic regression analyses with IFD and death as dependent variables were performed. Outcome was assessed after propensity score matching IFD-patients to non-IFD-controls.

RESULTS

421 patients received V-A ECMO. 392 patients with full electronic datasets were included. The prevalence of IFD, invasive candidiasis and probable invasive pulmonary aspergillosis was 4.6%, 3.8% and 1.0%. Severity of acute disease, pre-existing moderate-to-severe renal disease and continuous kidney replacement therapy were predictive of IFD. In-hospital mortality (94% (17/18) compared to 67% (252/374) in non-IFD patients (p = 0.0156)) was predicted by female sex, SOFA score at admission, SAVE score and IFD (for IFD: OR: 8.31; CI: 1.60-153.18; p: 0.044). There was no difference in outcome after matching IFD-cases to non-IFD-controls.

CONCLUSIONS

IFD are detected in about one in 20 patients on V-A ECMO, indicating mortality >90%. However, IFD do not contribute to prognosis in this population.

High-Dose Corticosteroid Use in Severe to Critically Ill Patients With COVID-19: A Nationwide Population-Based Matched Cohort Study

BACKGROUND

Systemic corticosteroids have become the standard of care for severe to critically ill patients with coronavirus disease 2019 (COVID-19). However, the real-world efficacy and safety outcomes associated with a higher dose of corticosteroids remain uncertain.

METHODS

We conducted a nationwide, population-based, matched cohort study of severe to critically ill adult patients with COVID-19 between January 2020 and June 2021 in Korea using the National Health Information Database. Patients using systemic corticosteroids were included and high-dose corticosteroid use was defined as a daily mean prescribed dose of more than 6 mg of dexamethasone. We then employed a proportional hazard regression model to identify prognostic factors for 28-day all-cause mortality and conducted a Fine and Gray regression model to assess risk factors for developing COVID-19-associated pulmonary aspergillosis (CAPA).

RESULTS

During the study period, 102,304 patients with COVID-19 were screened, 5,754 met the eligibility criteria, and 2,138 were successfully matched. The mean prescribed daily dose was 4.2 mg and 13.4 mg in the standard- and high-dose groups, respectively, and the mean duration of use was not different between the groups. High-dose corticosteroid use independently increased all-cause mortality at 28 days (adjusted hazard ratio [aHR], 1.48; 95% confidence interval [CI], 1.25-1.76) and 90 days (aHR, 1.63; CI, 1.44-1.85) after admission. Subgroup analysis revealed a statistically significant elevation in the risk of mortality among patients using low-flow or high-flow nasal cannulas, with aHRs of 1.41 and 1.46, respectively. No significant impact of high-dose steroids was observed, even in patients who underwent mechanical ventilation at 28 days (aHR, 1.17; CI, 0.79-1.72). As a safety outcome, high-dose corticosteroid use showed an association with the development of CAPA (aHR, 2.97; 95% CI, 0.94-9.43).

CONCLUSION

Among severe to critically ill patients with COVID-19, high-dose corticosteroid use was associated with increased 28-day all-cause mortality and showed a trend toward the development of CAPA.

Investigation of risk factors for invasive pulmonary aspergillosis among patients with COVID-19

COVID-19 associated pulmonary aspergillosis (CAPA) had been reported, and raised concern about this secondary infection due to the high mortality. This study aimed to investigate the risk factors for CAPA. The enrolled 114 COVID-19 patients were further divided into CAPA group and non-CAPA group. Demographic characteristics, underlying diseases, laboratory parameters and therapeutic schedule between the two groups were compared to identify the independent risk factors for CAPA by univariate analysis and multivariable logistic regression analysis. Sensitivity and specificity of independent risk factors were confirmed by receiver operating characteristic (ROC) curve analysis. Univariate analysis showed that renal transplant, IL-6 and CRP levels, decreased CD4 + T cell and CD8 + T cell, duration of antibiotics therapy, and prolonged mechanical ventilation were risk factors for development of CAPA. These factors were further analyzed by multivariable logistic regression analysis and the results indicated that elevated IL-6 level, decreased CD4 + T cell and prolonged mechanical ventilation could be recognized as independent risk factors for CAPA in COVID-19 patients. Identification of these risk factors is essential to initiate antifungal therapy as soon as possible to improve outcome of patients with CAPA.

The Utility of Real-Time PCR, Metagenomic Next-Generation Sequencing, and Culture in Bronchoalveolar Lavage Fluid for Diagnosis of Pulmonary Aspergillosis

Timely detection of Aspergillus infection is crucial given the high mortality rate of pulmonary aspergillosis (PA). Here, the diagnostic performances for PA of mycological culture, Aspergillus real-time PCR, and metagenomic next-generation sequencing (mNGS) assay from bronchoalveolar lavage fluid, were evaluated. In total, 139 patients with suspected fungal pneumonia were enrolled between December 2021 and July 2023, collecting 139 bronchoalveolar lavage fluid samples for real-time PCR and culture, with 87 undergoing mNGS assay. The sensitivity, specificity, positive predictive value, negative predictive value, and area under the curve with 95% CIs of these assays for PA were as follows: 35.3% (14.2%-61.7%), 100.0% (94.0%-100.0%), 100.0% (54.1%-100.0%), 84.5% (79.3%-88.6%), and 0.676 (0.560-0.779), respectively, for culture; 82.4% (56.6%-96.2%), 98.3% (91.1%-100.0%), 93.3% (66.4%-99.0%), 95.2% (87.6%-98.2%), and 0.903 (0.815-0.959), respectively, for same diagnostic performance of real-time PCR and mNGS; and 94.1% (71.3%-99.9%), 96.7% (88.5%-99.6%), 88.9% (67.1%-96.9%), 98.3% (89.6%-99.7%), and 0.954 (0.880-0.989), respectively, for real-time PCR combining mNGS; real-time PCR, mNGS, and their combination significantly improved in area under the curve values over culture (P < 0.001), but real-time PCR testing and mNGS had no significant difference with each other and their combination. Overall, the performance of culture was limited by low sensitivity; both real-time PCR and mNGS assays as single diagnostic tests are promising compared with culture and combined tests.

Metagenomic next generation sequencing of bronchoalveolar lavage fluids for the identification of pathogens in patients with pulmonary infection: A retrospective study

Due to the limitations of traditional laboratory methods (TMs), identification of causative pathogens of numerous pulmonary infections (PIs) remains difficult. This study evaluated the value of metagenomic next generation sequencing (mNGS) in the identification of various respiratory pathogens. A total of 207 patients with TMs and mNGS data were collected for this retrospective study. TMs included sputum culture, blood, and bronchoalveolar lavage fluid (BALF) analysis, or polymerase chain reaction analysis of throat swabs. Otherwise, BALF was collected and analyzed using mNGS. For bacterial pathogens, sensitivities of mNGS as compared to TMs were 76.74 % and 58.14 % (P=0.012). For fungal pathogens, the detection rate of mNGS sensitivity was higher as compared to that of TMs (93.68 % vs 22.11 %; P<0.001). The positive predictive value and negative predictive value were also greater for mNGS. Use of mNGS for BALF analysis offers good specificity and thus facilitates to the clinical diagnosis of PIs.

Fungal coinfection/superinfection in COVID-19 patients in a tertiary hospital in Mexico

Introduction

Data on the prevalence of fungal coinfections/superinfections in patients with COVID-19 are limited.

Objective

To describe the prevalence of fungal coinfections/superinfections in patients with COVID-19, as well as risk factors and demographic, clinical, and microbiological characteristics.

Material and methods

We included patients with a confirmed COVID-19 diagnosis and a confirmed fungal infection hospitalized in the ICU from March 2020 to December 2021. We collected data on age, sex, comorbidities, hospital length of stay (days), laboratory (ferritin) and microbiological results, treatment for COVID-19, antifungal therapy, and outcomes obtained from the clinical records.

Results

Only 11 out of 740 patients met the inclusion criteria. The coinfection rate was 0.3% and the superinfection was 1.2%. The most affected population was male adults. The coinfections/superinfections diagnosed were candiduria and candidemia, caused by Candida albicans, C. tropicalis, C. glabrata, C. lusitaniae, and Kluyveromyces marxianus (C. kefyr). In addition, tracheobronchitis due to Aspergillus fumigatus was found. The most used antifungals were fluconazole and caspofungin. The lethality in patients with fungal coinfections was 50% and superinfections, 22%. The length of hospital stay was 11-65 days. Eight patients required mechanical ventilation and six received corticosteroids. The main comorbidity was diabetes mellitus (81.8%).

Conclusions

The rate of fungal coinfections/superinfections in COVID-19 patients was low, but the lethality found urges for routine fungal screening in patients with severe COVID-19 to timely detect fungal infections that may further compromise the patient’s life.

Clinical characteristics and outcomes of patients with candidemia during the COVID-19 pandemic: Insights from experience in the Omicron era

BACKGROUND

In Taiwan, COVID-19 outbreaks caused by the Omicron variant occurred in 2022. We investigated the incidence of candidemia during COVID-19 pandemic and the mortality of candidemia patients with COVID-19 in Taiwan.

METHODS

The incidence of candidemia and fluconazole susceptibility of Candida species before (2015-2019) and during COVID-19 pandemic (2020-2023) at Kaohsiung Chang Gung Memorial Hospital were investigated. The associated factors with mortality in candidemia patients during COVID-19 pandemic were analyzed. Candidemia patients who had COVID-19 within the prior 90 days (case group, n = 34) were propensity-score matched for age, ICU admission, and abdominal surgery in a 1:4 ratio with candidemia patients without COVID-19 (control group, n = 136).

RESULTS

Age (adjusted odds ratio [AOR] = 1.02, 95% CI: 1.01-1.03), ICU stay (AOR = 1.84, 95% CI: 1.29-2.62), higher Charlson comorbidity index (AOR = 1.08, 95% CI: 1.03-1.13), corticosteroid use (AOR = 1.50, 95% CI: 1.04-2.17) were associated with increased risk of mortality; abdominal surgery (AOR = 0.47, 95% CI: 0.29-0.74) and infected by Candida parapsilosis (AOR = 0.61, 95% CI: 0.38-0.98) were associated with decreased risk of mortality. After matching, there was no significant difference in mortality rates between the case and control groups. The incidence of candidemia increased from 196 to 278 patients/100,000 admissions during COVID-19 pandemic, while the causative species of candidemia and fluconazole susceptibility rates were similar.

CONCLUSION

While the incidence of candidemia increased during COVID-19 pandemic, there was no significant difference in mortality between candidemia patients with and without COVID-19 in the Omicron era.

Emerging Microorganisms and Infectious Diseases: One Health Approach for Health Shared Vision

Emerging infectious diseases (EIDs) are newly emerging and reemerging infectious diseases. The National Institute of Allergy and Infectious Diseases identifies the following as emerging infectious diseases: SARS, MERS, COVID-19, influenza, fungal diseases, plague, schistosomiasis, smallpox, tick-borne diseases, and West Nile fever. The factors that should be taken into consideration are the genetic adaptation of microbial agents and the characteristics of the human host or environment. The new approach to identifying new possible pathogens will have to go through the One Health approach and omics integration data, which are capable of identifying high-priority microorganisms in a short period of time. New bioinformatics technologies enable global integration and sharing of surveillance data for rapid public health decision-making to detect and prevent epidemics and pandemics, ensuring timely response and effective prevention measures. Machine learning tools are being more frequently utilized in the realm of infectious diseases to predict sepsis in patients, diagnose infectious diseases early, and forecast the effectiveness of treatment or the appropriate choice of antibiotic regimen based on clinical data. We will discuss emerging microorganisms, omics techniques applied to infectious diseases, new computational solutions to evaluate biomarkers, and innovative tools that are useful for integrating omics data and electronic medical records data for the clinical management of emerging infectious diseases.

A prediction model for secondary invasive fungal infection among severe SARS-CoV-2 positive patients in ICU

Background

The global COVID-19 pandemic has resulted in over seven million deaths, and IFI can further complicate the clinical course of COVID-19. Coinfection of COVID-19 and IFI (secondary IFI) pose significant threats not only to healthcare systems but also to patient lives. After the control measures for COVID-19 were lifted in China, we observed a substantial number of ICU patients developing COVID-19-associated IFI. This creates an urgent need for predictive assessment of COVID-19 patients in the ICU environment for early detection of suspected fungal infection cases.

Methods

This study is a single-center, retrospective research endeavor. We conducted a case-control study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive patients. The cases consisted of patients who developed any secondary IFI during their ICU stay at Jilin University China-Japan Union Hospital in Changchun, Jilin Province, China, from December 1st, 2022, to August 31st, 2023. The control group consisted of SARS-CoV-2 positive patients without secondary IFI. Descriptive and comparative analyses were performed, and a logistic regression prediction model for secondary IFI in COVID-19 patients was established. Additionally, we observed an increased incidence of COVID-19-associated pulmonary aspergillosis (CAPA) during this pandemic. Therefore, we conducted a univariate subgroup analysis on top of IFI, using non-CAPA patients as the control subgroup.

Results

From multivariate analysis, the prediction model identified 6 factors that are significantly associated with IFI, including the use of broad-spectrum antibiotics for more than 2 weeks (aOR=4.14, 95% CI 2.03-8.67), fever (aOR=2.3, 95%CI 1.16-4.55), elevated log IL-6 levels (aOR=1.22, 95% CI 1.04-1.43) and prone position ventilation (aOR=2.38, 95%CI 1.15-4.97) as independent risk factors for COVID-19 secondary IFI. High BMI (BMI ≥ 28 kg/m2) (aOR=0.85, 95% CI 0.75-0.94) and the use of COVID-19 immunoglobulin (aOR=0.45, 95% CI 0.2-0.97) were identified as independent protective factors against COVID-19 secondary IFI. The Receiver Operating Curve (ROC) area under the curve (AUC) of this model was 0.81, indicating good classification.

Conclusion

We recommend paying special attention for the occurrence of secondary IFI in COVID-19 patients with low BMI (BMI < 28 kg/m2), elevated log IL-6 levels and fever. Additionally, during the treatment of COVID-19 patients, we emphasize the importance of minimizing the duration of broad-spectrum antibiotic use and highlight the potential of immunoglobulin application in reducing the incidence of IFI.

Sodium Houttuyfonate Ameliorates DSS-induced Colitis Aggravated by Candida albicans through Dectin-1/NF-κB/miR-32-5p/NFKBIZ Axis Based on Intestinal microRNA Profiling

Our previous research indicated that Sodium houttuyfonate (SH) can effectively ameliorate dextran sulfate sodium (DSS)-induced colitis exacerbated by Candida albicans. However, the underlying protective mechanism of SH remains unclear. Therefore, in this study, a mice colitis model was infected with C. albicans, and the total colonic miRNAs were assessed. Furthermore, the differentially expressed miRNAs were enriched, clustered, and analyzed. Moreover, based on the dual luciferase analysis of NFKBIZ modulation by miR-32-5p, the in vitro and in vivo therapeutic effects of SH on inflammatory response, fungal burden, oxidative stress, and apoptosis were assessed at transcriptional and translational levels in the presence of agonist and antagonist. A total of 1157 miRNAs were identified, 84 of which were differentially expressed. Furthermore, qRT-PCR validated that SH treatment improved 17 differentially expressed miRNAs with > fourfold upregulation or > sixfold downregulation. Similar to most differentially altered miRNA, C. albicans significantly increased Dectin-1, NF-κB, TNF-α, IL-1β, IL-17A, and decreased miR-32-5p which negatively targeted NFKBIZ. In addition, SH treatment reduced inflammatory response and fungal burden in a colitis model with C. albicans infection. Further analyses indicated that in C. albicans infected Caco2 cells, SH inhibited fungal growth, oxidative stress, and apoptosis by increasing Dectin-1, NF-κB, NFKBIZ, TNF-α, IL-1β, IL-17A, and decreasing miR-32-5p. Therefore, SH can ameliorate the severity of colitis aggravated by C. albicans via the Dectin-1/NF-κB/miR-32-5p/NFKBIZ axis.

Demographic characteristics and risk factors for invasive fungal sinusitis in the context of COVID-19: A systematic review and meta-analysis

OBJECTIVES

To identify the demographic characteristics and potential risk factors of invasive fungal sinusitis (IFS) patients with Coronavirus Disease in 2019 (COVID-19).

METHODS

Web of Science, Embase, the Cochrane Library, and PubMed were searched from database inception to August 2023 using the combination of medical searching heading terms "invasive fungal sinusitis" and "COVID-19" and their free words. The research protocol was registered on PROSPERO (CRD42023467175).

RESULTS

A total of 53 studies were included. The mean age of IFS patients with COVID-19 was 53.72 (95% credible interval [CI]: 51.08, 56.36), with 66% males (95% CI: 0.62, 0.70), and 81% diabetes (95% CI: 0.77, 0.86). The mean time from COVID-19 diagnosis to IFS onset was 19.09 days (95% CI: 16.96, 21.22). The percentage of patients with COVID-19 PCR positivity was 33% (95% CI: 0.21, 0.45). Overall, 71% of patients receiving steroid therapy during COVID-19 infection (95% CI: 0.63, 0.78). The odds ratio of diabetes mellitus, steroid administration, and COVID-19 PCR positivity were 6.09, 2.21, and 1.82, respectively. COVID-19 infection did not affect the IFS stage.

CONCLUSION

IFS patients with COVID-19 had an average age of 53.72 years and were predominantly males, with a mean interval of 19.09 days from COVID-19 diagnosis to IFS onset. Diabetes, steroid administration, and COVID-19 PCR positivity were risk factors.

Invasive Fungal Infections in Inpatient Solid Organ Transplant Recipients With COVID-19: A Multicenter Retrospective Cohort

BACKGROUND

The prevalence and outcomes of COVID-19-associated invasive fungal infections (CAIFIs) in solid organ transplant recipients (SOTRs) remain poorly understood.

METHODS

A retrospective cohort study of SOTRs with COVID-19 admitted to 5 hospitals within Johns Hopkins Medicine was performed between March 2020 and March 2022. Cox regression multilevel mixed-effects ordinal logistic regression was used.

RESULTS

In the cohort of 276 SOTRs, 22 (8%) developed IFIs. The prevalence of CAIFIs was highest in lung transplant recipients (20%), followed by recipients of heart (2/28; 7.1%), liver (3/46; 6.5%), and kidney (7/149; 4.7%) transplants. In the overall cohort, only 42 of 276 SOTRs (15.2%) required mechanical ventilation; these included 11 of 22 SOTRs (50%) of the CAIFI group and 31 of 254 SOTRs (12.2%) of the no-CAIFI group. Compared with those without IFIs, SOTs with IFIs had worse outcomes and required more advanced life support (high-flow oxygen, vasopressor, and dialysis). SOTRs with CAIFIs had higher 1-y death-censored allograft failure (hazard ratio 1.6 5.1 16.4 , P  = 0.006) and 1-y mortality adjusting for oxygen requirement (adjusted hazard ratio 1.1 2.4 5.1 , P  < 0.001), compared with SOTRs without CAIFIs.

CONCLUSIONS

The prevalence of CAIFIs in inpatient SOTRs with COVID-19 is substantial. Clinicians should be alert to the possibility of CAIFIs in SOTRs with COVID-19, particularly those requiring supplemental oxygen, regardless of their intubation status.

The "COVID effect" in culture-based clinical microbiology: Changes induced by COVID-19 pandemic in a Hungarian tertiary care center

BACKGROUND

The presence of bacterial and fungal coinfections plays an important role in the mortality of patients with coronavirus 2019 (COVID-19). We compared data from the 3 years before and 3 years after the COVID-19 pandemic outbreak to evaluate its effect on the traits of bacterial and fungal diseases.

METHODS

We retrospectively collected and analyzed data on positive respiratory tract samples (n = 13,133 samples from 7717 patients) and blood cultures (n = 23,652 from 9653 patients) between 2017 and 2022 from the Clinical Center of the University of Szeged, Hungary. We also evaluated antimicrobial susceptibility test results derived from 169,020 respiratory samples and 549,729 blood cultures to gain insight into changes in antimicrobial resistance.

RESULTS

The most common respiratory pathogen in the pre-COVID era was Pseudomonas aeruginosa, whereas Candida albicans was the most frequent during the pandemic. The number of respiratory isolates of Acinetobacter baumannii was also markedly increased. In blood cultures, Staphylococcus epidermidis, Escherichia coli, and S. aureus were dominant during the study period, and A. baumannii was widespread in blood cultures during the pandemic years. Resistance to ofloxacin, penicillin, piperacillin-tazobactam, ceftazidime, cefepime, imipenem, ceftolozane-tazobactam, and itraconazole increased significantly in the COVID era.

CONCLUSIONS

During the COVID-19 pandemic, there were changes in the prevalence of respiratory and blood culture pathogens at the Clinical Center of the University of Szeged. C. albicans became the predominant respiratory pathogen, and the number of A. baumannii isolates increased dramatically. Additionally, antimicrobial resistance notably increased during this period.

Severe mold fungal infections in critically ill patients with COVID-19

The SARS-CoV-2 pandemic put an unprecedented strain on modern societies and healthcare systems. A significantly higher incidence of invasive fungal co-infections was noted compared with the pre-COVID-19 era, adding new diagnostic and therapeutic challenges in the critical care setting. In the current narrative review, we focus on invasive mold infections caused by Aspergillus and Mucor species in critically ill COVID-19 patients. We discuss up-to-date information on the incidence, pathogenesis, diagnosis and treatment of these mold-COVID-19 co-infections, as well as recommendations on preventive and prophylactic interventions. Traditional risk factors were often not recognized in COVID-19-associated aspergillosis and mucormycosis, highlighting the role of other determinant risk factors. The associated patient outcomes were worse compared with COVID-19 patients without mold co-infection.

An enhanced IL17 and muted type I interferon nasal epithelial cell state characterizes severe COVID-19 with fungal coinfection

Recent case reports and epidemiological data suggest that fungal infections represent an underappreciated complication among people with severe COVID-19. However, the frequency of fungal colonization in patients with COVID-19 and associations with specific immune responses in the airways remain incompletely defined. We previously generated a single-cell RNA-sequencing data set characterizing the upper respiratory microenvironment during COVID-19 and mapped the relationship between disease severity and the local behavior of nasal epithelial cells and infiltrating immune cells. Our previous study, in agreement with findings from related human cohorts, demonstrated that a profound deficiency in host immunity, particularly in type I and type III interferon signaling in the upper respiratory tract, is associated with rapid progression to severe disease and worse clinical outcomes. We have now performed further analysis of this cohort and identified a subset of participants with severe COVID-19 and concurrent detection of Candida species-derived transcripts within samples collected from the nasopharynx and trachea. Here, we present the clinical characteristics of these individuals. Using matched single-cell transcriptomic profiles of these individuals' respiratory mucosa, we identify epithelial immune signatures suggestive of IL17 stimulation and anti-fungal immunity. Further, we observe a significant expression of anti-fungal inflammatory cascades in the nasal and tracheal epithelium of all participants who went on to develop severe COVID-19, even among participants without detectable genetic material from fungal pathogens. Together, our data suggest that IL17 stimulation-in part driven by Candida colonization-and blunted interferon signaling represent a common feature of severe COVID-19 infection.

IMPORTANCE

In this paper, we present an analysis suggesting that symptomatic and asymptomatic fungal coinfections can impact patient disease progression during COVID-19 hospitalization. By looking into the presence of other pathogens and their effect on the host immune response during COVID-19 hospitalizations, we aim to offer insight into an underestimated scenario, furthering our current knowledge of determinants of severity that could be considered for future diagnostic and intervention strategies.

COVID-19-associated pulmonary aspergillosis (CAPA) in hematological patients: Could antifungal prophylaxis be necessary? A nationwide study

BACKGROUND

COVID-19-associated pulmonary aspergillosis (CAPA) has emerged as a relatively common complication. Multiple studies described this relationship in critical patients, however its incidence and outcome in other risk groups such as immunosuppressed patients remains unknown. In this sense, we aimed to evaluate the rates and outcomes of CAPA in hematological patients and according to the different hematological malignances, comparing to invasive pulmonary aspergillosis (IPA) in non-COVID-19 ones.

METHODS

Nationwide, population-based and retrospective observational cohort study including all adult patients with hematological malignancies admitted in Spain since March 1, 2020 to December 31, 2021. The main outcome variable was the diagnosis of IPA during hospitalization in hematological patients with or without COVID-19 at admission. The rate of CAPA compared to IPA in non-COVID-19 patients in each hematological malignancy was also performed, as well as survival curve analysis.

FINDINGS

COVID-19 was diagnosed in 3.85 % (4367 out of 113,525) of the hematological adult inpatients. COVID-19 group developed more fungal infections (5.1 % vs. 3 %; p < 0.001). Candida spp. showed higher rate in non-COVID-19 (74.2 % vs. 66.8 %; p = 0.015), meanwhile Aspergillus spp. confirmed its predominance in COVID-19 hematological patients (35.4 % vs. 19.1 %; p < 0.001). IPA was diagnosed in 703 patients and 11.2 % (79 cases) were CAPA. The multivariate logistic regression analysis found that the diagnosis of COVID-19 disease at hospital admission increased more than two-fold IPA development [OR: 2.5, 95CI (1.9-3.1), p < 0.001]. B-cell malignancies - specifically B-cell non-Hodgkin lymphoma, multiple myeloma, chronic lymphocytic leukemia and acute lymphoblastic leukemia - showed between four- and six-fold higher CAPA development and 90-day mortality rates ranging between 50 % and 72 %. However, myeloid malignancies did not show higher CAPA rates compared to IPA in non-COVID-19 patients.

CONCLUSION

COVID-19 constitutes an independent risk factor for developing aspergillosis in B-cell hematological malignancies and the use of antifungal prophylaxis during hospitalizations may be warranted.

Evaluation of some immunological markers in co-infection of COVID-19 with thrush candidiasis

OBJECTIVE

COVID-19 infection poses significant risks, including life-threatening consequences and fungus synchronization, making it a significant concern. This study seeks to assess the effect of concurrent infection of COVID-19 with Thrush Candida albicans on the patient's health state by measuring the proportion of immune cells and certain interleukins such as IL-8, -10, -17, and -33.

METHODS

The study involved 70 patients (30 patients with COVID-19, 17 patients with thrush candidiasis, and 23 patients with Thrush Candida albicans) and 50 healthy individuals as a control group. COVID-19 was identified using RT-PCR, while C. albicans were identified through culture media, biochemical testing, and oral swabs. Ruby equipment and ELISA kits were used for blood counts and interleukin detection.

RESULTS

COVID-19, thrush candidiasis, and Thrush Candida albicans infections occur in a wide range of age groups (4-80 years), with no significant differences between sexes (p>0.05). Immunologically, our study found that Thrush Candida albicans patients had the highest rate of neutrophils (89.6%) and basophils (2.01%), while corona patients had the highest percentage of lymphocytes (70.12%) and eosinophils (7.11%), and patients with thrush candidiasis had the highest percentage of monocytes. Thrush Candida albicans patients showed increased IL-8 (56.7 pg/mL) and IL-17 (101.1 pg/mL) concentrations, with the greatest concentration of IL-33 (200.5 pg/mL) in COVID-19, and a decrease in the level of IL-10 in patient groups compared with controls.

CONCLUSION

Patient groups showed increased neutrophils, lymphocytes, monocytes, and IL-8 levels, with a significant linear association between proinflammatory interleukins and these cells.

Inferring fungal growth rates from optical density data

Quantifying fungal growth underpins our ability to effectively treat severe fungal infections. Current methods quantify fungal growth rates from time-course morphology-specific data, such as hyphal length data. However, automated large-scale collection of such data lies beyond the scope of most clinical microbiology laboratories. In this paper, we propose a mathematical model of fungal growth to estimate morphology-specific growth rates from easy-to-collect, but indirect, optical density (OD600) data of Aspergillus fumigatus growth (filamentous fungus). Our method accounts for OD600 being an indirect measure by explicitly including the relationship between the indirect OD600 measurements and the calibrating true fungal growth in the model. Therefore, the method does not require de novo generation of calibration data. Our model outperformed reference models at fitting to and predicting OD600 growth curves and overcame observed discrepancies between morphology-specific rates inferred from OD600 versus directly measured data in reference models that did not include calibration.

Risk factors for COVID-19 associated pulmonary aspergillosis and outcomes in patients with acute respiratory failure in a respiratory sub-intensive care unit

BACKGROUND

COVID-19-associated pulmonary aspergillosis (CAPA) is burdened by high mortality. Data are lacking about non-ICU patients. Aims of this study were to: (i) assess the incidence and prevalence of CAPA in a respiratory sub-intensive care unit, (ii) evaluate its risk factors and (iii) impact on in-hospital mortality. Secondary aims were to: (i) assess factors associated to mortality, and (ii) evaluate significant features in hematological patients.

MATERIALS AND METHODS

This was a single-center, retrospective study of COVID-19 patients with acute respiratory failure. A cohort of CAPA patients was compared to a non-CAPA cohort. Among patients with CAPA, a cohort of hematological patients was further compared to another of non-hematological patients.

RESULTS

Three hundred fifty patients were included in the study. Median P/F ratio at the admission to sub-intensive unit was 225 mmHg (IQR 155-314). 55 (15.7%) developed CAPA (incidence of 5.5%). Eighteen had probable CAPA (37.3%), 37 (67.3%) possible CAPA and none proven CAPA. Diagnosis of CAPA occurred at a median of 17 days (IQR 12-31) from SARS-CoV-2 infection. Independent risk factors for CAPA were hematological malignancy [OR 1.74 (95%CI 0.75-4.37), p = 0.0003], lymphocytopenia [OR 2.29 (95%CI 1.12-4.86), p = 0.02], and COPD [OR 2.74 (95%CI 1.19-5.08), p = 0.014]. Mortality rate was higher in CAPA cohort (61.8% vs 22.7%, p < 0.0001). CAPA resulted an independent risk factor for in-hospital mortality [OR 2.92 (95%CI 1.47-5.89), p = 0.0024]. Among CAPA patients, age > 65 years resulted a predictor of mortality [OR 5.09 (95% CI 1.20-26.92), p = 0.035]. No differences were observed in hematological cohort.

CONCLUSION

CAPA is a life-threatening condition with high mortality rates. It should be promptly suspected, especially in case of hematological malignancy, COPD and lymphocytopenia.

Incidence and Mortality of COVID-19-Associated Invasive Fungal Infections Among Critically Ill Intubated Patients: A Multicenter Retrospective Cohort Analysis

Background

An association between coronavirus disease 2019 (COVID-19)-associated invasive fungal infections (CAIFIs) and high mortality among intubated patients has been suggested in previous research. However, some of the current evidence was derived from small case series and multicenter studies conducted during different waves of the COVID-19 pandemic. We examined the incidence of CAIFIs and their associated mortality using a large, multicenter COVID-19 database built throughout the pandemic.

Methods

We conducted a retrospective analysis of the National COVID Cohort Collaborative (N3C) database collected from 76 medical centers in the United States between January 2020 and August 2022. Patients were 18 years or older and intubated after severe acute respiratory syndrome coronavirus 2 infection. The primary outcomes were incidence and all-cause mortality at 90 days. To assess all-cause mortality, we fitted Cox proportional hazard models after adjusting for confounders via inverse probability weighting.

Results

Out of the 4 916 229 patients with COVID-19 diagnosed during the study period, 68 383 (1.4%) met our cohort definition. The overall incidence of CAIFI was 2.80% (n = 1934/68 383). Aspergillus (48.2%; n = 933/1934) and Candida (41.0%; n = 793/1934) were the most common causative organisms. The incidence of CAIFIs associated with Aspergillus among patients who underwent BAL was 6.2% (n = 83/1328). Following inverse probability weighting, CAIFIs caused by Aspergillus (hazard ratio [HR], 2.0; 95% CI, 1.8-2.2) and Candida (HR, 1.7; 95% CI, 1.5-1.9) were associated with increased all-cause mortality. Systemic antifungals reduced mortality in 17% of patients with CAIFI with Aspergillus and 24% of patients with CAIFI with Candida.

Conclusions

The incidence of CAIFI was modest but associated with higher 90-day all-cause mortality among intubated patients. Systemic antifungals modified mortality.

Resurgence of orbital mucormycosis during COVID-19 pandemic: Study from a tertiary care center in Eastern India

PURPOSE

A sudden surge of Mucormycosis cases during the second wave of Covid 19 was observed in certain parts of India. The reasons for this upsurge remain unknown. However its impact on the overall healthcare system was quite overwhelming. In this context this study was decided to estimate and assess the spectrum of orbital involvement in patients with Mucormycosis, to find its association with coexisting disease entities if any, and at the same time evaluate the therapeutic response to established treatment regimens.

MATERIALS AND METHODS

This descriptive longitudinal study was conducted over a period of six months. Patients presenting with symptoms of Mucormycosis were jointly evaluated by a multi speciality team. After confirmation of diagnosis, patients were treated with intravenous Amphotericin B, surgical debridement of affected sinuses and orbital exenteration when indicated. They were followed up for three months after discharge.

RESULTS

Forty-three patients were enrolled in this study. Thirty-seven (86.04%) were COVID positive. All of them had history of steroid exposure during COVID treatment. Ninety five percent of study participants had diabetes mellitus. Twenty-seven (62.79%) patients had orbital involvement. Most common clinical presentation was peri-orbital or facial pain and edema. Besides medical treatment, thirty-nine patients (90.69%) required sinus debridement and nine patients (20.9%) required orbital exenteration. Thirteen patients (30.23%) expired during the follow up period. With treatment disease regressed in twenty patients (46.51%).

CONCLUSION

Diabetes and use of steroids to prevent anticipated cytokine storm may be the inciting factors for Orbital Mucormycosis in COVID patients. Early diagnosis, treatment and control of risk factors are keys for recovery and survival..

COVID-19 associated candidemia: From a shift in fungal epidemiology to a rise in azole drug resistance

Our understanding of fungal epidemiology and the burden of antifungal drug resistance in COVID-19-associated candidemia (CAC) patients is limited. Therefore, we conducted a retrospective multicenter study in Iran to explore clinical and microbiological profiles of CAC patients. Yeast isolated from blood, were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and subjected to antifungal susceptibility testing (AFST) using the broth microdilution method M27-A3 protocol. A total of 0.6% of the COVID-19 patients acquired CAC (43/6174). Fluconazole was the most widely used antifungal, and 37% of patients were not treated. Contrary to historic candidemia patients, Candida albicans and C. tropicalis were the most common species. In vitro resistance was high and only noted for azoles; 50%, 20%, and 13.6% of patients were infected with azole-non-susceptible (ANS) C. tropicalis, C. parapsilosis, and C. albicans isolates, respectively. ERG11 mutations conferring azole resistance were detected for C. parapsilosis isolates (Y132F), recovered from an azole-naïve patient. Our study revealed an unprecedented rise in ANS Candida isolates, including the first C. parapsilosis isolate carrying Y132F, among CAC patients in Iran, which potentially threatens the efficacy of fluconazole, the most widely used drug in our centers. Considering the high mortality rate and 37% of untreated CAC cases, our study underscores the importance of infection control strategies and antifungal stewardship to minimize the emergence of ANS Candida isolates during COVID-19.

Epidemiology of fungal infection in COVID 19 in Spain during 2020 and 2021: a nationwide study

We realize a nationwide population-based retrospective study to analyze the characteristics and risk factors of fungal co-infections in COVID-19 hospitalized patients as well as describe their causative agents in the Spanish population in 2020 and 2021. Data were obtained from records in the Minimum Basic Data Set of the National Surveillance System for Hospital Data in Spain, provided by the Ministry of Health, and annually published with two years lag. The assessment of the risk associated with the development of healthcare-associated fungal co-infections was assessed using an adjusted logistic regression model. The incidence of fungal co-infection in COVID-19 hospitalized patients was 1.41%. The main risk factors associated were surgery, sepsis, age, male gender, obesity, and COPD. Co-infection was associated with worse outcomes including higher in-hospital and in ICU mortality, and higher length of stay. Candida spp. and Aspergillus spp. were the microorganisms more frequent. This is the first study analyzing fungal coinfection at a national level in hospitalized patients with COVID-19 in Spanish population and one of the few studies available that demonstrate that surgery was an independent risk factor of Aspergillosis coinfection in COVID-19 patients.

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.

An observational cohort study of bronchoalveolar lavage fluid galactomannan and Aspergillus culture positivity in patients requiring mechanical ventilation

Rationale

Critically ill patients who develop invasive pulmonary aspergillosis (IPA) have high mortality rates despite antifungal therapy. Diagnosis is difficult in these patients. Bronchoalveolar lavage (BAL) fluid galactomannan (GM) is a helpful marker of infection, although the optimal cutoff for IPA is unclear. We aimed to evaluate the BAL fluid GM and fungal culture results, demographics, and outcomes among a large cohort of mechanically ventilated patients with suspected pneumonia.

Methods

A single-center cohort study of patients enrolled in the Successful Clinical Response in Pneumonia Therapy (SCRIPT) study from June 2018 to March 2023. Demographics, BAL results, and outcomes data were extracted from the electronic health record and compared between groups of patients who grew Aspergillus on a BAL fluid culture, those who had elevated BAL fluid GM levels (defined as >0.5 or >0.8) but did not grow Aspergillus on BAL fluid culture, and those with neither.

Results

Of over 1700 BAL samples from 688 patients, only 18 BAL samples grew Aspergillus. Patients who had a BAL sample grow Aspergillus (n=15) were older (median 71 vs 62 years, p=0.023), had more days intubated (29 vs 11, p=0.002), and more ICU days (34 vs 15, p=0.002) than patients whose BAL fluid culture was negative for Aspergillus (n=672). The BAL fluid galactomannan level was higher from samples that grew Aspergillus on culture than those that did not (median ODI 7.08 vs 0.11, p<0.001), though the elevation of BAL fluid GM varied across BAL samples for patients who had serial sampling. Patients who grew Aspergillus had a similar proportion of underlying immunocompromise compared with the patients who did not, and while no statistically significant difference in overall unfavorable outcome, had longer duration of ventilation and longer ICU stays.

Conclusions

In this large cohort of critically ill patients with a high number of BAL samples with GM levels, we found a relatively low rate of Aspergillus growth. Patients who eventually grew Aspergillus had inconsistently elevated BAL fluid GM, and many patients with elevated BAL fluid GM did not grow Aspergillus. These data suggest that the pre-test probability of invasive pulmonary aspergillosis should be considered low in a general ICU population undergoing BAL evaluation to define the etiology of pneumonia. Improved scoring systems are needed to enhance pre-test probability for diagnostic test stewardship purposes.

Exponential Rise of Fungal Infection Reported in Rajkot Civil Hospital in Covid Pandemic Era: A Retrospective Study

Mucormycosis is a rare but serious angio-invasive infection caused by a group of fungi called mucormycetes. Mucormycosis is an aggressive, life-threatening infection requiring prompt diagnosis and early treatment. Wide spread use of steroid and higher antibiotics may cause immune irregulation in post covid patients. A hallmark of mucormycosis infection is the presence of extensive angioinvasion with resultant vessel thrombosis and tissue necrosis. We reported exponential rising cases of fungal infection in covid pandemic era. Here we published epidemiological data of 773 fungal infected cases operated in ENT department of PDU Medical college, Rajkot in 2021. We have documented patients demographic data with comorbidity, paranasal sinuses with orbital, palatal and cerebral involvement, evaluation method, surgical and post surgical management protocol which we followed in our institute to treat all cases. We got promising result in terms of survival and less morbidity. Early presentation, less comorbidity, proper evaluation and immediate debridement with systemic antifungal coverage for adequate duration proved to be mainstay treatment of fungal infection in covid pandemic era.

Aspergillus and the Lung

The filamentous fungus Aspergillus causes a wide spectrum of diseases in the human lung, with Aspergillus fumigatus being the most pathogenic and allergenic subspecies. The broad range of clinical syndromes that can develop from the presence of Aspergillus in the respiratory tract is determined by the interaction between host and pathogen. In this review, an oversight of the different clinical entities of pulmonary aspergillosis is given, categorized by their main pathophysiological mechanisms. The underlying immune processes are discussed, and the main clinical, radiological, biochemical, microbiological, and histopathological findings are summarized.

Acute Invasive Pulmonary Aspergillosis: Clinical Presentation and Treatment

Among all clinical manifestations of pulmonary aspergillosis, invasive pulmonary aspergillosis (IPA) is the most acute presentation. IPA is caused by Aspergillus hyphae invading the pulmonary tissue, causing either tracheobronchitis and/or bronchopneumonia. The degree of fungal invasion into the respiratory tissue can be seen as a spectrum, going from colonization to deep tissue penetration with angio-invasion, and largely depends on the host's immune status. Patients with prolonged, severe neutropenia and patients with graft-versus-host disease are at particularly high risk. However, IPA also occurs in other groups of immunocompromised and nonimmunocompromised patients, like solid organ transplant recipients or critically ill patients with severe viral disease. While a diagnosis of proven IPA is challenging and often warranted by safety and feasibility, physicians must rely on a combination of clinical, radiological, and mycological features to assess the likelihood for the presence of IPA. Triazoles are the first-choice regimen, and the choice of the drug should be made on an individual basis. Adjunctive therapy such as immunomodulatory treatment should also be taken into account. Despite an improving and evolving diagnostic and therapeutic armamentarium, the burden and mortality of IPA still remains high. This review aims to give a comprehensive and didactic overview of the current knowledge and best practices regarding the epidemiology, clinical presentation, diagnosis, and treatment of acute IPA.

COVID-19-associated pulmonary aspergillosis in intensive care unit: A real-life experience

Since 2020, cases of COVID-19-associated pulmonary aspergillosis (CAPA) have been frequently described, representing an important cause of mortality, especially among patients admitted to intensive care unit (ICU). A predisposition to invasive infection caused by Aspergillus spp. in SARS-CoV-2 infected patients can be ascribed either to the direct viral-mediated damage of the respiratory epithelium or to the dysregulated immunity associated with COVID-19. In this case series we have collected the clinical, laboratory and radiological data of 10 patients admitted to the ICU with diagnosis of probable CAPA, according to the recent expert consensus statement, from March 2020 to December 2022 in the Teaching Hospital of Catanzaro in Italy. Overall, 249 patients were admitted to the COVID-19-ICU from March 2020 to December 2022; out of these, 4% developed a probable CAPA. Most of patients were male with a mean age of 62 years. Only two patients had an underlying immunocompromising condition. The observed mortality was 70%. In our institution, all COVID-19 patients requiring invasive mechanical ventilation systematically underwent bronchoscopy with bronchoalveolar lavage for an early evaluation of bacterial and/or fungal co- or super-infections, including galactomannan test. Patients were re-evaluated by an infectious diseases consultant team every 24-48 hours and the galactomannan test was systematically repeated based on patient's clinical course. Even though the numbers in this study are very small, we report our experience about the role of early diagnosis and careful choice of antifungal therapy, considering the fragility of these patients, and its relationship with outcomes. Despite a systemic approach allowing early diagnosis and initiation of anti-fungal therapy, the mortality rate turned out to be very high (70%).

Covid-19-associated pulmonary aspergillosis in mechanically ventilated patients: incidence and outcome in a French multicenter observational cohort (APICOVID)

BACKGROUND

Recent studies identified coronavirus disease 2019 (COVID-19) as a risk factor for invasive pulmonary aspergillosis (IPA) but produced conflicting data on IPA incidence and impact on patient outcomes. We aimed to determine the incidence and outcomes of COVID-19-associated pulmonary aspergillosis (CAPA) in mechanically ventilated patients.

METHODS

We performed a multicenter retrospective observational cohort study in consecutive adults admitted to 15 French intensive care units (ICUs) in 2020 for COVID-19 requiring mechanical ventilation. CAPA was diagnosed and graded according to 2020 ECMM/ISHAM consensus criteria. The primary objective was to determine the incidence of proven/probable CAPA, and the secondary objectives were to identify risk factors for proven/probable CAPA and to assess associations between proven/probable CAPA and patient outcomes.

RESULTS

The 708 included patients (522 [73.7%] men) had a mean age of 65.2 ± 10.8 years, a median mechanical ventilation duration of 15.0 [8.0-27.0] days, and a day-90 mortality rate of 28.5%. Underlying immunosuppression was present in 113 (16.0%) patients. Corticosteroids were used in 348 (63.1%) patients. Criteria for probable CAPA were met by 18 (2.5%) patients; no patient had histologically proven CAPA. Older age was the only factor significantly associated with probable CAPA (hazard ratio [HR], 1.04; 95% CI 1.00-1.09; P = 0.04). Probable CAPA was associated with significantly higher day-90 mortality (HR, 2.07; 95% CI 1.32-3.25; P = 0.001) but not with longer mechanical ventilation or ICU length of stay.

CONCLUSION

Probable CAPA is a rare but serious complication of severe COVID-19 requiring mechanical ventilation and is associated with higher day-90 mortality.

Clinical courses and outcomes of COVID-19 associated pulmonary aspergillosis in 168 patients with the SARS-CoV-2 omicron variant

PURPOSE

We aimed to analyze the clinical features of COVID-19-associated pulmonary aspergillosis (CAPA) during the SARS-CoV-2 Omicron variant pandemic and to reveal the risk factors for CAPA and death.

METHODS

A retrospective cohort study was conducted on 168 CAPA patients from December 8, 2022 to January 31, 2023. 168 COVID-19 patients without secondary fungal infection during this period were matched 1:1 using propensity score matching as controls.

RESULTS

The incidence of CAPA was 3.8% (168/4421). Compared with patients without fungal infection, CAPA patients had a higher mortality (43.5% vs. 10.1%, P < 0.001). Patients in the death group (n = 73) were more likely to be admitted to ICU (91.8% vs. 26.3%, p < 0.001), had a shorter ICU length of hospitalization (10 (IQR, 6 ~ 16.5) days vs. 14 (IQR, 8 ~ 37) days, p = 0.012). Immunocompromised status (p = 0.023), NLR ≥ 5.7 (p = 0.004), CRP ≥ 50 mg/L (p = 0.043), and the number of antibiotics ≥ 3 (p < 0.001) were all risk factors for CAPA; NLR ≥ 5.7 (p = 0.009) and the number of antibiotics ≥ 3 (p = 0.018) were all independent risk factors for death.

CONCLUSIONS

During the Omicron variant pandemic, CAPA increased death and ICU length of hospitalization. The risk factors of CAPA and death obtained from the study can help us further understand the disease characteristics of CAPA and better guide our clinical decision-making.

Case Report of COVID-19 and Pneumocystis coinfection in a pediatric patient with a history of receiving high dose steroid therapy

We report the first case of a critically ill pediatric patient coinfected with coronavirus disease 2019 (COVID-19) and Pneumocystis jirovecii pneumonia (PCP). Instances of coinfection of COVID-19 and PCP are being increasingly reported as the COVID-19 pandemic continues. Because the combination can be life-threatening, timely diagnosis and treatment for PCP is necessary in cases where an immunocompromised patient contracts COVID-19.

Clinical characteristics, bacterial coinfections and outcomes in COVID-19-associated pulmonary aspergillosis in a third-level Mexican hospital during the COVID-19 pre-vaccination era

BACKGROUND

Damage due to respiratory viruses increases the risk of bacterial and fungal coinfections and superinfections. High rates of invasive aspergillosis are seen in severe influenza and COVID-19. This report describes CAPA cases diagnosed during the first wave in the biggest reference centre for severe COVID-19 in Mexico.

OBJECTIVES

To describe the clinical, microbiological and radiological characteristics of patients with invasive pulmonary aspergillosis associated with critical COVID-19, as well as to describe the variables associated with mortality.

METHODS

This retrospective study identified CAPA cases among individuals with COVID-19 and ARDS, hospitalised from 1 March 2020 to 31 March 2021. CAPA was defined according to ECMM/ISHAM consensus criteria. Prevalence was estimated. Clinical and microbiological characteristics including bacterial superinfections, antifungal susceptibility testing and outcomes were documented.

RESULTS

Possible CAPA was diagnosed in 86 patients among 2080 individuals with severe COVID-19, representing 4.13% prevalence. All CAPA cases had a positive respiratory culture for Aspergillus species. Aspergillus fumigatus was the most frequent isolate (64%, n = 55/86). Seven isolates (9%, n = 7/80) were resistant to amphotericin B (A. fumigatus n = 5/55, 9%; A. niger, n = 2/7, 28%), two A. fumigatus isolates were resistant to itraconazole (3.6%, n = 2/55). Tracheal galactomannan values ranged between 1.2 and 4.05, while serum galactomannan was positive only in 11% (n = 3/26). Bacterial coinfection were documented in 46% (n = 40/86). Gram negatives were the most frequent cause (77%, n = 31/40 isolates), from which 13% (n = 4/31) were reported as multidrug-resistant bacteria. Mortality rate was 60% and worse prognosis was seen in older persons, high tracheal galactomannan index and high HbA1c level.

CONCLUSIONS

One in 10 individuals with CAPA carry a resistant Aspergillus isolate and/or will be affected by a MDR bacteria. High mortality rates are seen in this population.

COVID-19-associated pulmonary aspergillosis in mechanically ventilated patients: a prospective, multicentre UK study

BACKGROUND

Invasive pulmonary aspergillosis is a complication of severe COVID-19, with regional variation in reported incidence and mortality. We describe the incidence, risk factors and mortality associated with COVID-19-associated pulmonary aspergillosis (CAPA) in a prospective, multicentre UK cohort.

METHODS

From March 2020 to March 2021, 266 mechanically ventilated adults with COVID-19 were enrolled across 5 UK hospital intensive care units (ICUs). CAPA was defined using European Confederation for Medical Mycology and the International Society for Human and Animal Mycology criteria and fungal diagnostics performed on respiratory and serum samples.

RESULTS

Twenty-nine of 266 patients (10.9%) had probable CAPA, 14 (5.2%) possible CAPA and none proven CAPA. Probable CAPA was diagnosed a median of 9 (IQR 7-16) days after ICU admission. Factors associated with probable CAPA after multivariable logistic regression were cumulative steroid dose given within 28 days prior to ICU admission (adjusted OR (aOR) 1.16; 95% CI 1.01 to 1.43 per 100 mg prednisolone-equivalent), receipt of an interleukin (IL)-6 inhibitor (aOR 2.79; 95% CI 1.22 to 6.48) and chronic obstructive pulmonary disease (COPD) (aOR 4.78; 95% CI 1.13 to 18.13). Mortality in patients with probable CAPA was 55%, vs 46% in those without. After adjustment for immortal time bias, CAPA was associated with an increased risk of 90-day mortality (HR 1.85; 95% CI 1.07 to 3.19); however, this association did not remain statistically significant after further adjustment for confounders (adjusted HR 1.57; 95% CI 0.88 to 2.80). There was no difference in mortality between patients with CAPA prescribed antifungals (9 of 17; 53%) and those who were not (7 of 12; 58%) (p=0.77).

INTERPRETATION

In this first prospective UK study, probable CAPA was associated with corticosteroid use, receipt of IL-6 inhibitors and pre-existing COPD. CAPA did not impact mortality following adjustment for prognostic variables.

COVID-19-associated pulmonary aspergillosis (CAPA): identification of Aspergillus species and determination of antifungal susceptibility profiles

Among the co-infectious agents in COVID-19 patients, Aspergillus species cause invasive pulmonary aspergillosis (IPA). IPA is difficult to diagnose and is associated with high morbidity and mortality. This study is aimed at identifying Aspergillus spp. from sputum and tracheal aspirate (TA) samples of COVID-19 patients and at determining their antifungal susceptibility profiles. A total of 50 patients with COVID-19 hospitalized in their intensive care units (ICU) were included in the study. Identification of Aspergillus isolates was performed by phenotypic and molecular methods. ECMM/ISHAM consensus criteria were used for IPA case definitions. The antifungal susceptibility profiles of isolates were determined by the microdilution method. Aspergillus spp. was detected in 35 (70%) of the clinical samples. Among the Aspergillus spp., 20 (57.1%) A. fumigatus, six (17.1%) A. flavus, four (11.4%) A. niger, three (8.6%) A. terreus, and two (5.7%) A. welwitschiae were identified. In general, Aspergillus isolates were susceptible to the tested antifungal agents. In the study, nine patients were diagnosed with possible IPA, 11 patients were diagnosed with probable IPA, and 15 patients were diagnosed with Aspergillus colonization according to the used algorithms. Serum galactomannan antigen positivity was found in 11 of the patients diagnosed with IPA. Our results provide data on the incidence of IPA, identification of Aspergillus spp., and its susceptibility profiles in critically ill COVID-19 patients. Prospective studies are needed for a faster diagnosis or antifungal prophylaxis to manage the poor prognosis of IPA and reduce the risk of mortality.

Post-COVID pulmonary fungal infections: An unanticipated predicament or a ticking time bomb? Clinico-microbiological profile of cases encountered during the second wave of COVID-19 pandemic at a teaching hospital in the Himalayas with a brief literature review

Introduction

This study attempts to generate preliminary data regarding post-COVID pulmonary fungal infections, namely, COVID-19-associated pulmonary aspergillosis (CAPA), COVID-19-associated pulmonary mucormycosis (CAPM), and mixed infections from the Himalayas and compares the micro-radio-clinical profile and outcomes of the affected patients.

Materials and Methods

A retrospective data analysis was conducted, where clinical profiles, microbiological and radiological reports, and outcomes of n = 16 patients of post-COVID pulmonary infections were compared.

Results

Of n = 16 patients, n = 7 had CAPA (n = 5 Aspergillus fumigatus, n = 1 Aspergillus flavus, and n = 1 Aspergillus niger), n = 5 CAPM (Rhizopus arrhizus), and n = 4 with mixed infections (n = 3 infected with Aspergillus fumigatus and Rhizopus spp. and n = 1 with Aspergillus flavus and Rhizopus arrhizus). Thick-walled cavitary lesions, air-fluid levels, and multiple centrilobular nodules were some of the common radiological findings reported among these patients.

Conclusion

The immuno-compromised state following COVID-19 infection and treatment might be responsible for the progression of regular exposure to the dense Himalayan vegetation into an invasive pulmonary fungal infection. Suspecting post-COVID pulmonary fungal infection is necessary for primary care physicians to ensure timely referral to higher centers. Mixed pulmonary fungal infections (coinfection with Aspergillus spp. and Rhizopus spp.) are also emerging as important sequelae of COVID-19.

Bronchial aspirate obtained during bronchoscopy yields increased fungal load compared to bronchoalveolar lavage fluid in patients at risk of invasive aspergillosis and Pneumocystis pneumonia

Bronchoalveolar lavage fluid (BALF) is a standard respiratory sample for diagnosing invasive fungal diseases like Pneumocystis pneumonia (PCP) and invasive pulmonary aspergillosis (IPA). However, procedural variations exist across medical centers and wards. This study aimed to compare the diagnostic potential of BALF and bronchial aspirate (BA) obtained during bronchoscopy in 173 patients suspected of fungal infections. A prospective observational study was conducted from April 2020 to November 2021. BALF and BA were collected during bronchoscopy and subjected to direct examination, fungal culture, Aspergillus fumigatus qPCR (AfqPCR), and Pneumocystis jirovecii qPCR (PjqPCR). Galactomannan detection was performed on BALF. Patients were classified based on established European Organization for Research and Treatment of Cancer (EORTC) criteria. Out of 173 patients, 75 tested positive for at least one test in BA or BALF. For Aspergillus, proportion of positive AfqPCR (14.5% vs. 9.2%; P < 0.0001) and fungal loads (Cq of 31.3 vs. 32.8; P = 0.0018) were significantly higher in BA compared to BALF. For Pneumocystis, fungal loads by PjqPCR was also higher in BA compared to BALF (Cq of 34.2 vs. 35.7; P = 0.003). BA only detected A. fumigatus and P. jirovecii in 12 (42.9%) and 8 (19.5%) patients, respectively. BA obtained during a BAL procedure can be a suitable sample type for increased detection of P. jirovecii and A. fumigatus by qPCR. The use of BA in diagnostic algorithms requires further investigation in prospective studies.

Association between Pulmonary Aspergillosis and Cytomegalovirus Reactivation in Critically Ill COVID-19 Patients: A Prospective Observational Cohort Study

COVID-19-associated invasive pulmonary aspergillosis (CAPA) is common and is associated with poor outcomes in critically ill patients. This prospective observational study aimed to explore the association between CAPA development and the incidence and prognosis of cytomegalovirus (CMV) reactivation in critically ill COVID-19 patients. We included all consecutive critically ill adult patients with confirmed COVID-19 infection who were admitted to three COVID-19 intensive care units (ICUs) in an Italian hospital from 25 February 2020 to 8 May 2022. A standardized procedure was employed for early detection of CAPA. Risk factors associated with CAPA and CMV reactivation and the association between CMV recurrence and mortality were estimated using adjusted Cox proportional hazard regression models. CAPA occurred in 96 patients (16.6%) of the 579 patients analyzed. Among the CAPA population, 40 (41.7%) patients developed CMV blood reactivation with a median time of 18 days (IQR 7-27). The CAPA+CMV group did not exhibit a significantly higher 90-day mortality rate (62.5% vs. 48.2%) than the CAPA alone group (p = 0.166). The CAPA+CMV group had a longer ICU stay, fewer ventilation-free days, and a higher rate of secondary bacterial infections than the control group of CAPA alone. In the CAPA population, prior immunosuppression was the only independent risk factor for CMV reactivation (HR 2.33, 95% C.I. 1.21-4.48, p = 0.011). In critically ill COVID-19 patients, CMV reactivation is common in those with a previous CAPA diagnosis. Basal immunosuppression before COVID-19 appeared to be the primary independent variable affecting CMV reactivation in patients with CAPA. Furthermore, the association of CAPA+CMV versus CAPA alone appears to impact ICU length of stay and secondary bacterial infections but not mortality.

Chronic Candida albicans meningitis following critical COVID-19 and serial measurements of (1,3)-β-D-glucan in cerebrospinal fluid

Co-infections with invasive candidiasis have been reported to be overrepresented in severe COVID-19. This report presents an unusual case of chronic Candida meningitis following intensive care for COVID-19.

Severe Candida infections in critically ill patients with COVID-19

The frequency of co-infections with bacterial or fungal pathogens has constantly increased among critically ill patients with coronavirus disease 2019 (COVID-19) during the pandemic. Candidemia was the most frequently reported invasive fungal co-infection. The onset of candidemia in COVID-19 patients was often delayed compared to non-COVID-19 patients. Additionally, Candida invasive infections in COVID-19 patients were more often linked to invasive procedures (e.g., invasive mechanical ventilation or renal replacement therapy) during the intensive care stay and the severity of illness rather than more "classic" risk factors present in patients without COVID-19 (e.g., underlying diseases and prior hospitalization). Moreover, apart from the increased incidence of candidemia during the pandemic, a worrying rise in fluconazole-resistant strains was reported, including a rise in the multidrug-resistant Candida auris. Regarding outcomes, the development of invasive Candida co-infection had a negative impact, increasing morbidity and mortality compared to non-co-infected COVID-19 patients. In this narrative review, we present and critically discuss information on the diagnosis and management of invasive fungal infections caused by Candida spp. in critically ill COVID-19 patients.

ChatGPT and mycosis- a new weapon in the knowledge battlefield

As current trend for physician tools, ChatGPT can sift through massive amounts of information and solve problems through easy-to-understand conversations, ultimately improving efficiency. Mycosis is currently facing great challenges, including high fungal burdens, high mortality, limited choice of antifungal drugs and increasing drug resistance. To address these challenges, We asked ChatGPT for fungal infection scenario-based questions and assessed its appropriateness, consistency, and potential pitfalls. We concluded ChatGPT can provide compelling responses to most prompts, including diagnosis, recommendations for examination, treatment and rational drug use. Moreover, we summarized exciting future applications in mycosis, such as clinical work, scientific research, education and healthcare. However, the largest barriers to implementation are deficits in indiviudal advice, timely literature updates, consistency, accuracy and data safety. To fully embrace the opportunity, we need to address these barriers and manage the risks. We expect that ChatGPT will become a new weapon in in the battlefield of mycosis.

Association Between Candida albicans and COVID-19 in Complete Denture Wearers: An Observational Study

Introduction The phenomenon of coronavirus disease 2019 (COVID-19)-related candidiasis is gaining increased attention and acknowledgment as an integral component of the severe consequences of COVID-19. The aim of the present study was to assess the association between Candida albicans and COVID-19 in complete denture wearers. Materials and methods An observational study was conducted on 45 complete denture wearers, who were divided into three groups as follows: Group 1, 15 subjects with mild to moderate COVID-19 infection; Group 2, 15 subjects with severe COVID-19 infection; and Group 3, 15 subjects without COVID-19 infection. Mean colony forming units (CFU) were observed on agar plates containing Sabouraud dextrose in the salivary samples of the participants. Analysis of variance, followed by post-hoc analysis by Tukey's test, was used to compare CFU between the groups. Pearson's correlation coefficient was used to study the correlation between variables. Results The highest average colony-forming units of Candida albicans were observed in Group 2, followed by Group 1, compared to the control group, and a significant (p<0.001) difference was found. A weak positive correlation was found between the age of the patients and the duration of denture usage, as well as between age and the counts of Candida albicans in Groups 1 and 3. This correlation was more pronounced in Group 3. A strong positive correlation was observed in all groups between the Candida albicans count and the duration of denture usage by the patients. Conclusion The association between Candida albicans and denture wear was compounded by the presence of COVID-19. Consequently, the timely identification of Candida albicans infection in patients with COVID-19 is important to establish more efficacious approaches for antifungal treatment and prophylactic interventions.

COVID-19 associated Mucormycosis among ICU patients: risk factors, control, and challenges

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic is still difficult to be controlled. The spread of this virus and the emergence of new variants are considered a great challenge worldwide. Disturbance in infection control guidelines implementation, use of steroids, antibiotics, hospital crowdedness, and repeated use of oxygen masks during the management of critically ill COVID-19 patients lead to an increase in the rate of opportunistic infections. So, patients need to fight both the virus with its different variants and opportunistic pathogens including bacteria and fungi especially patients with diabetes mellitus, malignancy, or those who undergo hemodialysis and receive deferoxamine. During the pandemic, many cases of Mucormycosis associated with COVID-19 infection were observed in many countries. In this review, we discuss risk factors that increase the chance of infection by opportunistic pathogens, especially fungal pathogens, recent challenges, and control measures.

Reconstructive cranial surgery for invasive and non-responsive mucormycosis

The incidence of mucormycosis showed a sharp rise during the COVID-19 pandemic in vulnerable populations like people with diabetes. Here, we report a case of mucormycosis of the frontal and ethmoid sinuses in a man in his mid-50s with a background of diabetes mellitus and COVID-19 infection requiring steroids and oxygen support. The infection had remained persistent despite initial debridement by functional endoscopic sinus surgery of the anterior frontal sinus wall and re-exploration, followed by debridement using the brow incision. The patient had received an entire course of systemic antifungal therapy during the postoperative period. A bifrontal craniotomy, excision of the supraorbital ridge and complete removal of bilateral frontal sinuses managed the persistent fungal infection. The defect was reconstructed with a custom-made three-dimensional-printed MRI-compatible titanium cranioplasty mesh. The patient had no signs of infection on the 9-month follow-up.

The Clinical Significance of Aspergillus Detected in Lower-Respiratory-Tract Samples of Critically Ill COVID-19-Positive Patients

Objective: Critically ill patients with acute respiratory distress syndrome (ARDS) due to viral infection are at risk for secondary complications, including invasive aspergillosis. Our study aimed to characterize the clinical significance and outcome of Aspergillus species isolated from lower-respiratory-tract samples of critically ill OVID-19 patients at a single center. Design: We conducted a retrospective cohort study to evaluate the characteristics of patients with COVID-19 and aspergillus isolated from the lower respiratory tract and to identify predictors of outcomes in this population. Setting: The setting was a single-center hospital system within the metropolitan Detroit region. Results: The prevalence of Aspergillus isolated in hospitalized COVID-19 patients was 1.18% (30/2461 patients), and it was 4.6% in critically ill ICU patients with COVID-19. Probable COVID-19-associated invasive pulmonary aspergillosis (CAPA) was found in 21 critically ill patients, and 9 cases were classified as colonization. The in-hospital mortality of critically ill patients with CAPA and those with aspergillus colonization were high but not significantly different (76% vs. 67%, p = 1.00). Furthermore, the in-hospital mortality for ICU patients with or without Aspergillus isolated was not significantly different 73.3% vs. 64.5%, respectively (OR 1.53, CI 0.64-4.06, p = 0.43). In patients in whom Aspergillus was isolated, antifungal therapy (p = 0.035, OR 12.3, CI 1.74-252); vasopressors (0.016, OR 10.6, CI 1.75-81.8); and a higher mSOFA score (p = 0.043, OR 1.29 CI 1.03-1.72) were associated with a worse outcome. In a multivariable model adjusting for other significant variables, FiO2 was the only variable associated with in-hospital mortality in patients in whom Aspergillus was isolated (OR 1.07, 95% CI 1.01-1.27). Conclusions: The isolation of Aspergillus from lower-respiratory-tract samples of critically ill patients with COVID-19 is associated with high mortality. It is important to have a low threshold for superimposed infections such as CAPA in critically ill patients with COVID-19.

COVID-19 and candiduria: an investigation of the risk factors and immunological aspects

Secondary fungal infections are frequently observed in COVID-19 patients. However, the occurrence of candiduria in these patients and its risk factors are underexplored. We evaluated the risk factors of candiduria in COVID-19 patients, including inflammatory mediators that could be used as prognostic markers. Clinical information, laboratory test results, and outcomes were collected from severely ill COVID-19 patients with and without candiduria. Candida species identification, antifungal susceptibility, and plasma inflammatory mediators' measurements were performed. Regression logistic and Cox regression model were used to evaluate the risk factors. A higher risk of longer hospitalization and mortality were observed in patients with candiduria compared to those with COVID-19 only. Candiduria was caused by Candida albicans, C. glabrata, and C. tropicalis. Isolates with intermediate susceptibility to voriconazole and resistant to caspofungin were identified. Classic factors such as the use of corticosteroids and antibacterials, the worsening of renal function, and hematological parameters (hemoglobin and platelets) were found to predispose to candiduria. The mediators IL-1β, IL-1ra, IL-2, CXCL-8, IL-17, IFN-γ, basic FGF, and MIP-1β were significantly increased in patients with COVID-19 and candiduria. Furthermore, IFN-γ, IL-1ra, and CXCL-8 were associated with the occurrence of candiduria in COVID-19 patients, whereas basic FGF, IL-1β, and CXCL-8 were associated with the risk of death in these patients. Classical and immunological factors were associated with worse prognosis among patients with COVID-19 and candiduria. Some mediators, especially CXCL-8, can be a reliable biomarker of fungal coinfection and may guide the diagnostic and the treatment of these patients.

Prevalence, predictors, and outcome of pulmonary mucormycosis in COVID-19 associated rhino orbital mucormycosis in a tertiary care center in South India

Background and Purpose

India witnessed an explosive rise in mucormycosis following COVID-19 infection. Pulmonary mucormycosis closely followed rhino orbital mucormycosis as the most common presentation. The need for advanced resources and lack of clinical suspicion for COVID-19-associated pulmonary mucormycosis led to widespread underdiagnosis and poor response to late therapy. The present study aimed to assess the prevalence of pulmonary mucormycosis in COVID-19-associated rhino-orbital mucormycosis using non-invasive techniques, such as sputum microscopy and chest imaging.

Materials and Methods

A prospective observational study was conducted at the Institute of Internal Medicine, Rajiv Gandhi Government General Hospital in Chennai, India between June 2021 and July 2021. All hospitalized patients with proven rhino orbital mucormycosis with or without cerebral involvement within three months of confirmed COVID-19 infection who had clinical symptoms compatible with pulmonary mucormycosis were included in this study. These patients were screened for probable and possible COVID-19-associated pulmonary mucormycosis using computed tomography (CT) chest imaging and sputum microscopy within 48 h of hospital admission.

Results

Based on the findings, 8 (16%) out of 50 patients with rhino-orbital mucormycosis, had associated possible or probable pulmonary mucormycosis. All 8 patients were diabetics and had characteristic CT chest findings while only half of them had positive sputum microscopy. A higher prevalence of probably disseminated COVID-19-associated mucormycosis was noted among 51-60-year-old males with the use of corticosteroids and oxygen for COVID-19 therapy. The mortality rate was 100% in probably disseminated mucormycosis, 50% in possible disseminated mucormycosis, and only 9.5% in isolated rhino-orbital mucormycosis.

Conclusion

Non-invasive and feasible methods, such as sputum microscopy and chest imaging can be considered for early screening and intensive management of probably disseminated mucormycosis to improve prognosis.