Microbiological Laboratory Testing in the Diagnosis of Fungal Infections in Pulmonary and Critical Care Practice. An Official American Thoracic Society Clinical Practice Guideline

Development of biological techniques to prevent corrosion of reinforcing steel bars

The electrochemical corrosive processes compromise the passivity of reinforcing steel, potentially leading to structural integrity loss and, in extreme cases, concrete infrastructure failures. While bio-inspired concretes show promise in mitigating strength degradation and enabling self-healing of concrete flaws, their interaction with steel reinforcement remains underexplored. Thus, this investigation aimed to establish a protective strategy by fostering biofilm growth on rebar surfaces. To achieve this, Bacillus subtilis and Escherichia coli bacteria were utilized as biofilm-forming agents, aided by magnetic iron oxide and zeolite micro-nano particles. The study encompassed a thorough assessment of split tensile strength, corrosion resistance of bio-treated embedded steel bars, and a comprehensive biofilm characterization, along with a meticulous examination of the microstructure at the steel-concrete interface. The findings underscored a significant improvement in split tensile strength, demonstrating a remarkable 84.2 % increase when bacterial species were combined with iron oxide nanoparticles, in contrast to the control specimens. Furthermore, the bio-treated bars exhibited an impressive corrosion inhibition potential of 78.5 % relative to their unaltered counterparts. These outcomes are attributed to the discernible refinement of microstructural features surrounding the steel reinforcement and the heightened densification of the inter-transitional zone between steel and concrete.

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.

Diagnostic limitations and challenges in current clinical guidelines and potential application of metagenomic sequencing to manage pulmonary invasive fungal infections in patients with haematological malignancies

BACKGROUND

Pulmonary invasive fungal infections (pIFI) disproportionately affect patients with haematological malignancies (HM). Establishing a rapid and accurate diagnosis of pIFI is challenging. Multiple guidelines recommend diagnostic testing of invasive fungal infections but lack consensus and may contribute to inconsistent diagnostic approaches.

OBJECTIVE

To identify key diagnostic challenges and review metagenomic sequencing data.

SOURCES

PubMed, professional consortium, and scientific society websites search to identify relevant, published, evidence-based clinical guidelines within the past 5 years. PubMed searchs for papers describing clinically relevant novel diagnostic technologies.

CONTENT

Current guidelines for patients with HM and suspected pIFI recommend chest computed tomography imaging and specimen testing with microscopic examination (including calcofluor white stain, histopathology, cytopathology, etc.), Aspergillus galactomannan, β-D-glucan, PCR, and culture, each with certain limitations. Emerging real-world data support the adjunctive use of metagenomic sequencing-based tests for the timely diagnosis of pIFI.

IMPLICATIONS

High-quality evidence from robust clinical trials is needed to determine whether guidelines should be updated to include novel diagnostic technologies. Trials should ask whether the combination of powerful novel diagnostics, such as pathogen-agnostic metagenomic sequencing technologies in conjunction with conventional testing can optimize the diagnostic yield for all potential pIFI pathogens that impact the health of patients with HM.

Anti-Infection of Oral Microorganisms from Herbal Medicine of Piper crocatum Ruiz & Pav

The WHO Global Status Report on Oral Health 2022 reveals that oral diseases caused by infection with oral pathogenic microorganisms affect nearly 3.5 billion people worldwide. Oral health problems are caused by the presence of S. mutans, S. sanguinis, E. faecalis and C. albicans in the oral cavity. Synthetic anti-infective drugs have been widely used to treat oral infections, but have been reported to cause side effects and resistance. Various strategies have been implemented to overcome this problem. Synthetic anti-infective drugs have been widely used to treat oral infections, but they have been reported to cause side effects and resistance. Therefore, it is important to look for safe anti-infective alternatives. Ethnobotanical and ethnopharmacological studies suggest that Red Betel leaf (Piper crocatum Ruiz & Pav) could be a potential source of oral anti-infectives. This review aims to discuss the pathogenesis mechanism of several microorganisms that play an important role in causing health problems, the mechanism of action of synthetic oral anti-infective drugs in inhibiting microbial growth in the oral cavity, and the potential of red betel leaf (Piper crocatum Ruiz & Pav) as an herbal oral anti-infective drug. This study emphasises the importance of researching natural components as an alternative treatment for oral infections that is more effective and can meet global needs.

Universal digital high-resolution melting for the detection of pulmonary mold infections

Invasive mold infections (IMIs) are associated with high morbidity, particularly in immunocompromised patients, with mortality rates between 40% and 80%. Early initiation of appropriate antifungal therapy can substantially improve outcomes, yet early diagnosis remains difficult to establish and often requires multidisciplinary teams evaluating clinical and radiological findings plus supportive mycological findings. Universal digital high-resolution melting (U-dHRM) analysis may enable rapid and robust diagnoses of IMI. A universal fungal assay was developed for U-dHRM and used to generate a database of melt curve signatures for 19 clinically relevant fungal pathogens. A machine learning algorithm (ML) was trained to automatically classify these pathogen curves and detect novel melt curves. Performance was assessed on 73 clinical bronchoalveolar lavage samples from patients suspected of IMI. Novel curves were identified by micropipetting U-dHRM reactions and Sanger sequencing amplicons. U-dHRM achieved 97% overall fungal organism identification accuracy and a turnaround time of ~4 hrs. U-dHRM detected pathogenic molds (Aspergillus, Mucorales, Lomentospora, and Fusarium) in 73% of 30 samples classified as IMI, including mixed infections. Specificity was optimized by requiring the number of pathogenic mold curves detected in a sample to be >8 and a sample volume to be 1 mL, which resulted in 100% specificity in 21 at-risk patients without IMI. U-dHRM showed promise as a separate or combination diagnostic approach to standard mycological tests. U-dHRM's speed, ability to simultaneously identify and quantify clinically relevant mold pathogens in polymicrobial samples, and detect emerging opportunistic pathogens may aid treatment decisions, improving patient outcomes.

IMPORTANCE

Improvements in diagnostics for invasive mold infections are urgently needed. This work presents a new molecular detection approach that addresses technical and workflow challenges to provide fast pathogen detection, identification, and quantification that could inform treatment to improve patient outcomes.

Long-Term Follow-Up of a Case of Probable Aspergillus Skull Base Osteomyelitis With Galactomannan Test and Literature Review

We report a probable case of Aspergillus basicranial infection diagnosed by pathogenic serological examination presenting atypical initial manifestations, and highlight the importance of serological examination to avoid treatment delay and disease management. An 84-year-old diabetic patient presented with right peripheral nerve palsy, intolerable otalgia, hearing loss, dysphagia, hoarseness, and bucking. The patient was diagnosed a probable Aspergillus skull base osteomyelitis with cranial neuritis and meningitis of central nervous system. Galactomannan test was used in combination with 1-3-β-D-glucan and magnetic resonance imaging to follow-up during the continuous treatment of voriconazole. To date, the patient has remained in clinical remission for over 39 months but the drug cannot be stopped safely.

Amphotericin B in the Era of New Antifungals: Where Will It Stand?

Amphotericin B (AmB) has long stood as a cornerstone in the treatment of invasive fungal infections (IFIs), especially among immunocompromised patients. However, the landscape of antifungal therapy is evolving. New antifungal agents, boasting novel mechanisms of action and better safety profiles, are entering the scene, presenting alternatives to AmB's traditional dominance. This shift, prompted by an increase in the incidence of IFIs, the growing demographic of immunocompromised individuals, and changing patterns of fungal resistance, underscores the continuous need for effective treatments. Despite these challenges, AmB's broad efficacy and low resistance rates maintain its essential status in antifungal therapy. Innovations in AmB formulations, such as lipid complexes and liposomal delivery systems, have significantly mitigated its notorious nephrotoxicity and infusion-related reactions, thereby enhancing its clinical utility. Moreover, AmB's efficacy in treating severe and rare fungal infections and its pivotal role as prophylaxis in high-risk settings highlight its value and ongoing relevance. This review examines AmB's standing amidst the ever-changing antifungal landscape, focusing on its enduring significance in current clinical practice and exploring its potential future therapeutic adaptations.

Plasma Microbial Cell-Free DNA Sequencing in Immunocompromised Patients With Pneumonia: A Prospective Observational Study

BACKGROUND

Pneumonia is a common cause of morbidity and mortality, yet a causative pathogen is identified in a minority of cases. Plasma microbial cell-free DNA sequencing may improve diagnostic yield in immunocompromised patients with pneumonia.

METHODS

In this prospective, multicenter, observational study of immunocompromised adults undergoing bronchoscopy to establish a pneumonia etiology, plasma microbial cell-free DNA sequencing was compared to standardized usual care testing. Pneumonia etiology was adjudicated by a blinded independent committee. The primary outcome, additive diagnostic value, was assessed in the Per Protocol population (patients with complete testing results and no major protocol deviations) and defined as the percent of patients with an etiology of pneumonia exclusively identified by plasma microbial cell-free DNA sequencing. Clinical additive diagnostic value was assessed in the Per Protocol subgroup with negative usual care testing.

RESULTS

Of 257 patients, 173 met Per Protocol criteria. A pneumonia etiology was identified by usual care in 52/173 (30.1%), plasma microbial cell-free DNA sequencing in 49/173 (28.3%) and the combination of both in 73/173 (42.2%) patients. Plasma microbial cell-free DNA sequencing exclusively identified an etiology of pneumonia in 21/173 patients (additive diagnostic value 12.1%, 95% confidence interval [CI], 7.7% to 18.0%, P < .001). In the Per Protocol subgroup with negative usual care testing, plasma microbial cell-free DNA sequencing identified a pneumonia etiology in 21/121 patients (clinical additive diagnostic value 17.4%, 95% CI, 11.1% to 25.3%).

CONCLUSIONS

Non-invasive plasma microbial cell-free DNA sequencing significantly increased diagnostic yield in immunocompromised patients with pneumonia undergoing bronchoscopy and extensive microbiologic and molecular testing.

CLINICAL TRIALS REGISTRATION

NCT04047719.

A Diagnostic Approach to Fungal Pneumonia: An Infectious Diseases Perspective

Although bacteria significantly exceed fungi as the most common cause of lower respiratory tract infection, the incidence of fungal pneumonia is increasing because of a growing at-risk population of immunocompromised individuals as well as anthropogenic global heating and environmental disruption. When a patient presents with a clinical syndrome of pneumonia, a constellation of factors must be considered to determine the probability of a fungal pneumonia, including host factors, epidemiologic exposures, suggestive radiographic patterns, and the presence of a non-resolving pneumonia. In addition, knowledge of clinically important fungal pathogens, their epidemiology, and associated clinical syndromes are key in guiding appropriate diagnostic testing and result interpretation, and ultimately rendering a correct diagnosis of a fungal pneumonia. This article aims to provide a framework for the evaluation and appropriate diagnostic testing of patients with suspected fungal pneumonia.

Lung and sinus fungal infection imaging in immunocompromised patients

BACKGROUND

Imaging is a key diagnostic modality for suspected invasive pulmonary or sinus fungal disease and may help to direct testing and treatment. Fungal diagnostic guidelines have been developed and emphasize the role of imaging in this setting. We review and summarize evidence regarding imaging for fungal pulmonary and sinus disease (in particular invasive aspergillosis, mucormycosis and pneumocystosis) in immunocompromised patients.

OBJECTIVES

We reviewed data on imaging modalities and findings used for diagnosis of invasive fungal pulmonary and sinus disease.

SOURCES

References for this review were identified by searches of PubMed, Google Scholar, Embase and Web of Science through 1 April 1 2023.

CONTENT

Computed tomography imaging is the method of choice for the evaluation of suspected lung or sinus fungal disease. Although no computed tomography radiologic pattern is pathognomonic of pulmonary invasive fungal disease (IFD) the halo sign firstly suggests an angio-invasive pulmonary aspergillosis while the Reversed Halo Sign is more suggestive of pulmonary mucormycosis in an appropriate clinical setting. The air crescent sign is uncommon, occurring in the later stages of invasive aspergillosis in neutropenic patients. In contrast, new cavitary lesions should suggest IFD in moderately immunocompromised patients. Regarding sinus site, bony erosion, peri-antral fat or septal ulceration are reasonably predictive of IFD.

IMPLICATIONS

Imaging assessment of the lung and sinuses is an important component of the diagnostic work-up and management of IFD in immunocompromised patients. However, radiological features signs have sensitivity and specificity that often vary according to underlying disease states. Periodic review of imaging studies and diagnostic guidelines characterizing imaging findings may help clinicians to consider fungal infections in clinical care thereby leading to an earlier confirmation and treatment of IFD.

Metagenomic next-generation sequencing for detecting Aspergillosis pneumonia in immunocompromised patients: a retrospective study

Purpose

The identification of Aspergillus by metagenomic next-generation sequencing (mNGS) remains a challenging task due to the difficulty of nucleic acid extraction. The objective of this study was to determine whether mNGS could provide an accurate and efficient method for detecting invasive pulmonary aspergillosis (IPA) in immunocompromised patients (ICP).

Methods

A total of 133 ICP admitted to the ICU between January 2020 and September 2022 were enrolled in the study, of which 46 were diagnosed with IPA and 87 were non-IPA cases. The bronchoalveolar lavage fluid (BALF) was analyzed for the presence of Aspergillosis and other co-pathogens using mNGS, and its diagnostic performance was compared to conventional microbial tests (CMTs) that included smear, cultures, serum and BALF galactomannan (GM) test. Clinical composite diagnosis was used as the reference standard.

Results

mNGS had a sensitivity, specificity, and accuracy of 82.6%, 97.7%, and 92.5%, respectively, in diagnosing IPA. These findings were comparable to those of the combination of multiple CMTs. Interestingly, the sensitivity of mNGS was superior to that of any single CMT method, as demonstrated by comparisons with smears (8.7%, P < 0.001), culture (39.1%, P < 0.001), serum GM (23.9%, P < 0.001) and BALF GM (69.6%, P = 0.031). mNGS was capable of accurately distinguish strains of Aspergillus genus, with a consistency of 77.8% with culture. Furthermore, mNGS also identified A. fumigatus, A. flavus, A. terrestris, A. oryzae and Mucor spp. in culture-negative cases. The sequencing reads of Aspergillus by mNGS exhibited extensive variation, ranging from 11 to1702. A positive correlation was observed between the optical density index of BALF GM and unique reads by mNGS (r = 0.607, P = 0.001) in BALF-GM positive patients. Notably, mNGS was able to diagnose 35 out of 37 cases with mixed infection, with P. jirovecii and cytomegalovirus being the most common co-pathogens.

Conclusions

mNGS presents a feasible and remarkably sensitive approach for detecting Aspergillus in ICP, thereby serving as a valuable adjunctive tool to CMT. Furthermore, mNGS's ability to accurately identify fungal species and co-pathogens can assist in guiding appropriate antimicrobial therapy.

Diagnosis of invasive pulmonary fungal infections by a real-time panfungal PCR assay in non-neutropenic patients

This study explored the utility of quantitative real-time panfungal PCR assay in diagnosing invasive pulmonary fungal diseases (IPFD) in non-neutropenic patients. Panfungal PCR assay was performed on respiratory tract specimens from patients whose clinical signs could not exclude fungal infection. At the same time, the samples were subjected to bacterial and fungal culture, microscopic examination and galactomannan antigen (GM) test in order to find the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the 4 diagnostic methods in proven and probable cases. 518 specimens were collected while 63 respiratory tract specimens tested by PCR had positive results. According to diagnostic criteria, 40 patients were diagnosed with IPFD, with 12 proven, 20 probable and 8 possible cases. Among these, 33 patients of PCR results were positive, most of which were from BALF samples (44.12%). 23 cases were caused by Aspergillus species, with Aspergillus fumigatus was the major cause. Other Aspergillus species, including Aspergillus flavus, Aspergillus terreus and Aspergillus nidulans were found in 1 sample respectively. Candida species were found in 5 samples, Pneumocystis jeroveci pneumonia (PJP) in 4 samples and Mucormycosis in 1 sample. An analysis of proven/probable diagnosis showed a sensitivity of 78.13%, specificity of 92.18%, PPV of 39.68% and NPV of 98.46% for PCR and 50%, 85.27%, 35.7%, 95.65% for GM test respectively. The Ct value difference between proven/probable and possible cases had no statistical significance (P = .824). Fungal culture showed a sensitivity of 17.5% while microscopic examination sensitivity of 32.5%. Through stratified analysis, no apparent correlation was found between the Ct value of the PCR assay and GM value (r: 0.223, P = .294). But a conjunction of the 2 tests raised the PPV of Aspergillus to 90%. As shown in this study, the panfungal RT-PCR assay has high sensitivity and consistency with serological test and culture. Its high PPV in the detection of Aspergillus and PJP were also evident.

Performance of mNGS in bronchoalveolar lavage fluid for the diagnosis of invasive pulmonary aspergillosis in non-neutropenic patients

The diagnosis of invasive pulmonary aspergillosis (IPA) diseases in non-neutropenic patients remains challenging. It is essential to develop optimal non-invasive or minimally invasive detection methods for the rapid and reliable diagnosis of IPA. Metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) can be a valuable tool for identifying the microorganism. Our study aims to evaluate the performance of mNGS in BALF in suspected IPA patients and compare it with other detection tests, including serum/BALF galactomannan antigen (GM) and traditional microbiological tests (BALF fungal culture and smear and lung biopsy histopathology). Ninety-four patients with suspicion of IPA were finally enrolled in our study. Thirty-nine patients were diagnosed with IPA, and 55 patients were non-IPA. There was significance between the IPA and non-IPA groups, such as BALF GM (P < 0.001), history of glucocorticoid use (P = 0.004), and pulmonary comorbidities (P = 0.002), as well as no significance of the other demographic data including age, sex, BMI, history of cigarette, blood GM assay, T-SPOT.TB, and NEUT#/LYMPH#. The sensitivity of the BALF mNGS was 92.31%, which was higher than that of the traditional tests or the GM assays. The specificity of BALF mNGS was 92.73%, which was relatively similar to that of the traditional tests. The AUC of BALF mNGS was 0.925, which presented an excellent performance compared with other traditional tests or GM assays. Our study demonstrated the important role of BALF detection by the mNGS platform for pathogen identification in IPA patients with non-neutropenic states, which may provide an optimal way to diagnose suspected IPA disease.

Diffuse Alveolar Hemorrhage in Hematopoietic Cell Transplantation

Diffuse alveolar hemorrhage (DAH) is a morbid syndrome that occurs after autologous and allogeneic hematopoietic cell transplantation in children and adults. DAH manifests most often in the first few weeks following transplantation. It presents with pneumonia-like symptoms and acute respiratory failure, often requiring high levels of oxygen supplementation or mechanical ventilatory support. Hemoptysis is variably present. Chest radiographs typically feature widespread alveolar filling, sometimes with peripheral sparing and pleural effusions. The diagnosis is suspected when serial bronchoalveolar lavages return increasingly bloody fluid. DAH is differentiated from infectious causes of alveolar hemorrhage when extensive microbiological testing reveals no pulmonary pathogens. The cause is poorly understood, though preclinical and clinical studies implicate pretransplant conditioning regimens, particularly those using high doses of total-body-irradiation, acute graft-versus-host disease (GVHD), medications used to prevent GVHD, and other factors. Treatment consists of supportive care, systemic corticosteroids, platelet transfusions, and sometimes includes antifibrinolytic drugs and topical procoagulant factors. Therapeutic blockade of tumor necrosis factor-α showed promise in observational studies, but its benefit for DAH remains uncertain after small clinical trials. Even with these treatments, mortality from progression and relapse is high. Future investigational therapies could target the vascular endothelial cell biology theorized to contribute to alveolar bleeding and pathways that contribute to susceptibility, inflammation, cellular resilience, and tissue repair. This review will help clinicians navigate through the limited evidence to diagnose and treat DAH, counsel patients and families, and plan for future research.

Culture-independent diagnostic approaches for invasive aspergillosis in solid organ transplant recipients

Prompt and accurate diagnosis of invasive aspergillosis (IA) is crucial for immunocompromised patients, including those who have received a solid organ transplant (SOT). Despite their low sensitivity, microscopic detection and conventional culture are considered the 'gold standard' methods. In conjunction with conventional culture, culture-independent assays such as serum galactomannan testing and Aspergillus polymerase chain reaction (PCR) have been incorporated into the diagnostic process for IA. The recently revised consensus definitions from the European Organization for Research and Treatment of Cancer and the Mycosis Study Group have adjusted the threshold for positive galactomannan testing based on the sample type, and have excluded 1,3-β-D-glucan testing as a mycological criterion. Following extensive standardization efforts, positive Aspergillus PCR tests using serum, plasma, or bronchoalveolar lavage fluid have been added. However, there are limited studies evaluating the clinical utility of these culture-independent assays for the early diagnosis of IA in SOT recipients. Therefore, further research is required to determine whether these assays could aid in the early diagnosis of IA in SOT recipients, particularly in relation to the organ transplanted. In this review, we examine the culture-independent diagnostic methods for IA in SOT recipients, as well as the clinical utility of these assays.

Utility of multimodal sampling and testing during advanced bronchoscopy for diagnosing atypical respiratory infections in a Coccidioides-endemic region

Background

The role of advanced diagnostic bronchoscopy (ADB) for assessing atypical respiratory infections is unclear. The purpose of this study was to ascertain: (I) the diagnostic utility of ADB-tissue sampling in patients with focal thoracic lesions due to atypical respiratory infections; (II) how multimodal bronchoscopic sampling and testing enhance diagnosis in a Coccidioides-endemic region.

Methods

A retrospective observational cohort study analyzing all ADBs performed over a 10-year period in patients with focal thoracic lesions diagnosed with a non-malignant disorder. Only cases which procured lower respiratory tract secretion and tissue samples by ADB, and had both cytohistology and culture results available were included.

Results

Among 403 subjects with non-malignant disease, 136 (33.7%) were diagnosed with atypical respiratory infections, with ADB contributing a diagnosis in 119 (87.5%) of these. Coccidioidal disease was independently associated with a cytohistologic diagnosis [odds ratio =7.64, 95% confidence interval (CI): 2.51-23.26; P<0.001]. Mycobacteria were more effectively identified by culture (overall yield of 8.4%, vs. 2.7% by cytohistology; P<0.001). Among subjects for which both respiratory secretion and tissue sampling were dual-tested with culture and cytology/cytohistology, adding ADB-guided transbronchial needle aspiration and/or forceps biopsy (TBNA/TBFB) to bronchoalveolar lavage and/or bronchial washings (BAL/BW) more than doubled the yield for dimorphic fungi, from 7.1% to 15.1% (increase of 8.0%, 95% CI: 5.2-11.9%). For lung lesions, adding tissue culture to dual TBNA/TBFB cytohistology-tested lung samples doubled the proportion diagnosed with atypical infection over using TBNA-cytohistology alone (increase of 15.8%, 95% CI: 10.4-23.1%). Adding lymph node to lung sampling increased the proportion diagnosed with coccidioidomycosis by 8.8% (95% CI: 4.8-15%). Among subjects with atypical respiratory infections, major ADB-related complications occurred in 1.5%.

Conclusions

ADB is useful for diagnosing atypical respiratory infections manifesting as focal thoracic lesions. A multimodal approach to both sampling and testing enhances yield, while maintaining a favorable procedure safety profile. Cytohistology testing and nodal sampling are beneficial for pulmonary coccidioidomycosis, and culture for mycobacterial disease. The approach to ADB-sampling should be adjusted according to clinical context and regional infection patterns.

Challenges in the Management of Invasive Fungal Infections in the Middle East: Expert Opinion to Optimize Management Using a Multidisciplinary Approach

Invasive fungal infection (IFI) is a significant global healthcare concern among critically ill and immunocompromised patients. In Middle Eastern countries, IFI has been steadily increasing among hospitalized patients in the past two decades. Diagnosis of IFI at an early stage is crucial for efficient management. Invasive fungal infection management is complex and requires the involvement of physicians from different specialties. There are several challenges associated with IFI management in the countries in the Middle East. This review aims to understand the key challenges associated with IFI management in the Middle East, encompassing epidemiology, diagnosis, therapeutic options, and optimizing a multidisciplinary approach. In addition, this review aims to incorporate expert opinions from multidisciplinary fields for optimizing IFI management in different Middle Eastern countries by addressing key decision points throughout the patient's journey. Lack of epidemiological data on fungal infections, slow and poorly sensitive conventional culture-based diagnostic tests, limited availability of biomarker testing, lack of awareness of clinical symptoms of the disease, limited knowledge on fungal infections, lack of local practice guidelines, and complicated disease management are the major challenges associated with IFI diagnosis and management in the Middle Eastern countries. Implementation of a multidisciplinary approach, antifungal stewardship, improved knowledge of fungal infections, the use of rapid diagnostic tests, and enhanced epidemiological research are warranted to lower the IFI burden in the Middle East.

Opportunistic Fungal Invasion in COVID-19 Pandemic: A Critical Review in Diagnosis and Management

Severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) is the culprit behind the pandemic across the globe in recent decades. Variants of SARS-CoV especially coronavirus disease 2019 (COVID-19)-related fungus might not be identified or might be misdiagnosed on a worldwide scale. Patients of COVID-19 acquired invasive mycoses, especially if they are very ill or immunosuppressed. Clinical intervention based on various standard guidelines would be necessary to guarantee that Aspergillus and Candida -infected COVID-19 patients are adequately treated. To facilitate clinical professionals, doctors, paramedics, and laboratory staff in the treatment of various variants of COVID-19 patients with concurrent aspergillosis, candidiasis, mucormycosis, or cryptococcosis, a tabulation format is drafted in this study. We believe it is prudent to take into account the general nature, and variety of the mycosis that is arriving, the strength and limits of the diagnostic tools, clinical conditions, and the need for standardized or customized therapy in various coronavirus-infected patients.

Post-COVID Fungal Osteomyelitis-Another Killer

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been sweeping across the globe as a pandemic. Based on a retrospective analysis of SARS data from worldwide, it is summarized that the fungal co-infections associated with global COVID-19 might be missed or misdiagnosed. Along with, we report case series of fungal infections in the maxilla and in the orbit, who were successfully treated for covid-19 and are on regular follow-up.

Impact of Infection Patterns on the Outcomes of Patients with Hematological Malignancies in Southwest China: A 10-Year Retrospective Case-Control Study

Background

This study aimed to assess the effect of infection patterns on the outcomes of patients with hematological malignancies (HM) and to identify the determinants of in-hospital mortality.

Methods

A case-control study was retrospectively conducted in a tertiary teaching hospital in Chongqing, Southwest China from 2011 to 2020. Clinical characteristics, microbial findings, and outcomes of HM patients with infections were retrieved from the hospital information system. Chi-square or Fisher's exact test was adopted to test the significance of mortality rate. Kaplan-Meier survival analysis and Log rank test were applied to evaluate and compare the 30-day survival rates of those groups. Binary logistic regression, Cox proportional hazards regression, and receiver operating characteristic curves were used to investigate the determinants of in-hospital mortality.

Results

Of 1,570 enrolled participants, 43.63% suffered from acute myeloid leukemia, 69.62% received chemotherapy, and 25.73% had hematopoietic stem cell transplantation (HSCT). Microbial infection was documented in 83.38% of participants. Co-infection and septic shock were reported in 32.87% and 5.67% of participants, respectively. Patients with septic shock suffered a significantly lower 30-day survival rate, while those with distinct types of pathogens or co-infections had a comparable 30-day survival rate. The all-cause in-hospital mortality was 7.01% and higher mortality rate was observed in patients with allo-HSCT (7.20%), co-infection (9.88%), and septic shock (33.71%). Cox proportional hazards regression illustrated that elderly age, septic shock, and elevated procalcitonin (PCT) were independent predictors of in-hospital mortality. A PCT cut-off value of 0.24 ng/mL predicted in-hospital mortality with a sensitivity of 77.45% and a specificity of 59.80% (95% CI = 0.684-0.779, P<0.0001).

Conclusion

Distinct infectious patterns of HM inpatients were previously unreported in Southwest China. It was the severity of infection, not co-infection, source of infection, or type of causative pathogen that positively related to poor outcome. PCT guided early recognition and treatment of septic shock were advocated.

Invasive Pulmonary Aspergillosis in Coronavirus Disease 2019 Patients Lights and Shadows in the Current Landscape

Invasive pulmonary aspergillosis (IPA) presents a known risk to critically ill patients with SARS-CoV-2; quantifying the global burden of IPA in SARS-CoV-2 is extremely challenging. The true incidence of COVID-19-associated pulmonary aspergillosis (CAPA) and the impact on mortality is difficult to define because of indiscriminate clinical signs, low culture sensitivity and specificity and variability in clinical practice between centers. While positive cultures of upper airway samples are considered indicative for the diagnosis of probable CAPA, conventional microscopic examination and qualitative culture of respiratory tract samples have quite low sensitivity and specificity. Thus, the diagnosis should be confirmed with serum and BAL GM test or positive BAL culture to mitigate the risk of overdiagnosis and over-treatment. Bronchoscopy has a limited role in these patients and should only be considered when diagnosis confirmation would significantly change clinical management. Varying diagnostic performance, availability, and time-to-results turnaround time are important limitations of currently approved biomarkers and molecular assays for the diagnosis of IA. The use of CT scans for diagnostic purposes is controversial due to practical concerns and the complex character of lesions presented in SARS-CoV-2 patients. The key objective of management is to improve survival by avoiding misdiagnosis and by initiating early, targeted antifungal treatment. The main factors that should be considered upon selection of treatment options include the severity of the infection, concomitant renal or hepatic injury, possible drug interactions, requirement for therapeutic drug monitoring, and cost of therapy. The optimal duration of antifungal therapy for CAPA is still under debate.

Fungal Pathogens as Causes of Acute Respiratory Illness in Hospitalized Veterans: Frequency of Fungal Positive Test Results Using Rapid Immunodiagnostic Assays

Fungal respiratory illnesses caused by endemic mycoses can be nonspecific and are often mistaken for viral or bacterial infections. We performed fungal testing on serum specimens from patients hospitalized with acute respiratory illness (ARI) to assess the possible role of endemic fungi as etiologic agents. Patients hospitalized with ARI at a Veterans Affairs hospital in Houston, Texas, during November 2016-August 2017 were enrolled. Epidemiologic and clinical data, nasopharyngeal and oropharyngeal samples for viral testing (PCR), and serum specimens were collected at admission. We retrospectively tested remnant sera from a subset of patients with negative initial viral testing using immunoassays for the detection of Coccidioides and Histoplasma antibodies (Ab) and Cryptococcus, Aspergillus, and Histoplasma antigens (Ag). Of 224 patient serum specimens tested, 49 (22%) had positive results for fungal pathogens, including 30 (13%) by Coccidioides immunodiagnostic assays, 19 (8%) by Histoplasma immunodiagnostic assays, 2 (1%) by Aspergillus Ag, and none by Cryptococcus Ag testing. A high proportion of veterans hospitalized with ARI had positive serological results for fungal pathogens, primarily endemic mycoses, which cause fungal pneumonia. The high proportion of Coccidioides positivity is unexpected as this fungus is not thought to be common in southeastern Texas or metropolitan Houston, though is known to be endemic in southwestern Texas. Although serological testing suffers from low specificity, these results suggest that these fungi may be more common causes of ARI in southeast Texas than commonly appreciated and more increased clinical evaluation may be warranted.

Candida spp. DNA Extraction in the Age of Molecular Diagnosis

The standard procedure for the detection of candidemia is blood culture, a method that might require 3-5 days for a positive result. Compared with culturing, molecular diagnosis techniques can provide faster diagnosis. The current paper aimed to present the main strengths and constraints of current molecular techniques for Candida spp. DNA extraction, analyzing their efficiency from a time, price, and ease of usage point of view. A comprehensive search was conducted using the PubMed NIH database for peer-reviewed full-text articles published before October 2022. The studies provided adequate data on the diagnosis of the infection with the Candida spp. DNA extraction is a relevant step in yielding pure qualitative DNA to be amplified in molecular diagnostic techniques. The most used fungal DNA extraction strategies are: mechanical (bead beating, ultrasonication, steel-bullet beating), enzymatic (proteinase K, lysozyme, lyticase), and chemical extraction (formic acid, liquid nitrogen, ammonium chloride). More clinical studies are needed to formulate adequate guidelines for fungal DNA extraction as the current paper highlighted discrepancies in the reported outcome.

Ventilator-Associated Pneumonia in Immunosuppressed Patients

Immunocompromised patients-including patients with cancer, hematological malignancies, solid organ transplants and individuals receiving immunosuppressive therapies for autoimmune diseases-account for an increasing proportion of critically-ill patients. While their prognosis has improved markedly in the last decades, they remain at increased risk of healthcare- and intensive care unit (ICU)-acquired infections. The most frequent of these are ventilator-associated lower respiratory tract infections (VA-LTRI), which include ventilator-associated pneumonia (VAP) and tracheobronchitis (VAT). Recent studies have shed light on some of the specific features of VAP and VAT in immunocompromised patients, which is the subject of this narrative review. Contrary to previous belief, the incidence of VAP and VAT might actually be lower in immunocompromised than non-immunocompromised patients. Further, the relationship between immunosuppression and the incidence of VAP and VAT related to multidrug-resistant (MDR) bacteria has also been challenged recently. Etiological diagnosis is essential to select the most appropriate treatment, and the role of invasive sampling, specifically bronchoscopy with bronchoalveolar lavage, as well as new molecular syndromic diagnostic tools will be discussed. While bacteria-especially gram negative bacteria-are the most commonly isolated pathogens in VAP and VAT, several opportunistic pathogens are a special concern among immunocompromised patients, and must be included in the diagnostic workup. Finally, the impact of immunosuppression on VAP and VAT outcomes will be examined in view of recent papers using improved statistical methodologies and treatment options-more specifically empirical antibiotic regimens-will be discussed in light of recent findings on the epidemiology of MDR bacteria in this population.

Bronchoalveolar lavage fluid polymerase chain reaction for invasive pulmonary aspergillosis among high-risk patients: a diagnostic meta-analysis

BACKGROUND

Polymerase chain reaction (PCR) assays are perceived to facilitate the diagnosis of fungal infections. However, due to lack of standardization, the value of bronchoalveolar lavage (BAL) fluid PCR in diagnosis of invasive pulmonary aspergillosis (IPA) remains unclear.

METHODS

We conducted a systematic meta-analysis to evaluate the accuracy of BAL fluid PCR in IPA diagnosis among high-risk patients. All studies involving patients at risk for IPA were included. The sensitivity, specificity, positive and negative likelihood ratios of BAL fluid PCR were summarized for diagnosis of proven/probable IPA, or proven IPA only. Potential heterogeneity was assessed by subgroup analyses and meta-regression.

RESULTS

Forty-one studies involving 5668 patients were analyzed. The summary sensitivity, specificity, positive and negative likelihood ratios of BAL fluid PCR for proven/probable IPA were 0.75 (95% CI = 0.67-0.81), 0.94 (95% CI = 0.90-0.96), 11.8 (95% CI = 7.7-18.1) and 0.27 (95% CI = 0.20-0.36), respectively. Whereas for proven IPA only, sensitivity and specificity were 0.91 (95% CI = 0.68-0.98) and 0.80 (95% CI = 0.74-0.85) in fourteen studies involving 2061 patients. Significant heterogeneity was present due to the underlying disease, antifungal treatment and differences in DNA extraction techniques and choice of PCR assay. Compared to patients with hematological malignancies (HM) and hematopoietic stem cell/solid organ transplantation (HSCT/SOT), sensitivity was higher in the population with disease such as chronic obstructive pulmonary disease, solid tumor, autoimmune disease with prolonged use of corticosteroids, etc. (0.88 vs. 0.68, P < 0.001), which was related to the concurrent use of antifungal prophylaxis among patients with HM and HSCT/SOT.

CONCLUSION

BAL fluid PCR is a useful diagnostic tool for IPA in immunocompromised patients and is also effective for diagnosing IPA in patients without HM and HSCT/SOT. Furthermore, standard protocols for DNA extraction and PCR assays should be focused on to improve the diagnostic accuracy. Trial registration PROSPERO, registration number CRD42021239028.

The clinical significance of Aspergillus-positive respiratory samples

BACKGROUND

Aspergilli moulds are frequently detected in sputum and other respiratory samples. It is not known what the significance of these findings is, or how to differentiate contamination, temporary or persistent colonisation from clinical infection when Aspergilli are found in respiratory samples.

OBJECTIVES

In this study we studied the clinical significance of Aspergillus findings from respiratory samples.

METHODS

We retrospectively evaluated 299 patients who had provided Aspergillus-positive respiratory samples in 2007-2016, which provided a follow-up time of 3-13 years. Data were collected from laboratory registry and Helsinki University Hospital medical records. Underlying diseases, immunosuppression, reasons for sample collection, clinical significance of positive Aspergillus culture, antifungal medication, and patient survival were assessed.

RESULTS

Underlying pulmonary disease had 88% of patients, most commonly asthma (44%), bronchiectasis (30%) or COPD (21%). Corticosteroids (orally or inhalation therapy) prior to positive samples used 78%; the use of corticosteroids did not explain the development of Aspergillus disease. Pulmonary disease caused by Aspergillus was identified in 88 (29%) of the reviewed patients; remaining samples did not represent clinical disease. Chronic cavitary or fibrosing pulmonary aspergillosis (CCPA or CFPA) had 44 (49%) of the diseased. The probability of Aspergillus disease increased when Aspergillus-positive samples were given repeatedly within 1 year (p = .001). Mortality for all reasons was 45%. The repeated positive samples did not predict survival (p = .084), but the diagnosis of CPA did (p < .001).

CONCLUSIONS

The possibility of Aspergillus disease increases when Aspergilli are found repeatedly, collection of samples should be repeated due to method insensitivity. Diagnosis of CPA predicted significantly lower survival.

Post-cardiac surgery fungal mediastinitis: clinical features, pathogens and outcome

OBJECTIVES

The occurrence of mediastinitis after cardiac surgery remains a rare and severe complication associated with poor outcomes. Whereas bacterial mediastinitis have been largely described, little is known about their fungal etiologies. We report incidence, characteristics and outcome of post-cardiac surgery fungal mediastinitis.

METHODS

Multicenter retrospective study among 10 intensive care units (ICU) in France and Belgium of proven cases of fungal mediastinitis after cardiac surgery (2009-2019).

RESULTS

Among 73,688 cardiac surgery procedures, 40 patients developed fungal mediastinitis. Five were supported with left ventricular assist device and five with veno-arterial extracorporeal membrane oxygenation before initial surgery. Twelve patients received prior heart transplantation. Interval between initial surgery and mediastinitis was 38 [17-61] days. Only half of the patients showed local signs of infection. Septic shock was uncommon at diagnosis (12.5%). Forty-three fungal strains were identified: Candida spp. (34 patients), Trichosporon spp. (5 patients) and Aspergillus spp. (4 patients). Hospital mortality was 58%. Survivors were younger (59 [43-65] vs. 65 [61-73] yo; p = 0.013), had lower body mass index (24 [20-26] vs. 30 [24-32] kg/m²; p = 0.028) and lower Simplified Acute Physiology Score II score at ICU admission (37 [28-40] vs. 54 [34-61]; p = 0.012).

CONCLUSION

Fungal mediastinitis is a very rare complication after cardiac surgery, associated with a high mortality rate. This entity should be suspected in patients with a smoldering infectious postoperative course, especially those supported with short- or long-term invasive cardiac support devices, or following heart transplantation.

Rapid preparation of Candida genomic DNA: combined use of enzymatic digestion and thermal disruption

Nucleic acid based molecular technologies are the most promising tools for the early diagnosis of Candida infection. A simple and effective DNA preparation method is of critical for standardizing and applying molecular diagnostics in clinic laboratories. The goal of this study was to develop a Candida DNA preparation method that was quick to do, easy to perform, and bio-safe. Snailase and lyticase were screened and combined in this work to enhance the lysis of Candida cells. The lysis solution composition and metal bath were optimized to boost amplification efficiency and biosafety. A duplex real-time PCR was established to evaluate the sensitivity and specificity of the preparation method. Using the supernatant from the rapid preparation method as templates, the duplex PCR sensitivities for five common Candida species were determined to be as low as 10⁰ CFUs. When compared to conventional preparation methods, the samples prepared by our method showed higher PCR detection sensitivity. PCR identification and ITS sequencing were 100% consistent, which was better than biochemical identification. This study demonstrates a rapid method for Candida DNA preparation that has the potential to be used in clinical laboratories. Meanwhile, the practical application of the method for clinical samples needs to be proven in future investigations.

Machine learning algorithm as a prognostic tool for venous thromboembolism in allogeneic transplant patients

As a serious complication after allogenic hematopoietic stem cell transplantation (allo-HSCT), venous thromboembolism (VTE) is significantly related to increased nonrelapse mortality. Therefore distinguishing patients at high risk of death who should receive specific therapeutic management is key to improving survival. This study aimed to establish a machine learning-based prognostic model for the identification of post-transplantation VTE patients who have a high risk of death. We retrospectively evaluated 256 consecutive VTE patients who underwent allo-HSCT at our center between 2008 and 2019. These patients were further randomly divided into (1) a derivation (80%) cohort of 205 patients and (2) a test (20%) cohort of 51 patients. The least absolute shrinkage and selection operator (LASSO) approach was used to choose the potential predictors from the primary dataset. Eight machine learning classifiers were used to produce 8 candidate models. A 10-fold cross-validation procedure was used to internally evaluate the models and to select the best-performing model for external assessment using the test cohort. In total, 256 of 7238 patients were diagnosed with VTE after transplantation. Among them, 118 patients (46.1%) had catheter-related venous thrombosis, 107 (41.8%) had isolated deep-vein thrombosis (DVT), 20 (7.8%) had isolated pulmonary embolism (PE), and 11 (4.3%) had concomitant DVT and PE. The 2-year overall survival (OS) rate of patients with VTE was 68.8%. Using LASSO regression, 8 potential features were selected from the 54 candidate variables. The best-performing algorithm based on the 10-fold cross-validation runs was a logistic regression classifier. Therefore a prognostic model named BRIDGE was then established to predict the 2-year OS rate. The areas under the curves of the BRIDGE model were 0.883, 0.871, and 0.858 for the training, validation, and test cohorts, respectively. The Hosmer-Lemeshow goodness-of-fit test showed a high agreement between the predicted and observed outcomes. Decision curve analysis indicated that VTE patients could benefit from the clinical application of the prognostic model. A BRIDGE risk score calculator for predicting the study result is available online (47.94.162.105:8080/bridge/). We established the BRIDGE model to precisely predict the risk for all-cause death in VTE patients after allo-HSCT. Identifying VTE patients who have a high risk of death can help physicians treat these patients in advance, which will improve patient survival.

Associated microbiota and treatment of severe fever with thrombocytopenia syndrome complicated with infections

The purpose of this study is to assess the incidence and management of co-infections in hospitalized severe fever with thrombocytopenia syndrome bunyavirus (SFTSV) patients. We retrospectively evaluated the microbiological database records of the SFTS patients in the first affiliated hospital of Anhui Medical University from January 1, 2018, to December 1, 2021. According to the obtained results, co-infections including pulmonary infection, bloodstream infection, biliary tract infection, urinary tract infection, and abdominal infection were observed in SFTS patients. The incidence rate of fungal infections was found to be high in SFTS patients. Furthermore, we suggest that old age people should be evaluated for the risk of fungal infection. In comparison to the non-infection group, patients in the co-infection group were more likely to get mechanical ventilation, antibacterial treatment, antifungal treatment, and blood product therapy (p < 0.001), with a significantly longer length of stay (p < 0.05). In SFTS patients, the most prevalent strains were Aspergillus fumigatus, Aspergillus flavus, Candida, Klebsiella pneumonia, and Escherichia coli. In this investigation, 66.2% (106/160) of patients were given antibiotics, most often Piperacillin/tazobactam or minocycline. 15.6% (25/160) of patients were treated with antifungal drugs: 13.1% (21/160) with voriconazole. Patients with SFTS Associated Pulmonary Aspergillosis (SAPA) received active antifungal treatment, but the mortality rate was still 23.5% (8/34). Only 6 of the 11 patients with SFTS Associated Candidiasis were treated with antifungal drugs with no mortality. Due to the high frequency of fungal pulmonary infection in SFTS patients, more standardized fungal detection program should be strengthened.

Radical treatment for blastomycosis following unsuccessful liposomal amphotericin

Pulmonary blastomycosis is a respiratory disease that is caused by the fungus Blastomyces spp, which is acquired through inhalation of the fungal spores. Blastomycosis is relatively uncommon, with yearly incidence rate of 1-2 cases per 100 000 people. Blastomycosis is a disease that is endemic to the midwest and southern regions of the USA, most commonly affecting immunocompromised patients. About 50% of patients are asymptomatic, but for those who progress to acute respiratory distress syndrome (ARDS) mortality can be as high as 80%. Patients with severe blastomycosis are initially treated with intravenous amphotericin B, followed by long-term itraconazole maintenance therapy. In this Grand Round, we present the case of an immunocompetent 35-year-old man diagnosed with chronic pulmonary blastomycosis who had a poor response to 10 days of intravenous liposomal amphotericin B (L-AmB). He was endotracheally intubated and eventually cannulated for extracorporeal membrane oxygenation (ECMO), due to worsening respiratory function. L-AmB was replaced with a continuous infusion of intravenous amphotericin B deoxycholate (AmB-d). He improved significantly and was decannulated from ECMO on day 9 of AmBd continuous infusion and extubated on day 12 Although L-AmB is considered first-line treatment for blastomycosis, mortality remains high for patients with ARDS associated with blastomycosis. This case highlights the importance of considering AmB-d continuous infusions for patients with severe blastomycosis who might have poor clinical responses to L-AmB.

Diagnosis and Antifungal Prophylaxis for COVID-19 Associated Pulmonary Aspergillosis

The COVID-19 pandemic has redemonstrated the importance of the fungal-after-viral phenomenon, and the question of whether prophylaxis should be used to prevent COVID-19-associated pulmonary aspergillosis (CAPA). A distinct pathophysiology from invasive pulmonary aspergillosis (IPA), CAPA has an incidence that ranges from 5% to 30%, with significant mortality. The aim of this work was to describe the current diagnostic landscape of CAPA and review the existing literature on antifungal prophylaxis. A variety of definitions for CAPA have been described in the literature and the performance of the diagnostic tests for CAPA is limited, making diagnosis a challenge. There are only six studies that have investigated antifungal prophylaxis for CAPA. The two studied drugs have been posaconazole, either a liquid formulation via an oral gastric tube or an intravenous formulation, and inhaled amphotericin. While some studies have revealed promising results, they are limited by small sample sizes and bias inherent to retrospective studies. Additionally, as the COVID-19 pandemic changes and we see fewer intubated and critically ill patients, it will be more important to recognize these fungal-after-viral complications among non-critically ill, immunocompromised patients. Randomized controlled trials are needed to better understand the role of antifungal prophylaxis.

When to Initiate Antifungal Treatment in COVID-19 Patients with Secondary Fungal Co-infection

Purpose of Review

Severe-acute respiratory coronavirus 2 (SARS-CoV-2) has been driving the health care delivery system for over 2 years. With time, many issues related to co-infections in COVID-19 patients are constantly surfacing. There have been numerous reports about various fungal co-infections in patients with COVID-19. The extent of severity of fungal pathogens has been recognized as a substantial cause of morbidity and mortality in this population. Awareness, understanding, and a systematic approach to managing fungal co-infections in COVID-19 patients are important. No guidelines have enumerated the stepwise approach to managing the fungal infections co-occurring with COVID-19. This review is intended to present an overview of the fungal co-infections in COVID-19 patients and their stepwise screening and management.

Recent Findings

The most common fungal infections that have been reported to co-exist with COVID-19 are Candidemia, Aspergillosis, and Mucormycosis. Prevalence of co-infections in COVID-19 patients has been reported to be much higher in hospitalized COVID-19 patients, especially those in intensive care units. While clear pathogenetic mechanisms have not been delineated, COVID-19 patients are at a high risk of invasive fungal infections.

Summary

As secondary fungal infections have been challenging to treat in COVID-19 patients, as they tend to affect the critically ill or immunocompromised patients, a delay in diagnosis and treatment may be fatal. Antifungal drugs should be initiated with caution after carefully assessing the immune status of the patients, drug interactions, and adverse effects. The crucial factors in successfully treating fungal infections in COVID-19 patients are optimal diagnostic approach, routine screening, and timely initiation of antifungal therapy.

Progress and challenges in fungal lung disease in cystic fibrosis

PURPOSE OF REVIEW

This review is an overview of the recent progress made for the diagnosis and understanding of fungal lung disease in people with cystic fibrosis (CF), with a focus on Aspergillus fumigatus , the most common filamentous fungus in the CF airway. Currently, the longstanding question of the clinical significance of Aspergillus fumigatus and other fungi in CF respiratory cultures, in the absence of allergy, remains. Clinical criteria and biomarkers are needed to classify fungal lung disease and determine who may warrant therapy.

RECENT FINDINGS

Several retrospective and prospective studies have described the prevalence of A. fumigatus and other fungi in the CF lung and factors contributing to the changes in fungal epidemiology. Selective fungus culture testing for the detection of fungi in CF sputa has been well studied, yet a standardized fungus culture protocol has yet to be defined. Culture-independent molecular studies and other fungal diagnostic testing have been conducted in the CF population, leading to efforts to better understand the clinical role of these tests. Recent works have aimed to determine whether chronic A. fumigatus colonization is associated with lung disease progression measured by FEV 1 percentage predicted, structural lung disease, lung clearance index and respiratory quality-of-life. However, the existing knowledge gaps remain: definition of a fungal respiratory infection, the association between fungal infection and clinical outcomes, and indications for antifungal therapy.

SUMMARY

Significant progress has been made for the detection and diagnosis of fungal lung disease. Yet, the role and impact of A. fumigatus and other fungal infections on respiratory health in people with CF remains to be determined.

COVID-19-associated pulmonary aspergillosis: an underdiagnosed or overtreated infection?

PURPOSE OF REVIEW

Coronavirus disease (COVID-19)-associated pulmonary aspergillosis (CAPA) may concern up to one third of intensive care unit (ICU) patients. The purpose of this review is to discuss the diagnostic criteria, the pathogenesis, the risk factors, the incidence, the impact on outcome, and the diagnostic and therapeutic management of CAPA in critically ill patients.

RECENT FINDINGS

The incidence of CAPA ranges 3--28% of critically ill patients, depending on the definition used, study design, and systematic or triggered screening. COVID-19 is associated with direct damage of the respiratory epithelium, immune dysregulation, and common use of immunosuppressive drugs which might promote Aspergillus respiratory tract colonization and invasion. Positive Aspergillus tests among COVID-19 critically patients might reflect colonization rather than invasive disease. CAPA usually appears during the second week after starting invasive mechanical ventilation and is independently associated with ICU mortality.

SUMMARY

Further studies are needed to validate CAPA case definitions, to determine the accurate incidence of CAPA in comparison to adequate controls, and its evolution during the pandemic. A pro-active diagnostic strategy, based on risk stratification, clinical assessment, and bronchoalveolar lavage could be recommended to provide early antifungal treatment in patients with high probability of CAPA and clinical deterioration.

Progranulin aggravates lethal Candida albicans sepsis by regulating inflammatory response and antifungal immunity

Candida albicans is the most frequent pathogen of fungal sepsis associated with substantial mortality in critically ill patients and those who are immunocompromised. Identification of novel immune-based therapeutic targets from a better understanding of its molecular pathogenesis is required. Here, we reported that the production of progranulin (PGRN) levels was significantly increased in mice after invasive C.albicans infection. Mice that lacked PGRN exhibited attenuated kidney injury and increased survival upon a lethal systemic infection with C. albicans. In mice, PGRN deficiency protected against systemic candidiasis by decreasing aberrant inflammatory reactions that led to renal immune cell apoptosis and kidney injury, and by enhancing antifungal capacity of macrophages and neutrophils that limited fungal burden in the kidneys. PGRN in hematopoietic cell compartment was important for this effect. Moreover, anti-PGRN antibody treatment limited renal inflammation and fungal burden and prolonged survival after invasive C. albicans infection. In vitro, PGRN loss increased phagocytosis, phagosome formation, reactive oxygen species production, neutrophil extracellular traps release, and killing activity in macrophages or neutrophils. Mechanistic studies demonstrated that PGRN loss up-regulated Dectin-2 expression, and enhanced spleen tyrosine kinase phosphorylation and extracellular signal-regulated kinase activation in macrophages and neutrophils. In summary, we identified PGRN as a critical factor that contributes to the immunopathology of invasive C.albicans infection, suggesting that targeting PGRN might serve as a novel treatment for fungal infection.

Fatal acute respiratory distress syndrome caused by blastomycosis after recent orthotopic liver transplantation in a non-endemic area

In blastomycosis, immunosuppression such as that following solid organ transplantation appears to be a risk factor for the development of overwhelming lung infection fulfilling criteria for the acute respiratory distress syndrome. Our transplant center, located outside traditional endemic areas for Blastomyces spp, experienced a case of fatal acute respiratory distress syndrome secondary to blastomycosis pneumonia in a recipient of recent orthotopic liver transplantation. The patient expired despite support with veno-venous extracorporeal membrane oxygenation.

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Immunosuppression is associated with overwhelming pneumonia and lung injury in blastomycosis.

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Acute respiratory distress syndrome from blastomycosis poses a danger to recipients of solid organ transplantation.

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We describe a fatal case of ARDS from blastomycosis in a recipient of recent orthotopic liver transplantation in a non-endemic region.

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Pre-transplant lung nodules could represent asymptomatic blastomycosis that could become overt after immunosuppression.

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This case underscores the need to evaluate suspicious lung nodules prior to transplantation, resorting to biopsy if required.

Challenges in Serologic Diagnostics of Neglected Human Systemic Mycoses: An Overview on Characterization of New Targets

Systemic mycoses have been viewed as neglected diseases and they are responsible for deaths and disabilities around the world. Rapid, low-cost, simple, highly-specific and sensitive diagnostic tests are critical components of patient care, disease control and active surveillance. However, the diagnosis of fungal infections represents a great challenge because of the decline in the expertise needed for identifying fungi, and a reduced number of instruments and assays specific to fungal identification. Unfortunately, time of diagnosis is one of the most important risk factors for mortality rates from many of the systemic mycoses. In addition, phenotypic and biochemical identification methods are often time-consuming, which has created an increasing demand for new methods of fungal identification. In this review, we discuss the current context of the diagnosis of the main systemic mycoses and propose alternative approaches for the identification of new targets for fungal pathogens, which can help in the development of new diagnostic tests.

Comparison of the Performance of Two Galactomannan Detection Tests: Platelia Aspergillus Ag and Aspergillus Galactomannan Ag Virclia Monotest

The use of nonculture-based biomarkers such as the determination of galactomannan is sought for the diagnosis of invasive aspergillosis. To investigate the comparative yield of two tests for the detection of galactomannan in patients with or without proven or probable invasive aspergillosis. Overall, 327 samples (327 patients) were analyzed in a retrospective/prospective study performed in 3 hospitals in Madrid, comparing the determination results in serum or bronchoalveolar lavage of two techniques for galactomannan detection, namely, Platelia Aspergillus Ag (Bio-Rad) and Aspergillus galactomannan Ag Virclia Monotest (Vircell S.L.), following the manufacturer's instructions. Both techniques can automate the process, but the second technique has the advantage of individual processing and assembly of each sample without the need for the additional expense of single-dose strips in controls. In total, 288 of the 327 tests performed showed concordant results between both techniques. The agreement between both methods was к = 0.722, and the correlation between indices was ρ = 0.718. Only 39 samples showed discordant results. In those 39 cases, there were 15 patients with proven or probable invasive aspergillosis criteria. For the samples with clinical criteria as a reference, the areas under the curve of the receiver operating characteristic (ROC) curve were 0.962 for Platelia and 0.968 for VirClia. The VirClia test has been proven to be an alternative for diagnosis due to its friendlier automated format than that of the usual Platelia routine test. The VirClia test also allows individual action and, therefore, a more immediate clinical response. IMPORTANCE Invasive mycoses are increasingly present in immunosuppressed or hospitalized patients with serious illnesses, leading to high rates of morbidity and mortality. Invasive aspergillosis is an infection caused, in a percentage greater than 50%, by the genus Aspergillus. It is vitally important to make an early diagnosis that leads to the application of antifungals in the initial stage of the infection. Therefore, tools are required to help with the early diagnosis of the infection. This comparative study of two enzyme immunoassays is based on the detection of galactomannan antigen in serum and bronchoalveolar lavage samples. A new design based on chemiluminescence and presented in an automated single-dose format is compared to a conventional ELISA technique marketed for years. The results obtained from the prospective and retrospective study indicate a high correlation and degree of agreement between both techniques, as well as in their diagnostic performance.

Approach to fever in patients with neutropenia: a review of diagnosis and management

Febrile neutropenia (FN) is associated with mortality rates as high as 40%, highlighting the importance of appropriate clinical management in this patient population. The morbidity and mortality of FN can be attributed largely to infectious processes, with specific concern for infections caused by pathogens with antimicrobial resistance. Expeditious identification of responsible pathogens and subsequent initiation of empiric antimicrobial therapy is imperative. There are four commonly used guidelines, which have variable recommendations for empiric therapy in these populations. All agree that changes could be made once patients are stable and/or with an absolute neutrophil count (ANC) over 500 cells/mcL. Diagnostic advances have the potential to improve knowledge of pathogens responsible for FN and decrease time to results. In addition, more recent data show that rapid de-escalation or discontinuation of empiric therapy, regardless of ANC, may reduce days of therapy, adverse effects, and cost, without affecting clinical outcomes. Antimicrobial and diagnostic stewardship should be performed to identify, utilize, and respond to appropriate rapid diagnostic tests that will aid in the definitive management of this population.

Effective Inhibition of Invasive Pulmonary Aspergillosis by Silver Nanoparticles Biosynthesized with Artemisia sieberi Leaf Extract

Aspergillus fumigatus is one of the most common fungal pathogens that can cause a diversity of diseases ranging from invasive pulmonary aspergillosis (IPA) and aspergilloma to allergic syndromes. In this study, we investigated the antifungal effect of silver nanoparticles biosynthesized with Artemisia sieberi leaf extract (AS-AgNPs) against A. fumigatus in vitro and in vivo. The biosynthesized AS-AgNPs were characterized by imaging (transmission electron microscopy (TEM)), UV-VIS spectroscopy, X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). The microdilution method showed the antifungal activity of AS-AgNPs against A. fumigatus, with an MIC of 128 µg/mL. AS-AgNPs significantly inhibited the growth of hyphae in all directions, as imaged by SEM. Additionally, TEM on biofilm revealed invaginations of the cell membrane, a change in the vacuolar system, and the presence of multilamellar bodies within vacuoles. Interestingly, AS-AgNPs displayed low cytotoxicity on the A549 human lung cell line in vitro. Treatment of an invasive pulmonary aspergillosis (IPA) mouse model with AS-AgNPs demonstrated the potency of AS-AgNPs to significantly reduce lung tissue damage and to suppress the elevated levels of pro-inflammatory cytokines, tumor necrosis factor-alpha (TNF-α), interleukin-1 (IL-1), and interleukin-17 (IL-17). The therapeutic potential of AS-AgNPs was found to be due to their direct action to suppress the fungal burden and gliotoxin production in the lungs. In addition, AS-AgNPs reduced the oxidative stress in the lungs by increasing the enzymatic activities of catalase (CAT) and superoxide dismutase (SOD). Thus, our data indicate the biosynthesized AS-AgNPs as a novel antifungal alternative treatment against aspergillosis.

Aspergillosis: Emerging risk groups in critically ill patients

Information on invasive aspergillosis (IA) and other invasive filamentous fungal infections is limited in non-neutropenic patients admitted to the intensive care unit (ICU) and presenting with no classic IA risk factors. This review is based on the critical appraisal of relevant literature, on the authors' own experience and on discussions that took place at a consensus conference. It aims to review risk factors favoring aspergillosis in ICU patients, with a special emphasis on often overlooked or neglected conditions. In the ICU patients, corticosteroid use to treat underlying conditions such as chronic obstructive pulmonary disease (COPD), sepsis, or severe COVID-19, represents a cardinal risk factor for IA. Important additional host risk factors are COPD, decompensated cirrhosis, liver failure, and severe viral pneumonia (influenza, COVID-19). Clinical observations indicate that patients admitted to the ICU because of sepsis or acute respiratory distress syndrome are more likely to develop probable or proven IA, suggesting that sepsis could also be a possible direct risk factor for IA, as could small molecule inhibitors used in oncology. There are no recommendations for prophylaxis in ICU patients; posaconazole mold-active primary prophylaxis is used in some centers according to guidelines for other patient populations and IA treatment in critically ill patients is basically the same as in other patient populations. A combined evaluation of clinical signs and imaging, classical biomarkers such as the GM assay, and fungal cultures examination, remain the best option to assess response to treatment.

LAY SUMMARY

The use of corticosteroids and the presence of co-morbidities such as chronic obstructive pulmonary disease, acute or chronic advanced liver disease, or severe viral pneumonia caused by influenza or Covid-19, may increase the risk of invasive aspergillosis in intensive care unit patients.

Risk factors of severe blastomycosis and comparison of diagnosis and outcomes between immunocompetent and immunocompromised patients

BACKGROUND

Blastomycosis is an endemic fungal infection that causes pulmonary and systemic disease. It can occur irrespective of the patient's immune status. The risk factors associated with the severity of the disease are not well studied.

METHODS

This is a retrospective study of patients admitted with blastomycosis at the University of Kentucky Hospital from 2004 to 2019. Logistic regression was used to identify variables associated with severe blastomycosis.

RESULTS

A total of 76 patients were identified; 22 (28.9%) had at least one immunosuppressive condition. Pulmonary blastomycosis was reported in 49/76 (65%) of the patients and disseminated infection in 27/76 (35.5%). All diagnostic tests were not significantly different in diagnostic results in immunocompromised vs immunocompetent patients. Cultures and histopathology were positive in 56/61 (91.8%) and 54/63 (85.7%) respectively. Blastomyces or Histoplasma antigen test was positive in 13/17 (76.4%) in immunocompromised patients compared to 26/42 (61.9%) in immunocompetent patients. Immunocompromised patients were more likely to be admitted to the hospital and ICU compared to immunocompetent patients. In the multivariate analysis, pulmonary multilobar disease (RR 5.68; 95% CI 2.13-15.15), obesity (RR 2.39; 95% CI 1.26-4.51), diabetes mellitus (RR 3.50; 95% CI 1.38-8.90) and immunosuppression (RR 2.28; 95% CI 1.14-4.56) were significant independent risk factors for severe blastomycosis. Inpatient mortality proportion was higher in immunocompromised patients but not statistically significant.

CONCLUSION

Pulmonary multilobar disease, obesity, diabetes mellitus and immunosuppression were risk factors associated with severe blastomycosis. Immunocompromised patients required more frequent hospitalisations compared to immunocompetent patients.

Liquid Biopsy for Invasive Mold Infections in Hematopoietic Cell Transplant Recipients With Pneumonia Through Next-Generation Sequencing of Microbial Cell-Free DNA in Plasma

BACKGROUND

Noninvasive diagnostic options are limited for invasive mold infections (IMIs). We evaluated the performance of a plasma microbial cell-free DNA sequencing (mcfDNA-Seq) test for diagnosing pulmonary IMI after hematopoietic cell transplant (HCT).

METHODS

We retrospectively assessed the diagnostic performance of plasma mcfDNA-Seq next-generation sequencing in 114 HCT recipients with pneumonia after HCT who had stored plasma obtained within 14 days of diagnosis of proven/probable Aspergillus IMI (n = 51), proven/probable non-Aspergillus IMI (n = 24), possible IMI (n = 20), and non-IMI controls (n = 19). Sequences were aligned to a database including >400 fungi. Organisms above a fixed significance threshold were reported.

RESULTS

Among 75 patients with proven/probable pulmonary IMI, mcfDNA-Seq detected ≥1 pathogenic mold in 38 patients (sensitivity, 51% [95% confidence interval {CI}, 39%-62%]). When restricted to samples obtained within 3 days of diagnosis, sensitivity increased to 61%. McfDNA-Seq had higher sensitivity for proven/probable non-Aspergillus IMI (sensitivity, 79% [95% CI, 56%-93%]) compared with Aspergillus IMI (sensitivity, 31% [95% CI, 19%-46%]). McfDNA-Seq also identified non-Aspergillus molds in an additional 7 patients in the Aspergillus subgroup and Aspergillus in 1 patient with possible IMI. Among 19 non-IMI pneumonia controls, mcfDNA-Seq was negative in all samples, suggesting a high specificity (95% CI, 82%-100%) and up to 100% positive predictive value (PPV) with estimated negative predictive values (NPVs) of 81%-99%. The mcfDNA-Seq assay was complementary to serum galactomannan index testing; in combination, they were positive in 84% of individuals with proven/probable pulmonary IMI.

CONCLUSIONS

Noninvasive mcfDNA-Seq had moderate sensitivity and high specificity, NPV, and PPV for pulmonary IMI after HCT, particularly for non-Aspergillus species.

Metagenomic Next-Generation Sequencing for Pulmonary Fungal Infection Diagnosis: Lung Biopsy versus Bronchoalveolar Lavage Fluid

Purpose

Metagenomic next-generation sequencing (mNGS) is widely used for pulmonary infection; nonetheless, the experience from its clinical use in diagnosing pulmonary fungal infections is sparse. This study aimed to compare mNGS results from lung biopsy and bronchoalveolar lavage fluid (BALF) and determine their clinical diagnostic efficacy.

Patients and Methods

A total of 106 patients with suspected pulmonary fungal infection from May 2018 to January 2020 were included in this retrospective study. All patients' lung biopsy and BALF specimens were collected through bronchoscopy. Overall, 45 (42.5%) patients had pulmonary fungal infection. The performance of lung biopsy and BALF used for mNGS in diagnosing pulmonary fungal infections and identifying pathogens was compared. Additionally, mNGS was compared with conventional tests (pathology, galactomannan test, and cultures) with respect to the diagnosis of pulmonary fungal infections.

Results

Lung biopsy-mNGS and BALF-mNGS exhibited no difference in terms of sensitivity (80.0% vs 84.4%, P=0.754) and specificity (91.8% vs 85.3%, P=0.39). Additionally, there was no difference in specificity between mNGS and conventional tests; however, the sensitivity of mNGS (lung biopsy, BALF) in diagnosing pulmonary fungal infections was significantly higher than that of conventional tests (conventional tests vs biopsy-mNGS: 44.4% vs 80.0%, P<0.05; conventional tests vs BALF-mNGS: 44.4% vs 84.4%, P<0.05). Among 32 patients with positive mNGS results for both biopsy and BALF specimens, 23 (71.9%) cases of consistency between the two tests for the detected fungi and nine (28.1%) cases of a partial match were identified. Receiver operating curve analysis revealed that the area under the curve for the combination of biopsy and BALF was significantly higher than that for BALF-mNGS (P=0.018).

Conclusion

We recommend biopsy-based or BALF-based mNGS for diagnosing pulmonary fungal infections because of their diagnostic advantages over conventional tests. The combination of biopsy and BALF for mNGS can be considered when higher diagnostic efficacy is required.

Identifying Mucormycosis Severity in Indian COVID-19 Patients: A Nano-Based Diagnosis and the Necessity for Critical Therapeutic Intervention

The COVID-19 infection caused by the new SARS-CoV-2 virus has been linked to a broad spectrum of symptoms, from a mild cough to life-threatening pneumonia. As we learn more about this unusual COVID-19 epidemic, new issues are emerging and being reported daily. Mucormycosis, also known as zygomycosis or phycomycosis, causes severe fungal illness to individuals with a weakened immune system. It is a devastating fungal infection, and the most frequent kind is the rhino cerebral type. As a devastating second wave of COVID-19 sweeps India, doctors report several instances involving a strange illness-sometimes known as the "black fungus"-among returning and recovered COVID-19 patients. This paper analyzes the existing statistical data to address the severity of prevalence and further notes the nano-based diagnostic parameters, clinical presentations, its connection with other conditions like diabetes, hypertension, and GI disorders, and the importance of anti-fungal therapy in treating the same. Anti-fungal therapies, as well as surgical interventions, are currently used for the treatment of the disease. Proper and timely diagnosis is necessary, along with the reduction in the spread of COVID-19. From the review, it was found that timely pharmacologic interventions and early diagnosis by using a nano-based diagnostic kit can help control the disease. Additionally, this paper provides novel information about the nanotechnology approaches such as fungal detection biosensors, nucleic acids-based testing, point-of-care tests, and galactomannans detection, in the diagnosis of mucormycosis, and thereby reinforces the need for further research on the topic.