Diagnosis of Fungal Infections. A Systematic Review and Meta-Analysis Supporting American Thoracic Society Practice Guideline

INTERPRETABLE MACHINE LEARNING FOR PREDICTING RISK OF INVASIVE FUNGAL INFECTION IN CRITICALLY ILL PATIENTS IN THE INTENSIVE CARE UNIT: A RETROSPECTIVE COHORT STUDY BASED ON MIMIC-IV DATABASE

ABSTRACT

The delayed diagnosis of invasive fungal infection (IFI) is highly correlated with poor prognosis in patients. Early identification of high-risk patients with invasive fungal infections and timely implementation of targeted measures is beneficial for patients. The objective of this study was to develop a machine learning-based predictive model for invasive fungal infection in patients during their intensive care unit (ICU) stay. Retrospective data was extracted from adult patients in the MIMIC-IV database who spent a minimum of 48 h in the ICU. Feature selection was performed using LASSO regression, and the dataset was balanced using the BL-SMOTE approach. Predictive models were built using six machine learning algorithms. The Shapley additive explanation algorithm was used to assess the impact of various clinical features in the optimal model, enhancing interpretability. The study included 26,346 ICU patients, of whom 379 (1.44%) were diagnosed with invasive fungal infection. The predictive model was developed using 20 risk factors, and the dataset was balanced using the borderline-SMOTE (BL-SMOTE) algorithm. The BL-SMOTE random forest model demonstrated the highest predictive performance (area under curve = 0.88, 95% CI = 0.84-0.91). Shapley additive explanation analysis revealed that the three most influential clinical features in the BL-SMOTE random forest model were dialysis treatment, APSIII scores, and liver disease. The machine learning model provides a reliable tool for predicting the occurrence of IFI in ICU patients. The BL-SMOTE random forest model, based on 20 risk factors, exhibited superior predictive performance and can assist clinicians in early assessment of IFI occurrence in ICU patients. Importance: Invasive fungal infections are characterized by high incidence and high mortality rates characteristics. In this study, we developed a clinical prediction model for invasive fungal infections in critically ill patients based on machine learning algorithms. The results show that the machine learning model based on 20 clinical features has good predictive value.

Lower (1,3)-beta-d-glucan sensitivity and in vitro levels in Candida auris and Candida parapsilosis strains

OBJECTIVES

The serum (1,3)-beta-d-glucan (BDG) assay gives quicker results and has higher sensitivity than blood cultures, therefore it is advised for early diagnosis of invasive candidemia and/or discontinuation of empirical therapy. Its sensitivity may depend on different factors. The aim of our study was to analyse the in vitro and in vivo BDG levels in clinical isolates of three species of Candida responsible for candidemia.

METHODS

C. albicans, C. parapsilosis, and C. auris strains were collected from blood cultures of patients who had a concurrent (-1 to +3 days) serum BDG test (Fungitell assay). Supernatants of all strains were tested in quadruplicate for BDG levels.

RESULTS

Twenty-two C. auris, 14 C. albicans, and ten C. parapsilosis strains were included. The median BDG levels in supernatants were 463 pg/mL (interquartile range [IQR] 379-648) for C. auris, 1080 pg/mL (IQR 830-1276) for C. albicans, and 755 pg/mL (IQR 511-930) for C. parapsilosis, with the significant difference among the species (p < 0.0001). Median serum BDG levels (IQR) were significantly lower in case C. auris and C. parapsilosis vs. C. albicans (p < 0.0001), respectively, 50 pg/mL (IQR 15-161) and 57 pg/mL (IQR 18-332), vs. 372 pg/mL (IQR 102-520). Sensitivity of serum BDG was 39% (95% confidence interval [CI], 18-64) in case of C. auris, 30% (95% CI, 8-65) C. parapsilosis and 78% (95% CI, 49-94) C. albicans candidemia.

DISCUSSION

In our centre C. auris and C. parapsilosis strains have lower BDG content as compared with C. albicans, with a potential impact on serum BDG performance for the diagnosis of candidemia.

Antimicrobial De-Escalation in Critically Ill Patients

Antimicrobial de-escalation (ADE) is defined as the discontinuation of one or more antimicrobials in empirical therapy, or the replacement of a broad-spectrum antimicrobial with a narrower-spectrum antimicrobial. The aim of this review is to provide an overview of the available literature on the effectiveness and safety of ADE in critically ill patients, with a focus on special conditions such as anti-fungal therapy and high-risk categories. Although it is widely considered a safe strategy for antimicrobial stewardship (AMS), to date, there has been no assessment of the effect of de-escalation on the development of resistance. Conversely, some authors suggest that prolonged antibiotic treatment may be a side effect of de-escalation, especially in high-risk categories such as neutropenic critically ill patients and intra-abdominal infections (IAIs). Moreover, microbiological documentation is crucial for increasing ADE rates in critically ill patients with infections, and efforts should be focused on exploring new diagnostic tools to accelerate pathogen identification. For these reasons, ADE can be safely used in patients with infections, as confirmed by high-quality and reliable microbiological samplings, although further studies are warranted to clarify its applicability in selected populations.

Blastomycosis Complicated by Adult Respiratory Distress Syndrome in an Immunocompetent Adult: A Case Report and Literature Review

Blastomycosis is an endemic mycotic infection caused by inhalation of thermally dimorphic fungi from the genus Blastomyces. Blastomyces dermatitidis is the species most related to human infection in the USA and North America. Adult respiratory distress syndrome (ARDS) is a rare complication of blastomycosis and is associated with high mortality. Due to its rarity, evidence-based guidelines for diagnosing and treating ARDS associated with blastomycosis are scarce. In this case presentation, a 22-year-old male with a history of chronic cannabis use presented with severe respiratory symptoms, initially treated as community-acquired pneumonia. Despite antibiotic treatment, his condition deteriorated, necessitating intubation and resulting in the development of ARDS. A delayed diagnosis of pulmonary blastomycosis was confirmed through polymerase chain reaction testing. Treatment with amphotericin B and corticosteroids proved successful in addressing the fungal infection, leading to the recovery of the patient from his severe clinical condition. This case highlights the challenges associated with diagnosing and treating blastomycosis, particularly when complicated by ARDS, emphasizing the importance of considering fungal infections in the differential diagnosis of non-responsive pulmonary infections. Additionally, it suggests the potential utility of corticosteroids in severe cases and emphasizes the crucial role of early diagnosis and a combination of diagnostic modalities for the timely management of this rare and potentially life-threatening condition.

Molecular Pathway, Epidemiological Data and Treatment Strategies of Fungal Infection (Mycoses): A Comprehensive Review

The recent increase in fungal infections is a health crisis. This surge is directly tied to the increase in immunocompromised people caused by changes in medical practice, such as the use of harsh chemotherapy and immunosuppressive medicines. Immunosuppressive disorders such as HIV have exacerbated the situation dramatically. Subcutaneous or superficial fungal infections can harm the skin, keratinous tissues, and mucous membranes. This category includes some of the most common skin disorders that impact millions of people worldwide. Despite the fact that they are seldom fatal, they can have a catastrophic impact on a person's quality of life and, in rare situations, spread to other people or become obtrusive. The majority of fungal infections under the skin and on the surface are simply and quickly cured. An opportunistic organism that preys on a weak host or a natural intruder can both result in systemic fungal infections. Furthermore, it might be exceedingly lethal and dangerous to one's life. Dimorphic fungi may pose a hazard to healthy populations that are not exposed to endemic fungi. Increased surveillance, the availability of quick, noninvasive diagnostic tests, monitoring the emergence of antifungal medication resistance, and research on the pathophysiology, prevention, and management of fungal infections are just a few potential solutions to these new health problems. The goal of this review is to summarize the data available for fungal infections and the different therapies which are involved in their treatment. Additionally, it also summarizes the molecular and scientific data of the plants which contain anti-fungal activity. Data are acquired using Google, PubMed, Scholar, and other online sources.

Identification and production of novel potential pathogen-specific biomarkers for diagnosis of histoplasmosis

IMPORTANCE

Histoplasmosis is considered one of the most important mycoses due to the increasing number of individuals susceptible to develop severe clinical forms, particularly those with HIV/AIDS or receiving immunosuppressive biological therapies, the high mortality rates reported when antifungal treatment is not initiated in a timely manner, and the limitations of conventional diagnostic methods. In this context, there is a clear need to improve the capacity of diagnostic tools to specifically detect the fungal pathogen, regardless of the patient's clinical condition or the presence of other co-infections. The proposed novel pathogen-specific biomarkers have the potential to be used in immunodiagnostic platforms and antifungal treatment monitoring in histoplasmosis. In addition, the bioinformatics strategy used in this study could be applied to identify potential diagnostic biomarkers in other models of fungal infection of public health importance.

β-(1→3)-D-glucan- and mannan-guided early termination of antifungal therapy in ICU patients: a randomized controlled study

Candida spp. are frequently encountered in specimens from ICUs. However, most of these detections represent colonization. Nevertheless, clinical practice shows that a considerable proportion of these patients will receive antifungal therapy (AT). β-(1→3)-D-glucan (BDG) and mannan are fungal biomarkers with high negative predictive values. We aimed to examine whether biomarker-guided discontinuation of AT can reduce the antifungal consumption. Therefore, we conducted a prospective, randomized intervention study between 1 April 2019 and 31 March 2020. All adult ICU patients with a newly started systemic AT but without fungal infection were eligible for inclusion. Enrolled patients were randomized into an intervention and a control group. In both groups, serum BDG and mannan were determined on days 1 and 2 of AT. If all measurements were negative, AT was discontinued in the intervention group. The primary endpoint was antifungal use. The study was terminated after 12 months. Until this time-point, 41 patients had been included. In the intervention group (n = 19), AT was stopped in only two patients because all others showed either positive BDG and/or mannan levels. One of these two patients developed candidemia and AT had to be restarted. There was no significant difference in the primary and secondary endpoints. In summary, the strategy of using two negative BDG and mannan levels to stop AT failed to reduce antifungal consumption in our cohort. Indeed, there will inevitably be patients with invasive candidiasis in whom necessary AT is discontinued. The optimal patient population, biomarker set, and termination criteria are critical to the success of biomarker-based termination strategies.

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.

An Overview of Systematic Reviews of Polymerase Chain Reaction (PCR) for the Diagnosis of Invasive Aspergillosis in Immunocompromised People: A Report of the Fungal PCR Initiative (FPCRI)-An ISHAM Working Group

This overview of reviews (i.e., an umbrella review) is designed to reappraise the validity of systematic reviews (SRs) and meta-analyses related to the performance of Aspergillus PCR tests for the diagnosis of invasive aspergillosis in immunocompromised patients. The methodological quality of the SRs was assessed using the AMSTAR-2 checklist; the quality of the evidence (QOE) within each SR was appraised following the GRADE approach. Eight out of 12 SRs were evaluated for qualitative and quantitative assessment. Five SRs evaluated Aspergillus PCR on bronchoalveolar lavage fluid (BAL) and three on blood specimens. The eight SRs included 167 overlapping reports (59 evaluating PCR in blood specimens, and 108 in BAL), based on 107 individual primary studies (98 trials with a cohort design, and 19 with a case-control design). In BAL specimens, the mean sensitivity and specificity ranged from 0.57 to 0.91, and from 0.92 to 0.97, respectively (QOE: very low to low). In blood specimens (whole blood or serum), the mean sensitivity ranged from 0.57 to 0.84, and the mean specificity from 0.58 to 0.95 (QOE: low to moderate). Across studies, only a low proportion of AMSTAR-2 critical domains were unmet (1.8%), demonstrating a high quality of methodological assessment. Conclusions. Based on the overall methodological assessment of the reviews included, on average we can have high confidence in the quality of results generated by the SRs.

Plasma Microbial Cell-Free DNA Sequencing from over 15,000 Patients Identified a Broad Spectrum of Pathogens

Microbial cell-free DNA (mcfDNA) sequencing is an emerging infectious disease diagnostic tool which enables unbiased pathogen detection and quantification from plasma. The Karius Test, a commercial mcfDNA sequencing assay developed by and available since 2017 from Karius, Inc. (Redwood City, CA), detects and quantifies mcfDNA as molecules/μL in plasma. The commercial sample data and results for all tests conducted from April 2018 through mid-September 2021 were evaluated for laboratory quality metrics, reported pathogens, and data from test requisition forms. A total of 18,690 reports were generated from 15,165 patients in a hospital setting among 39 states and the District of Columbia. The median time from sample receipt to reported result was 26 h (interquartile range [IQR] 25 to 28), and 96% of samples had valid test results. Almost two-thirds (65%) of patients were adults, and 29% at the time of diagnostic testing had ICD-10 codes representing a diverse array of clinical scenarios. There were 10,752 (58%) reports that yielded at least one taxon for a total of 22,792 detections spanning 701 unique microbial taxa. The 50 most common taxa detected included 36 bacteria, 9 viruses, and 5 fungi. Opportunistic fungi (374 Aspergillus spp., 258 Pneumocystis jirovecii, 196 Mucorales, and 33 dematiaceous fungi) comprised 861 (4%) of all detections. Additional diagnostically challenging pathogens (247 zoonotic and vector-borne pathogens, 144 Mycobacterium spp., 80 Legionella spp., 78 systemic dimorphic fungi, 69 Nocardia spp., and 57 protozoan parasites) comprised 675 (3%) of all detections. This is the largest reported cohort of patients tested using plasma mcfDNA sequencing and represents the first report of a clinical grade metagenomic test performed at scale. Data reveal new insights into the breadth and complexity of potential pathogens identified.

Diagnosis and Management of Severe Water-Related Skin and Soft Tissue Sepsis: A Summative Review of the Literature

BACKGROUND

Skin and soft tissue infections (SSTIs) are common presentations in the emergency department. However, this is less common after contact with contaminated saltwater or freshwater. This review presents the diagnosis and management of water-related soft tissue sepsis in this vulnerable and difficult-to-treat subgroup of necrotizing soft tissue sepsis.

METHODS

A summative literature overview is presented regarding bacterial and fungal SSTI after contact with contaminated water, with practical diagnostic and management aspects.

RESULTS

The literature indicates that these wounds and infections remain difficult to treat. An approach using appropriate diagnostic tools with both medical and surgical management strategies is provided.

CONCLUSIONS

SSTIs due to water contamination of wounds involve unusual organisms with unusual resistance patterns, and require a nuanced and directed diagnostic approach with an adaptation of the usual antibiotic or antifungal selection to achieve a successful cure, along with aggressive debridement and wound care.

Aspergillus Galactomannan Titer as a Diagnostic Marker of Invasive Pulmonary Aspergillosis in Lung Transplant Recipients: A Single-Center Retrospective Cohort Study

Invasive pulmonary aspergillosis (IPA) can occur in immunocompromised patients, and an early detection and intensive treatment are crucial. We sought to determine the potential of Aspergillus galactomannan antigen titer (AGT) in serum and bronchoalveolar lavage fluid (BALF) and serum titers of beta-D-glucan (BDG) to predict IPA in lung transplantation recipients, as opposed to pneumonia unrelated to IPA. We retrospectively reviewed the medical records of 192 lung transplant recipients. Overall, 26 recipients had been diagnosed with proven IPA, 40 recipients with probable IPA, and 75 recipients with pneumonia unrelated to IPA. We analyzed AGT levels in IPA and non-IPA pneumonia patients and used ROC curves to determine the diagnostic cutoff value. The Serum AGT cutoff value was 0.560 (index level), with a sensitivity of 50%, specificity of 91%, and AUC of 0.724, and the BALF AGT cutoff value was 0.600, with a sensitivity of 85%, specificity of 85%, and AUC of 0.895. Revised EORTC suggests a diagnostic cutoff value of 1.0 in both serum and BALF AGT when IPA is highly suspicious. In our group, serum AGT of 1.0 showed a sensitivity of 27% and a specificity of 97%, and BALF AGT of 1.0 showed a sensitivity of 60% and a specificity of 95%. The result suggested that a lower cutoff could be beneficial in the lung transplant group. In multivariable analysis, serum and BALF AGT, with a minimal correlation between the two, showed a correlation with a history of diabetes mellitus.

Dual Disseminated Aspergillosis and Mucormycosis Diagnosed at Autopsy: A Report of Two Cases of Coinfection and a Review of the Literature

Coinfection with invasive aspergillosis and mucormycosis in immunocompromised patients has been reported but is rarely confirmed by tissue histology or autopsy. Serum fungal biomarkers and culture are the primary diagnostic tools but are suboptimal for detecting fungal coinfection. Here, we present the cases of two patients who were immunocompromised due to hematologic malignancy where disseminated aspergillosis and mucormycosis coinfection was only diagnosed upon autopsy despite extensive fungal diagnostic workup, and also review recent literature of such instances of coinfection.

A scoring system based on novel biomarkers and clinical risk factors to predict invasive candidiasis in immunocompetent critically ill patients

Background

Delayed diagnosis further increases the mortality of invasive candidiasis (IC) in intensive care unit (ICU) patients. This study aimed to develop and validate a score based on novel serological biomarkers and clinical risk factors for predicting IC in immunocompetent ICU patients.

Methods

We retrospectively collected clinical data and novel serological markers on admission to ICU. Multivariate logistic regression was used to identify the risk factors associated with IC, which were adopted to establish a scoring system.

Results

Patients with IC had a higher C-reactive protein-to-albumin ratio (CAR) and neutrophil-to-lymphocyte ratio (NLR) and lower prognostic nutritional index than those without IC. The NLR, CAR, sepsis, total parenteral nutrition, 1,3-β-D-glucan (BDG)-positivity, and Sequential Organ Failure Assessment score were identified as independent risk factors for IC by multivariate logistic regression analysis and entered into the final scoring system. The area under receiver operating characteristic curve of the score were 0.883 and 0.892, respectively, in the development and validation cohort, higher than Candida score (0.883 vs.0.730, p &lt; 0.001).

Conclusion

We established a parsimonious score based on NLR, CAR, BDG-positivity, and clinical risk factors, which can accurately identify IC in ICU patients to give treatment on time and reduce mortality.

How to use biomarkers of infection or sepsis at the bedside: guide to clinicians

Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response to infection. In this context, biomarkers could be considered as indicators of either infection or dysregulated host response or response to treatment and/or aid clinicians to prognosticate patient risk. More than 250 biomarkers have been identified and evaluated over the last few decades, but no biomarker accurately differentiates between sepsis and sepsis-like syndrome. Published data support the use of biomarkers for pathogen identification, clinical diagnosis, and optimization of antibiotic treatment. In this narrative review, we highlight how clinicians could improve the use of pathogen-specific and of the most used host-response biomarkers, procalcitonin and C-reactive protein, to improve the clinical care of patients with sepsis. Biomarker kinetics are more useful than single values in predicting sepsis, when making the diagnosis and assessing the response to antibiotic therapy. Finally, integrated biomarker-guided algorithms may hold promise to improve both the diagnosis and prognosis of sepsis. Herein, we provide current data on the clinical utility of pathogen-specific and host-response biomarkers, offer guidance on how to optimize their use, and propose the needs for future research.

Prevalence and pattern of isolated fungi from bronchoalveolar lavage among patients with lung cancer: a prospective cross-sectional study

Background

Fungal colonization or infection has recently been reported in patients with lung cancer, and it is possible that it has a role in the pathogenesis of lung cancer or having an effect on treatment and outcome. Aim of work was to assess the prevalence and pattern of isolated fungi from patients with lung cancer at the time of diagnosis. In this prospective cross-sectional observational study, patients with suspected lung tumors were subjected to fiberoptic bronchoscopy (FOB) for biopsy, bronchoalveolar lavage (BAL) with its culture for fungal growth. After a pathological diagnosis, 100 cases of confirmed lung cancer were entered into the study analysis. The prevalence and type of isolated fungi have been determined and compared to the characteristics of the participants and cell types of lung cancer.

Results

Fungi were isolated from 68% of the studied lung cancer cases. The most common isolated fungi were Candida albicans (32%), Aspergillus niger (28%), and Aspergillus fumigatus (8%). Fungi were isolated with a higher frequency in lung cancer cases with the following characteristics: males (p = 0.008), current or ex-smokers (p = 0.002), and chronic obstructive pulmonary disease (COPD) association (p = 0.01). In comparison to lung cancer cases with negative fungal culture, detection of fungal colonization was more associated with increasing severity of clinical presentation: higher grades of dyspnea (grade 1 vs. grade 2, p 0.001), a higher cough score (score 1 versus score 3, p 0.001), a higher chest pain score (score 0 versus score 1, p 0.001), and higher scores of hemoptysis (score 0 versus score 3, p 0.001). Otherwise, no difference was detected regarding age, frequency of comorbidities, chest computed tomography (CT) findings, lung cancer cell type, and staging in lung cancer patients with fungal colonization (p > 0.05).

Conclusion

Fungi were isolated in more than two thirds of lung cancer cases at the time of diagnosis with higher frequency among males, smokers, and those having associated COPD. This may negatively affect the response to treatment and prognosis of lung cancer. ClinicalTrials.gov (NCT 05575388).

Paracoccidioidomycosis: Current Status and Future Trends

Paracoccidioidomycosis (PCM), initially reported in 1908 in the city of São Paulo, Brazil, by Adolpho Lutz, is primarily a systemic and neglected tropical mycosis that may affect individuals with certain risk factors around Latin America, especially Brazil. Paracoccidioides brasiliensis sensu stricto, a classical thermodimorphic fungus associated with PCM, was long considered to represent a monotypic taxon. However, advances in molecular taxonomy revealed several cryptic species, including Paracoccidioides americana, P. restrepiensis, P. venezuelensis, and P. lutzii, that show a preference for skin and mucous membranes, lymph nodes, and respiratory organs but can also affect many other organs. The classical diagnosis of PCM benefits from direct microscopy culture-based, biochemical, and immunological assays in a general microbiology laboratory practice providing a generic identification of the agents. However, molecular assays should be employed to identify Paracoccidioides isolates to the species level, data that would be complemented by epidemiological investigations. From a clinical perspective, all probable and confirmed cases should be treated. The choice of treatment and its duration must be considered, along with the affected organs, process severity, history of previous treatment failure, possibility of administering oral medication, associated diseases, pregnancy, and patient compliance with the proposed treatment regimen. Nevertheless, even after appropriate treatment, there may be relapses, which generally occur 5 years after the apparent cure following treatment, and also, the mycosis may be confused with other diseases. This review provides a comprehensive and critical overview of the immunopathology, laboratory diagnosis, clinical aspects, and current treatment of PCM, highlighting current issues in the identification, treatment, and patient follow-up in light of recent Paracoccidioides species taxonomic developments.

How to Identify Invasive Candidemia in ICU-A Narrative Review

The incidence of invasive fungal infection in ICUs has increased over time, and Candida spp. is the most common cause. Critical care patients are a particular set of patients with a higher risk of invasive fungal infections; this population is characterized by extensive use of medical devices such as central venous lines, arterial lines, bladder catheters, hemodialysis and mechanical intubation. Blood cultures are the gold standard diagnosis; still, they are not an early diagnostic technique. Mannan, anti-mannan antibody, 1,3-β-D-glucan, Candida albicans germ tube antibody, Vitek 2, PNA-FISH, MALDI-TOF, PCR and T2Candida panel are diagnostic promising microbiological assays. Scoring systems are tools to distinguish patients with low and high risk of infection. They can be combined with diagnostic tests to select patients for pre-emptive treatment or antifungal discontinuation. Candidemia is the focus of this narrative review, an approach to contributing factors and diagnosis, with an emphasis on critical care patients.

Comparison of Indirect Fungal Diagnostic Tests in Patients With Proven Histoplasmosis

BACKGROUND

Histoplasmosis is a common cause of invasive fungal infection in endemic regions and accurate diagnosis is difficult without direct tissue culture or pathology. Indirect fungal antigen testing for various fungal pathogens are typically performed to assist with diagnostic workup, though cross-reaction can lead to difficulty in interpreting results. We aimed to compare indirect fungal diagnostic tests and evaluate prevalence of positive antigen testing for non-Histoplasma fungal pathogens in patients with proven histoplasmosis.

METHODS

We performed a single-center retrospective review of adult patients with proven histoplasmosis diagnosed by fungal culture and/or cytology from January 2010 to March 2018. Patient demographics, clinical characteristics, and results of fungal antigen testing for Histoplasma, Blastomyces, Aspergillus, Cryptococcus, and (1→3)-β-D-glucan were evaluated. Two different urine Histoplasma antigen assays were used during the study period.

RESULTS

Fifty-seven of 182 (31.3%) patients reviewed had proven histoplasmosis and presented with acute pulmonary (n = 10), chronic pulmonary (n = 7), and disseminated (n = 40) disease. Forty-one (72%) of these patients were immunosuppressed. Urine Blastomyces antigen (93%) and serum (1→3)-β-D-glucan (88%) were commonly positive in patients with histoplasmosis, whereas Aspergillus antigen was detected in 50% of patients and Cryptococcus antigenemia was rare (5%). In patients with disseminated disease, the MiraVista urine Histoplasma antigen assay had higher sensitivity than the Viracor urine Histoplasma antigen assay (86% vs 50%, respectively; P = .019).

CONCLUSIONS

Noninvasive fungal antigen assays are helpful diagnostic tools; however, given their low specificity, clinicians must be aware of the various clinical presentations of invasive fungal infections and be aware of the limitations of these tests.

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.

Metabolomic profiling of exhaled breath condensate for the diagnosis of pulmonary aspergillosis

Objective

This study aims to ascertain the unique metabolic profile of exhaled breath condensate (EBC) samples in pulmonary aspergillosis (PA) patients, and explore their usefulness for the diagnosis of PA.

Methods

A total of 133 patients were included in the study, including 66 PA patients (invasive pulmonary aspergillosis, n=3; chronic pulmonary aspergillosis, n=60; allergic bronchopulmonary aspergillosis, n=3) and controls (n=67). Ultra high-performance liquid chromatography coupled with high-resolution mass spectrometry(UHPLC-HRMS) was used to analyze EBC samples. Metabolic profiling of EBC samples that were collected from 22 CPA patients at various times during treatment (before treatment, &lt;1 month, 1–2 months, 2–3 months, 3–6 months, and ≥6 months after treatment initiation) were performed using UHPLC-HRMS. Potential biomarkers were evaluated using cluster analysis, Venn diagram and receiver operating characteristic analysis (ROC).

Results

A total of 47 metabolites of potential interest were detected in the EBC samples. Further investigation showed that Asperpyrone C, Kotanin, Terphenyllin, Terrelumamide B, and Cyclotryprostatin D could be used as a diagnostic biomarker for PA. The classification between metabolic profiling of EBC samples from PA patients and controls was good with a sensitivity of 100%, specificity 89.6% for patients with PA, respectively. Venn diagram analysis of these biomarker candidates displayed three main types of compounds, which could be used for the further discrimination of aspergilloma and chronic cavitary PA. In addition, antifungal treatment had a limited influence on the value of the EBC results.

Conclusions

This metabolomic approach using UHPLC-HRMS could be used as a noninvasive method for the diagnosis of PA.

Sensitivity of Serum Beta-D-Glucan in Candidemia According to Candida Species Epidemiology in Critically Ill Patients Admitted to the Intensive Care Unit

Serum beta-D-glucan (BDG) determination plays an important role in the diagnosis of candidemia among critically ill patients admitted to the intensive care unit (ICU). However, BDG levels measured may be lower in the case of infections caused by some non-albicans species, such as C. parapsilosis and C. auris. The aim of this single-center study was to investigate the sensitivity of serum BDG for the diagnosis of candidemia stratified according to causative Candida species in ICU patients. This was a single-center, retrospective study, including all adult patients admitted to ICU during the period 2018–2021. All episodes of candidemia with a determination of BDG available within 3 days before or after positive blood culture were recorded. The preplanned primary objective was to investigate the sensitivity of serum BDG to detect candidemia early and the effect of different Candida species. The secondary objective was to measure serum BDG in patients with candidemia from different Candida species. In total, 146 candidemia episodes in 118 patients were analyzed. Median BDG value for C. albicans candidemia (182 pg/mL) was higher than that observed for C. parapsilosis (78 pg/mL, p = 0.015) and C. auris (48 pg/mL, p = 0.022). The overall sensitivity of BDG for the diagnosis of candidemia was low (47%, 95% CI 39–55%). In conclusion, in critically ill patients admitted to ICU, serum BDG levels for candidemia were different among species, with lower levels confirmed for C. parapsilosis and C. auris. Serum BDG sensitivity for early detection of candidemia was lower than previously reported in other ICU populations.

Noninvasive Testing and Surrogate Markers in Invasive Fungal Diseases

Invasive fungal infections continue to increase as at-risk populations expand. The high associated morbidity and mortality with fungal diseases mandate the continued investigation of novel antifungal agents and diagnostic strategies that include surrogate biomarkers. Biologic markers of disease are useful prognostic indicators during clinical care, and their use in place of traditional survival end points may allow for more rapid conduct of clinical trials requiring fewer participants, decreased trial expense, and limited need for long-term follow-up. A number of fungal biomarkers have been developed and extensively evaluated in prospective clinical trials and small series. We examine the evidence for these surrogate biomarkers in this review and provide recommendations for clinicians and regulatory authorities.

Recent Advances in Fungal Infections: From Lung Ecology to Therapeutic Strategies With a Focus on Aspergillus spp

Fungal infections are estimated to be the main cause of death for more than 1.5 million people worldwide annually. However, fungal pathogenicity has been largely neglected. This is notably the case for pulmonary fungal infections, which are difficult to diagnose and to treat. We are currently facing a global emergence of antifungal resistance, which decreases the chances of survival for affected patients. New therapeutic approaches are therefore needed to face these life-threatening fungal infections. In this review, we will provide a general overview on respiratory fungal infections, with a focus on fungi of the genus Aspergillus. Next, the immunological and microbiological mechanisms of fungal pathogenesis will be discussed. The role of the respiratory mycobiota and its interactions with the bacterial microbiota on lung fungal infections will be presented from an ecological perspective. Finally, we will focus on existing and future innovative approaches for the treatment of respiratory fungal infections.

Challenges with Utilizing the 1,3-Beta-d-Glucan and Galactomannan Assays To Diagnose Invasive Mold Infections in Immunocompromised Children

Establishing the diagnosis of invasive mold infections (IMI) in immunocompromised children is challenging due to nonspecific clinical presentations and the limited sensitivity of traditional culture-based methods. Rapid non-culture-based diagnostics such as the 1,3-beta-d-glucan and galactomannan assays have emerged as promising adjuncts to conventional diagnostic tests in adults. Available data suggest that 1,3-beta-d-glucan has limited accuracy in the pediatric population and is not recommended to be used for the diagnosis of IMI in children. On the other hand, the diagnostic performance of the serum and bronchoalveolar lavage galactomannan in immunocompromised children is comparable to results observed in adults and can be used as a screening tool in children at high risk of developing invasive aspergillosis (IA) who are not receiving mold-active antifungal prophylaxis and as a diagnostic tool in symptomatic children suspected of having IA. Herein, we summarize the available evidence for the use of these rapid non-culture-based diagnostics in immunocompromised children. We also summarize potential causes of false positivity for the 1,3-beta-d-glucan and galactomannan assays.

Diagnosis of Pulmonary Infections Due to Endemic Fungi

Endemic mycoses including Histoplasma, Blastomyces, Coccidioides, Paracoccidioides, and Talaromyces are dimorphic fungi that can cause a variety of clinical manifestations, including respiratory infections. Their pulmonary presentations are variable, and diagnosis is often delayed as they can mimic other infectious and non-infectious causes of pulmonary disease. Delay in diagnosis can lead to unnecessary antibiotic use, repeat hospitalizations, and increased morbidity and mortality. The diagnosis of endemic fungal pulmonary infections often relies on multiple diagnostic tests including culture, tissue histopathology, antigen assays, and antibody assays. Due to the increased use of immunosuppressive agents and the widening geographic ranges where these infections are being found, the prevalence of endemic fungal infections is increasing. Physicians need to be aware of the clinical manifestations of pulmonary infections due to endemic fungal in order to ensure that the proper diagnostic work up is obtained promptly. A high index of suspicion is particularly important in patients with suspected pulmonary infections who have failed to improve despite antibiotics in the appropriate setting. We present a review diagnostic testing for pulmonary infections due to endemic mycoses.

Invasive pulmonary aspergillosis with brain dissemination in an immunocompetent host

Invasive aspergillosis is an uncommon infection, which is mainly seen among immunocompromised patients. In recent years, cases of aspergillosis involving immunocompetent hosts are increasingly being reported. Herein, we report the case of a 27-year-old man with fever, productive cough, shortness of breath, and left hemiparesis. He had suffered trauma to his head 25 days prior. Imaging of the chest showed bilateral cavitary lesions in the lungs, and neuroimaging revealed a space-occupying lesion in the right frontoparietal cerebrum. He was suspected of having an abscess or metastasis. He died on day 3 of hospitalization, and an autopsy was performed. The autopsy revealed the cause of death to be invasive pulmonary aspergillosis, with brain dissemination. Invasive aspergillosis is uncommon in apparently immunocompetent individuals, and we discuss the autopsy findings in detail.

Treatment of infections in cancer patients: an update from the neutropenia, infection and myelosuppression study group of the Multinational Association for Supportive Care in Cancer (MASCC)

INTRODUCTION

Patients with hematological and advanced solid malignancies have acquired immune dysfunction, often exacerbated by treatment, posing a significant risk for the development of infections. This review evaluates the utility of current clinical and treatment guidelines, in the setting of management of infections in cancer patients.

AREAS COVERED

These include causes of infection in cancer patients, management of patients with high-risk and low-risk febrile neutropenia, management of low-risk patients in an outpatient setting, the role of granulocyte colony-stimulating factor (G-CSF) in the prevention and treatment of neutropenia-related infections, management of lung infections in various clinical settings, and emerging challenges surrounding the risk of infection in cancer patients treated with novel treatments. The literature search was performed by accessing PubMed and other databases, focusing on published clinical trials of relevant anti-cancer agents and diseases, primarily covering the recent past, but also including several key studies published during the last decade and, somewhat earlier in a few cases.

EXPERT REVIEW

Notwithstanding the promise of gene therapy/gene editing in hematological malignancies and some types of solid cancers, innovations introduced in clinical practice include more discerning clinical management such as the generalized use of biosimilar formulations of G-CSF and the implementation of novel, innovative immunotherapies.

New clinical algorithm including fungal biomarkers to better diagnose probable invasive pulmonary aspergillosis in ICU

Background

The classification of invasive pulmonary aspergillosis (IPA) issued by the European Organization for the Research and Treatment of Cancer/Mycoses Study Group Education and Research Consortium (EORTC/MSGERC) is used for immunocompromised patients. An alternative algorithm adapted to the intensive care unit (ICU) population has been proposed (AspICU), but this algorithm did not include microbial biomarkers such as the galactomannan antigen and the Aspergillus quantitative PCR. The objective of the present pilot study was to evaluate a new algorithm that includes fungal biomarkers (BM-AspICU) for the diagnosis of probable IPA in an ICU population.

Patients and methods

Data from 35 patients with pathology-proven IPA according to European Organization for the Research and Treatment of Cancer/Mycosis Study Group (EORTC/MSGERC)-2008 criteria were extracted from the French multicenter database of the Invasive Fungal Infections Surveillance Network (RESSIF). The patients were investigated according to the AspICU algorithm, and the BM-AspICU algorithm in analyzing the clinical, imaging, and biomarker data available in the records, without taking into account the pathology findings.

Results

Eight patients had to be excluded because no imaging data were recorded in the database. Among the 27 proven IPAs with complete data, 16 would have been considered as putative IPA with the AspICU algorithm and 24 would have been considered as probable IPA using the new algorithm BM-AspICU. Seven out of the 8 patients with probable BM-AspICU IPA (and not classified with the AspICU algorithm) had no host factors and no Aspergillus-positive broncho-alveolar lavage fluid (BALF) culture. Three patients were non-classifiable with any of the two algorithms, because they did not have any microbial criteria during the course of the infection, and diagnosis of proven aspergillosis was done using autopsy samples.

Conclusion

Inclusion of biomarkers could be effective to identify probable IPA in the ICU population. A prospective study is needed to validate the routine application of the BM-AspICU algorithm in the ICU population.

Invasive candidiasis in critical care: challenges and future directions

Invasive candidiasis is the most common critical care-associated fungal infection with a crude mortality of ~ 40-55%. Important factors contributing to risk of invasive candidiasis in ICU include use of broad-spectrum antimicrobials, immunosuppressive drugs, and total parenteral nutrition alongside iatrogenic interventions which breach natural barriers to infection [vascular catheters, renal replacement therapy, extracorporeal membrane oxygenation (ECMO), surgery]. This review discusses three key challenges in this field. The first is the shift in Candida epidemiology across the globe to more resistant non-albicans species, in particular, the emergence of multi-resistant Candida glabrata and Candida auris, which pose significant treatment and infection control challenges in critical care. The second challenge lies in the timely and appropriate initiation and discontinuation of antifungal therapy. Early antifungal strategies (prophylaxis, empirical and pre-emptive) using tools such as the Candida colonisation index, clinical prediction rules and fungal non-culture-based tests have been developed: we review the evidence on implementation of these tools in critical care to aid clinical decision-making around the prescribing and cessation of antifungal therapy. The third challenge is selection of the most appropriate antifungal to use in critical care patients. While guidelines exist to aid choice, this heterogenous and complex patient group require a more tailored approach, particularly in cases of acute kidney injury, liver impairment and for patients supported by extracorporeal membrane oxygenation. We highlight key research priorities to overcome these challenges in the future.

The Diagnostic Utility and Clinical Implications of Bronchoalveolar Lavage in Cancer Patients With Febrile Neutropenia and Lung Infiltrates

Introduction Febrile neutropenia (FN) is a dreaded complication of cancer chemotherapy and frequently associated with respiratory infections. Flexible bronchoscopy (FB) serves as a useful diagnostic tool in this regard. Objective To determine the diagnostic yield, safety and clinical implications of bronchoalveolar lavage (BAL) in cancer patients with FN, having lung infiltrates on radiographic chest imaging. Methods We reviewed medical records of FN patients who underwent FB at Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, from July 2015 till July 2018. The culture yield of BAL, resultant change of management and outcome over the subsequent 30 days were retrospectively analysed. Statistical Package for Social Sciences (SPSS) version 20 (IBM Corp., Armonk, NY) was used for data analysis. Results Ninety FN patients, with mean age 26 ± 18 years and predominantly males (65.6%, n = 59) were included in the study. Seventy-seven (85.6%) had hematological and 13 (14.4%) solid organ malignancy. The mean absolute neutrophil count was 0.20 +/- 0.36/ µL. BAL cultures were diagnostic in 40 (44%) patients; the etiology was bacterial, fungal and mixed in 25 (62.5%), 14 (35%) and one (2.5%) patient, respectively. All patients were on empirical antibiotics prior to bronchoscopy: 32 (35.6%) on antibacterial alone and 58 (64.4%) on antibacterial plus antifungal therapy. Change of management occurred in 51 (56.7%) patients after BAL results, including de-escalation from dual antibiotics in 28 (55%) and initiation of new culture sensitive antibiotic in 23 (45%). FB-associated complications developed in three (5.6%) non-intensive care patients (ICU), including transient hypoxia in two and minor hemoptysis in one patient, while five (14.8%) mechanically ventilated patients in ICU experienced worsening of oxygenation parameters within 48 hours. Overall, 24 (26.7%) patients died. Mortality was 3.7% in non-ICU and 69% in ICU setting and significantly higher in patients with fungal pneumonias (p-value 0.01) and with prolonged neutropenia (p-value 0.001). Conclusions BAL is a safe diagnostic tool for FN patients with lung infiltrates, with minimal complications and sufficient diagnostic yield to improve diagnosis and management of such patients.

Introduction of a bead beating step improves fungal DNA extraction from selected patient specimens

In immunocompromised patients a colonisation with fungi carries the risk to develop serious invasive fungal infection. An early detection is therefore important, but not optimal hitherto. Fortunately, molecular genetic methods have increased the sensitivity of fungal detection and limited the time, until results are available. However, their success depends on an efficient extraction of genomic DNA from the fungal cell in the given diagnostic specimen. To improve the routine DNA preparation method for yeasts and moulds, the impact of bead beating on fungal DNA release was evaluated. PBS, blood and respiratory rinse were spiked with Candida glabrata or Aspergillus fumigatus. DNA was extracted by mechanical bead beating in addition to the different steps of the DNA preparation protocol, which comprised liquid nitrogen treatment, proteinase K digestion and DNA isolation using the EZ1 DNA Tissue Kit and Workstation. In every method variant tested, treatment with liquid nitrogen did not improve the DNA release. Bead beating once followed by proteinase K digestion and EZ1-work-up led to the highest DNA release from fungus, spiked in PBS, and increased the extracted DNA amount of C. glabrata about 100-fold and of A. fumigatus about 10-fold in relation to sole EZ1-work-up. In fungus-spiked respiratory rinse and blood, highest increase in DNA release was measured after triple bead beating with simultaneous proteinase K digestion. Fungal DNA release of C. glabrata increased for >100-fold in respiratory rinse and for >1000-fold in blood and of A. fumigatus for >10-fold in respiratory rinse and about 5- to 10-fold in blood. The data of this study clearly demonstrate that preparation of fungal DNA from human specimens is optimized by introduction of a bead beating step to the conventional DNA-preparation method without the necessity of a liquid nitrogen step.

Pulmonary Aspergillosis: What the Generalist Needs to Know

Aspergillus spp. is a ubiquitous mold found commonly in our environment that can cause a spectrum of pulmonary disorders, ranging from a hypersensitivity reaction to an acutely invasive disease with significant mortality. Allergic bronchopulmonary aspergillosis results from airway hypersensitivity from aspergillus colonization almost exclusively in patients with asthma and cystic fibrosis. Chronic pulmonary aspergillosis typically presents in immunocompetent patients with underlying lung pathology. Treatment is primarily with antifungal agents; however, other measures such as surgical resection may be necessary. Invasive pulmonary aspergillosis is a severe infection in immunocompromised patients and is characterized by invasion of pulmonary vasculature by the Aspergillus hyphae. Recent advances in the diagnosis and management of invasive pulmonary aspergillosis include emerging risk factors such as critically ill patients, and those with chronic obstructive pulmonary disease and liver disease. In addition, noninvasive biomarkers have made it easier to suspect and diagnose invasive pulmonary aspergillosis. There are more effective and better-tolerated antifungal agents that have improved patient outcomes. This review introduces the spectrum of pulmonary aspergillosis geared toward generalists, including disease manifestations, most recent diagnostic criteria, and first-line treatment options. Involving a multidisciplinary team is vital to the early diagnosis and management of these diseases.

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

Background: Fungal infections are of increasing incidence and importance in immunocompromised and immunocompetent patients. Timely diagnosis relies on appropriate use of laboratory testing in susceptible patients.Methods: The relevant literature related to diagnosis of invasive pulmonary aspergillosis, invasive candidiasis, and the common endemic mycoses was systematically reviewed. Meta-analysis was performed when appropriate. Recommendations were developed using the Grading of Recommendations Assessment, Development, and Evaluation approach.Results: This guideline includes specific recommendations on the use of galactomannan testing in serum and BAL and for the diagnosis of invasive pulmonary aspergillosis, the role of PCR in the diagnosis of invasive pulmonary aspergillosis, the role of β-d-glucan assays in the diagnosis of invasive candidiasis, and the application of serology and antigen testing in the diagnosis of the endemic mycoses.Conclusions: Rapid, accurate diagnosis of fungal infections relies on appropriate application of laboratory testing, including antigen testing, serological testing, and PCR-based assays.