Update on the laboratory diagnosis of invasive fungal infections

Microbiological Assessment of the FilmArray Blood Culture Identification 2 Panel: Potential Impact in Critically Ill Patients

Rapid pathogen detection and characterization from positive blood cultures are crucial in the management of patients with bloodstream infections (BSI) and in achieving their improved outcomes. In this context, the FilmArray Blood Culture Identification (BCID2) panel is an FDA approved molecular test, which can quickly identify different species and resistance determinants, thus making an impact in antimicrobial practice. In this study, we analyzed 136 positive blood cultures collected from septic critically ill patients from April 2021 to March 2023 by using the FilmArray BCID2 panel, and results obtained by fast molecular analysis were compared to those obtained by routine protocols. Overall, the BCID2 panel showed a strong concordance with conventional methods, particularly in the case of monomicrobial samples, whereas some discrepancies were found in 10/32 polymicrobial samples. Of note, this technique allowed us to identify a significant number of yeasts (37/94 samples) and to unravel the presence of several resistance markers, including both Gram-positive and Gram-negative organisms. These findings strongly support the potential use of the BCID2 panel as an adjunct to the conventional microbiology methods for the management of critically ill septic patients, thus accelerating blood pathogen and resistance genes identification, focusing antibiotic therapy, and avoiding inappropriate and excessive use of drugs.

Candida Species (Volatile) Metabotyping through Advanced Comprehensive Two-Dimensional Gas Chromatography

Microbial metabolomics is a challenge strategy that allows a comprehensive analysis of metabolites within a microorganism and may support a new approach in microbial research, including the microbial diagnosis. Thus, the aim of this research was to in-depth explore a metabolomics strategy based on the use of an advanced multidimensional gas chromatography for the comprehensive mapping of cellular metabolites of C. albicans and non-C. albicans (C. glabrata and C. tropicalis) and therefore contributing for the development of a comprehensive platform for fungal detection management and for species distinction in early growth times (6 h). The volatile fraction comprises 126 putatively identified metabolites distributed over several chemical families: acids, alcohols, aldehydes, hydrocarbons, esters, ketones, monoterpenic and sesquiterpenic compounds, norisoprenoids, phenols and sulphur compounds. These metabolites may be related with different metabolic pathways, such as amino acid metabolism and biosynthesis, fatty acids metabolism, aromatic compounds degradation, mono and sesquiterpenoid synthesis and carotenoid cleavage. These results represent an enlargement of ca. 70% of metabolites not previously reported for C. albicans, 91% for C. glabrata and 90% for C. tropicalis. This study represents the most detailed study about Candida species exometabolome, allowing a metabolomic signature of each species, which signifies an improvement towards the construction of a Candida metabolomics platform whose application in clinical diagnostics can be crucial to guide therapeutic interventions.

Novel Antifungal Agents and Their Activity against Aspergillus Species

There is a need for new antifungal agents, mainly due to increased incidence of invasive fungal infections (IFI), high frequency of associated morbidity and mortality and limitations of the current antifungal agents (e.g., toxicity, drug-drug interactions, and resistance). The clinically available antifungals for IFI are restricted to four main classes: polyenes, flucytosine, triazoles, and echinocandins. Several antifungals are hampered by multiple resistance mechanisms being present in fungi. Consequently, novel antifungal agents with new targets and modified chemical structures are required to combat fungal infections. This review will describe novel antifungals, with a focus on the Aspergillus species.

Systemic Fusariosis: A Rare Complication in Children with Acute Lymphoblastic Leukemia

Fusarium species are ubiquitous pathogens causing opportunistic infections in immunocompromised patients. Clinical presentation depends on a host’s immunity and can be localized or disseminated. Since there are few reports of disseminated fusariosis in children, we described an unusual case of Fusarium solani infection in a 9-year-old child with acute lymphoblastic leukemia (ALL). This patient presented a deep wound in the elbow at diagnosis. During the induction phase of chemotherapy, he developed multiple skin lesions and severe pneumonia; Fusarium solani was cultured from the skin lesions. He was treated with a high dose of liposomal amphotericin B, followed by voriconazole. Starting from this peculiar case, we collected all patients with acute leukemia affected by Fusarium infection, treated in the pediatric Onco-Hematology Division of Padua University Hospital during the last 20 years. We identified another six cases: all these patients were affected by acute myeloid leukemia (AML) and five of them presented a relapsed/refractory disease. Two out of seven patients died because of infection; five patients recovered from infection, but three out of seven died because of leukemia. Skin lesions in immunocompromised patients should rise the suspicion of disseminated fusariosis. Furthermore, considering the emergence of filamentous fungi in immunocompromised patients, we all should be aware of Fusarium infection, reminding us that the diagnosis is important to cure the infection.

Phenotypic typing and epidemiological survey of antifungal resistance of Candida species detected in clinical samples of Italian patients in a 17 months' period

INTRODUCTION

Yeast pathogens are emerging agents of nosocomial as well as community-acquired infections and their rapid and accurate identification is crucial for a better management of high-risk patients and for an adequate treatment.

METHODS

We performed a retrospective review of 156 yeast isolates collected during a 17 months' period of regular clinical practice at the Microbiology Department of San Camillo Hospital in Treviso, Italy and analyzed by the traditional culture-based method combined with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).

RESULTS

Out of all the samples collected MALDI-TOF MS was able to characterize with a MT score ≥1.7 (accurate result at species level) 12 different yeast and yeast-like species from 140 samples: Candida albicans (63.7%), Candida glabrata (13.6%), Saccharomyces cerevisiae (6.5%), Candida parapsilosis (5.7%), Candida tropicalis (2.1%), Candida pararugosa (2.1%), Candida guilliermondii (2.1%), Candida kefyr (1.4%), Candida lusitaniae (0.7%), Candida palmioleophila (0.7%), Geotrichum silvicola (0.7%), Rhodotorula mucilaginosa (0.7%). Susceptibility testing toward seven common antifungal agents showed a characteristic MIC distribution of C. albicans isolates for echinocandins: particularly we noticed that 72% and 46% of C. albicans showed an MIC value close to clinical breakpoint as defined by EUCAST, respectively for anidulafungin and micafungin.

CONCLUSION

Accurate identification of microorganisms and the study of their antifungal susceptibility allow to understand the epidemiology of a particular area, permitting the choice of the most appropriate early antifungal treatment.

Shedding light on Aspergillus niger volatile exometabolome

An in-depth exploration of the headspace content of Aspergillus niger cultures was performed upon different growth conditions, using a methodology based on advanced multidimensional gas chromatography. This volatile fraction comprises 428 putatively identified compounds distributed over several chemical families, being the major ones hydrocarbons, alcohols, esters, ketones and aldehydes. These metabolites may be related with different metabolic pathways, such as amino acid metabolism, biosynthesis and metabolism of fatty acids, degradation of aromatic compounds, mono and sesquiterpenoid synthesis and carotenoid cleavage. The A. niger molecular biomarkers pattern was established, comprising the 44 metabolites present in all studied conditions. This pattern was successfully used to distinguish A. niger from other fungi (Candida albicans and Penicillium chrysogenum) with 3 days of growth by using Partial Least Squares-Discriminant Analysis (PLS-DA). In addition, PLS-DA-Variable Importance in Projection was applied to highlight the metabolites playing major roles in fungi distinction; decreasing the initial dataset to only 16 metabolites. The data pre-processing time was substantially reduced, and an improvement of quality-of-fit value was achieved. This study goes a step further on A. niger metabolome construction and A. niger future detection may be proposed based on this molecular biomarkers pattern.

MALDI-TOF mass spectrometry: any use for Aspergilli?

Recently, relentless efforts to develop rapid, cost-effective, and reliable laboratory methods for daily diagnosis of fungal diseases such as aspergillosis appear to be materialized in the relatively new, but revolutionary matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) technology. As for Aspergilli, MALDI-TOF MS profiling of isolates growing in culture--characteristic protein spectra are obtainable by means of simple and reproducible preanalytical and analytical procedures--ensures that single species within the different sections or complexes can be easily and accurately identified, including species that are morphologically and phylogenetically similar to each other. Thus, resort to longer and more onerous molecular biology techniques is restricted to those cases for which no spectra in the reference fungal database or library are available at the time of analysis. However, it is necessary to interrogate reference libraries composed of spectra that have been obtained using procedures similar to those used to obtain the test isolate's mass spectrum, as well as to continuously update these libraries for enriching them with fungal strains/species not (or not well) represented in their current versions. Compared to mold identification, very limited work was reported on the use of MALDI-TOF MS to perform strain typing or antifungal susceptibility testing for Aspergilli. If these complementing areas will be potentiated in the near future, MALDI-TOF MS could effectively support the clinical microbiology/mycology laboratory in its primary role of assisting either infection control specialists or physicians for the diagnosis and treatment of aspergillosis.

Antifungal susceptibility testing: current role from the clinical laboratory perspective

Despite availability of many antifungal agents, antifungal clinical resistance occurs, perhaps as a consequence of an infecting organism found to be resistant in vitro to one or more antifungals tested. From what derives the important current role of the in vitro antifungal susceptibility testing (AFST), that is to determine which agents are like to be scarcely effective for a given infection. Thus, AFST results, if timely generated by the clinical microbiology laboratory and communicated to clinicians, can aid them in the therapeutic decision making, especially for difficult-to-treat invasive candidiasis and aspergillosis. Although recently refined AFST methods are commercially available for allowing a close antifungal resistance surveillance in many clinical setting, novel assays such as flow cytometry or MALDI-TOF mass spectrometry are upcoming tools for AFST. Based on short-time antifungal drug exposure of fungal isolates, these assays could provide a reliable means for quicker and sensitive assessment of AFST.

MALDI-TOF mass spectrometry in the clinical mycology laboratory: identification of fungi and beyond

MALDI-TOF mass spectrometry (MS) is becoming essential in most clinical microbiology laboratories throughout the world. Its successful use is mainly attributable to the low operational costs, the universality and flexibility of detection, as well as the specificity and speed of analysis. Based on characteristic protein spectra obtained from intact cells - by means of simple, rapid and reproducible preanalytical and analytical protocols - MALDI-TOF MS allows a highly discriminatory identification of yeasts and filamentous fungi starting from colonies. Whenever used early, direct identification of yeasts from positive blood cultures has the potential to greatly shorten turnaround times and to improve laboratory diagnosis of fungemia. More recently, but still at an infancy stage, MALDI-TOF MS is used to perform strain typing and to determine antifungal drug susceptibility. In this article, the authors discuss how the MALDI-TOF MS technology is destined to become a powerful tool for routine mycological diagnostics.

Comparative evaluation of BD Phoenix and vitek 2 systems for species identification of common and uncommon pathogenic yeasts

The BD Phoenix system was evaluated for species-level identification of yeasts (250 clinical isolates) and compared with the Vitek 2 system, using ribosomal internal transcribed spacer (ITS) sequence analysis as the gold standard. Considering only the species included in each system's database, 96.3% (236/245) and 91.4% (224/245) of the isolates were correctly identified by BD Phoenix and Vitek 2, respectively.

Overview of invasive fungal infections

The incidence of invasive fungal infections (IFIs) has seen a marked increase in the last two decades. This is especially evident among transplant recipients, patients suffering from AIDS, in addition to those in receipt of immunosuppressive therapy. Worryingly, this increased incidence includes infections caused by opportunistic fungi and emerging fungal infections which are resistant to or certainly less susceptible than others to standard antifungal agents. As a direct response to this phenomenon, there has been a resolute effort over the past several decades to improve early and accurate diagnosis and provide reliable screening protocols thereby promoting the administration of appropriate antifungal therapy for fungal infections. Early diagnosis and treatment with antifungal therapy are vital if a patient is to survive an IFI. Substantial advancements have been made with regard to both the diagnosis and subsequent treatment of an IFI. In parallel, stark changes in the epidemiological profile of these IFIs have similarly occurred, often in direct response the type of antifungal agent being administered. The effects of an IFI can be far reaching, ranging from increased morbidity and mortality to increased length hospital stays and economic burden.

Detection of (1, 3)-β-D-glucan in bronchoalveolar lavage and serum samples collected from immunocompromised hosts

The incidence of invasive fungal infections (IFI) has increased in recent years, especially among immunocompromised hosts (ICH). In 2003, the Fungitell(®) assay received FDA clearance for the presumptive diagnosis of IFI using serum and detects (1-3)-β-D-glucan, which is a major cell wall component of certain fungi (e.g., Candida, Aspergillus, and Pneumocystis). The goal of the current study was to assess the performance of the assay on bronchoalveolar lavage (BAL) fluid and serum to identify IFI in ICH. Patients were classified as having proven, probable, possible, or no IFI according to the European Organization for Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG) guidelines. Among 109 patients for whom the results of Fungitell were compared to the EORTC/MSG criteria, Fungitell showed a low positive predictive value for the identification of IFI from both BAL (20.0%) and serum (26.7%). However, the negative predictive value of Fungitell was significantly higher for both sample types (BAL, 83.0%; serum, 84.8%). Interestingly, the results of Fungitell were positive in BAL and serum in 7/8 (87.5%) patients diagnosed with Pneumocystis pneumonia (PcP) by real-time, non-nested PCR. These data indicate that the Fungitell assay has a low positive predictive value for the diagnosis of IFI in ICH, regardless of the specimen type that is tested. However, testing of serum samples by Fungitell may permit a rapid and noninvasive initial screening approach in patients with presumed PcP.

Discrimination of motile bacteria from filamentous fungi using dynamic speckle

We present a dynamic laser speckle method to easily discriminate filamentous fungi from motile bacteria in soft surfaces, such as agar plate. The method allows the detection and discrimination between fungi and bacteria faster than with conventional techniques. The new procedure could be straightforwardly extended to different micro-organisms, as well as applied to biological and biomedical research, infected tissues analysis, and hospital water and wastewaters studies.

Diagnostic performance of 1→3-β-d-glucan in neonatal and pediatric patients with Candidemia

Fungal sepsis is one of the major problems in neonatal and pediatric care unit settings. The availability of new diagnostic techniques could allow medical practitioners to rapidly identify septic patients and to improve their outcome. The aim of this study was to evaluate the performance of the 1→3-β-d-glucan (BDG), individually and in comparison with the Candida mannan (CM) antigen, in ten preterm infants and five onco-haematological pediatric patients with Candida bloodstream infections already proven by positive culture. The serum levels of BDG were >80 pg/mL on the same day as a positive blood culture in all examined patients, while CM antigen was negative in the patients with C. parapsilosis fungemia and in one further case due to C. albicans. These results suggest that a regular monitoring of serum circulating antigens (i.e., 1→3-β-d-glucan) combined with other microbiological and clinical information, may allow earlier and accurate diagnosis. However, further studies are necessary to confirm its usefulness in routine clinical practice.