Use of mass spectrometry to identify clinical Fusarium isolates

Identification of Lutzomyia longipalpis' using MALDI-TOF peptide/protein profiles

Sand flies are vectors of great public health importance, since they constitute a group of hematophagous insects responsible for etiological agents transmission of zoonotic diseases such a visceral leishmaniasis. In face of the expansion of these diseases, efficient control strategies are needed which depend on comprehending the sand fly eco-epidemiology. In this regard, MALDI-TOF mass spectrometry has been used for bacteria, fungi and yeast detection studies through peptide/protein profiles. However, little is known about interference of biological factors associated with vector ecology, such as blood meal preferences and even sand fly age on the peptide/protein profiles. Thus, the present study aimed to evaluate the differences in peptide/protein profiles of the sand fly Lutzomyia longipalpis, by means of MALDI-TOF, due to the sand fly's age, sex, blood meal source and Leishmania infantum infection. Sample preparation was made removing both head and last abdomen segments keeping the thorax, its appendices and the rest of the abdomen. Five specimens per pool were used to obtain peptide/protein extract of which 1 μL solution was deposited over 1 μL MALDI matrix dried. Characteristic spectra were analyzed using principal coordinate analysis as well as indicator species analysis to discriminate differences in sand flies's peptide/protein profile by sex, age, blood meal source and L. infantum infection. The results show that the evaluated variables produced distinct peptide/protein profiles, demonstrated by the identification of specific diagnostic ions. It was found that the interference of biological factors should be taken into account when using the MALDI-TOF analysis of sand fly species identification and eco-epidemiological applications in field studies. Based on our results, we believe that it is possible to identify infected specimens and the source of blood meal in a collection of wild sand flies, serving to measure infectivity and understand the dynamics of the vector's transmission chain. Our results may be useful for epidemiological studies that look at the ecology of sand flies and leishmaniasis, as well as for raising awareness of biological characteristics' impact on peptide/protein profiles in sand fly species identification.

Pathogen detection via inductively coupled plasma mass spectrometry analysis with nanoparticles

Infections caused by viruses and bacteria pose a significant threat to global public health, emphasizing the critical importance of timely and precise detection methods. Inductively coupled plasma mass spectrometry (ICP-MS), a contemporary approach for pathogen detection, offers distinct advantages such as high sensitivity, a wide linear range, and multi-index capabilities. This review elucidates the underexplored application of ICP-MS in conjunction with functional nanoparticles (NPs) for the identification of viruses and bacteria. The review commences with an elucidation of the underlying principles, procedures, target pathogens, and NP requirements for this innovative approach. Subsequently, a thorough analysis of the advantages and limitations associated with these techniques is provided. Furthermore, the review delves into a comprehensive examination of the challenges encountered when utilizing NPs and ICP-MS for pathogen detection, culminating in a forward-looking assessment of the potential pathways for advancement in this domain. Thus, this review contributes novel perspectives to the field of pathogen detection in biomedicine by showcasing the promising synergy of ICP-MS and NPs.

Trans-kingdom fungal pathogens infecting both plants and humans, and the problem of azole fungicide resistance

Azole antifungals are abundantly used in the environment and play an important role in managing fungal diseases in clinics. Due to the widespread use, azole resistance is an emerging global problem for all applications in several fungal species, including trans-kingdom pathogens, capable of infecting plants and humans. Azoles used in agriculture and clinics share the mode of action and facilitating cross-resistance development. The extensive use of azoles in the environment, e.g., for plant protection and wood preservation, contributes to the spread of resistant populations and challenges using these antifungals in medical treatments. The target of azoles is the cytochrome p450 lanosterol 14-α demethylase encoded by the CYP51 (called also as ERG11 in the case of yeasts) gene. Resistance mechanisms involve mainly the mutations in the coding region in the CYP51 gene, resulting in the inadequate binding of azoles to the encoded Cyp51 protein, or mutations in the promoter region causing overexpression of the protein. The World Health Organization (WHO) has issued the first fungal priority pathogens list (FPPL) to raise awareness of the risk of fungal infections and the increasingly rapid spread of antifungal resistance. Here, we review the main issues about the azole antifungal resistance of trans-kingdom pathogenic fungi with the ability to cause serious human infections and included in the WHO FPPL. Methods for the identification of these species and detection of resistance are summarized, highlighting the importance of these issues to apply the proper treatment.

Fusarium spp. in Human Disease: Exploring the Boundaries between Commensalism and Pathogenesis

Fusarium is a large fungal genus that is widely distributed in the environment, mostly known for its plant pathogenicity. Rarely, it is involved in human pathology, where the type of infection caused is highly dependent upon the portal of entry and the immune status of the host. The study at hand aims to summarize routine methods used in diagnosing such infections as well as more advanced molecular diagnostic methods, techniques that can play a huge role in differentiating between colonization and infection when trying to decide the therapeutic outcome. Consequently, to further support our findings, two different strains (one isolated from corneal scrapings and one isolated from purulent discharge) were analyzed in a clinical context and thoroughly tested using classical and modern diagnostic methods: identification by macroscopical and microscopical examinations of the culture and mass spectrometry, completed by molecular methods such as PCR for trichothecene and ERIC-PCR for genetic fingerprinting. Isolation of a clinically relevant Fusarium spp. from a sample still remains a diagnostic challenge for both the clinician and the microbiologist, because differentiating between colonization and infection is very strenuous, but can make a difference in the treatment that is administered to the patient.

Determination of Pathogens by Electrophoretic and Spectrometric Techniques

In modern medical diagnostics, where analytical chemistry plays a key role, fast and accurate identification of pathogens is becoming increasingly important. Infectious diseases pose a growing threat to public health due to population growth, international air travel, bacterial resistance to antibiotics, and other factors. For instance, the detection of SARS-CoV-2 in patient samples is a key tool to monitor the spread of the disease. While there are several techniques for identifying pathogens by their genetic code, most of these methods are too expensive or slow to effectively analyze clinical and environmental samples that may contain hundreds or even thousands of different microbes. Standard approaches (e.g., culture media and biochemical assays) are known to be very time- and labor-intensive. The purpose of this review paper is to highlight the problems associated with the analysis and identification of pathogens that cause many serious infections. Special attention was paid to the description of mechanisms and the explanation of the phenomena and processes occurring on the surface of pathogens as biocolloids (charge distribution). This review also highlights the importance of electromigration techniques and demonstrates their potential for pathogen pre-separation and fractionation and demonstrates the use of spectrometric methods, such as MALDI-TOF MS, for their detection and identification.

Fusarium Keratitis From a Comprehensive Eye Health Care Facility in South India: Molecular Characterization by MALDI-TOF Versus PCR Sequencing, Species Complex Distribution, and Clinical Correlation

PURPOSE

Fusarium keratitis possesses significant diagnostic and therapeutic challenges. Medically relevant Fusaria belong to various species complexes and show prominent differences in their antifungal susceptibility profile which may influence the clinical outcome. Rapid diagnostic methods are warranted for precise identification of species complexes for prompt initiation of correct antifungals. The aim of the study was to compare between matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) and PCR sequencing for correct species-level identification and to analyze the clinical outcome among different Fusarium species complexes.

METHODS

Twenty-nine culture-proven Fusarium keratitis cases were included in this study. A phylogenetic tree was constructed after TEF1α gene sequencing and isolates were subjected to MALDI-TOF MS, followed by database expansion and identification. Clinical outcome and risk association among species complexes were analyzed retrospectively.

RESULTS

Maximum likelihood phylogeny categorized 68.9% isolates as Fusarium solani species complex (FSSC), 17.2% as Fusarium dimerum species complex (FDSC), followed by 13.7% as Fusarium fujikuroi species complex (FFSC). With extended database, MALDI-TOF MS could correctly speciate 96.5% (28/29) isolates. Previous antibiotic usage (P = 0.034) and preoperative antifungal treatment with natamycin, voriconazole, or ketoconazole (P = 0.025) were significantly higher in the FSSC group. The patients in the FFSC group had a significantly longer duration of symptoms at the time of clinical presentation to the clinic (15 days vs. 5 days, P = 0.030). Among 11 patients with a clinically poor outcome, 9 (31%) had FSSC infection.

CONCLUSIONS

Patients infected with the FSSC had more aggressive infection with poor prognosis. MALDI-TOF MS can serve as the best alternative method to conventional molecular identification with reduced turnaround time, which may help the ophthalmologists to consider the appropriate antifungals or early surgical intervention for improved outcome.

MALDI-TOF MS: application in diagnosis, dereplication, biomolecule profiling and microbial ecology

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized scientific research over the past few decades and has provided a unique platform in ongoing technological developments. Undoubtedly, there has been a bloom chiefly in the field of biological sciences with this emerging technology, and has enabled researchers to generate critical data in the field of disease diagnoses, drug development, dereplication. It has received well acceptance in the field of microbial identification even at strain level, as well as diversified field like biomolecule profiling (proteomics and lipidomics) has evolved tremendously. Additionally, this approach has received a lot more attention over conventional technologies due to its high throughput, speed, and cost effectiveness. This review aims to provide a detailed insight regarding the application of MALDI-TOF MS in the context of medicine, biomolecule profiling, dereplication, and microbial ecology. In general, the expansion in the application of this technology and new advancements it has made in the field of science and technology has been highlighted.

A New Filter Based Cultivation Approach for Improving Aspergillus Identification using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS)

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) is widely used in clinical laboratories for routine identification of bacteria and yeasts. However, methodological difficulties are still apparent when applied to filamentous fungi. The liquid cultivation method recommended by Bruker Daltonics GmbH for identification of filamentous fungi by MALDI-TOF MS is labour intensive and time-consuming. In this study, growth of Aspergillus species on different (porous) surfaces was investigated with the aim to develop a more reliable, quicker and less laborious identification method using MALDI-TOF MS. Mycelial growth without sporulation mimicking liquid cultivation and reliable MALDI-TOF MS spectra were obtained when A. fumigatus strains were grown on and in between a polycarbonate membrane filter on Sabouraud dextrose agar. A database of in-house reference spectra was created by growing Aspergillus reference strains (mainly focusing on sections Fumigati and Flavi) under these selected conditions. A test set of 50 molecularly identified strains grown under different conditions was used to select the best growth condition for identification and to perform an initial validation of the in-house database. Based on these results, the cultivation method on top of a polycarbonate filter proved to be most successful for species identification. This method was therefore selected for the identification of two sets of clinical isolates that mainly consisted of Aspergilli (100 strains originating from Indonesia, 70 isolates from Qatar). The results showed that this cultivation method is reliable for identification of clinically relevant Aspergillus species, with 67% and 76% correct identification of strains from Indonesia and Qatar, respectively. In conclusion, cultivation of Aspergilli on top of a polycarbonate filter showed improved results compared to the liquid cultivation protocol recommended by Bruker in terms of percentage of correct identification, ease of MSP creation, time consumption, cost and labour intensity. This method can be reliably applied for identification of clinically important Aspergilli and has potential for identification of other filamentous fungi.

Synthesis and Study of Antifungal Properties of New Cationic Beta-Glucan Derivatives

The interaction of positively charged polymers (polycations) with a biological membrane is considered to be the cause of the frequently observed toxicity of these macromolecules. If it is possible to obtain polymers with a predominantly negative effect on bacterial and fungal cells, such systems would have great potential in the treatment of infectious diseases, especially now when reports indicate the growing risk of fungal co-infections in COVID-19 patients. We describe in this article cationic derivatives of natural beta-glucan polymers obtained by reacting the polysaccharide isolated from Saccharomyces boulardii (SB) and Cetraria islandica (CI) with glycidyl trimethyl ammonium chloride (GTMAC). Two synthesis strategies were applied to optimize the product yield. Fungal diseases particularly affect low-income countries, hence the emphasis on the simplicity of the synthesis of such drugs so they can be produced without outside help. The three structures obtained showed selective anti-mycotic properties (against, i.e., Scopulariopsis brevicaulis, Aspergillus brasiliensis, and Fusarium solani), and their toxicity established using fibroblast 3T3-L1 cell line was negligible in a wide range of concentrations. For one of the polymers (SB derivative), using in vivo model of Aspergillus brasiliensis infection in Galleria mellonella insect model, we confirmed the promising results obtained in the preliminary study.

Recent developments in less known and multi-resistant fungal opportunists

Fungal infections have increased in recent years due to host factors, such as oncohaematological and transplant-related disorders, immunosuppressive therapy, and AIDS. Additionally, molecular and proteomic facilities have become available to identify previously unrecognizable opportunists. For these reasons, reports on less-known and recalcitrant mycoses, such as those caused by black fungi, hyaline filamentous fungi, coelomycetes, Mucorales, and non-Candida yeasts have emerged. In this review, novel taxonomy in these groups, which often are multi-resistant to one or several classes of antifungals, is discussed. Clinical presentations, diagnosis and current treatment of some major groups are summarised.

Fusarium: more than a node or a foot-shaped basal cell

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).

Clinical Origin and Species Distribution of Fusarium spp. Isolates Identified by Molecular Sequencing and Mass Spectrometry: A European Multicenter Hospital Prospective Study

Fusarium spp. are widespread environmental fungi as well as pathogens that can affect plants, animals and humans. Yet the epidemiology of human fusariosis is still cloudy due to the rapidly evolving taxonomy. The Mass Spectrometry Identification database (MSI) has been developed since 2017 in order to allow a fast, accurate and free-access identification of fungi by matrix-assisted laser desorption ionization—time of flight (MALDI-TOF) mass spectrometry. Taking advantage of the MSI database user network, we aim to study the species distribution of Fusarium spp. isolates in an international multicenter prospective study. This study also allowed the assessment of the abilities of miscellaneous techniques to identify Fusarium isolates at the species level. The identification was performed by PCR-sequencing and phylogenic-tree approach. Both methods are used as gold standard for the evaluation of mass spectrometry. Identification at the species complex was satisfactory for all the tested methods. However, identification at the species level was more challenging and only 32% of the isolates were correctly identified with the National Center for Biotechnology Information (NCBI) DNA database, 20% with the Bruker MS database and 43% with the two MSI databases. Improvement of the mass spectrometry database is still needed to enable precise identification at the species level of any Fusarium isolates encountered either in human pathology or in the environment.

Invasive Fusariosis in Nonneutropenic Patients, Spain, 2000-2015

Invasive fusariosis (IF) is associated with severe neutropenia in patients with concurrent hematologic conditions. We conducted a retrospective observational study to characterize the epidemiology of IF in 18 Spanish hospitals during 2000-2015. In that time, the frequency of IF in nonneutropenic patients increased from 0.08 cases per 100,000 admissions in 2000-2009 to 0.22 cases per 100,000 admissions in 2010-2015. Nonneutropenic IF patients often had nonhematologic conditions, such as chronic cardiac or lung disease, rheumatoid arthritis, history of solid organ transplantation, or localized fusariosis. The 90-day death rate among nonneutropenic patients (28.6%) and patients with resolved neutropenia (38.1%) was similar. However, the death rate among patients with persistent neutropenia (91.3%) was significantly higher. We used a multivariate Cox regression analysis to characterize risk factors for death: persistent neutropenia was the only risk factor for death, regardless of antifungal therapy.

Update on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Identification of Filamentous Fungi

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based species identification has found its place in many clinical routine diagnostic laboratories over the past years, allowing significantly reduced turnaround times and high-precision results. With regard to MALDI-TOF MS for filamentous fungi, here, we discuss different approaches for sample processing and growth conditions before analysis. In particular, we review the performances of different commercially available databases as well as the potential of complementary (self-constructed) in-house databases.

Humidity governs the wall-inhabiting fungal community composition in a 1600-year tomb of Emperor Yang

Biodeterioration caused by filamentous fungi is often a threat to the architectural heritage (i.e. tombs and historic sites). To specifically understand the deterioration phenomena caused by microorganisms in tombs and how these are shaped due to various environmental factors, the fungal communities in the coffin chamber of the Chinese emperor Yang (BC 569-618) were investigated at different heights using denaturant gradient gel electrophoresis (DGGE) fingerprinting. The associated environmental conditions, such as humidity, temperature, height and illumination, were also assessed. The results showed that a great diversity of fungal species (Cordyceps, Fusarium, Harpochytrium, Emericellopsis, Volutella, Cladosporium, Stachybotrys, Trichoderma, Cochlonema and two unknown fungal species) was present in emperor Yang's coffin chamber. The predominant species were Stachybotrys, Fusarium, Trichoderma and Cochlonema. Redundancy analysis (RDA) indicated that humidity, temperature, height and illumination were the most significantly related factors shaping the fungal communities. Humidity showed the highest degree of variance description (19.2%) than all other environmental factors, followed by illumination (18.3%) and height (12.8%). Furthermore, fungal richness and diversity indices showed a positive correlation with humidity (p < 0.05). These results help in understanding the fungal community in tombs, promoting the mitigation of deterioration phenomena of such building heritage for the present and future.

In Vitro Susceptibility of Fusarium to Isavuconazole

To evaluate the in vitro susceptibility of Fusarium to isavuconazole, 75 clinical isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry and then tested with a broth microdilution method (EUCAST) and the gradient concentration strip (GCS) technique. The activity of isavuconazole overall was shown to be limited, with an MIC₅₀ of >16 μg/ml, without significant differences between the species complexes. The categorical agreement between GCS and EUCAST was 97.4% to 100%, making the GCS as a valuable alternative.

First Comprehensive Report of Clinical Fusarium Strains Isolated in the State of Sao Paulo (Brazil) and Identified by MALDI-TOF MS and Molecular Biology

The aim of this study was to compare the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), phenotypic and molecular methods for the identification of Fusarium species complexes isolated from clinical cases in the State of Sao Paulo (Brazil) between the years 2001 and 2017. Sequencing of ITS region of ribosomal DNA and elongation factor 1 alpha gene (ET1α) were used as reference method in the analysis of a total of 108 Fusarium spp. clinical strains isolated from human hosts with superficial and systemic infections. Agreement between MALDI-TOF-MS and molecular data was observed for 97 out of 108 clinical isolates (89.8%), whereas five (4.6%) and six (5.5%) clinical isolates were misidentified and were not identified by MALDI-TOF MS, respectively. ITS region sequences and MALDI-TOF MS mass spectra identified and grouped correctly most of Fusarium clinical isolates at species complex level. This investigation highlights the potential of MALDI-TOF MS technique as a fast and cost-efficient alternative for clinical Fusarium identification. However, MALDI-TOF MS requires a more accurate and larger database. This work is the first comprehensive report for Fusarium population, based on phenotypic analyses, proteomic profile by MALDI-TOF and phylogenetic analyses of Fusarium species complexes isolated from clinical cases in the State of Sao Paulo, Brazil.

Adaptive-Cognitive Kalman Filter and Neural Network for an Upgraded Nondispersive Thermopile Device to Detect and Analyze Fusarium Spores

Noises such as thermal noise, background noise or burst noise can reduce the reliability and confidence of measurement devices. In this work, a recursive and adaptive Kalman filter is proposed to detect and process burst noise or outliers and thermal noise, which are popular in electrical and electronic devices. The Kalman filter and neural network are used to preprocess data of three detectors of a nondispersive thermopile device, which is used to detect and quantify Fusarium spores. The detectors are broadband (1 µm to 20 µm), λ 1 (6.09 ± 0.06 µm) and λ 2 (9.49 ± 0.44 µm) thermopiles. Additionally, an artificial neural network (NN) is applied to process background noise effects. The adaptive and cognitive Kalman Filter helps to improve the training time of the neural network and the absolute error of the thermopile data. Without applying the Kalman filter for λ 1 thermopile, it took 12 min 09 s to train the NN and reach the absolute error of 2.7453 × 104 (n. u.). With the Kalman filter, it took 46 s to train the NN to reach the absolute error of 1.4374 × 104 (n. u.) for λ 1 thermopile. Similarly, to the λ 2 (9.49 ± 0.44 µm) thermopile, the training improved from 9 min 13 s to 1 min and the absolute error of 2.3999 × 105 (n. u.) to the absolute error of 1.76485 × 105 (n. u.) respectively. The three-thermopile system has proven that it can improve the reliability in detection of Fusarium spores by adding the broadband thermopile. The method developed in this work can be employed for devices that encounter similar noise problems.

Application of MALDI-TOF MS to rapid identification of anaerobic bacteria

BACKGROUND

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been rapidly developed and widely used as an analytical technique in clinical laboratories with high accuracy in microorganism identification.

OBJECTIVE

To validate the efficacy of MALDI-TOF MS in identification of clinical pathogenic anaerobes.

METHODS

Twenty-eight studies covering 6685 strains of anaerobic bacteria were included in this meta-analysis. Fixed-effects models based on the P-value and the I-squared were used for meta-analysis to consider the possibility of heterogeneity between studies. Statistical analyses were performed by using STATA 12.0.

RESULTS

The identification accuracy of MALDI-TOF MS was 84% for species (I² = 98.0%, P < 0.1), and 92% for genus (I² = 96.6%, P < 0.1). Thereinto, the identification accuracy of Bacteroides was the highest at 96% with a 95% CI of 95-97%, followed by Lactobacillus spp., Parabacteroides spp., Clostridium spp., Propionibacterium spp., Prevotella spp., Veillonella spp. and Peptostreptococcus spp., and their correct identification rates were all above 90%, while the accuracy of rare anaerobic bacteria was relatively low. Meanwhile, the overall capabilities of two MALDI-TOF MS systems were different. The identification accuracy rate was 90% for VITEK MS vs. 86% for MALDI biotyper system.

CONCLUSIONS

Our research showed that MALDI-TOF-MS was satisfactory in genus identification of clinical pathogenic anaerobic bacteria. However, this method still suffers from different drawbacks in precise identification of rare anaerobe and species levels of common anaerobic bacteria.

Increased species-assignment of filamentous fungi using MALDI-TOF MS coupled with a simplified sample processing and an in-house library

In this study we evaluated the capacity of MALDI-TOF MS (Bruker Daltonics, Bremen, Germany) to identify clinical mould isolates. We focused on two aspects of MALDI-TOF MS identification: the sample processing and the database. Direct smearing of the sample was compared with a simplified processing consisting of mechanical lysis of the moulds followed by a protein extraction step. Both methods were applied to all isolates and the Filamentous Fungi Library 1.0 (Bruker Daltonics) was used for their identification. This approach allowed the correct species-level identification of 25/34 Fusarium spp. and 10/10 Mucor circinelloides isolates using the simplified sample processing. In addition, 7/34 Fusarium spp. and 1/21 Pseudallescheria/Scedosporium spp. isolates were correctly identified at the genus level. The remaining isolates-60-could not be identified using the commercial database, mainly because of the low number of references for some species and the absence of others. Thus, an in-house library was built with 63 local isolates previously characterized using DNA sequence analysis. Its implementation allowed the accurate identification at the species level of 94 isolates (91.3%) and the remaining nine isolates (8.7%) were correctly identified at the genus level. No misidentifications at genus level were detected. In conclusion, with improvements of both the sample preparation and the feeding of the database, MALDI-TOF MS is a reliable, ready to use method to identify moulds of clinical origin in an accurate, rapid, and cost-effective manner.

Identification of Mucorales by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry

More than 20 different species of Mucorales can be responsible for human mucormycosis. Accurate identification to the species level is important. The morphological identification of Mucorales is not reliable, and the currently recommended identification standard is the molecular technique of sequencing the internal transcribed spacer regions. Nevertheless, matrix-assisted laser desorption ionization time-of-flight mass spectrometry has been shown to be an accurate alternative for the identification of bacteria, yeasts, and even filamentous fungi. Therefore, 38 Mucorales isolates, belonging to 12 different species or varieties, mainly from international collections, including 10 type or neo-type strains previously identified by molecular methods, were used to evaluate the usefulness of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for the identification of human pathogenic Mucorales to the species level. One to three reference strains for each species were used to create a database of main spectrum profiles, and the remaining isolates were used as test isolates. A minimum of 10 spectra was used to build the main spectrum profile of each database strain. Interspecies discrimination for all the isolates, including species belonging to the same genus, was possible. Twenty isolates belonging to five species were used to test the database accuracy, and were correctly identified to the species level with a log-score >2. In summary, matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a reliable and rapid method for the identification of most of the human pathogenic Mucorales to the species level.

Rapid characterization of aquatic hyphomycetes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Protein fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI--TOF MS) is a rapid, reliable, and economical method to characterize isolates of terrestrial fungi and other microorganisms. The objective of our study was to evaluate the suitability of MALDI-TOF MS for the identification of aquatic hyphomycetes, a polyphyletic group of fungi that play crucial roles in stream ecosystems. To this end, we used 34 isolates of 21 aquatic hyphomycete species whose identity was confirmed by spore morphology and internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) nuc rDNA sequencing. We tested the efficiency of three protein extraction methods, including chemical and mechanical treatments using 13 different protocols, with the objective of producing high-quality MALDI-TOF mass spectra. In addition to extraction protocols, mycelium age was identified as a key parameter affecting protein extraction efficiency. The dendrogram based on mass-spectrum similarity indicated good and relevant taxonomic discrimination; the tree structure was comparable to that of the phylogram based on ITS sequences. Consequently, MALDI-TOF MS could reliably identify the isolates studied and provided greater taxonomic accuracy than classical morphological methods. MALDI-TOF MS seems suited for rapid characterization and identification of aquatic hyphomycete species.

Fluorine-18-fluorodeoxyglucose PET/CT in hematopoietic stem cell transplant patients with fusariosis: initial findings of a case series review

BACKGROUND

Fusariosis is an opportunistic fungal infection that affects mostly leukemic and hematopoietic stem cell transplant patients. Locally invasive and disseminated infection may occur. Treatment is challenging, and besides evaluation of immune status, one also needs to take into account organ involvement to predict the duration and prognosis.

OBJECTIVE

The aim of this study was to present the findings and clinical follow-up from a series of cases of Fusarium spp. infections in patients subjected to hematopoietic stem cell transplant evaluated with one or more fluorine-18-fluorodeoxyglucose (18F-FDG) PET/CT scans, according to the source of clinical culture sample (blood or wound secretion).

RESULTS

Ten patients were included. In this series, 18F-FDG PET/CT was able to detect osteomyelitis in three patients.

CONCLUSION

Although having a small number of patients and lack of standard approach, 18F-FDG PET/CT seemed useful to discriminate uncomplicated cases of primary bloodstream infections and detect occult foci of metastatic infection in patients with positive cutaneous lesions cultures.

Fusarium: The versatile pathogen

Fusarium is an emerging human opportunistic pathogen of growing importance, especially among immunosuppressed haematology patients due to an increased incidence of disseminated infections over the past two decades. This trend is expected only to continue due to the advances in medical and surgical technologies that will prolong the lives of the severely ill, making these patients susceptible to rare opportunistic infections. Production of mycotoxins, enzymes such as proteases, angio-invasive property and an intrinsically resistant nature, makes this genus very difficult to treat. Fusarium is frequently isolated from the cornea and less commonly from nail, skin, blood, tissue, Continuous Ambulatory Peritoneal Dialysis (CAPD) fluid, urine and pleural fluid. Conventional microscopy establishes the genus, but accurate speciation requires multilocus sequence typing with housekeeping genes such as internal transcribed spacer, translation elongation factor-1α and RPB1 and 2 (largest and second largest subunits of RNA polymerase), for which expansive internet databases exist. Identifying pathogenic species is of epidemiological significance, and the treatment includes immune reconstitution by granulocyte-colony-stimulating factor, granulocyte macrophage-colony-stimulating factor and a combination of the most active species - specific antifungals, typically liposomal amphotericin-B and voriconazole. However, patient outcome is difficult to predict even with in vitro susceptibility with these drugs. Therefore, prevention methods and antifungal prophylaxis have to be taken seriously for these vulnerable patients by vigilant healthcare workers. The current available literature on PubMed and Google Scholar using search terms 'Fusarium', 'opportunistic invasive fungi' and 'invasive fusariosis' was summarised for this review.

Sugarcane cells as origin of acid beverage floc in cane sugar

Brazil stands out as the largest producer of crystal sugar in the world, exporting much of its production to the soft drinks industry. However, the chemical composition of sugar may contain numerous compounds that promote the formation of acid beverage flocs (ABF), reducing product acceptance. This study aimed to identify the chemical composition of ABF using different analytical techniques. We could observe the ABF are formed by several chemical classes. Regarding the histochemical analysis, we observed the presence of cellular sugarcane tissues, which are not fully removed in sugarcane processing. Mineral compounds, such as silicon, were found in great amounts by the Scanning electron microscopy and energy dispersive system (SEM/EDS) analysis. The mass spectrometry, high resolution mass by Q-ToF analysis and MALDI-MS allowed identification of compounds, such as p-hydroxybenzaldehyde, vanillin, triacontanoic acid, hexadecanoic acid, octadecanoic acid and n-octacosanoic acid, in the ABF composition. These compounds are widely found in vegetable tissues, confirming that the ABF are formed by tiny particles of plant cells of sugar cane.

Performance of VITEK mass spectrometry V3.0 for rapid identification of clinical Aspergillus fumigatus in different culture conditions based on ribosomal proteins

Fast and accurate discrimination of Aspergillus fumigatus is significant, since misidentification may lead to inappropriate clinical therapy. This study assessed VITEK mass spectrometry (MS) V3.0 for A. fumigatus identification using extracted fungal ribosomal proteins. A total of 52 isolates preliminarily identified as A. fumigatus by traditional morphological methods were inoculated in three different culture media and cultured at two different temperatures. The specific spectral fingerprints of different culture time points (48, 72, 96, and 120 h) were obtained. Of all strains, 88.5% (46/52) were discriminated as A. fumigatus, while the remaining 11.5% (6/52) produced results inconsistent with morphological analysis. Molecular sequencing, as a reference method for species identification, was used to validate the morphological analysis and matrix-assisted laser desorption/ionization time of flight MS. Chi-square tests (χ² test, P=0.05) demonstrated that the culture medium and incubation temperature had no effects on identification accuracy; however, identification accuracy of the strains in the 48-h group was lower than that in other groups. In addition, we found that ribosomal proteins extracted from A. fumigatus can be stored in different environments for at least 1 week, with their profiles remaining stable and strain identification results showing no change. This is beneficial for medical institutions with no mass spectrometer at hand. Overall, this study showed the powerful ability of VITEK MS V 3.0 in identifying A. fumigatus.

Matrix-assisted laser desorption/ionization–time of flight mass spectrometry: protocol standardization and database expansion for rapid identification of clinically important molds

Aim: To standardize the matrix-assisted laser desorption ionization–time of flight mass spectrometry protocols and expansion of existing Bruker Biotyper database for mold identification. Materials & methods: Four different sample preparation methods (protocol A, B, C and D) were evaluated. Results: On analyzing each protein extraction method, reliable identification and best log scores were achieved through protocol D. The same protocol was used to identify 153 clinical isolates. Of these 153, 123 (80.3%) were accurately identified by using existing database and remaining 30 (19.7%) were not identified due to unavailability in database. On inclusion of missing main spectrum profile in existing database, all 153 isolates were identified. Conclusion: Matrix-assisted laser desorption ionization–time of flight mass spectrometry can be used for routine identification of clinically important molds.

Lipid and protein fingerprinting for Fusarium oxysporum f. sp. cubense strain-level classification

Banana is one of the most popular fruits in the world but has been substantially impaired by Panama disease in the last years. Fusarium oxysporum f. sp. cubense (Foc) is the causal agent and colonizes banana cultivars from many subgroups with different aggressiveness levels, often leading to plant death while compromising new crops in infested areas. This study has evaluated the ability of MALDI-MS protein and lipid fingerprinting to provide intraspecies classification of Foc isolates and to screen biomolecules related to host-pathogen relationship. The MS data, when inspected via partial least square discriminant analysis (PLS-DA), distinguished the isolates by aggressiveness as well as by specific location and host. Although both lipids and proteins show discriminating tendencies, these differences were more clearly perceived via the protein profiles. Considering that Cavendish cultivar is the more resistant option to endure Foc presence in the field, the lipids and proteins related to this subgroup might have an important role in pathogen adaptation. This study reports a new application of MALDI-MS for the analysis of a banana pathogen with intraspecies classification ability. Graphical abstract MALDI-MS classified Foc isolates by aggressiveness level on banana revealing the additional influence of location and host cultivar on the expression of lipids and proteins.

Characterization of the fungal flora of dolo, a traditional fermented beverage of Burkina Faso, using MALDI-TOF mass spectrometry

A cross-sectional study was conducted in Bobo-Dioulasso, Burkina Faso, to identify the yeast diversity associated with the manufacture of dolo, a traditional fermented beverage of Burkina Faso. From sixty specimens spread onto chromogenic medium plates, sixty-two strains were isolated then identified using MALDI-TOF analysis. Seven yeast species were identified, Saccharomyces cerevisiae (39%) followed by Pichia manshurica (18%) being the most frequent. Forty-three percent of the samples contained Candida species, notably Candida albicans. In conclusion, the combined use of a chromogenic medium and MALDI-TOF analysis reveals a higher diversity in yeast species present in the dolo than previously thought.

Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry systems for the identification of clinical filamentous fungi

Infections caused by filamentous fungi have become a health concern, and require rapid and accurate identification in order for effective treatment of the pathogens. To compare the performance of two MALDI-TOF MS systems (Bruker Microflex LT and Xiamen Microtyper) in the identification of filamentous fungal species. A total of 374 clinical filamentous fungal isolates sequentially collected in the Clinical Laboratory at the Beijing Tongren Hospital between January 2014 and December 2015 were identified by traditional phenotypic methods, Bruker Microflex LT and Xiamen Microtyper MALDI-TOF MS, respectively. The discrepancy between these methods was resolved by sequencing for definitive identification. Bruker Microflex LT and Xiamen Microtyper had similar correct species ID (98.9 vs. 99.2%), genus ID (99.7 vs. 100%), mis-ID (0.3 vs. 0%) and no ID (0 vs. 0). The rate of correct species identification by both MALDI-TOF MS (98.9 and 99.2%, respectively) was much higher compared with phenotypic approach (91.9%). Both MALDI-TOF MS systems provide accurate identification of clinical filamentous fungi compared with conventional phenotypic method, and have the potential to replace identification for routine identification of these fungi in clinical mycology laboratories. Both systems have similar performance in the identification of clinical filamentous fungi.

Emergence of the Molds Other than Aspergillus in Immunocompromised Patients

Immunocompromised patients are at high risk for invasive fungal infections (IFIs); although Aspergillus remains the most common IFI caused by molds, other fungi, such as Mucorales, dematiaceous molds, and Fusarium spp, are being seen with increasing frequency. Presentations can vary, but sinopulmonary and disseminated infections are common. Our understanding of the pathogenesis of these infections is rudimentary. Fungal cultures and histopathology remain the backbone of diagnostics, as no good serologic markers are available. Polymerase chain reaction tests are being developed but currently remain investigational. Management of these infections is usually multidisciplinary, requiring surgical debridement along with antifungal therapy.

Antifungal Susceptibility Testing of Fusarium: A Practical Approach

In vitro susceptibility testing of Fusarium is becoming increasingly important because of frequency and diversity of infections and because resistance profiles are species-specific. Reference methods for antifungal susceptibility testing (AFST) are those of Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility (EUCAST), but breakpoints (BPs) have not yet been established. One of the problems is that phylogenetic distances between Fusarium species are much smaller than between species of, e.g., Candida. Epidemiological cutoff values (ECVs) for some Fusarium species have been determined in order to differentiate wild-type from non-wild-type isolates. In clinical routine, commercially available assays such as Etest, Sensititre or others provide essential agreement with reference methods. Our objective is to summarize antifungal susceptibility testing of Fusarium genus in the clinical laboratory: how to do it, when to do it, and how to interpret it.

Decision criteria for MALDI-TOF MS-based identification of filamentous fungi using commercial and in-house reference databases

BACKGROUND

Several Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry protocols, which differ in identification criteria, have been developed for mold and dermatophyte identification. Currently, the most widely used approach is Bruker technology, although no consensus concerning the log(score) threshold has been established. Furthermore, it remains unknown how far increasing the number of spots to compare results might improve identification performance. In this study, we used in-house and Bruker reference databases as well as a panel of 422 isolates belonging to 126 species to test various thresholds. Ten distinct identification algorithms requiring one to four spots were tested.

RESULTS

Our findings indicate that optimal results were obtained by applying a decisional algorithm in which only the highest score of four spots was taken into account with a 1.7 log(score) threshold. Testing the entire panel enabled identification of 87.41% (in-house database) and 35.15% (Bruker database) of isolates, with a positive predictive value (PPV) of 1 at the genus level for both databases as well as 0.89 PPV (in-house database) and 0.72 PPV (Bruker database) at the species level. Applying the same rules to the isolates for which the species were represented by at least three strains in the database enabled identification of 92.1% (in-house database) and 46.6% (Bruker database) of isolates, with 1 PPV at the genus level for both databases as well as 0.95 PPV (in-house database) and 0.93 PPV (Bruker database) at the species level.

CONCLUSIONS

Depositing four spots per extract and lowering the threshold to 1.7, a threshold which is notably lower than that recommended for bacterial identification, decreased the number of unidentified specimens without altering the reliability of the accepted results. Nevertheless, regardless of the criteria used for mold and dermatophyte identification, commercial databases require optimization.

[Clusters of Fusarium solani infection in juvenile captive born Caretta caretta sea turtles]

Various yeasts and filamentous fungi are described as the cause of infection in sea turtles. Among them, Fusarium solani is responsible both for superficial and invasive infection in weakened adults (capture, stranding), and wild nest contamination, causing massive losses during hatching. We illustrate the pathogenicity of this fungus in sea turtles, through our experience with the species Caretta caretta (loggerhead turtle) and its reproduction, which was obtained for the first time in 2010 at the marine park Marineland, Antibes and renewed in 2011 and 2013. The first generation (6 viable newborns e.g. 0.9% of the nest) was severely affected by an infectious agent causing skin and multifocal organ lesions. Microbiological samples allowed to establish F. solani as the etiological agent. Antifungal therapy with posaconazole cured 2 (33%) of the brood. Epidemiological investigations, infection control and hygiene measures as well as diagnosis criteria, preemptive and curative treatment procedures allowed better prevention and cure and finally higher survival rates in subsequent broods, in 2011 and 2013 (80 viable newborns e.g. 6.6% of the nest and 50% survival rate). F. solani appears as a major threat for the successful reproduction of sea turtles in the wild. As observed, this threat is also of concern during captive breeding. The conditions of transmission and pathogenicity of Fusarium spp. in these animals are discussed in light of the literature cases that occurred in adult sea turtles and in wild nests, and of our breeding experience.

Major phytopathogens and strains from cocoa (Theobroma cacao L.) are differentiated by MALDI-MS lipid and/or peptide/protein profiles

Phytopathogens are the main disease agents that promote attack of cocoa plantations in all tropical countries. The similarity of the symptoms caused by different phytopathogens makes the reliable identification of the diverse species a challenge. Correct identification is important in the monitoring and management of these pests. Here we show that matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) in combination with multivariate data analysis is able to rapidly and reliably differentiate cocoa phytopathogens, namely Moniliophthora perniciosa, Phytophthora palmivora, P. capsici, P. citrophthora, P. heveae, Ceratocystis cacaofunesta, C. paradoxa, and C. fimbriata. MALDI-MS reveals unique peptide/protein and lipid profiles which differentiate these phytopathogens at the level of genus, species, and single strain coming from different hosts or cocoa tissues collected in several plantations/places. This fast methodology based on molecular biomarkers is also shown to be sufficiently reproducible and selective and therefore seems to offer a suitable tool to guide the correct application of sanitary defense approaches for infected cocoa plantations. International trading of cocoa plants and products could also be efficiently monitored by MALDI-MS. It could, for instance, prevent the entry of new phytopathogens into a country, e.g., as in the case of Moniliophthora roreri fungus that is present in all cocoa plantations of countries bordering Brazil, but that has not yet attacked Brazilian plantations. Graphical Abstract Secure identification of phytopathogens attacking cocoa plantations has been demonstrated via typical chemical profiles provided by mass spectrometric screening.

Identification of Stachybotrys spp. by MALDI-TOF mass spectrometry

Stachybotrys (S.) spp. are omnipresent cellulolytic molds. Some species are highly toxic owing to their ability to synthesize various secondary metabolites such as macrocyclic trichothecenes or hemolysins. The reliable identification of Stachybotrys at species level is currently limited to genome-based identification. This study aimed to establish a fast and reliable MALDI-TOF MS identification method by optimizing the pre-analytical steps for protein extraction for subsequent generation of high-quality fingerprint mass spectra. Eight reference strains of the American Type Culture Collection and the Technical University of Denmark were cultivated in triplicate (biological repetitions) for 2 days in malt extract broth. The mycelia (1.5 ml) were first washed with 75 % ethanol and an additional washing step with dimethyl sulfoxide (10 %) was added to remove unspecific low weight masses. Furthermore, mycelia were broken with roughened glass beads in formic acid (70 %) and acetonitrile. The method was successfully applied to a total of 45 isolates of Stachybotrys originating from three different habitats (indoor, feed, and food samples; n = 15 each): Twenty-seven isolates of S. chartarum and 18 isolates of S. chlorohalonata could be identified by MALDI-TOF MS. The data obtained exactly matched those obtained by genome-based identification. The mean score values for S. chartarum ranged from 2.509 to 2.739 and from 2.148 to 2.622 for S. chlorohalonata with a very good reproducibility: the relative standard deviations were between 0.3 % and 6.8 %. Thus, MALDI-TOF MS proved to be a fast and reliable alternative to identification of Stachybotrys spp. by nucleotide amplification and sequencing.

Performance of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Aspergillus, Scedosporium, and Fusarium spp. in the Australian Clinical Setting

We developed an Australian database for the identification of Aspergillus, Scedosporium, and Fusarium species (n = 28) by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In a challenge against 117 isolates, species identification significantly improved when the in-house-built database was combined with the Bruker Filamentous Fungi Library compared with that for the Bruker library alone (Aspergillus, 93% versus 69%; Fusarium, 84% versus 42%; and Scedosporium, 94% versus 18%, respectively).

Emerging infections due to filamentous fungi in humans and animals: only the tip of the iceberg?

Over the last few decades, the number of patients susceptible to invasive filamentous fungal infections has steadily increased, especially in populations suffering from hematological diseases. The pathogens responsible for such mycoses are now quite well characterized, such as Aspergillus spp. - the most commonly isolated mold -, Mucorales, Fusarium spp., Scedosporium spp. or melanized fungi. An increase in the incidence of this category of 'emerging' fungi has been recently highlighted, evoking a shift in fungal ecology. Starting from these medical findings, taking a step back and adopt a wider perspective offers possible explanations of this phenomenon on an even larger scale than previously reported. In this review, we illustrate the link between emerging fungi in medicine and changes in ecology or human behaviours, and we encourage integrative approaches to apprehend the adverse effects of progress and develop preventive measures in vast domains, such as agriculture or medicine.

Evaluation of two methods for direct detection of Fusarium spp. in water

Fusarium is a waterborne fungus that causes severe infections especially in patients with prolonged neutropenia. Traditionally, the detection of Fusarium in water is done by culturing which is difficult and time consuming. A faster method is necessary to prevent exposure of susceptible patients to contaminated water. The objective of this study was to develop a molecular technique for direct detection of Fusarium in water. A direct DNA extraction method from water was developed and coupled to a genus-specific PCR, to detect 3 species of Fusarium (verticillioides, oxysporum and solani). The detection limits were 10 cells/L and 1 cell/L for the molecular and culture methods, respectively. To our knowledge, this is the first method developed to detect Fusarium directly from water.