Development of a clinically comprehensive database and a simple procedure for identification of molds from solid media by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Intra-abdominal nocardiosis and scedosporiosis in a dog: case report and literature review

A 2-y-old, intact female, mixed-breed dog was presented to the veterinary hospital with abdominal distension, anemia, and lethargy following a chronic history of nonspecific gastrointestinal signs. CBC and serum biochemistry revealed moderate nonregenerative anemia with neutrophilia, hypoalbuminemia, hyperglobulinemia, hypoglycemia, decreased urea and creatinine, and hypercholesterolemia. Abdominal radiographs and ultrasound revealed a large heterogeneous mesenteric mass and ascites. Abdominocentesis confirmed septic peritonitis with filamentous bacteria. Fine-needle aspiration of the mass yielded pyogranulomatous inflammation and hyphae. An exploratory laparotomy revealed a large cranial abdominal mass with granulomas present throughout the abdominal cavity. Due to the poor prognosis and disseminated disease, the owner elected euthanasia. Postmortem and histologic examinations detected intralesional mycetomas and bacterial colonies within the mesenteric masses. 16S ribosomal RNA gene PCR and sequencing using formalin-fixed, paraffin-embedded sections identified Nocardia yamanashiensis, Nocardioides cavernae, and Nocardioides zeicaulis. Fungal culture, PCR, and sequencing confirmed Scedosporium apiospermum. Our report highlights the importance of molecular methods in conjunction with culture and histologic findings for diagnosing coinfections caused by infrequent etiologic agents. Additionally, we provide a comprehensive literature review of Scedosporium apiospermum infections in dogs.

Occurrence, Molecular Serogroups, Antimicrobial Susceptibility and Identification by MALDI-TOF MS of Listeria monocytogenes Isolated from RTE Meat Products in Southern Poland

L. monocytogenes is considered one of the most dangerous foodborne pathogens. This study aimed to determine the occurrence of L. monocytogenes in RTE meat products from southern Poland, including serogroups and antimicrobial susceptibility, and to assess the usefulness of MALDI-TOF MS as a tool for identifying L. monocytogenes. A total of 848 production batches of RTE meat products were analyzed for L. monocytogenes. All L. monocytogenes isolates were serotyped using the multiplex PCR method, tested for antimicrobial susceptibility using the disk diffusion method and identified using the MALDI-TOF MS method. L. monocytogenes was detected in 52/848 batches of RTE meat products (6.13%). The isolates belonged to four serogroups: 17/52 (33%) isolates to IVb; 15/52 (29%) isolates to IIa; 10/52 (19%) isolates to IIc and 10/52 (19%) isolates to IIb. All isolates (52/52) showed susceptibility to the tested antimicrobials. Using MALDI-TOF MS, 10/52 isolates (19.2%) were identified at the level of secure genus identification, probable species identification; 37/52 isolates (71.2%) were identified at the level of probable genus identification; 3/52 isolates (5.8%) were incorrectly identified as L. innocua; and 2/52 isolates (3.8%) were not identified. The occurrence of L. monocytogenes in RTE meat products was low. Almost half of the analyzed isolates were L. monocytogenes of serogroups, which are most often associated with listeriosis in humans in Poland. All isolates showed susceptibility to five commonly used antimicrobials for treating listeriosis. The use of MALDI-TOF MS as a tool for the identification of L. monocytogenes indicated its limitations related to the insufficient representation of the pathogen in the reference database.

Formic acid sandwich method is well-suited for filamentous fungi identification and improves turn around time using Zybio EXS2600 mass spectrometry

OBJECTIVES

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is extensively employed for the identification of filamentous fungi on MALDI Biotyper (Bruker Daltonics) and Vitek MS (biomerieux), but the performance of fungi identification on new EXS2600 (Zybio) is still unknow. Our study aims to evaluate the new EXS2600 system's (Zybio) ability to rapidly identify filamentous fungi and determine its effect on turnaround time (TAT) in our laboratory.

METHODS

We tested 117 filamentous fungi using two pretreatment methods: the formic acid sandwich (FA-sandwich) and a commercial mold extraction kit (MEK, Zybio). All isolates were confirmed via sequence analysis. Laboratory data were extracted from our laboratory information system over two 9-month periods: pre-EXS (April to December 2022) and post-EXS (April to December 2023), respectively.

RESULTS

The total correct identification (at the species, genus, or complex/group level) rate of fungi was high, FA-sandwich (95.73%, 112/117), followed by MEK (94.02%, 110/117). Excluding 6 isolates not in the database, species-level identification accuracy was 92.79% (103/111) for FA-sandwich and 91.89% (102/111) for MEK; genus-level accuracy was 97.29% (108/111) and 96.39% (107/111), respectively. Both methods attained a 100% correct identification rate for Aspergillus, Lichtheimia, Rhizopus Mucor and Talaromyces species, and were able to differentiate between Fusarium verticillioides and Fusarium proliferatum within the Fusarium fujikuroi species complex. Notably, high confidence was observed in the species-level identification of uncommon fungi such as Trichothecium roseum and Geotrichum candidum. The TAT for all positive cultures decreased from pre EXS2600 to post (108.379 VS 102.438, P < 0.05), and the TAT for tissue decreased most (451.538 VS 222.304, P < 0.001).

CONCLUSIONS

The FA-sandwich method is more efficient and accurate for identifying filamentous fungi with EXS2600 than the MEK. Our study firstly evaluated the performance of fungi identification on EXS2600 and showed it is suitable for clinical microbiology laboratories use.

Scedosporiosis and lomentosporiosis: modern perspectives on these difficult-to-treat rare mold infections

SUMMARYAlthough Scedosporium species and Lomentospora prolificans are uncommon causes of invasive fungal diseases (IFDs), these infections are associated with high mortality and are costly to treat with a limited armamentarium of antifungal drugs. In light of recent advances, including in the area of new antifungals, the present review provides a timely and updated overview of these IFDs, with a focus on the taxonomy, clinical epidemiology, pathogenesis and host immune response, disease manifestations, diagnosis, antifungal susceptibility, and treatment. An expansion of hosts at risk for these difficult-to-treat infections has emerged over the last two decades given the increased use of, and broader population treated with, immunomodulatory and targeted molecular agents as well as wider adoption of antifungal prophylaxis. Clinical presentations differ not only between genera but also across the different Scedosporium species. L. prolificans is intrinsically resistant to most currently available antifungal agents, and the prognosis of immunocompromised patients with lomentosporiosis is poor. Development of, and improved access to, diagnostic modalities for early detection of these rare mold infections is paramount for timely targeted antifungal therapy and surgery if indicated. New antifungal agents (e.g., olorofim, fosmanogepix) with novel mechanisms of action and less cross-resistance to existing classes, availability of formulations for oral administration, and fewer drug-drug interactions are now in late-stage clinical trials, and soon, could extend options to treat scedosporiosis/lomentosporiosis. Much work remains to increase our understanding of these infections, especially in the pediatric setting. Knowledge gaps for future research are highlighted in the review.

Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management

Nosocomial clusters of fungal infections, whilst uncommon, cannot be predicted and are associated with significant morbidity and mortality. Here, we review reports of nosocomial outbreaks of invasive fungal disease to glean insight into their epidemiology, risks for infection, methods employed in outbreak detection including genomic testing to confirm the outbreak, and approaches to clinical and infection control management. Both yeasts and filamentous fungi cause outbreaks, with each having general and specific risks. The early detection and confirmation of the outbreak are essential for diagnosis, treatment of affected patients, and termination of the outbreak. Environmental sampling, including the air in mould outbreaks, for the pathogen may be indicated. The genetic analysis of epidemiologically linked isolates is strongly recommended through a sufficiently discriminatory approach such as whole genome sequencing or a method that is acceptably discriminatory for that pathogen. An analysis of both linked isolates and epidemiologically unrelated strains is required to enable genetic similarity comparisons. The management of the outbreak encompasses input from a multi-disciplinary team with epidemiological investigation and infection control measures, including screening for additional cases, patient cohorting, and strict hygiene and cleaning procedures. Automated methods for fungal infection surveillance would greatly aid earlier outbreak detection and should be a focus of research.

Mass spectrometry-based proteomics as an emerging tool in clinical laboratories

Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.

Intramedullary disseminated sporotrichosis in an immunocompetent patient: case report and review of the literature

BACKGROUND

Disseminated sporotrichosis is a severe opportunistic infection that often affects immunocompromised patients after a cutaneous inoculation. Here we present a rare case of disseminated sporotrichosis discovered as a solitary intramedullary thoracic spinal cord lesion in an immunocompetent patient.

CASE DESCRIPTION

A 37-year-old man presented with progressive lower limb weakness and sensory changes over 1 week. A spinal magnetic resonance imaging (MRI) revealed a contrast-enhancing intramedullary lesion centered at T10. The patient was afebrile and reported no history of trauma or cutaneous lesions. The lesion was unresponsive to a trial of corticosteroids. A thoracic laminectomy was performed and a biopsy obtained. A cutaneous lesion on the arm was concurrently discovered, which was also biopsied. Both the skin and spinal cord biopsies showed Sporothrix schenckii by macroscopic and microscopic morphology which were later confirmed by MALDI-TOF mass spectrometry.

CONCLUSION

This is a rare case of intramedullary disseminated sporotrichosis affecting the central nervous system of an immunocompetent patient. This unusual presentation should be taken into consideration when such intramedullary lesions are encountered.

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.

Comparison of Bruker Biotyper® and Vitek® MS matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry platforms for the identification of filamentous fungi

Aims: To evaluate the performance of two matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry platforms to identify molds isolated from clinical specimens. Methods: Fifty mold isolates were analyzed on Bruker Biotyper® and Vitek® MS platforms. Two Bruker Biotyper extraction protocols were assessed alongside the US FDA-approved extraction protocol for Vitek MS. Results: The Bruker Biotyper modified NIH-developed extraction protocol correctly identified more isolates than Bruker's protocol (56 vs 33%). For species in the manufacturers' databases, Vitek MS correctly identified 85% of isolates, with 8% misidentifications. The Bruker Biotyper identified 64%, with no misidentifications. For isolates not in the databases, the Bruker Biotyper did not misidentify any, and Vitek MS misidentified 36%. Conclusion: Both the Vitek MS and Bruker Biotyper accurately identified the fungal isolates, however Vitek MS was more likely to misidentify isolates than the Bruker Biotyper.

Review of Clinical and Laboratory Diagnostics for Coccidioidomycosis

Coccidioidomycosis is a fungal disease associated with soil exposure that frequently goes undiagnosed due at least in part to its nonspecific presentation and the lack of clinical suspicion by health care providers. Currently available diagnostics for coccidioidomycosis offer qualitative results that can suffer from low specificity, while semiquantitative assays are labor-intensive and complex and can require multiple days to complete. Furthermore, significant confusion exists regarding the optimal diagnostic algorithms and appropriate usage of available diagnostic tests. This review aims to inform clinical laboratorians and treating clinicians about the current diagnostic landscape, appropriate diagnostic strategies, and future diagnostic directions for coccidioidomycosis, which is expected to become more prevalent due to increased migration into areas of endemicity and climate changes.

Validation of an expanded, in-house library and an optimized preparation method for the identification of fungal isolates using MALDI-TOF mass spectrometry

The goal of this study was to validate an optimized sample preparation method for filamentous fungal isolates coupled with the use of an in-house library for the identification of moulds using Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) in a multicenter context. For that purpose, three Spanish microbiology laboratories participated in the identification of 97 fungal isolates using MALDI-TOF MS coupled with the Filamentous Fungi library 3.0 (Bruker Daltonics) and an in-house library containing 314 unique fungal references. The isolates analyzed belonged to 25 species from the genus Aspergillus, Fusarium, Scedosporium/Lomentospora, the Mucorales order and the Dermatophytes group. MALDI-TOF MS identification was carried out from hyphae resuspended in water and ethanol. After a high-speed centrifugation step, the supernatant was discarded and the pellet submitted to a standard protein extraction step. The protein extract was analyzed with the MBT Smart MALDI Biotyper system (Bruker Daltonics). The rate of accurate, species-level identification obtained ranged between 84.5% and 94.8% and the score values were 1.8 for 72.2-94.9% of the cases. Two laboratories failed to identify only one isolate of Syncephalastrum sp. and Trichophyton rubrum, respectively and three isolates could not be identified in the third center (F. proliferatum, n = 1; T.interdigitale, n = 2). In conclusion, the availability of an effective sample preparation method and an extended database allowed high rates of correct identification of fungal species using MALDI-TOF MS. Some species, such as Trichophyton spp. are still difficult to identify. Although further improvements are still required, the developed methodology allowed the reliable identification of most fungal species.

Evaluation of the MALDI-TOF mass spectrometry technique for the identification of dermatophytes: Use of an extended database

BACKGROUND

Identification of dermatophytes is usually performed through morphological analyses. However, it may be hindered due to the discovery of new species and complexes and, with some isolates, by the absence of fructification. Matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF MS) seems to be an option for improving identification.

AIMS

To develop a database (DB) for the identification of dermatophytes with MALDI-TOF MS, including 32 isolates from the Red de Micología de la Ciudad Autónoma de Buenos Aires [Mycology Network of the Autonomous City of Buenos Aires] (RMCABA) and one reference isolate (RMCABA DB), and evaluate its performance when added to the DB from the supplier, Bruker (Bruker DB).

METHODS

All the isolates in the RMCABA DB were identified based on morphology and sequencing. To evaluate the performance of the extended DB (Bruker DB plus RMCABA DB), 136 clinical isolates were included.

RESULTS

The percentages of identification at the species level increased from 45% to 88%, but the identification at the genus level decreased from 23% to 7%.

CONCLUSIONS

MALDI-TOF MS yielded better performance in the identification of dermatophytes after including the RMCABA DB, which encompassed local isolates.

Performance of the MSI-2 Database for Fungal Identification by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry from Cleanroom Environments

Accurate mold identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is dependent on robust organism representation in available databases. The Mass Spectrometry Identification (MSI) platform has proven successful for mold identification in clinical and veterinary settings but has yet to be studied with a large set of environmental isolates. Here, we performed a retrospective study using spectra collected by the Bruker MALDI Biotyper (MBT) v4.1 microflex LT instrument to evaluate the MSI-2 database alongside the combined use of the Bruker MBT (including the MBT Filamentous Fungi Library) and the National Institutes of Health (NIH) mold database (MBT/NIH databases). Analysis was performed for 462 environmental fungal isolates (representing 73 different fungi) cultured from the hospital pharmacy and cellular therapy suites as part of the current good manufacturing practices (cGMP) environmental monitoring program at the NIH. When used alone, MSI-2 identified 237 spectra (51.3%) at its higher score threshold (index A), while the MBT/NIH databases identified only 183 spectra (39.6%; P < 0.001) at the equivalent threshold of ≥2.0. The combination of all three databases at the respective high thresholds improved identification sensitivity to 327 spectra (70.8%). The combination of MSI-2 with the MBT/NIH databases at a lowered threshold (index B or ≥1.7, respectively) identified 400/462 environmental spectra (86.6%). Our results show that the MSI-2 database, in combination with existing databases, may be useful for environmental surveillance, particularly by clinical or industry laboratories involved in cGMP or current good tissue practices (cGTP) applications, such as cellular therapy manufacturing facilities and sterile compounding pharmacies.

A Practical Workflow for the Identification of Aspergillus, Fusarium, Mucorales by MALDI-TOF MS: Database, Medium, and Incubation Optimization

There is an increasing body of literature on the utility of MALDI-TOF MS in the identification of filamentous fungi. However, the process still lacks standardization. In this study, we attempted to establish a practical workflow for the identification of three clinically important molds: Aspergillus, Fusarium, and Mucorales using MALDI-TOF MS. We evaluated the performance of Bruker Filamentous Fungi database v3.0 for the identification of these fungi, highlighting when there would be a benefit of using an additional database, the MSI-2 for further identification. We also examined two other variables, namely, medium effect and incubation time on the accuracy of fungal identification. The Bruker database achieved correct species level identification in 85.7% of Aspergillus and 90% of Mucorales, and correct species-complex level in 94.4% of Fusarium. Analysis of spectra using the MSI-2 database would also offer additional value for species identification of Aspergillus species, especially when suspecting species with known identification limits within the Bruker database. This issue would only be of importance in selected cases where species-level identification would impact therapeutic options. Id-Fungi plates (IDFP) had almost equivalent performance to Sabouraud dextrose agar (SDA) for species-level identification of isolates and enabled an easier harvest of the isolates with occasional faster identification. Our study showed accurate identification at 24 h for Fusarium and Mucorales species, but not for Aspergillus species, which generally required 48 h.

Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in veterinary medicine: Recent advances (2019-present)

Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) has become a valuable laboratory tool for rapid diagnostics, research, and exploration in veterinary medicine. While instrument acquisition costs are high for the technology, cost per sample is very low, the method requires minimal sample preparation, and analysis is easily conducted by end-users requiring minimal training. Matrix-assisted laser desorption ionization-time-of-flight MS has found widespread application for the rapid identification of microorganisms, diagnosis of dermatophytes and parasites, protein/lipid profiling, molecular diagnostics, and the technique demonstrates significant promise for 2D chemical mapping of tissue sections collected postmortem. In this review, an overview of the MALDI-TOF technique will be reported and manuscripts outlining current uses of the technology for veterinary science since 2019 will be summarized. The article concludes by discussing gaps in knowledge and areas of future growth.

Mass spectrometry in research laboratories and clinical diagnostic: a new era in medical mycology

Diagnosis by clinical mycology laboratory plays a critical role in patient care by providing definitive knowledge of the cause of infection and antimicrobial susceptibility data to physicians. Rapid diagnostic methods are likely to improve patient. Aggressive resuscitation bundles, adequate source control, and appropriate antibiotic therapy are cornerstones for success in the treatment of patients. Routine methods for identifying clinical specimen fungal pathogen are based on the cultivation on different media with the subsequent examination of its phenotypic characteristics comprising a combination of microscopic and colony morphologies. As some fungi cannot be readily identified using these methods, molecular diagnostic methods may be required. These methods are fast, but it can cost a lot. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs. It can be considered an alternative for conventional biochemical and molecular identification systems in a microbiological laboratory. The reliability and accuracy of this method have been scrutinized in many surveys and have been compared with several methods including sequencing and molecular methods. According to these findings, the reliability and accuracy of this method are very high and can be trusted. With all the benefits of this technique, the libraries of MALDI-TOF MS need to be strengthened to enhance its performance. This review provides an overview of the most recent research literature that has investigated the applications and usage of MT-MS to the identification of microorganisms, mycotoxins, antifungal susceptibility examination, and mycobiome research.

Molecular Diagnosis of Two Major Implantation Mycoses: Chromoblastomycosis and Sporotrichosis

Chromoblastomycosis and sporotrichosis are the two main implantation mycoses that are now recognized as fungal neglected tropical diseases (NTDs). Their laboratory diagnosis mainly relies on direct microscopy, histopathology, and identification of the fungus by culture. However, to be appropriately used, these techniques require mycological expertise that is not widely available and may be absent in peripheral health care facilities in endemic areas. In addition, they lack sensitivity and specificity, and the culture for isolation and identification can have a long time-to-results period. Molecular methods, including matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), have been developed in well-equipped reference laboratories. They greatly improve the rapidity and accuracy of diagnosis; in particular, for species identification. Recently, PCR and sequencing have paved the way for more user-friendly point-of-care tests, such as those based on LAMP or RCA technologies, which can be used in basic healthcare settings and even in field consultations.

Performance of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Scedosporium, Acremonium-Like, Scopulariopsis, and Microascus Species

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a powerful microorganism identification tool. Research on MALDI-TOF MS identification of rare filamentous fungi is still lacking. This study aimed to evaluate the performance of MALDI-TOF MS in the identification of Scedosporium, Acremonium-like, Scopulariopsis, and Microascus species. Sabouraud broth cultivation and formic acid/acetonitrile protein extraction were used for MALDI-TOF MS identification by a Bruker Biotyper system. An in-house database containing 29 isolates of Scedosporium, Acremonium-like, Scopulariopsis, and Microascus spp. was constructed. A total of 52 clinical isolates were identified using the Bruker Filamentous Fungi Library v1.0 (FFL v1.0) alone, and Filamentous Fungi Library v1.0 plus the in-house library, respectively. The mass spectrum profile (MSP) dendrograms of the 28 Scedosporium isolates, 26 Acremonium-like isolates, and 27 Scopulariopsis and Microascus isolates were constructed by MALDI Biotyper OC 4.0 software, respectively. The correct species identification rate significantly improved when using the combined databases compared with that when using FFL v1.0 alone (Scedosporium spp., 75% versus 0%; Acremonium-like spp., 100% versus 0%; Scopulariopsis and Microascus spp., 100% versus 62.5%). The MSP dendrograms differentiated Acremonium-like species, Scopulariopsis and Microascus species clearly, but cannot distinguish species in the Scedosporium apiospermum complex. In conclusion, with an expanded database, MALDI-TOF MS is an effective tool for the identification of Scedosporium, Acremonium-like, Scopulariopsis, and Microascus species.

Evaluation of Formic Acid Sandwich (FA-sandwich), A Pretreatment method for Filamentous Fungi, for the Identification of Clinically Relevant Filamentous Fungi by Two MALDI-TOF MS systems

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been successfully applied to identify microorganisms. However, unlike bacteria and yeast where identification results can be obtained rapidly and accurately by using a simple direct-coating pretreatment method, the traditional pretreatment methods for filamentous fungi are more complex, involving ethanol, formic acid, acetonitrile, and a protein extraction process by centrifugation, i.e., the EtOH-FA full extraction. This cumbersome pretreatment for filamentous fungi is a major reason for the lack of widespread use of MALDI-TOF MS for the identification of filamentous fungi in clinical settings. The present study describes an alternative method, the FA-sandwich, and demonstrates that the approach is efficient and effective. 148 clinical filamentous fungal isolates collected from three large general hospitals in Hubei Province, China, were processed by the FA-sandwich method and identified by two MALDI-TOF MS platforms, Autof ms and Vitek MS. The FA-sandwich allowed a 93.9% species-level identification with Autof ms, and 97.3% species-level identification rates were found for Vitek MS when the IVD, the RUO and in-house databases are used in combination. Further comparison of the ease of FA-sandwich with the EtOH-FA full extraction showed that the FA-sandwich is a more convenient, time- and reagent-saving, and sensitive pretreatment method. These findings indicate that the FA-sandwich method is suitable for pretreating filamentous fungi followed by MALDI-TOF MS identification in clinical microbiology laboratories.

Discrimination of Tilletia controversa from the T. caries/T. laevis complex by MALDI-TOF MS analysis of teliospores

The fungal genus Tilletia includes a large number of plant pathogens of Poaceae. Only a few of those cause bunt of wheat, but these species can lead to significant yield losses in crop production worldwide. Due to quarantine regulations and specific disease control using appropriate seed treatments for the different disease agents, it is of high importance to distinguish Tilletia caries and Tilletia laevis as causal agents of common bunt accurately from Tilletia controversa, the causal agent of the dwarf bunt. Several studies have shown that matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a useful tool to differentiate closely related fungal species. The aim of this study was to assess whether MALDI-TOF MS analysis is able to distinguish specimens of the three closely related pathogens T. caries, T. laevis, and T. controversa and whether it may constitute an alternative method to the morphology-based identification or germination tests. Spectral data are available via ProteomeXchange with identifier PXD030401. Spectra-based hierarchical cluster analysis (HCA) and discriminant analysis of principal components (DAPC) of the obtained mass spectra showed two main clusters. One cluster included specimens of T. controversa, whereas the second cluster comprised T. laevis and T. caries specimens. Even though main spectral profiles (MSPs) for species identification are missing, MALDI-TOF MS has proven to be a useful method for distinguishing between T. controversa and the two causal agents of common bunt, using direct analysis of teliospores, but was unable to separate T. caries and T. laevis species. KEY POINTS: • MALDI-TOF MS was developed to classify Tilletia species causing bunt of wheat. • Best results were achieved when combining HCA and DAPC analysis. • The method resulted in an accuracy of 98.51% testing 67 Tilletia specimens.

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.

Candida auris Identification and Profiling by MALDI-ToF Mass Spectrometry

MALDI-ToF MS has become the standard method for routine identification of most medically important yeasts in clinical and public health laboratories and has largely replaced phenotypic identification methods as a first-line identification tool. Fungal identification is based on extensive and well-curated mass spectra libraries usually provided by the manufacturer of the MALDI-ToF MS platform; however, many centers do create specialized or in-house database collections to aid analysis. Most MALDI-ToF MS systems offer simple and standardized workflows for the identification of clinically relevant yeasts to species level with a high throughput, high accuracy, and a low overall cost per test. This makes MALDI-ToF MS an ideal platform for use in routine clinical, diagnostic, and research microbiology laboratories which may lack experience or expertise in the identification of pathogenic fungi.In this chapter we review three standard protocols for the proteomic-based identification of Candida auris isolated from cultures of clinical or environmental surveillance samples in diagnostic and research laboratories.

Fungal infections diagnosis - Past, present and future

Despite the scientific advances observed in the recent decades and the emergence of new methodologies, the diagnosis of systemic fungal infections persists as a problematic issue. Fungal cultivation, the standard method that allows a proven diagnosis, has numerous disadvantages, as low sensitivity (only 50% of the patients present positive fungal cultures), and long growth time. These are factors that delay the patient's treatment and, consequently, lead to higher hospital costs. To improve the accuracy and quickness of fungal infections diagnosis, several new methodologies attempt to be implemented in clinical microbiology laboratories. Most of these innovative methods are independent of pathogen isolation, which means that the diagnosis goes from being considered proven to probable. In spite of the advantage of being culture-independent, the majority of the methods lack standardization. PCR-based methods are becoming more and more commonly used, which has earned them an important place in hospital laboratories. This can be perceived now, as PCR-based methodologies have proved to be an essential tool fighting against the COVID-19 pandemic. This review aims to go through the main steps of the diagnosis for systemic fungal infection, from diagnostic classifications, through methodologies considered as "gold standard", to the molecular methods currently used, and finally mentioning some of the more futuristic approaches.

Assessing the effects of common topical exposures on skin bacteria associated with atopic dermatitis

Background

While patients and families struggling with atopic dermatitis (AD) have documented concerns for a contributory role of skin care products in AD pathology, nearly all the skin microbiome studies to date have asked participants to avoid topical products (such as soaps or select medications) for the preceding days to weeks prior to sample collection. Thus, given the established role of the microbiome in AD, the interactions between topical exposures, dysbiosis and AD remains underrepresented in the academic literature.

Objectives

To address this knowledge gap, we expanded our previous evaluations to test the toxicological effects of a broader range of common chemicals, AD treatment lotions, creams and ointments using both health- and AD-associated strains of Roseomonas mucosa and Staphylococcus spp.

Methods

Use of in vitro culture techniques and mouse models were deployed to identify chemicals with dysbiotic or pre-biotic potential. A proof-of-concept study was subsequently performed in healthy volunteers to assess global microbiome shifts after exposure to select chemicals using dermatologic patch testing.

Results

Numerous chemicals possessed antibiotic properties, including many not marketed as anti-microbials. Through targeted combination of potentially beneficial chemicals, we identified combinations which promoted the growth of health-associated isolates over disease-associated strains in bacterial culture and enhanced microbe-specific outcomes in an established mouse model of AD; the most promising of which was the combination of citral and colophonium (often sold as lemon myrtle oil and pine tar). Additional studies would likely further optimize the combination of ingredients use. Similar results were seen in the proof-of-concept human studies.

Conclusions

Our results could offer a systematic, multiplex approach to identify which products carry dysbiotic potential and thus may guide formulation of new topicals to benefit patients with AD.

Multicenter evaluation of three different MALDI-TOF MS systems for identification of clinically relevant filamentous fungi

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) holds promise as a potential tool for clinical identification of filamentous fungi. However, due to the lack of an appropriate extraction protocol and the difficulty of database building, the identification power of each system differs. In this study, we selected 126 clinical mould isolates comprising 28 species identified using internal transcribed spacer (ITS) sequencing as the reference method to evaluate three MALDI-TOF MS systems. When using cultures and sample preparation as recommended by the respective vendors, of the 126 strains tested, VITEK MS identified 121 (96.0%) to species-level and 124 (98.4%) to genus-level; Biotyper identified 53 (42.1%) to species-level and 54 (42.9%) to genus-level; Autof identified 74 (58.7%) to species-level and 76 (60.3%) to genus-level. For the Autof system, the tube extraction method recommended by the vendor performed better (59%) than the on-plate lysis (51%). Our study demonstrates that MALDI-TOF MS systems can successfully identify most clinically relevant fungi, while performance is still highly dependent on the database and sample preparation protocol.

Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.

Developing Two Rapid Protein Extraction Methods Using Focused-Ultrasonication and Zirconia-Silica Beads for Filamentous Fungi Identification by MALDI-TOF MS

Filamentous fungi identification by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been challenging due to the lack of simple and rapid protein extraction methods and insufficient species coverage in the database. In this study, we created two rapid protein extraction methods for filamentous fungi: a one-step zirconia-silica beads method (ZSB) and a focused-ultrasonication method (FUS). The identification accuracy of two methods were evaluated with the VITEK MS, as well as number of spectra peaks and signal-to-noise ratio (S/N) with M-Discover 100 MALDI-TOF MS compared to the routine method. The better method was applied to build a filamentous fungi in-house spectra library for the M-Discover 100 MS, and then another one and routine method were performed in parallel to verify the accuracy and commonality of the in-house library. Using the two optimized methods, the dedicated operating time before MALDI-TOF MS analysis was reduced from 30 min to 7 (ZSB) or 5 (FUS) min per sample, with only a few seconds added for each additional strain. And both two methods identified isolates from most mold types equal to or better than the routine method, and the total correct identification rate using VITEK MS was 79.67, 76.42, and 76.42%, respectively. On the other hand, the two rapid methods generally achieved higher maximum and minimum S/N ratios with these isolates tested as compared to the routine method. Besides, the ZSB method produced overall mean of maximum and minimum S/N ratio higher than that by FUS. An in-house library of M-Discover MS was successfully built from 135 isolates from 42 species belonging to 18 genera using the ZSB method. Analysis of 467 isolates resulted in 97.22% correctly identified isolates to the species level by the ZSB method versus 95.50% by the routine method. The two novel methods are time- and cost-effective and allow efficient identification of filamentous fungi while providing a simplified procedure to build an in-house library. Thus, more clinical laboratories may consider adopting MALDI-TOF MS for filamentous fungi identification in the future.

Scedosporium apiospermum infection presenting as a mural urinary bladder mass and focal peritonitis in a Border Collie

Scedosporium apiospermum is an opportunistic mold that is an emerging disease in humans and animals. This report describes a case of S. apiospermum infection inciting a mural urinary bladder mass and focal peritonitis in a dog that had a history of multiple traumatic events several years prior. For diagnosis, culture followed by MALDI-ToF, PCR, and sequencing was performed to accurately identify the species. Susceptibility testing was also performed due to the inherent resistance of S. apiospermum to numerous antifungal agents.

Recognition of Diagnostic Gaps for Laboratory Diagnosis of Fungal Diseases: Expert Opinion from the Fungal Diagnostics Laboratories Consortium (FDLC)

Fungal infections are a rising threat to our immunocompromised patient population, as well as other nonimmunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics. To jointly address this diagnostic challenge, the Fungal Diagnostics Laboratory Consortium (FDLC) was recently created. The FDLC consists of 26 laboratories from the United States and Canada that routinely provide fungal diagnostic services for patient care. A survey of fungal diagnostic capacity among the 26 members of the FDLC was recently completed, identifying the following diagnostic gaps: lack of molecular detection of mucormycosis; lack of an optimal diagnostic algorithm incorporating fungal biomarkers and molecular tools for early and accurate diagnosis of Pneumocystis pneumonia, aspergillosis, candidemia, and endemic mycoses; lack of a standardized molecular approach to identify fungal pathogens directly in formalin-fixed paraffin-embedded tissues; lack of robust databases to enhance mold identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; suboptimal diagnostic approaches for mold blood cultures, tissue culture processing for Mucorales, and fungal respiratory cultures for cystic fibrosis patients; inadequate capacity for fungal point-of-care testing to detect and identify new, emerging or underrecognized, rare, or uncommon fungal pathogens; and performance of antifungal susceptibility testing. In this commentary, the FDLC delineates the most pressing unmet diagnostic needs and provides expert opinion on how to fulfill them. Most importantly, the FDLC provides a robust laboratory network to tackle these diagnostic gaps and ultimately to improve and enhance the clinical laboratory's capability to rapidly and accurately diagnose fungal infections.

Detection of azole resistance in Aspergillus fumigatus complex isolates using MALDI-TOF mass spectrometry

OBJECTIVES

The main goal of this study was to accurately detect azole resistance in species of the Aspergillus fumigatus complex by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).

METHODS

Identification of isolates (n = 868) was done with MALDI-TOF MS using both commercial and in-house libraries. To determine azole susceptibility, the EUCAST E.Def. 9.3.2 method was applied as the reference standard. Identification of resistant isolates was confirmed by DNA sequence analysis. Protein spectra obtained by MALDI-TOF MS were analysed to differentiate species within the A. fumigatus complex and to detect azole-resistant A. fumigatus sensu stricto isolates.

RESULTS

Correct discrimination of A. fumigatus sensu stricto from cryptic species was accomplished in 100% of the cases applying principal component analysis (PCA) to protein spectra generated by MALDI-TOF MS. Furthermore, a specific peak (4586 m/z) was found to be present only in cryptic species. The application of partial least squares (PLS) discriminant analysis allowed 98.43% (±0.038) discrimination between susceptible and azole-resistant A. fumigatus sensu stricto isolates. Finally, based on PLS and SVM, A. fumigatus sensu stricto isolates with different cyp51A gene mutations were correctly clustered in 91.5% of the cases.

CONCLUSIONS

MALDI-TOF MS combined with peak analysis is a novel tool that allows the differentiation of A. fumigatus sensu stricto from other species within the A. fumigatus complex, as well as the detection of azole-resistant A. fumigatus sensu stricto. Although further studies are still needed, the results reported here show the great potential of MALDI-TOF and machine learning for the rapid detection of azole-resistant Aspergillus fumigatus isolates from clinical origins.

MALDI-TOF MS in a Medical Mycology Laboratory: On Stage and Backstage

The implementation of MALDI-TOF MS in medical microbiology laboratories has revolutionized practices and significantly reduced turnaround times of identification processes. However, although bacteriology quickly benefited from the contributions of this technique, adjustments were necessary to accommodate the specific characteristics of fungi. MALDI-TOF MS is now an indispensable tool in clinical mycology laboratories, both for the identification of yeasts and filamentous fungi, and other innovative uses are gradually emerging. Based on the practical experience of our medical mycology laboratory, this review will present the current uses of MALDI-TOF MS and the adaptations we implemented, to allow their practical execution in a daily routine. We will also introduce some less mainstream applications, like those for fungemia, or even still under development, as is the case for the determination of sensitivity to antifungal agents or typing methods.

Bringing Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging to the Clinics

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is an emerging analytical technique that promises to change tissue-based diagnostics. This article provides a brief introduction to MALDI MSI as well as clinical diagnostic workflows and opportunities to apply this powerful approach. It describes various MALDI MSI applications, from more clinically mature applications such as cancer to emerging applications such as infectious diseases and drug distribution. In addition, it discusses the analytical considerations that need to be considered when bringing these approaches to different diagnostic problems and settings.

Matrix-assisted laser desorption/ionisation-time of flight mass spectrometry: Protocol standardisation, comparison and database expansion for faster and reliable identification of dermatophytes

BACKGROUND

Accurate and early identification of dermatophytes enables prompt antifungal therapy. However, phenotypic and molecular identification methods are time-consuming. MALDI-TOF MS-based identification is rapid, but an optimum protocol is not available.

OBJECTIVES

To develop and validate an optimum protein extraction protocol for the efficient and accurate identification of dermatophytes by MALDI-TOF MS.

MATERIALS/METHODS

Trichophyton mentagrophytes complex (n = 4), T. rubrum (n = 4) and Microsporum gypseum (n = 4) were used for the optimisation of protein extraction protocols. Thirteen different methods were evaluated. A total of 125 DNA sequence confirmed clinical isolates of dermatophytes were used to create and expand the existing database. The accuracy of the created database was checked by visual inspection of MALDI spectra, MSP dendrogram and composite correlation index matrix analysis. The protocol was validated further using 234 isolates.

RESULT

Among 13 protein extraction methods, six correctly identified dermatophytes but with a low log score (≤1.0). The modified extraction protocol developed provided an elevated log score of 1.6. Significant log score difference was observed between the modified protocol and other existing protocols (T. mentagrophytes complex: 1.6 vs. 0.2-1.0, p < .001; T. rubrum: 1.6 vs. 0.4-1.0, p < .001; M. gypseum:1.6 vs. 0.2-1.0, p < .001). Expansion of the database enabled the identification of all 234 isolates (73.5% with log score ≥2.0 and 26.4% with log scores range: 1.75-1.99). The results were comparable to DNA sequence-based identification.

CONCLUSION

MALDI-TOF MS with an updated database and efficient protein extraction protocol developed in this study can identify dermatophytes accurately and also reduce the time for identifying them.

Matrix-Assisted Laser Desorption Ionization Time-of-Flight for Fungal Identification

Many studies have shown successful performance of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for rapid yeast and mold identification, yet few laboratories have chosen to apply this technology into their routine clinical mycology workflow. This review provides an overview of the current status of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for fungal identification, including key findings in the literature, processing and database considerations, updates in technology, and exciting future prospects. Significant advances toward standardization have taken place recently; thus, accurate species-level identification of yeasts and molds should be highly attainable, achievable, and practical in most clinical laboratories.

Using MALDI-ToF mass spectrometry to identify mushroom species: Proof of concept analysis of Amanita genus specimens

Food poisoning caused by toxic mushrooms, such as species in the Amanita genus, occurs frequently around the world. To properly treat these patients, it is important to rapidly and accurately identify the causal species. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry is a rapid technique that has been used in medical laboratories for the past three decades to identify bacteria, yeasts, and filamentous fungi.Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-Tof MS) is a rapid method used for the past three decades to identify microorganisms. In this study, we created and internally validated a MALDI-Tof MS reference database comprising 15 Amanita species frequently encountered in France, and we challenged this database with 38 Amanita specimens from four French locations, using a free online application for MALDI-ToF spectra identifications.Assessment of the database showed that mass spectra can be obtained by analyzing any portion of a carpophore and that all portions enabled identification of the carpophore at the species level. Most carpophores were correctly identified using our database, with the exception of specimens from the Vaginatae section. Decay tests also demonstrated that decayed portions (like those found in the kitchen garbage can) of Amanita phalloides mushrooms could be properly identified using MALDI-ToF MS.Our findings provide important insight for toxicology laboratories that often rely on DNA sequencing to identify meal leftovers implicated in food poisoning. In future developments, this technique could also be used to detect counterfeit mushrooms by including other genera in the reference database.

LAY SUMMARY

MALDI-ToF MS is a powerful identification tool for microorganisms. We demonstrate that the technique can be applied to Amanita specimens. This will prevent food intoxications as a rapid and definite identification can be obtained, and it can also be used for food remnants.

[Trichophyton benhamiae, an emergent zoonotic pathogen in Argentina associated with Guinea pigs: Description of 7cases in Buenos Aires]

Trichophyton benhamiae is a zoonotic dermatophyte that can cause tinea corporis, tinea faciei and tinea capitis, producing inflammatory lesions, especially in children. In this publication, we describe 7clinical cases of pediatric patients that occurred in our institution between July 2019 and January 2020. All patients underwent a conventional mycological study. The identification of fungi isolates was confirmed by MALDI-TOF MS and sequencing of the ribosomal DNA. T. benhamiae was identified as the etiological agent, whose epidemiological link in all cases was the contact with Guinea pigs. This is the first description of infections caused by T. benhamiae in Argentina. This dermatophyte can be misidentified as other more frequent dermatophytes when performing conventional studies. Molecular technology should be used to reach a definitive diagnosis. It is important to have epidemiological data from patients such as contact with non-traditional pets, especially Guinea pigs, for an adequate presumptive diagnosis of this dermatophytosis.

Diagnosis of histoplasmosis: current status and perspectives

Histoplasmosis is a worldwide-distributed systemic mycosis caused by the dimorphic fungus Histoplasma capsulatum. Its clinical manifestations range from subclinical or mild respiratory illness to progressive disseminated histoplasmosis (PDH), a life-threatening disease, whose accurate diagnosis is still challenging and limited in many countries, where this disease is highly endemic. In this regard, Histoplasma antigen testing is now included in the WHO Essential Diagnostics List. The final diagnosis of histoplasmosis is established by culture and/or visualization of the yeast cells by cytology or histopathology using specific stains. However, both procedures have limited sensitivity to detect the disease and cultures are time-consuming. Antibody detection assays are effective for the subacute and chronic clinical forms of histoplasmosis. However, their sensitivity is low in the immunocompromised host. Several molecular "in-house" tests were also developed and showed promising results, but none of these tests are commercially available and their standardization and validation are still pending. Antigen detection assays have high sensitivity in PDH cases and are of great value for the follow-up of patients with histoplasmosis; however, cross-reactivity with other related fungi are common. In addition, this assay is expensive and only performed in few laboratories. Novel protein antigen candidates have been recently identified and produced by DNA-recombinant techniques in order to obtain standardized and specific reagents for the diagnosis of histoplasmosis, as opposed to the unspecific antigens or crude extracts currently used. This review describes the currently available assays, highlighting their strengths and limitations and reports the latest approaches to achieve reliable and rapid diagnostic tests for histoplasmosis. KEY POINTS: • PDH causes thousands of deaths per year globally. • Rapid accurate diagnosis of PDH is unfeasible in many regions. • Fast, accurate, and low-cost diagnostic alternatives are currently under development.

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

Johnson E, Littlechild J, Winlove CP, Vollmer F, Gow NAR. Biosensors and Diagnostics for Fungal Detection

Early detection is critical to the successful treatment of life-threatening infections caused by fungal pathogens, as late diagnosis of systemic infection almost always equates with a poor prognosis. The field of fungal diagnostics has some tests that are relatively simple, rapid to perform and are potentially suitable at the point of care. However, there are also more complex high-technology methodologies that offer new opportunities regarding the scale and precision of fungal diagnosis, but may be more limited in their portability and affordability. Future developments in this field are increasingly incorporating new technologies provided by the use of new format biosensors. This overview provides a critical review of current fungal diagnostics and the development of new biophysical technologies that are being applied for selective new sensitive fungal biosensors to augment traditional diagnostic methodologies.

Epidemiology and Diagnostic Perspectives of Dermatophytoses

Dermatophytoses affect about 25% of the world population, and the filamentous fungus Trichophyton rubrum is the main causative agent of this group of diseases. Dermatomycoses are caused by pathogenic fungi that generally trigger superficial infections and that feed on keratinized substrates such as skin, hair, and nails. However, there are an increasing number of reports describing dermatophytes that invade deep layers such as the dermis and hypodermis and that can cause deep infections in diabetic and immunocompromised patients, as well as in individuals with immunodeficiency. Despite the high incidence and importance of dermatophytes in clinical mycology, the diagnosis of this type of infection is not always accurate. The conventional methods most commonly used for mycological diagnosis are based on the identification of microbiological and biochemical features. However, in view of the limitations of these conventional methods, molecular diagnostic techniques are increasingly being used because of their higher sensitivity, specificity and rapidity and have become more accessible. The most widely used molecular techniques are conventional PCR, quantitative PCR, multiplex PCR, nested, PCR, PCR-RFLP, and PCR-ELISA. Another promising technique for the identification of microorganisms is the analysis of protein profiles by MALDI-TOF MS. Molecular techniques are promising but it is necessary to improve the quality and availability of the information in genomic and proteomic databases in order to streamline the use of bioinformatics in the identification of dermatophytes of clinical interest.

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.

Evaluating VITEK MS for the identification of clinically relevant Aspergillus species

Aspergillus spp. identification has become more relevant in clinical practice since azole-resistant cryptic species have been related to invasive fungal infections. Conventional morphologic identification is not able to discriminate Aspergillus species, and DNA sequencing is not feasible for clinical laboratories. MALDI-TOF mass spectrometry is an emergent technology that has been explored to provide fast and accurate identification of microorganisms, including clinically relevant moulds. However, only a few studies have explored the platform VITEK MS for the identification of Aspergillus species. Hence, we provided additional data regarding the performance of the VITEK MS system for the identification of Aspergillus species, including azole-resistant ones. We also improved the RUO system by adding additional spectral profiles from well-identified Aspergillus strains belonging to different noncryptic and cryptic species. The IVD library correctly identified 91.6% of the organisms at genus and section level, and 84.7% at species level, including the azole-resistant Aspergillus lentulus and Aspergillus calidoustus. The organisms belonging to Aspergillus cryptic species had only 31.2% of correct species identification. The RUO library plus our in-house SuperSpectra correctly identified 100% of the organisms at genus and section level and 91.6% at species level. Among organisms belonging to Aspergillus cryptic species, 68.7% had correct species identification. Some closely related Aspergillus cryptic species showed similar spectral profiles and were difficult to be differentiated.

Development and Validation of an In-House Library for Filamentous Fungi Identification by MALDI-TOF MS in a Clinical Laboratory in Medellin (Colombia)

Identification of filamentous fungi by conventional phenotypic methods are time-consuming, and a correct identification at the species level is prone to errors. Therefore, a more accurate and faster time-to-results, and cost-effective technique, is required, such as the Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). In this study, we describe the development of an in-house spectra library for the identification of filamentous fungi frequently isolated from patients with infections. An in-house spectra library was constructed using 14 reference strains grown in solid medium. Clinical isolates were identified either by the in-house spectra library or the Biotyper commercial library from Bruker Daltonics. Fungal identification was carried following the Biotyper’s established scores: ≤1.699: not reliably identified (NRI); 1.700–1.999: genus-level; ≥2.000: species-level. Clinical isolates were identified, with the in-house library, at species- and genus-level at 88.70% (55) and 3.22% (2), respectively. While 4.80% (3) was NRI and 3.22% (2) was discrepant concerning sequencing. On the contrary, identification up to species and genus-level with the commercial library was 44.44% (16) and 22.22% (8), respectively. NRI and the discrepancy was 30.55% (11) and 2.77% (1), respectively. For the reaming 26 isolates, 16 from Neoscytalidium dimidiatum and 10 from Sporothrix spp., respectively, the absence of spectrum and the specific spectra within the Sporothrix complex in the commercial library resulted in the inability to obtain an identification. In conclusion, the current results advocate the importance that each clinical microbiological laboratory needs to develop an ad hoc library associated with the MALDI-TOF MS fungal identification to overcome the limitations of the available commercial libraries.

Evaluation of the new Id-Fungi plates from Conidia for MALDI-TOF MS identification of filamentous fungi and comparison with conventional methods as identification tool for dermatophytes from nails, hair and skin samples

OBJECTIVES

We first compare the efficiency of mould/dermatophyte identification by MALDI-TOF MS using a new medium called Id-Fungi plates (IDFP) from Conidia^® and two different databases. For the second purpose, we evaluated a new version of the medium supplemented with cycloheximide, Id-Fungi plates Plus (IDFPC) for the direct inoculation of nails, hair and skin samples and compared the efficiency of MALDI-TOF MS identification of dermatophytes to classical methods based on culture and microscopy.

METHODS

A total of 71 strains have been cultured IDFP and Sabouraud gentamicin plates (SGC2) and were identified by MALDI-TOF MS. For the evaluation of the combination IDFPC/ MALDI-TOF MS as a method of identification for dermatophytes, 428 samples of hair nails and skin were cultivated in parallel on IDFPC and Sabouraud + cycloheximide medium (SAB-ACTI).

RESULTS

For Aspergillus sp and non-Aspergillus moulds, the best performances were obtained on IDFP after maximum 48-h growth, following protein extraction. For dermatophytes, the best condition was using the IDFP at 72 hours, after extended direct deposit. Regarding the direct inoculation of nails, hair skin on IDFPC, 129/428 (30.1%) showed a positive culture against 150/428 (35%) on SAB-ACTI medium. Among the 129 positive strains, the identification by MALDI-TOF MS was correct for 92/129 (71.4%).

CONCLUSION

The IDFP allows the generation of better spectra by MALDI-TOF MS compared to SGC2. It facilitates sampling and deposit. Regarding the use of IDFPC, this medium seems less sensitive than SAB-ACTI but among positive strains, the rate of correct identification by MALDI-TOF MS is satisfactory.

Subcutaneous phaeohyphomycosis caused by Hongkongmyces snookiorum in a kidney transplant patient: a case report

BACKGROUND

Morbidity and mortality in transplant patients is increased by infection caused mainly by rare opportunistic pathogens. The present study reports a case where Hongkongmyces snookiorum caused subcutaneous phaeohyphomycosis in a kidney transplant patient.

CASE PRESENTATION

A 47-year old Chinese woman with chronic kidney disease 5 underwent kidney transplantation 3 years ago. Her regular medications included Tacrolimus (1 mg, two times daily), Mycophenolate Mofetil (two times 250 mg, twice daily) and Prednisone acetate tablets (5 mg daily). Eighteen months ago, her proximal right index finger was red, painful and swollen. After admission, a hard and fluctuating 1 cm × 1 cm abscess was found on the dorsal side of the right index finger. Gram and fluorescence staining of a direct smear of a syringe extraction from the abscess revealed presence of filamentous fungi. White velvet colonies (2-3 mm) were found on blood plate and Sabouraud glucose agar (SGA) after 1 week, and grey aerial hyphae were observed. After 15 days, a 26 mm gray colony was also observed on SGA. The homology between this filamentous fungus and Hongkongmyces snookiorum ILLS00125755 (Genbank Sequence ID: MH161189.1) was 99.66%. An in vitro antifungal susceptibility test showed that this filamentous fungus was sensitive to azoles such as itraconazole and voriconazole.

CONCLUSIONS

We report an opportunistic fungus infection caused by Hongkongmyces snookiorum in a transplant patient. Our finding shows that prevention of subcutaneous fungal infection is necessary for kidney transplantation patients.

Sporotrichosis in the Highlands of Madagascar, 2013-20171

Sporotrichosis is a saprozoonotic fungal infection found mostly in tropical and subtropical areas. Few case reports in Madagascar have been published. To document sporotrichosis epidemiology in Madagascar, we conducted a cross-sectional study. During March 2013–June 2017, we recruited from select hospitals in Madagascar patients with chronic cutaneous lesions suggestive of dermatomycosis. Sporotrichosis was diagnosed for 63 (42.5%) of 148 patients. All but 1 patient came from the central highlands, where the prevalence was 0.21 cases/100,000 inhabitants. Frequency was high (64.7%) among patients <18 years of age. Sporotrichosis was diagnosed for 73.8% of patients with arm lesions, 32.3% with leg lesions, and 15.4% with lesions at other sites. Molecular identification identified 53 Sporothrix schenckii isolates. Among the 32 patients who were followed up, response to itraconazole was complete or major for 15 and minor for 17. Overall, endemicity of sporotrichosis in Madagascar was high, concentrated in the highlands.

Mass Spectrometry: A Rosetta Stone to Learn How Fungi Interact and Talk

Fungi are a highly diverse group of heterotrophic organisms that play an important role in diverse ecological interactions, many of which are chemically mediated. Fungi have a very versatile metabolism, which allows them to synthesize a large number of still little-known chemical compounds, such as soluble compounds that are secreted into the medium and volatile compounds that are chemical mediators over short and long distances. Mass spectrometry (MS) is currently playing a dominant role in mycological studies, mainly due to its inherent sensitivity and rapid identification capabilities of different metabolites. Furthermore, MS has also been used as a reliable and accurate tool for fungi identification (i.e., biotyping). Here, we introduce the readers about fungal specialized metabolites, their role in ecological interactions and provide an overview on the MS-based techniques used in fungal studies. We particularly present the importance of sampling techniques, strategies to reduce false-positive identification and new MS-based analytical strategies that can be used in mycological studies, further expanding the use of MS in broader applications. Therefore, we foresee a bright future for mass spectrometry-based research in the field of mycology.