Identification of yeast isolated from dermatological patients by MALDI-TOF mass spectrometry

MALDI-TOF MS-Based Clustering and Antifungal Susceptibility Tests of Talaromyces marneffei Isolates from Fujian and Guangxi (China)

Introduction

Talaromyces marneffei is a life-threatening pathogen that causes systemic talaromycosis in immunocompromised and acquired immunodeficiency syndrome (AIDS) patients. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a tool to cluster T. marneffei isolates is rarely reported and the data on antifungal susceptibility of T. marneffei isolated in the southern region of China, especially in Fujian, is hardly found.

Methods

MALDI-TOF MS was used to cluster 135 T. marneffei isolates, and the minimum inhibitory concentration (MIC) values of amphotericin B, itraconazole, posaconazole, voriconazole, fluconazole, anidulafungin, micafungin, caspofungin and 5-fluorocytosine with Sensititre YeastOne™ YO10 assay were measured during January 2017 to October 2020 in Fujian and Guangxi.

Results

MALDI-TOF MS correctly identified 100% of the T. marneffei isolates. Hierarchical clustering of MALDI-TOF peak profiles identified four different clusters. MICs for itraconazole, posaconazole, voriconazole and amphotericin B were as follows: ≤0.015–0.03 μg/mL, ≤0.008–0.03 μg/mL, ≤0.008–0.06 μg/mL, ≤0.12–1 μg/mL, respectively. MICs for echinocandins and fluconazole were comparatively high.

Conclusion

Since only simple sample preparation is required and since results are available in a short period of time, MALDI-TOF MS can be considered as a method for identification and clustering of T. marneffei. Itraconazole, posaconazole, voriconazole and amphotericin B can be used to treat T. marneffei infected patients due to the low MICs.

Saprochaete clavata Invasive Infections - A New Threat to Hematological-Oncological Patients

Background

Saprochaete clavata (formerly Geotrichum clavatum, now proposed as Magnusiomyces clavatus) is a filamentous yeast-like fungus that has recently been described as an emerging pathogen mostly in patients with acute leukemia.

Methods

This is a retrospective study of patients diagnosed with proven and probable S. clavata infection at the University Hospital, Hradec Králové, Czechia between March 2005 and December 2017. Previous cases were identified from the literature and FungiScope^® database.

Results

Six new cases (5 females, 1 male) of blood-stream S. clavata infections at the hemato-oncological department were described including epidemiological data of additional 48 patients colonized with the species. Overall, 116 strains of S. clavata were isolated from different clinical specimens of 54 patients; most of them belonged to the respiratory tract (60.3%). S. clavata was the most frequent species among arthroconidial yeasts (Trichosporon, Galactomyces, Magnusiomyces) recovered from the blood. All our patients with S. clavata infection had profound neutropenia, a central venous catheter, broad-spectrum antibiotics and antifungal prophylaxis; four had a history of a biliary tract system disease. The diagnosis was based on a positive blood culture in all patients. Four patients died of multiorgan failure and sepsis despite treatment with lipid-based amphotericin B and/or voriconazole. From the literature and FungiScope database, 67 previous cases of S. clavata infections were evaluated in context of our cases.

Conclusion

Saprochaete clavata infection represents a life-threatening mycosis in severely immunocompromised patients. The successful outcome of treatment seems to be critically dependent on the early diagnosis and the recovery of underlying conditions associated with immune dysfunction or deficiency.

White Piedra: Clinical, Mycological, and Therapeutic Experience of Fourteen Cases

Background

White piedra (WP) is an asymptomatic superficial mycosis that affects the hair stems, forming whitish nodules caused by various species of the genus Trichosporon.

Objective

To present a case series of WP of the head, its epidemiological data, as well as clinical, mycological, and therapeutic experience.

Methods

We conducted a 12-year retrospective and observational study of WP cases tested by dermoscopy, mycological study, and the identification of species through morphology, biochemistry, and proteomics (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry). The treatment was based on ketoco-nazole shampoo as well as keratolytics.

Results

We included 14 cases of WP, all located in the head and 1 case with both head and scrotum affected. Nine cases (64.3%) presented in children aged < 15 years. The majority of the cases (13/14, 92.8%) were women. Two cases were associated with hyperkeratosis and intertrigo. Most patients had long hair and excessive moisture. In all cases hair nodules were observed and Trichosporon inkin (11/14, 78.6%) was usually isolated. Eleven cases (78.6%) were cured by administering 2% ketoconazole shampoo.

Conclusion

WP was observed in school-age girls. The diagnosis was based on the observation of hair nodules and its main etiologic agent was T. inkin, with good response to treatment in most cases.

Comparison of Vitek Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Versus Conventional Methods in Candida Identification

Candida species are generally identified by conventional methods such as germ tube or morphological appearance on corn meal agar, biochemical methods using API kits and molecular biological methods. Alternative to these methods, rapid and accurate identification methods of microorganisms called matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDİ-TOF MS) has recently been described. In this study, Candida identification results by API Candida kit, API 20C AUX kit and identifications on corn meal agar (CMA) are compared with the results obtained on Vitek-MS. All results were confirmed by sequencing internal transcribed spacer (ITS) regions of rDNA. Totally, 97 Candida strains were identified by germ tube test, CMA, API and Vitek-MS. Vitek-MS results were compatible with 74.2 % of API 20C AUX and 81.4 % of CMA results. The difference between the results of API Candida and API 20C AUX was detected. The ratio of discrepancy between Vitek-MS and API 20C AUX was 25.8 %. Candida species mostly identified as C. famata or C. tropicalis by and not compatible with API kits were identified as C. albicans by Vitek-MS. Sixteen Candida species having discrepant results with Vitek-MS, API or CMA were randomly chosen, and ITS sequence analysis was performed. The results of sequencing were compatible 56.2 % with API 20C AUX, 50 % with CMA and 93.7 % with Vitek-MS. When compared with conventional identification methods, MS results are more reliable and rapid for Candida identification. MS system may be used as routine identification method in clinical microbiology laboratories.

Comparative evaluation of two matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems for the identification of clinically significant yeasts

OBJECTIVES

To prospectively evaluate the performance of two matrix-assisted laser desorption/ionization time-of-flight mass spectrometry systems (MALDI-TOF MS) for the identification of clinically significant yeast isolates compared to the VITEK 2 system.

METHODS

One hundred and eighty-eight consecutive yeast isolates were analyzed by Bruker Biotyper and VITEK MS. The results were compared with the conventional VITEK 2 yeast identification system. Discrepant results were resolved by direct sequencing of rDNA.

RESULTS

Accurate identification by VITEK 2, VITEK MS, and Bruker Biotyper MS was 94.1% (177/188), 93.0% (175/188), and 92.6% (174/188), respectively. Three isolates were not identified by VITEK MS, while nine Candida orthopsilosis were misidentified as Candida parapsilosis, as this species is not present in its database. Eleven isolates were not identified or were wrongly identified by Bruker Biotyper and although another 14 were correctly identified, the score was unreliable at <1.7.

CONCLUSION

The overall accuracy of rapid MALDI-TOF MS systems was essentially comparable to that of the conventional VITEK 2 yeast identification system. However, future expansion of the databases may further improve the outcome and accuracy of identification of yeast species.

Accuracy of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinical pathogenic fungi: a meta-analysis

Fungal infections in the clinic have become increasingly serious. In many cases, the identification of clinically relevant fungi remains time-consuming and may also be unreliable. Matrix-assisted laser desorption ionization-time of flight mass spectroscopy (MALDI-TOF MS) is a newly developed diagnostic tool that is increasingly being employed to rapidly and accurately identify clinical pathogenic microorganisms. The present meta-analysis aimed to systematically evaluate the accuracy of MALDI-TOF MS for the identification of clinical pathogenic fungi. After a rigorous selection process, 33 articles, involving 38 trials and a total of 9,977 fungal isolates, were included in the meta-analysis. The random-effects pooled identification accuracy of MALDI-TOF MS increased from 0.955 (95% confidence interval [CI], 0.939 to 0.969) at the species level to 0.977 (95% CI, 0.955 to 0.993) at the genus level (P < 0.001; χ(2) = 15.452). Subgroup analyses were performed at the species level for several categories, including strain, source of strain, system, system database, and modified outcomes, to calculate the accuracy and to investigate heterogeneity. These analyses revealed significant differences between the overall meta-analysis and some of the subanalyses. In parallel, significant differences in heterogeneity among different systems and among different methods for calculating the identification ratios were found by multivariate metaregression, but none of the factors, except for the moderator of outcome, was significantly associated with heterogeneity by univariate metaregression. In summary, the MALDI-TOF MS method is highly accurate for the identification of clinically pathogenic fungi; future studies should analyze the comprehensive capability of this technology for clinical diagnostic microbiology.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology

Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.

Identification and antifungal susceptibility of a large collection of yeast strains isolated in Tunisian hospitals

In this study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used as a rapid method to identify yeasts isolated from patients in Tunisian hospitals. When identification could not be exstablished with this procedure, sequencing of the internal transcribed spacer with 5.8S ribosomal DNA (rDNA) (ITS1-5.8S-ITS2) and D1/D2 domain of large-subunit (LSU rDNA) were employed as a molecular approach for species differentiation. Candida albicans was the dominant species (43.37% of all cases), followed by C. glabrata (16.55%), C. parapsilosis (13.23%), C. tropicalis (11.34%), C. dubliniensis (4.96%), and other species more rarely encountered in human diseases such as C. krusei, C. metapsilosis, C. lusitaniae, C. kefyr, C. palmioleophila, C. guilliermondii, C. intermedia, C. orthopsilosis, and C. utilis. In addition, other yeast species were obtained including Saccharomyces cerevisiae, Debaryomyces hansenii (anamorph known as C. famata), Hanseniaspora opuntiae, Kodamaea ohmeri, Pichia caribbica (anamorph known as C. fermentati), Trichosporon spp. and finally a novel yeast species, C. tunisiensis. The in vitro antifungal activities of fluconazole and voriconazole were determined by the agar disk diffusion test and Etest, while the susceptibility to additional antifungal agents was determined with the Sensititre YeastOne system. Our results showed low incidence of azole resistance in C. albicans (0.54%), C. tropicalis (2.08%) and C. glabrata (4.28%). In addition, caspofungin was active against most isolates of the collection with the exception of two K. ohmeri isolates. This is the first report to describe caspofungin resistant isolates of this yeast.

Identification of medically relevant species of arthroconidial yeasts by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was used for an extensive identification study of arthroconidial yeasts, using 85 reference strains from the CBS-KNAW yeast collection and 134 clinical isolates collected from medical centers in Qatar, Greece, and Romania. The test set included 72 strains of ascomycetous yeasts (Galactomyces, Geotrichum, Saprochaete, and Magnusiomyces spp.) and 147 strains of basidiomycetous yeasts (Trichosporon and Guehomyces spp.). With minimal preparation time, MALDI-TOF MS proved to be an excellent diagnostic tool that provided reliable identification of most (98%) of the tested strains to the species level, with good discriminatory power. The majority of strains were correctly identified at the species level with good scores (>2.0) and seven of the tested strains with log score values between 1.7 and 2.0. The MALDI-TOF MS results obtained were consistent with validated internal transcribed spacer (ITS) and/or large subunit (LSU) ribosomal DNA sequencing results. Expanding the mass spectrum database by increasing the number of reference strains for closely related species, including those of nonclinical origin, should enhance the usefulness of MALDI-TOF MS-based diagnostic analysis of these arthroconidial fungi in medical and other laboratories.

Evaluation of four pretreatment procedures for MALDI-TOF MS yeast identification in the routine clinical laboratory

MALDI-TOF MS-based yeast identification requires a pretreatment step for which four are described in the literature, i.e., direct smear, fast formic acid and two complete formic acid/acetonitrile extractions. In this study we compared the impact of these procedures on the performance of MALDI-TOF MS-based yeast identification of samples from colonies grown on Sabouraud or chromogenic media. A total of 103 yeast isolates recovered from clinical samples were identified in parallel using the four pretreatment procedures. The proportions of both correct identifications (regardless of LogScore values) and of reliable identifications (i.e., correct identifications with a LogScore 2, as recommended by the manufacturer) obtained with the four techniques were compared. Even if the proportion of correct identifications exceeded 85% independent of the pretreatment procedure, results obtained with complete formic acid/acetonitril extractions of colonies grown on Sabouraud media were significantly superior to those with smear and fast formic acid extraction procedures. If one considers only reliable identifications, then both smear and fast formic acid extraction procedures yielded lower (<40%) correct identification rates than the use of the two complete extraction procedures (>77%) of portions of colonies on both Sabouraud and chromogenic media. The data would indicate that the direct smear and fast formic acid procedures cannot be recommended due to the LogScore values which were continually below those recommended by the manufacturer for biological validation. Thus, complete extraction methods are better suited for MALDI-TOF MS-based yeast identification in the clinical laboratory setting although they are more labor-intensive.

[New apects in the diagnosis and therapy of dermatomycoses]

Recent observations indicate that Arthroderma benhamiae can cause bullous tinea, that onychomycosis increasingly occurs in children and that molds can cause tinea-like lesions. If a mycotic infection is suspected, the pathogen needs to be identified. The first genetic assays for the detection of dermatophytes have successfully been tested under routine conditions. Using appropriate techniques, genetic diagnosis is faster and more sensitive than a culture. Laboratory standards that would facilitate widespread implementation of genetic identification of dermatophytes have not yet been established. For the identification of yeasts, MALDI-TOF has already been established in many laboratories. This method is being refined for the diagnosis of hyphomycetes too. Newer antimycotics that are approved for certain systemic mycoses such as the triazoles voriconazole and posaconazole and the echinocandines caspofungin, micafungin und anidulafungin may be considered for dermatomycoses that cannot be treated by other therapies. Thermotherapy and photodynamic therapy are additional options in particularly difficult cases.

Optimization of the preanalytical steps of matrix-assisted laser desorption ionization-time of flight mass spectrometry identification provides a flexible and efficient tool for identification of clinical yeast isolates in medical laboratories

We report here that modifications of the preanalytical steps of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification of yeasts, with regard to the original protocol provided by the manufacturers, appear to be efficient for the reliable routine identification of clinical yeast isolates in medical laboratories. Indeed, when one colony was sampled instead of five and the protein extraction protocol was modified, the performance of MALDI-TOF MS was superior to that of the API ID 32C method (discrepancies were confirmed by using molecular identification), allowing the correct identification of 94% of the 335 clinical isolates prospectively tested. We then demonstrated that the time for which the primary cultures were preincubated on CHROMagar did not impact the identification of yeasts by MALDI-TOF MS, since 95.1 and 96.2% of the 183 clinical yeast isolates prospectively tested were correctly identified after 48 and 72 h of preincubation, respectively.