Evaluation of a new matrix-assisted laser desorption/ionization time-of-flight mass spectrometry system for the identification of yeast isolation

Rapid and accurate identification of yeast subspecies by MALDI-MS combined with a cell membrane disruption reagent

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been widely used for microbial analysis. However, due to the impenetrable shell of fungi the direct identification of fungi remains challenges. Targeting on this problem, the yeast Saccharomyces cerevisiae (S. cerevisiae) was selected as a model fungus, and a new fungal cell membrane disruption reagent C18-G1 was used before MALDI-MS detection. As a result, much more intensive peaks which distributed in wider m/z range of S. cerevisiae have been identified in comparison with the use of traditional fungal pretreatment methods. Furthermore, a differential peak at m/z 4993 between two subspecies of S. cerevisiae has been identified. The corresponding protein with exclusive sequence of the specific peak was obtained based on MS/MS fragments and database searching. In addition, the method was successfully applied for the discrimination of four commercial yeasts.

A head-to-head comparison of three MALDI-TOF mass spectrometry systems with 16S rRNA gene sequencing

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized diagnostics in culture-based microbiology. Commonly used MALDI-TOF MS systems in clinical microbiology laboratories are MALDI Biotyper (Bruker Daltonics) and Vitek MS (bioMérieux), but recently the new EXS2600 (Zybio) has been launched. This study aimed to evaluate the performance of the three devices by comparing the results to 16S rRNA gene sequencing. A set of 356 previously collected difficult-to-identify bacteria was tested in parallel with the three systems. Only the direct smear method and simple formic acid extraction were applied. Valid results were achieved for 98.6%, 94.4%, and 93.3% of all isolates by MALDI Biotyper, EXS2600, and Vitek MS, respectively. Of all valid results, agreement with sequencing data was achieved in 98.9%, 98.5%, and 99.7% by MALDI Biotyper, EXS2600, and Vitek MS, respectively. Considering only the isolates with valid measurements at the single-species level, misidentification rates were 0%, 2.6%, and 1.1% for MALDI Biotyper, EXS2600, and Vitek MS, respectively. Apart from minor performance differences, our data demonstrate that the three systems provide comparable results and are suitable for use in medical diagnostic laboratories.

Identification of Pathogenic and Opportunistic Yeasts in Pigeon Excreta by MALDI-TOF Mass Spectrometry and Their Prevalence in Chon Buri Province, Thailand

Pigeon excreta can cause environmental and public health issues, particularly in urban and public areas. They are reservoirs of several human pathogens including fungi, bacteria, and viruses. Epidemiological data of pathogenic and opportunistic yeasts in pigeon droppings in Chon Buri, one of the most reputable tourist cities of Thailand, are scarce. The present study aimed to identify yeasts in pigeon droppings by MALDI-TOF mass spectrometry, and to study their prevalence in Chon Buri, Thailand. A total of 200 pigeon fecal samples were collected randomly from all 11 districts of Chon Buri. A sum of 393 yeast-like colonies were isolated on Sabourand's dextrose agar and CHROMagar media. These isolates were further confirmed for their species by MALDI-TOF MS. Twenty-four yeast species belonging to 11 different genera were identified in pigeon fecal samples. Candida spp., predominantly C. krusei (14.32%), were the most prevalent yeast species. Other yeast species, including C. glabrata (12.73%), C. metapsilosis (11.93%), Lodderomyces elongisporus (10.87%), C. tropicalis (7.16%), C. albicans (5.83%), and Cryptococcus neoformans (4.77%) were identified. This study provides valuable epidemiological data and diversity of yeasts in pigeon droppings in Chon Buri, Thailand, and also supports the use of MALDI-TOF MS for yeast identification and epidemiological surveillance.

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.

Substantial Improvement in Nontuberculous Mycobacterial Identification Using ASTA MicroIDSys Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry with an Upgraded Database

Identifying Mycobacterium using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is challenging. We evaluated the performance of MALDI-TOF MS in identifying nontuberculous mycobacteria (NTM) using the ASTA MicroIDSys system (ASTA Inc., Suwon, Korea) with the MycoDB v1.95s and upgraded MycoDB v2.0-beta databases. We tested 124 NTM isolates collected from Ogawa medium at Severance Hospital, Seoul, Korea, between January and April 2019. MicroIDSys scores were categorized into three groups: ≥140, reliable identification; 130-139, ambiguous identification; and <130, invalid identification. To validate the results, we used the reverse blot hybridization assay (Molecutech REBA MycoID, YD Diagnostics Corp., Korea). Initial analysis using MycoDB v1.95s resulted in 26.6% (33/124) reliable, 43.5% (54/124) ambiguous, and 29.8% (37/124) invalid identifications. Re-analysis using the upgraded MycoDB v2.0-beta database resulted in 94.4% (117/124) reliable, 4.0% (5/124) ambiguous, and 1.6% invalid (2/124) identifications. The percentage of reliable identifications that matched with the reference increased from 26.6% (33/124) with MycoDB v1.95s to 93.5% (116/124) with MycoDB v2.0-beta. The upgraded databases enable substantially improved NTM identification through deep learning in the inference algorithm and by considering more axes in the correlation analysis. MALDI-TOF MS using the upgraded database unambiguously identified most NTM species. Our study lays a foundation for applying MALDI-TOF MS for the simple and rapid identification of NTM isolated from solid media.

Comparison of Six Antifungal Susceptibilities of 11 Candida Species Using the VITEK2 AST-YS08 Card and Broth Microdilution Method

We used a Vitek 2 AST-YS08 (YS08) system and the broth microdilution method (BMD) adopted by the Clinical and Laboratory Standards Institute (CLSI) to compare the susceptibility of 184 isolates of 11 Candida species to fluconazole, voriconazole, micafungin, caspofungin, amphotericin B, and flucytosine. In Candida albicans, the categorical agreement (CA) was 79.2%, 91.7%, 95.8%, and 95.8% for fluconazole, voriconazole, micafungin, and caspofungin, respectively. About 12.5% and 4.2% of very major errors were detected for fluconazole and voriconazole, respectively. C. glabrata showed excellent essential agreements (EAs) (>90%) for azoles but different MIC distributions for fluconazole and caspofungin. The CA between BMD fluconazole MICs and YS08 voriconazole MICs by the method-specific clinical breakpoint (CBP) was 90% in C. glabrata. Over 80% of C. glabrata and C. krusei isolates identified as micafungin-susceptible were labeled intermediate or resistant to caspofungin in YS08. In C. parapsilosis, 5.3% of very major errors and 10.5% of minor errors were found, whereas 33.3% of minor errors were observed in C. tropicalis for fluconazole. For C. tropicalis, 13 (61.9%) non-wild type (WT) isolates of fluconazole and 7 (33.3%) non-WTs of voriconazole were classified in YS08 as WT. For C. auris, the EAs were 93.3%, 100%, 82.2%, 97.8%, and 97.8% for fluconazole, voriconazole, micafungin, caspofungin, and amphotericin B, respectively. YS08 showed comparable results to the BMD. However, considering the lower YS08 fluconazole MIC results compared with BMD in Candida species and YS08 caspofungin results in C. glabrata and C. krusei, improvements are needed. IMPORTANCE The new Vitek 2 AST-YS08 (YS08) card has been updated to reflect the recently revised Clinical and Laboratory Standards Institute (CLSI) guideline. In this study, antifungal drug susceptibility tests were performed using the YS08 card and compared with the CLSI broth microdilution (BMD) method. In conclusion, YS08 showed similar results to BMD, including with C. auris. However, about 12.5% and 4.2% of major errors were detected for fluconazole and voriconazole, respectively, in C. albicans. More than 80% of C. glabrata and C. krusei isolates identified as susceptible to micafungin were labeled moderate or resistant to caspofungin in YS08. The categorical agreement between BMD fluconazole MICs and YS08 voriconazole MICs was 90% by the method-specific CBP of voriconazole, 80% by the current epidemiological cutoff value (ECV) (0.25 μg/mL) of voriconazole, and 85% by the previous ECV (0.5 μg/mL) of voriconazole. Further improvements in YS08 for the detection of fluconazole and echinocandin resistance are thus needed.

Comparative Evaluation of Bruker Biotyper and ASTA MicroIDSys for Species Identification in a Clinical Microbiology Laboratory

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) has been widely used for microbial identification, because of its speed and accuracy, since its introduction to clinical microbiology laboratories. In this study, we evaluated the performance of ASTA MicroIDSys, a newly developed MALDI–TOF, and compared it with the widely used Bruker Biotyper. Microbial identification with the Bruker Biotyper system was performed by using a direct smear method and the Bruker Biotyper database (reference library version 6.0.0.0). The isolates were also tested in parallel, using the ASTA MicroIDSys system with a direct smear method and the MicroIDSys database, CoreDB v1.26. A total of 914 clinical isolates were recovered from the clinical specimens. Identical results with confidence scores (≥2.0, for the Bruker Biotyper) and acceptable scores (≥140 for the ASTA MicroIDSys) were obtained for 840 (91.9%) isolates. The minor errors were defined as misidentification at the species level, and the rate was 1.1% (9/792) for Bruker Biotyper and 1.6% (13/792) for ASTA MicroIDSys. Major errors were defined as misidentification at the genus level, and the rate was 0.3% (2/792) for both Bruker Biotyper and ASTA MicroIDSys. ASTA MicroIDSys showed reliable performance for microbial identification, which was comparable to that of the Bruker Biotyper. Therefore, ASTA MicroIDSys can be applied for the identification of microorganisms in clinical microbiology laboratories.

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.

Comparison of Autof ms1000 and Bruker Biotyper MALDI-TOF MS Platforms for Routine Identification of Clinical Microorganisms

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used in clinical microbiology laboratories because it is cost-effective, reliable, and fast. This study is aimed at comparing the identification performance of the recently developed Autof ms1000 (Autobio, China) with that of the Bruker Biotyper (Bruker Daltonics, Germany). From January to June 2020, 205 preserved strains and 302 clinical isolates were used for comparison. Bacteria were tested with duplicates of the direct transfer method, and formic acid extraction was performed if the results were not at the species level. Fungi were tested with formic acid extraction followed by ethanol extraction methods. 16S rRNA or ITS region sequence analysis was performed on isolates that could not be identified by any of the instruments and on isolates that showed inconsistent results. The time to result of each instrument was also compared. Among preserved strains, species-level identification results were obtained in 202 (98.5%) strains by the Autof ms1000 and 200 (97.6%) strains by the Bruker Biotyper. Correct identification at the species/complex level was obtained for 200 (97.6%) strains by the Autof ms1000 and for 199 (97.1%) strains by the Bruker Biotyper. Among clinical isolates, species-level identification results were obtained in 301 (99.7%) strains and 300 (99.3%) strains by the Autof ms1000 and Bruker Biotyper, respectively. Correct identification at the species/complex level was achieved for 299 (99.0%) strains by the Autof ms1000 and for 300 (99.3%) strains by the Bruker Biotyper. The time to analyze 96 spots was approximately 14 min for the Autof ms1000 and approximately 27 min for the Bruker Biotyper. The two instruments showed comparable performance for the routine identification of clinical microorganisms. In addition, the Autof ms1000 has a short test time, making it convenient for use in clinical microbiology laboratories.

Kazachstania slooffiae: An unexpected journey to a human pleural sample

We report a case of a 50-year-old shepherd hospitalized in intensive care unit for hiatal hernia complicated by an occlusive syndrome. In post-surgery, an acute respiratory distress occurs due to mediastinitis with large pleural effusion. At the laboratory, direct examination of the pleural sample revealed the presence of pseudohyphae. Kazachstania slooffiae was identified by Mass Spectrometry and confirmed by DNA sequencing. This uncommon yeast has never been previously described in human infections. Although its pathogenicity is not well known, K. slooffiae should be considered in the case of critically ill patients.

Yeasts in Liquid Swine Diets: Identification Methods, Growth Temperatures and Gas-Formation Potential

Liquid feed is susceptible to microbiological growth. Yeasts are said to cause sudden death in swine due to intestinal gas formation. As not all animals given high yeast content feed fall ill, growth and gas formation potential at body temperature were investigated as possible causally required properties. The best identification method for these environmental yeasts should be tested beforehand. Yeasts derived from liquid diets without (LD - S) and liquid diets with maize silage (LD + S) were examined biochemically (ID32C-test) and with MALDI-TOF with direct smear (DS) and an extraction method (EX). Growth temperature and gas-forming potential were measured. With MALDI-EX, most yeast isolates were identified: Candida krusei most often in LD - S, and C. lambica most often in LD + S, significantly more than in LD - S. Larger colonies, 58.75% of all yeast isolates, were formed at 25 °C rather than at 37 °C; 17.5% of all isolates did not grow at 37 °C at all. Most C. krusei isolates formed high gas amounts within 24 h, whereas none of the C. lambica, C. holmii and most other isolates did. The gas pressure formed by yeast isolates varied more than tenfold. Only a minority of the yeasts were able to produce gas at temperatures common in the pig gut.

Multilaboratory Evaluation of the MALDI-TOF Mass Spectrometry System, MicroIDSys Elite, for the Identification of Medically Important Filamentous Fungi

With the increasing number of fungal infections and immunocompromised patients, rapid and accurate fungal identification is required in clinical microbiology laboratories. We evaluated the applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system, MicroIDSys Elite (ASTA Corp., South Korea) for the identification of medically important filamentous fungi. A total of 505 strains comprising 37 genera and 90 species collected from 11 Korean hospitals were sent to the microbiology laboratory of International St. Mary's Hospital. All isolates were tested using MicroIDSys Elite, and data were analyzed using the MoldDB v.1.22 database (ASTA). Correct identification rates were compared with the multigene sequencing results. MicroIDSys Elite correctly identified 86.5% (437/505) and 88.9% (449/505) of all tested isolates at the species and genus level, respectively. About 98.2% of Aspergillus isolates were identified at the species level, including cryptic and rare species of A. calidoustus, A. tamarii, A. lentulus, A. versicolor and A. aculeatus. MicroIDSys Elite identified 75.0% of basidiomycetes, including Schizophyllum commune, and 84.3% of the dermatophytes. It also distinguished Sprothrix globosa at the species level. The mean scores of total isolates corresponding to correct species identification were significantly higher than those obtained for genus-level identification (253.5 ± 50.7 vs. 168.6 ± 30.3, P < 0.001). MicroIDSys Elite showed high accuracy for the identification of filamentous fungi, including cryptic and rare Aspergillus species. It is suitable for use in clinical laboratories as a rapid and efficient tool for clinical mold identification. Further evaluations are recommended for MicroIDSys Elite as a rapid and efficient tool for the identification of medically important filamentous fungi.

Evaluation of the ASTA MicroIDSys matrix-assisted laser desorption ionization time-of-flight mass spectrometry system for identification of mycobacteria directly from positive MGIT liquid cultures

OBJECTIVES

We evaluated the performance of the MicroIDSys Elite system, a newly developed matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry system for identification of mycobacteria directly from positive MGIT liquid cultures.

METHODS

Analytical specificity was evaluated with 63 reference strains grown in mycobacteria growth indicator tube media. Prospective performance evaluation was conducted with primary liquid cultures of sputum samples for identification of mycobacteria, and results were compared to multigenerational sequencing as the reference method. Liquid media subcultures were also analyzed.

RESULTS

The accuracy for the 63 reference strains was 98.4% (62/63). A total of 167 paired mycobacterial primary cultures and subcultures in liquid media, comprised of seven Mycobacterium tuberculosis isolates, 109 slowly growing nontuberculous mycobacterial isolates, and 51 rapidly growing nontuberculous mycobacterial isolates, was identified by the MicroIDSys Elite system. Using primary liquid cultures, the MicroIDSys Elite system correctly identified 143 (85.6%) isolates; 21 (12.6%) resulted in "no identification"; and three (1.8%) isolates were misidentified. Using liquid media subcultures with this system, 159 (95.2%) isolates were correctly identified; seven (4.2%) resulted in "no identification"; and one (0.6%) isolate was misidentified.

CONCLUSION

The MicroIDSys Elite system is a useful routine diagnostic tool for identification of mycobacterial species from liquid culture.

Saccharomyces cerevisiae and S. pastorianus species and strain differentiation by direct analysis in real time time-of-flight mass spectrometry

RATIONALE

Seventeen different dried yeast strains, including twelve strains of Saccharomyces cerevisiae and five strains of S. pastorianus, were analyzed using direct analysis in real time (DART) time-of-flight mass spectrometry. The resulting mass spectra were used for rapid species and strain differentiation based upon small-molecule metabolomic profiles.

METHODS

Yeast strains purchased from local shops were suspended in a 1:1 water-methanol solution. Solutions were sampled by dipping the sealed end of a melting point capillary into each vial. Six replicates were measured in positive-ion and negative-ion mode for each strain using an automated linear rail with the DART source operated with helium gas and a gas heater temperature of 350°C. Averaged and centroided mass spectra were exported for analysis with chemometric software.

RESULTS

Negative-ion DART mass spectra exhibited less chemical background and more distinctive components than positive-ion DART mass spectra. An on-line search of the Yeast Metabolome Database provided candidate metabolites for selection as features for chemometric analysis. Negative-ion DART mass spectra could distinguish both species and all strains. The DART analysis was also able to identify potential metabolomic differences between top-fermenting and bottom-fermenting yeast, between beer and baking yeast, and between red wine and champagne yeast.

CONCLUSIONS

All strains could be distinguished by their negative-ion DART mass spectra with 97.7% validation accuracy. Clear differences were observed between dry and liquid forms and Saccharomyces strains with different applications to baking or beverage fermentation. Possible differences in metabolite profiles were suggested, but not confirmed, by accurate mass data.

Comparison of the ASTA MicroIDSys and VITEK MS matrix-assisted laser desorption/ionization time-of-flight mass spectrometry systems for identification of clinical bacteria and yeasts

The ASTA MicroIDSys system (ASTA, Suwon, Korea) is a newly developed Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system for identification of microorganisms. We compared the performance of the ASTA MicroIDSys system with that of the VITEK MS system (bioMérieux, Marcy l'Etoile, France) for identifying clinical microorganisms. A total 2055 isolates including 1910 bacteria and 145 yeasts were tested. Among them, the VITEK MS correctly identified 1999 (97.3%) isolates to species level and 26 (1.3%) to the genus level. The ASTA MicroIDSys correctly identified 1988 (96.7%) isolates to species level and 28 (1.4%) to the genus level. The VITEK MS and ASTA MicroIDSys misidentified one isolate and four (0.2%) isolates, respectively, and provided no identification for 29 (1.4%) and 35 (1.7%) isolates, respectively. The performance of the ASTA MicroIDSys was comparable to that of the VITEK MS for identification of clinically relevant bacterial and yeast isolates.

Evaluation of a new matrix-assisted laser desorption/ionization time-of-flight mass spectrometry system for the identification of yeast isolation

BACKGROUND

Currently, three commercial in vitro diagnostic matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems are widely used in clinical laboratories. The ASTA MicroIDSys system (ASTA Inc, South Korea) is a newly developed MALDI-TOF MS system used for the identification of pathogenic microorganisms. In the present study, we assessed the performance of the ASTA MALDI-TOF MS system for the identification of pathogenic yeast from clinical samples.

METHODS

We tested 284 clinical yeast isolates from various clinical specimens using ASTA MALDI-TOF MS, and the results were compared with those using molecular sequencing of the ITS or D1-D2 regions of rDNA and biochemical assays.

RESULTS

A total of 284 isolates were tested and found to be distributed across 14 species including Candida albicans (n = 100) and other yeast species (n = 184). ASTA MALDI-TOF MS correctly identified 95.1% (270/284) of the yeast species compared to molecular sequencing. Among them, 262 isolates showed acceptable MALDI-TOF MS scores (≥140), and 98.1% (257/262) isolates were identified correctly. In addition, among 22 isolates with a MALDI-TOF MS score <140, 59.1% (13/22) of the isolates showed concordance with molecular typing at the species level. Clustering analysis revealed the effectiveness of the new MALDI-TOF MS system for the identification of yeast species.

CONCLUSIONS

ASTA MALDI-TOF MS showed high accuracy in the identification of yeast species; it involves facile sample preparation and extraction procedures. ASTA MALDI-TOF MS is expected to be useful for yeast identification in clinical microbiology laboratories due to its reliability and cost-effectiveness.