Identification of filamentous fungi including dermatophytes using MALDI-TOF mass spectrometry

A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases

The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.

Detection accuracy and clinical applications of DP-TOF mass spectrometry

OBJECTIVE

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently used in clinical microbiology laboratories. This study aimed to determine whether dual-polarity time-of-flight mass spectrometry (DP-TOF MS) could be applied to clinical nucleotide detection.

METHODS

This prospective study included 40 healthy individuals and 110 patients diagnosed with cardiovascular diseases. We used DP-TOF MS and Sanger sequencing to evaluate 17 loci across 11 genes associated with cardiovascular drug responses. In addition, we used DP-TOF MS to test 998 retrospectively collected clinical DNA samples with known results.

RESULTS

A, T, and G nucleotide detection by DP-TOF MS and Sanger sequencing revealed 100% concordance, whereas the C nucleotide concordance was 99.86%. Genotyping based on the results of the two methods showed 99.96% concordance. Regarding clinical applications, DP-TOF MS yielded a 99.91% concordance rate for known loci. The minimum detection limit for DNA was 0.4 ng; the inter-assay and intra-assay precision rates were both 100%. Anti-interference analysis showed that aerosol contamination greater than 1013 copies/µL in the laboratory environment could influence the results of DP-TOF MS.

CONCLUSIONS

The DP-TOF MS platform displayed good detection performance, as demonstrated by its 99.96% concordance rate with Sanger sequencing. Thus, it may be applied to clinical nucleotide detection.

Comparison of Autof Ms1000 and EXS3000 MALDI-TOF MS Platforms for Routine Identification of Microorganisms

Purpose

Matrix-assisted laser desorption-ionization-time of flight mass spectrometry (MALDI-TOF) has recently been widely used in clinical microbiology laboratories, with the advantages of being reliable, rapid, and cost-effective. Here, we reported the performance of two MALDI-TOF MS instruments, EXS3000 (Zybio, China) and Autof ms1000 (Autobio, China), which are commonly used in clinical microbiology field.

Methods

A total of 209 common clinical common isolates, including 70 gram-negative bacteria strains, 58 gram-positive bacteria strains, 33 yeast strains, 15 anaerobic bacteria strains, and 33 mold strains, and 19 mycobacterial strains were tested. All strains were identified by EXS3000 (Zybio, China) and Autof ms1000 (Autobio, China). Sequence analysis of 16S rRNA or ITS regions was used to verify all strains.

Results

Current study found that species-level discrimination was found to be 191 (91.39%) and 190 (90.91%) by EXS3000 and Autof ms1000, respectively. Genus-level discrimination was 205 (98.09%) by the EXS3000 and 205 (98.09%) by the Autof ms1000, respectively. The correct results at species level of the EXS3000 were 91.43% (64/70) for gram-negative bacteria, 93.1% (54/58) for gram-positive cocci, 93.94% (31/33) for yeast, 100% (15/15) for anaerobes and 81.82% (27/33) for filamentous fungi. The correct results at species level of the Autof ms1000 were 92.86% (65/70) for gram-negative bacteria, 91.38% (53/58) for gram-positive cocci, 93.94% (31/33) for yeast, 100% (15/15) for anaerobes and 78.79% (26/33) for filamentous fungi.

Conclusion

Although the results show that the EXS3000 and Autof ms1000 systems are equally good choices in terms of analytical efficiency for routine procedures, the test result of EXS3000 is slightly better than Autof ms1000. It's worth mentioning that the target plate of the EXS 3000 instrument is reusable, but the target plate of the Autof ms1000 is disposable, making the EXS3000 more effective in reducing costs.

Implementation of MALDI-TOF Mass Spectrometry to Identify Fungi From the Indoor Environment as an Added Value to the Classical Morphology-Based Identification Tool

Introduction

During the last decades, molds in the indoor environment have raised concern regarding their potential adverse health effects. The genera Aspergillus, Cladosporium, Penicillium, Alternaria, and yeasts, the most common fungi found indoors, include species with high allergenic and toxigenic potentials. Identification of these molds is generally performed by microscopy. This method has, however, some limitations as it requires mycologists with high expertise while identification is often limited to the genus level. Therefore, it is necessary to seek for fast and accurate tools, such as Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDITOF MS), enabling an identification to the species level and guiding general practitioners in their search for the underlying cause of a health problem.

Methods

In this study, 149 fungal air and dust isolates from 43 dwellings in Brussels were taken in collaboration with Brussels Environment RCIB/CRIPI and identified by both microscopy and MALDI-TOF MS in Sciensano's Indoor Mycology laboratory. Spectra obtained via MALDI-TOF MS were compared with data available in an in-house created reference database containing over 1,700 strains from the BCCM/IHEM fungal collection.

Results

A total of 149 isolates including 18 yeasts and 131 filamentous fungi were analyzed. Microscopic analysis indicated 18 yeast species and allowed identification of 79 isolates (53%) to the genus level. Only 36 isolates (24%) could be identified to the species complex level. Fifteen molds (10%) could not be identified, and one was indicated as sterile mycelia. No isolate was identified to species level. MALDI-TOF MS analysis identified 137 (92%) of the 149 isolates with a logscore > 1.7. Of these 137 isolates, 129 (87%) were identified to the species level (logscore > 2.0). For only 8 isolates (5%), identification was limited to the genus/section level (1.7 < logscore <2.0), and 12 isolates (8%) could not be identified.

Conclusion

A comparison of results obtained with both methods indicates an increased precision in identifications with MALDI-TOF MS analysis for 92% of the isolates, emphasizing its highly added value to the standard microscopic analysis in routine practice. In addition, MALDI-TOF MS also enables to assess the accuracy of microscopic identifications.