Comparison of the Vitek MS and Bruker Microflex LT MALDI-TOF MS platforms for routine identification of commonly isolated bacteria and yeast in the clinical microbiology laboratory

Analysis of the efficacy of MALDI-TOF MS technology in identifying microorganisms in cancer patients and oncology hospital environment

Rapid diagnostics of microbes in hospitals are crucial for promptly identifying infections, enabling timely and appropriate treatment. The study was conducted to evaluate the effectiveness of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF MS) technology in the microbial profiling of hospital environments and patient samples. The objective was to determine the microbial landscape in swabs collected from hospitalized patients and their immediate environments, using MALDI to compare the capabilities of two systems: BRUKER and ZYBIO. The analysis resulted in 1012 microbial identifications from patient samples (N = 81), encompassing 96 species, and 1496 identifications from hospital surface samples (N = 108), covering 124 species. Predominantly identified microorganisms in patients' samples included Staphylococcus epidermidis, Staphylococcus aureus, Staphylococcus capitis, Steptococcus salivarius, and Micrococcus luteus, whereas environmental samples chiefly yielded S. epidermidis, Staphylococcus hominis, Staphylococcus warneri, and Microcccus luteus. 33 species were found in both types of samples, highlighting a significant microbial interchange within hospital settings. Both MALDI systems showed high consistency in results at both genus and species levels. Nevertheless, mismatches in identification between both MALDI systems were noted, particularly within Brevibacterium, Streptococcus, Bacillus, Staphylococcus, and Neisseria genera. This study presents the precision of MALDI technology in microbial identification and highlights the need for ongoing enhancements, especially in the expansion and updating of databases, to bolster its diagnostic effectiveness further.

Evaluation of VITEK MS Version 3.0 MALDI-TOF for the identification of anaerobes, mycobacteria, Nocardia, and moulds

PURPOSE

The identification of anaerobes, Mycobacterium and Nocardia species, and moulds by MALDI-TOF-MS remains a challenge. This study aimed to evaluate the performance of MALDI-TOF in the identification of these organisms.

METHODS

A total of 382 strains, comprising 128 (33.5 %) anaerobes, 126(33.0 %) mycobacterial, 113(29.6 %), mycelial fungi, and 15(3.9 %) Nocardia species were evaluated by VITEK MS Version 3.0. The results were compared with the identification of the isolates by DNA sequence analysis. The DNA sequences used for analysis were the 16S rRNA for anaerobic bacteria, hsp65 gene for mycobacteria, whereas both 16S rRNA and hsp65 gene for Nocardia species, and internal transcribed spacer (ITS) and 28S rRNA gene's D1/D2 regions of fungi.

RESULTS

The VITEK-MS accurately identified 78.3 % (299/382) of the strains at the species, and 9.4 % (36/382) at the genus level. Misidentifications were observed in 3.9 % (15/382) isolates. Of isolates tested, 8.4 % (32/382) were not identified by the system, and 7.06 % (27/382) were not included in the IVD database.

CONCLUSION

An upgraded VITEK MS V3.0 database provides reasonably accurate and rapid identification of clinically relevant anaerobes, mycobacteria, Nocardia species, and moulds to the species level.

Identification of Food Spoilage Fungi Using MALDI-TOF MS: Spectral Database Development and Application to Species Complex

Fungi, including filamentous fungi and yeasts, are major contributors to global food losses and waste due to their ability to colonize a very large diversity of food raw materials and processed foods throughout the food chain. In addition, numerous fungal species are mycotoxin producers and can also be responsible for opportunistic infections. In recent years, MALDI-TOF MS has emerged as a valuable, rapid and reliable asset for fungal identification in order to ensure food safety and quality. In this context, this study aimed at expanding the VITEK® MS database with food-relevant fungal species and evaluate its performance, with a specific emphasis on species differentiation within species complexes. To this end, a total of 380 yeast and mold strains belonging to 51 genera and 133 species were added into the spectral database including species from five species complexes corresponding to Colletotrichum acutatum, Colletotrichum gloeosporioides, Fusarium dimerum, Mucor circinelloides complexes and Aspergillus series nigri. Database performances were evaluated by cross-validation and external validation using 78 fungal isolates with 96.55% and 90.48% correct identification, respectively. This study also showed the capacity of MALDI-TOF MS to differentiate closely related species within species complexes and further demonstrated the potential of this technique for the routine identification of fungi in an industrial context.

Comparison of the Bruker Microflex LT and Zybio EXS2600 MALDI TOF MS systems for the identification of clinical microorganisms

The emergence of Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI TOF MS) technology has expanded the capabilities for identifying microorganisms in clinical labs, replacing traditional biochemical testing with a proteomic approach. In the present study, we compared results between the two commercial MALDI TOF MS systems, Bruker Microflex LT Biotyper and Zybio EXS2600 Ex-Accuspec, for the identification of 1979 urinary isolates by direct extraction method. Current study found that both systems identified a high percentage of isolates to at least the genus level - Bruker 95.6 % of isolates, Zybio 92.4 %. In the case of 89.5 % of all analyzed spectra, the identification results were consistent between the used devices. The highest score values and the highest percentage of spectra identified to species were obtained for gram-negative bacteria. The results show that both systems are equally good choices in terms of analytical performance for routine microbiological diagnostic procedures.

A side-by-side comparison of the new VITEK MS PRIME and the MALDI Biotyper sirius in the clinical microbiology laboratory

PURPOSE

This study aims to evaluate the performance of two latest generation matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems in routine laboratory settings, focusing on turnaround time (TAT), time to results (TTR), hands-on time, and identification rate.

METHODS

We conducted a time and motion study on three workflow scenarios to simulate different laboratory settings. Overall, 618 bacterial isolates from a tertiary hospital's laboratory were processed using the VITEK MS PRIME (bioMérieux) and the MALDI Biotyper sirius (Bruker Daltonics) and their corresponding databases VITEK IVD Database 3.2 and MBT reference library 12.

RESULTS

The target preparation process showed no significant difference in TAT, but the Biotyper workflow had a shorter hands-on time by 3 to 6 min. In the measurement process, TTR was three to five times shorter for the Biotyper sirius while hands-on time was significantly shorter for VITEK MS PRIME (approximately 1.5 min per target). The identification rate without retesting was 97.9% for VITEK MS PRIME and 98.9% for Biotyper sirius. Both systems achieved 100% agreement at genus and 96.2% at species level.

CONCLUSION

Both systems exhibited excellent identification rates for routine bacterial isolates. Due to its high speed, the Biotyper sirius is suited for laboratories with high sample throughput and a workflow designed for processing larger batches. The VITEK MS PRIME, with its "load and go" system accommodating up to 16 targets, reduces hands-on time, making it a reasonable choice for laboratories with fewer identifications overall but a higher number of targets and a workflow designed for parallel processing on different workstations.

Challenges and Opportunities in Antimicrobial Stewardship among Hematopoietic Stem Cell Transplant and Oncology Patients

Antimicrobial stewardship programs play a critical role in optimizing the use of antimicrobials against pathogens in the era of growing multi-drug resistance. However, implementation of antimicrobial stewardship programs among the hematopoietic stem cell transplant and oncology populations has posed challenges due to multiple risk factors in the host populations and the infections that affect them. The consideration of underlying immunosuppression and a higher risk for poor outcomes have shaped therapeutic decisions for these patients. In this multidisciplinary perspective piece, we provide a summary of the current landscape of antimicrobial stewardship, unique challenges, and opportunities for unmet needs in these patient populations.

Multimodal analysis of south-eastern Black Sea sediment bacterial population diversity

This study focused on marine sediments from the Black Sea, mainly due to bacterial diversity-induced public health / biotechnology application value. Sediment samples were gathered from 14 locations at differing depths across Turkish shores on a seasonal basis over 10 months, with bacterial identifications performed through using multimodal analytical platforms. Overall, 26 differing, predominantly Gram-positive (57.5 %) bacterial species were identified for this region, including Bacillaceae (50.0 %) and Pseudomonadaceae (15.0 %). The most dominant classes were identified as Bacilli (52.5 %) and Gammaproteobacteria (40.0 %). Ten isolates (25 %) to the species level and thirty-six isolates (90 %) to the genus level were identified using VITEK® MS and Bruker Microflex® LT/SH, in comparison to 16S rRNA sequencing results. Identified species - particularly, novel reported species - can contribute to the knowledge of microbial life dwelling upon sediments of the south-eastern regions of the Black Sea.

A side-by-side comparison of the performance and time-and-motion data of VITEK MS

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry systems are designed for rapid and reliable microbial identification. VITEK MS PRIME is the bioMérieux's new generation instrument equipped with a continuous load-and-go sample loading system, urgent slide prioritization for critical patient samples and new internal components for faster identification. The aim of this study was to assess the performance of VITEK MS PRIME and to compare it to that of the VITEK MS system. In addition, at two sites, we performed a time-and-motion study to evaluate the efficiency of sample analysis from colony picking to slide removal from the instrument. We analyzed by VITEK MS and VITEK MS PRIME a total of 1413 isolates (1320 bacterial and 76 yeast) deriving from routine diagnostic samples that came into four laboratories in Canada, France, Italy, and Spain. VITEK MS PRIME and VITEK MS were concordant to the species and genus level for 1354/1413 (95.8%) and to the species level for 1341/1413 (94.9%). The identification and concordance rates in individual centers were largely homogenous. Overall, VITEK MS PRIME identified 1370/1413 (97.0%) of isolates compared to 1367/1413 (96.7%) identified by VITEK MS. Identification rates were consistently high for all microorganism categories. A time-and-motion study showed that the use of VITEK MS PRIME was associated with significant time saving. VITEK MS PRIME performs as well as VITEK MS and reduces the time necessary for pathogen identification. To fully optimize the laboratory process and obtain maximum efficiency, VITEK MS PRIME must be integrated into the laboratory workflow.

Impact of tissue processing on microbiological colonization in the context of placentophagy

A mother’s postpartum ingestion of raw or processed placental tissue—referred to as human maternal placentophagy—is an emerging health trend observed in industrialized nations. Placenta is commonly consumed as small pieces of raw tissue, or as raw or steamed dehydrated pulverized and encapsulated tissue. To investigate the potential neonatal health risks of this behavior, the present study focused on microbial colonization of processed placenta preparations with potentially pathogenic bacteria Streptococcus agalactiae (Group-B-Streptococci; GBS) and Escherichia coli (E. coli). In the clinical approach placentas from 24 mothers were analyzed. Two placentas, from 13 mothers with confirmed positive maternal GBS status, showed GBS-growth on their surface (2/13; 15.4%) independent from delivery mode or antibiotic treatment. All processed samples (n = 24) were free from GBS. In the experimental approach, a standardized inoculation protocol was introduced to resemble ascending vaginal and hematogenous colonization. Six placentas from elective term C-sections of GBS negative mothers were collected and artificially inoculated with highly concentrated suspensions of GBS and E. coli. Heat processing significantly reduced the number of colony forming units (CFU) for GBS and E. coli. Our results suggest placentophagy of processed tissue is an unlikely source of clinical infection.

A Piece of the Puzzle: The Role of Molecular Testing in Antimicrobial Stewardship

Molecular testing may have an important role in expediting the diagnosis of infectious diseases. Pediatric infectious diseases specialists need to be cognizant of the strengths and limitations of these existing and emerging technologies in order to ensure that they are used and interpreted appropriately.

Reducing time in detection of Listeria monocytogenes from food by MALDI-TOF mass spectrometry

In this study, direct detection of L. monocytogenes from liquid culture and enrichment broths containing foods was investigated by using MALDI-TOF MS. For determining the sole effect of food constituents on detection and accuracy of identification in enrichment broths, sterile foods were used before the experiments with food. L. monocytogenes could be detected in BHI broth after 24 h of incubation. Detection period was determined as 18 h for 3 × 10¹ cfu/mL initial bacterial count in BHI broth containing sterile food. The period extended in ONE broth containing sterile garnish, which was 24 and 30 h for 3 × 10¹ and 1 cfu/mL inoculum, respectively. It was found that identification times in UHT milk were longer than that of canned garnish. In the experiments performed with foods having a specific microbiota; White cheese, iceberg lettuce, parsley and watermelon were used. Although no reliable identification was obtained by using White cheese, iceberg lettuce and parsley, L. monocytogenes could be detected in 24 h in the enrichment broth containing watermelon. Detection was achieved during a single step enrichment in a reduced time of 24 h for even 1 cfu/mL initial inoculum.

Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS): basics and clinical applications

Background Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS) has been used for more than 30 years. Compared with other analytical techniques, it offers ease of use, high throughput, robustness, cost-effectiveness, rapid analysis and sensitivity. As advantages, current clinical techniques (e.g. immunoassays) are unable to directly measure the biomarker; rather, they measure secondary signals. MALDI-MS has been extensively researched for clinical applications, and it is set for a breakthrough as a routine tool for clinical diagnostics. Content This review reports on the principles of MALDI-MS and discusses current clinical applications and the future clinical prospects for MALDI-MS. Furthermore, the review assesses the limitations currently experienced in clinical assays, the advantages and the impact of MALDI-MS to transform clinical laboratories. Summary MALDI-MS is widely used in clinical microbiology for the screening of microbial isolates; however, there is scope to apply MALDI-MS in the diagnosis, prognosis, therapeutic drug monitoring and biopsy imaging in many diseases. Outlook There is considerable potential for MALDI-MS in clinic as a tool for screening, profiling and imaging because of its high sensitivity and specificity over alternative techniques.

Detection of Intrinsically Resistant Candida in Mixed Samples by MALDI TOF-MS and a Modified Naïve Bayesian Classifier

MALDI-TOF MS is one of the major methods for clinical fungal identification, but it is currently only suitable for pure cultures of isolated strains. However, multiple fungal coinfections might occur in clinical practice. Some fungi involved in coinfection, such as Candida krusei and Candida auris, are intrinsically resistant to certain drugs. Identifying intrinsically resistant fungi from coinfected mixed cultures is extremely important for clinical treatment because different treatment options would be pursued accordingly. In this study, we counted the peaks of various species generated by Bruker Daltonik MALDI Biotyper software and accordingly constructed a modified naïve Bayesian classifier to analyze the presence of C. krusei and C. auris in simulated mixed samples. When reasonable parameters were fixed, the modified naïve Bayesian classifier effectively identified C. krusei and C. auris in the mixed samples (sensitivity 93.52%, specificity 92.5%). Our method not only provides a viable solution for identifying the two highlighted intrinsically resistant Candida species but also provides a case for the use of MALDI-TOF MS for analyzing coinfections of other species.

Application and Perspectives of MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories

Early diagnosis of severe infections requires of a rapid and reliable diagnosis to initiate appropriate treatment, while avoiding unnecessary antimicrobial use and reducing associated morbidities and healthcare costs. It is a fact that conventional methods usually require more than 24–48 h to culture and profile bacterial species. Mass spectrometry (MS) is an analytical technique that has emerged as a powerful tool in clinical microbiology for identifying peptides and proteins, which makes it a promising tool for microbial identification. Matrix assisted laser desorption ionization–time of flight MS (MALDI–TOF MS) offers a cost- and time-effective alternative to conventional methods, such as bacterial culture and even 16S rRNA gene sequencing, for identifying viruses, bacteria and fungi and detecting virulence factors and mechanisms of resistance. This review provides an overview of the potential applications and perspectives of MS in clinical microbiology laboratories and proposes its use as a first-line method for microbial identification and diagnosis.

Effective discrimination of Yersinia pestis and Yersinia pseudotuberculosis by MALDI-TOF MS using multivariate analysis

Separating Yersinia pseudotuberculosis and Yersinia pestis is an important issue in plague diagnosis but can be extremely difficult because of the high similarity between the two species. MALDI-TOF MS has grown as a diagnostic tool with great potential in bacterial identification. Its application in this field is largely enhanced by multivariate analysis, especially in extracting subtle spectral differences. In this study, we built a complete MALDI-TOF MS data pipeline and found a Y. pestis-specific biomarker at 3063 Da closely related to Y. pestis plasminogen activation factor. Based on this, we achieved almost perfect separation between Y. pseudotuberculosis and Y. pestis (AUC = 0.999) using a supervised linear discriminant analysis (LDA) model. This is significantly better than the conventionally applied unsupervised spectral similarity comparison methods, such as hierarchical clustering analysis (HCA), which gave a separation accuracy of 75.0%. This new computing method paves the way for automatic differentiation between the two highly similar bacterial species with high separation accuracy.

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.

Application of MALDI-TOF MS to species complex differentiation and strain typing of food related fungi: Case studies with Aspergillus section Flavi species and Penicillium roqueforti isolates

Filamentous fungi are one of the main causes of food losses worldwide and their ability to produce mycotoxins represents a hazard for human health. Their correct and rapid identification is thus crucial to manage food safety. In recent years, MALDI-TOF emerged as a rapid and reliable tool for fungi identification and was applied to typing of bacteria and yeasts, but few studies focused on filamentous fungal species complex differentiation and typing. Therefore, the aim of this study was to evaluate the use of MALDI-TOF to identify species of the Aspergillus section Flavi, and to differentiate Penicillium roqueforti isolates from three distinct genetic populations. Spectra were acquired from 23 Aspergillus species and integrated into a database for which cross-validation led to more than 99% of correctly attributed spectra. For P. roqueforti, spectra were acquired from 63 strains and a two-step calibration procedure was applied before database construction. Cross-validation and external validation respectively led to 94% and 95% of spectra attributed to the right population. Results obtained here suggested very good agreement between spectral and genetic data analysis for both Aspergillus species and P. roqueforti, demonstrating MALDI-TOF applicability as a fast and easy alternative to molecular techniques for species complex differentiation and strain typing of filamentous fungi.

Bacterial identification using a SCIEX 5800 TOF/TOF MALDI research instrument and an external database

In our current study we were identifying 26 bacterial isolates using a SCIEX 5800 TOF/TOF MALDI instrument and an external database. The results were compared with the results of a Vitek® MS system and in case of discrepancies at the species level 16s rRNA sequencing was performed for further verification.

Identification and antifungal susceptibility profiles of Kodamaea ohmeri based on a seven-year multicenter surveillance study

Background

Kodamaea ohmeri has been a rare fungal pathogen in the past decades but is now becoming more common in various invasive fungal diseases, with high mortality. There are limited data on the occurrence and distribution of K. ohmeri.

Methods

Sixty-two K. ohmeri isolates collected from 24 hospitals in China over a 7-year period were studied. Performance of three phenotypic methods in the identification of this organism was assessed against a gold standard, 26S rDNA sequencing. Original identification results submitted by the participating local hospitals were reviewed. The Sensititre YeastOne YO10 (SYY) was evaluated in determining the in vitro antifungal susceptibilities using standard broth microdilution method (BMD) as a reference, and essential agreement (EA) was calculated.

Results

Accurate species identification was achieved in 82.3% and 96.8% of the cases by Vitek 2 Compact and Vitek mass spectrometry (MS), respectively. For Bruker MS, 12.9% and 96.8% of the isolates were correctly identified to species level using the direct transfer and protein extraction methods, respectively. Only 29 (46.8%) isolates were initially correctly identified as K. ohmeri by the local hospitals. The highest misidentification rate (100%, 16/16) was observed in CHROMagar. According to BMD, the highest MIC₉₀ was seen in fluconazole (8 μg/mL), followed by 1 μg/mL for micafungin, caspofungin, 5-fluorocytosine, and amphotericin B, 0.5 μg/mL for itraconazole, 0.25 μg/mL for posaconazole and voriconazole. Significant differences in EAs for different drugs were observed, ranging from 95.2% for amphotericin B to 22.6% for itraconazole between SYY and BMD.

Conclusion

Our study emphasizes the need for accurate identification of clinical K. ohmeri isolates and the importance of validating antifungal susceptibility by standard BMD.

Microbial Degradation of Epoxy

Epoxy resins have a wide range of applications, including in corrosion protection of metals, electronics, structural adhesives, and composites. The consumption of epoxy resins is predicted to keep growing in the coming years. Unfortunately, thermoset resins cannot be recycled, and are typically not biodegradable. Hence, they pose environmental pollution risk. Here, we report degradation of epoxy resin by two bacteria that are capable of using epoxy resin as a sole carbon source. These bacteria were isolated from soil samples collected from areas around an epoxy and polyurethanes manufacturing plant. Using an array of molecular, biochemical, analytical, and microscopic techniques, they were identified as Rhodococcus rhodochrous and Ochrobactrum anthropi. As epoxy was the only carbon source available for these bacteria, their measured growth rate reflected their ability to degrade epoxy resin. Bacterial growth took place only when the two bacteria were grown together, indicating a synergistic effect. The surface morphology of the epoxy droplets changed significantly due to the biodegradation process. The metabolic pathway of epoxy by these two microbes was investigated by liquid chromatography mass spectrometry. Bisphenol A, 3,3′-((propane-2,2-diylbis(4,1-phenylene))bis(oxy))bis(propane-1,2-diol) and some other constituents were identified as being consumed by the bacteria.

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.

Taxonomy and evolution of Aspergillus, Penicillium and Talaromyces in the omics era - Past, present and future

Aspergillus, Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species important to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxonomic studies on these fungi are essential since they could provide invaluable information on their evolutionary relationships and define criteria for species recognition. With the advancement of various biological, biochemical and computational technologies, different approaches have been adopted for the taxonomy of Aspergillus, Penicillium and Talaromyces; for example, from traditional morphotyping, phenotyping to chemotyping (e.g. lipotyping, proteotypingand metabolotyping) and then mitogenotyping and/or phylotyping. Since different taxonomic approaches focus on different sets of characters of the organisms, various classification and identification schemes would result. In view of this, the consolidated species concept, which takes into account different types of characters, is recently accepted for taxonomic purposes and, together with the lately implemented 'One Fungus - One Name' policy, is expected to bring a more stable taxonomy for Aspergillus, Penicillium and Talaromyces, which could facilitate their evolutionary studies. The most significant taxonomic change for the three genera was the transfer of Penicillium subgenus Biverticillium to Talaromyces (e.g. the medically important thermally dimorphic 'P. marneffei' endemic in Southeast Asia is now named T. marneffei), leaving both Penicillium and Talaromyces as monophyletic genera. Several distantly related Aspergillus-like fungi were also segregated from Aspergillus, making this genus, containing members of both sexual and asexual morphs, monophyletic as well. In the current omics era, application of various state-of-the-art omics technologies is likely to provide comprehensive information on the evolution of Aspergillus, Penicillium and Talaromyces and a stable taxonomy will hopefully be achieved.

Identification of Candida glabrata complex species: use of Vitek MS® RUO & Bruker ClinproTools®

AIM

Distinction of species within the Candida glabrata complex (i.e., C. glabrata sensu stricto, Candida nivariensis and Candida bracarensis) is relevant for epidemiological purposes and antifungal management.

MATERIALS & METHODS

Two commercial matrix-assisted laser desorption ionization-time of flight mass spectrometry systems were comprehensively evaluated for the identification of fungi within this complex.

RESULTS

None of the species (C. nivariensis and C. bracarensis) were identified correctly by Vitek mass spectrometry (MS^®) v2.0 In Vitro Diagnosis system and Bruker Biotyper MS^® v3.1, but all were correct by the Vitek MS^® Research Use Only system. The Bruker ClinProTools software showed 100% recognition capability and cross validation for the discrimination of C. nivariensis and C. bracarensis.

CONCLUSION

Using Vitek MS Research Use Only and Bruker ClinProTools can overcome limitations of the Vitek MS In Vitro Diagnosis and Bruker Biotyper databases in the identification of C. glabrata complex.

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

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

Head-to-head comparison of Microflex LT and Vitek MS systems for routine identification of microorganisms by MALDI-TOF mass spectrometry in Chile

Background

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a new and revolutionary identification method for microorganisms and has recently been introduced into clinical microbiology in many industrialized countries in Europe and North America.

Objectives

Our study aimed to compare the performance and practicality of two commercial MALDI-TOF MS platforms in a head-to head manner at a routine laboratory in Chile.

Methods

During a five-month period in 2012–13, the diagnostic efficiency (correct identification rate) and agreement between Microflex LT (Bruker Daltonics) and Vitek MS (bioMérieux) was compared in a parallel manner to conventional identification including genotypic analysis for difficult-to-identify strains. The study included 804 microbial isolates: 252 Enterobacteriaceae, 126 non-fermenters, 36 other gram-negative rods, 279 gram-positive cocci, 32 gram-positive rods, 32 anaerobes, and 47 yeasts. Other relevant factors of the two devices such as user friendliness and connectivity were also evaluated and compared.

Results

Both systems correctly identified the vast majority (98%) of the isolates to the genus level. Vitek MS reached higher rates of identification to species and species complex level than Microflex LT (81% vs. 85% and 87% vs. 93%, respectively), which was mainly based on the higher performance among coagulase negative staphylococci and Candida isolates. The evaluation of user friendliness and other technical aspects showed only marginal differences, which slightly favored Vitek MS, mainly due to its ready-to-use supplies, easier connectivity and workflow integration, and availability of local technical support.

Conclusions

Both MALDI-TOF MS systems permitted fast and accurate identification of most microbial strains and showed a high level of user-friendliness. The observed differences were marginal and slightly favored Vitek MS, mainly due to practicality and connectivity issues within our setting.

Identification and Antifungal Susceptibility Profiles of Candida nivariensis and Candida bracarensis in a Multi-Center Chinese Collection of Yeasts

Candida nivariensis and C. bracarensis are two emerging cryptic species within the C. glabrata complex. Thirteen of these isolates from 10 hospitals in China were studied for their species identification and antifungal susceptibilities. Phenotypic and molecular [rDNA ITS sequencing, D1/D2 sequencing and ITS sequencer-based capillary gel electrophoresis (SCGE)] and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS identification methods were compared for their performance in species identification. Twelve of 13 (92.3%) isolates were identified as C. nivariensis and one as C. bracarensis using ITS sequencing as the reference method. Results obtained by D1/D2 sequencing and ITS SCGE were concordant with ITS sequencing results for all (100%) isolates. SCGE was able to subtype 12 C. nivariensis into four ITS SCGE length types. All isolates failed to be identified by the Vitek MALDI-TOF MS system (bioMérieux), whilst the Bruker MS system (Bruker Daltoniks) correctly identified all C. nivariensis isolates but using a lowered (≥1.700) cut-off score for species assignment; the C. bracarensis isolate was identified but with score <1.700. The Vitek 2 Compact system could not identify 11 C. nivariensis and one C. bracarensis isolate and misidentified the remaining C. nivarensis strain as “C. glabrata.” All isolates were susceptible-dose dependent to fluconazole [minimum inhibitory concentration (MIC) range 0.5–4 μg/mL] and were classed as susceptible to echinocandins (MICs ≤ 0.06 μg/mL). All 13 isolates had low MICs for other azoles (MICs ≤ 0.5 μg/mL), amphotericin B (MICs ≤ 2 μg/mL) and 5-flucytosine (MICs ≤ 0.25 μg/mL). Our results reinforce the need for molecular differentiation of species of C. nivarensis and C. bracarensis. The performance of MALDI-TOF may be improved by adding mass spectral profiles (MSPs) into the current databases. The antifungal susceptibility profile of isolates should be monitored.

Clinical and Microbiological Aspects of β-Lactam Resistance in Staphylococcus lugdunensis

Antimicrobial susceptibility results from broth microdilution MIC testing of 993 Staphylococcus lugdunensis isolates recovered from patients at a tertiary care medical center from 2008 to 2015 were reviewed. Ninety-two oxacillin-susceptible isolates were selected to assess the accuracy of penicillin MIC testing, the penicillin disk diffusion test, and three β-lactamase tests, including the cefoxitin-induced nitrocefin test, penicillin cloverleaf assay, and penicillin disk zone edge test. The results of all phenotypic tests were compared to the results of blaZ PCR. The medical records of 62 patients from whom S. lugdunensis was isolated, including 31 penicillin-susceptible and 31 penicillin-resistant strains, were retrospectively reviewed to evaluate the clinical significance of S. lugdunensis isolation, the antimicrobial agents prescribed, if any, and the clinical outcome. MIC testing revealed that 517/993 (52.1%) isolates were susceptible to penicillin and 946/993 (95.3%) were susceptible to oxacillin. The induced nitrocefin test was 100% sensitive and specific for the detection of β-lactamase compared to the blaZ PCR results, whereas the penicillin disk zone edge and cloverleaf tests showed sensitivities of 100% but specificities of only 9.1% and 89.1%, respectively. The penicillin MIC test had 100% categorical agreement with blaZ PCR, while penicillin disk diffusion yielded one major error. Only 3/31 patients with penicillin-susceptible isolates were treated with a penicillin family antimicrobial. The majority of cases were treated with other β-lactams, trimethoprim-sulfamethoxazole, or vancomycin. These data indicate that nearly all isolates of S. lugdunensis are susceptible to narrow-spectrum antimicrobial agents. Clinical laboratories in areas with resistance levels similar to those described here can help promote the use of these agents versus vancomycin by effectively designing their antimicrobial susceptibility reports to convey this message.

Identification and Antifungal Susceptibility Profiles of Candida haemulonii Species Complex Clinical Isolates from a Multicenter Study in China

Candida haemulonii complex (Candida haemulonii, Candida haemulonii var. vulnera, and Candida duobushaemulonii) consists of emerging pathogens. Thirty-one isolates from 14 hospitals in China were studied for their species classification and antifungal susceptibilities. Performances of molecular (i.e., ribosomal DNA [rDNA] internal transcribed spacer [ITS] sequencing, D1/D2 sequencing, and ITS sequencer-based capillary gel electrophoresis [SCGE]) and phenotypic identification methods in species identification were compared. Twenty-six (83.9%) of 31 isolates were identified as C. haemulonii and 5 isolates were identified as C. duobushaemulonii by ITS sequencing as the reference method; results obtained by D1/D2 sequencing and ITS SCGE were concordant with those obtained by ITS sequencing for all (100%) of the isolates. All 31 isolates were identified as C. haemulonii by the Vitek matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system (bioMérieux, France), whereas the Bruker MS system (Bruker Daltoniks, Germany) correctly provided species identification for 77.4% and 100% of isolates using cutoff scores for species of ≥2.0 and ≥1.70, respectively. The Vitek 2 compact (bioMérieux) only identified 9 (29%) of 31 isolates. All isolates showed high MICs for amphotericin B (range, 2 to >8 μg/ml) and fluconazole (≥128 μg/ml) but low MICs (≤0.5 μg/ml) for the echinocandins. Our results reinforce the need for MALDI-TOF MS and/or molecular differentiation of species within the C. haemulonii complex. The multiresistant antifungal susceptibility profile of these isolates represents a challenge to therapy.

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS

There are a number of rare and, therefore, insufficiently described bacterial pathogens which are reported to cause severe infections especially in immunocompromised patients. In most cases only few data, mostly published as case reports, are available which investigate the role of such pathogens as an infectious agent. Therefore, in order to clarify the pathogenic character of such microorganisms, it is necessary to conduct epidemiologic studies which include large numbers of these bacteria. The methods used in such a surveillance study have to meet the following criteria: the identification of the strains has to be accurate according to the valid nomenclature, they should be easy to handle (robustness), economical in routine diagnostics and they have to generate comparable results among different laboratories. Generally, there are three strategies for identifying bacterial strains in a routine setting: 1) phenotypic identification characterizing the biochemical and metabolic properties of the bacteria, 2) molecular techniques such as 16S rRNA gene sequencing and 3) mass spectrometry as a novel proteome based approach. Since mass spectrometry and molecular approaches are the most promising tools for identifying a large variety of bacterial species, these two methods are described. Advances, limitations and potential problems when using these techniques are discussed.

A rare cause of infection, Raoultella planticola: emerging threat and new reservoir for carbapenem resistance

BACKGROUND

Severe cases of infections caused by Raoultella planticola are constantly being reported from all over the world with the increase in drug-resistance patterns. In this study, we retrospectively evaluated the clinical characteristics of R. planticola infections with patients' demographics and antimicrobial susceptibilities of the R. planticola isolates.

METHODS

R. planticola isolates were retrospectively evaluated. VITEK 2^® automated system was used for identification and antimicrobial susceptibility testing. Verification of the low-discriminated isolates was analyzed with MALDI-TOF method using VITEK MS^® system. Gene-Xpert^® system was used for detection of bla _IMP-1-, bla _KPC-, bla _NDM-1-, bla _OXA-48- and bla _VIM-type carbapenemases. The data of the patients with R. planticola infection were collected from hospital records.

RESULT

During the 4-year period, 42 episodes of R. planticola infections were detected. MALDI-TOF was used for 11 of the low-discriminated isolates, and 1 of which identified as R. terrigena was excluded. Carbapenems and aminoglycosides were the most effective antimicrobial agents. Extended spectrum beta-lactamases were detected in seven of the isolates. Three carbapenem-resistant isolates were detected as bla _OXA-48-type carbapenemase carrier. Nosocomial R. planticola infections constituted 80.9 % (n = 34) of the infections. Most common infections related with R. planticola were blood stream infections (n = 24) (p < 0.005). The presence of indwelling catheter and intensive care unit stay were the most common detected risk factors (p < 0.005). Diabetes mellitus and chronic renal insufficiency commonly accompanied the infections (p > 0.005).

CONCLUSIONS

Challenging infections caused by Raoultella spp., like those of multidrug resistant Klebsiella spp., will probably become a concern for clinicians as well as microbiologists . In literature, there were few cases, but we believe that the incidence of Raoultella spp. infections, which may result from misidentification, are more common than expected , and it is not unlikely that there will be a gradual increase and spread in multidrug-resistant isolates.

A Comprehensive Evaluation of the Bruker Biotyper MS and Vitek MS Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Systems for Identification of Yeasts, Part of the National China Hospital Invasive Fungal Surveillance Net (CHIF-NET) Study, 2012 to 2013

Among the 2,683 yeast isolates representing 41 different species (25 Candida and Candida-related species and 16 non-Candida yeast species) collected in the National China Hospital Invasive Fungal Surveillance Net (CHIF-NET) program (2012 to 2013), the Bruker Biotyper MS matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system exhibited significantly higher accuracy rates than the Vitek MS system for identification of all yeast isolates (98.8% versus 95.4%, P <0.001 by Pearson's chi-square test) and for all Candida and Candida-related species isolates (99.4% versus 95.5%, P < 0.001).

MALDI-TOF mass spectrometry for differentiation between Streptococcus pneumoniae and Streptococcus pseudopneumoniae

We compared the Vitek MS and Microflex MALDI-TOF mass spectrometry platform for species differentiation within the Streptococcus mitis group with PCR assays targeted at lytA, Spn9802, and recA as reference standard. The Vitek MS correctly identified 10/11 Streptococcus pneumoniae, 13/13 Streptococcus pseudopneumoniae, and 12/13 S. mitis/oralis. The Microflex correctly identified 9/11 S. pneumoniae, 0/13 S. pseudopneumoniae, and 13/13 S. mitis/oralis. MALDI-TOF is a powerful tool for species determination within the mitis group. Diagnostic accuracy varies depending on platform and database used.

MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hôpital Principal de Dakar, Senegal (West Africa)

Our team in Europe has developed the routine clinical laboratory identification of microorganisms by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). To evaluate the utility of MALDI-TOF MS in tropical Africa in collaboration with local teams, we installed an apparatus in the Hôpital Principal de Dakar (Senegal), performed routine identification of isolates, and confirmed or completed their identification in France. In the case of discordance or a lack of identification, molecular biology was performed. Overall, 153/191 (80.1%) and 174/191 (91.1%) isolates yielded an accurate and concordant identification for the species and genus, respectively, with the 2 different MALDI-TOF MSs in Dakar and Marseille. The 10 most common bacteria, representing 94.2% of all bacteria routinely identified in the laboratory in Dakar (Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus haemolyticus, Enterobacter cloacae, Enterococcus faecalis, and Staphylococcus epidermidis) were accurately identified with the MALDI-TOF MS in Dakar. The most frequent misidentification in Dakar was at the species level for Achromobacter xylosoxidans, which was inaccurately identified as Achromobacter denitrificans, and the bacteria absent from the database, such as Exiguobacterium aurientacum or Kytococcus schroeteri, could not be identified. A few difficulties were observed with MALDI-TOF MS for Bacillus sp. or oral streptococci. 16S rRNA sequencing identified a novel bacterium, “Necropsobacter massiliensis.” The robust identification of microorganisms by MALDI-TOF MS in Dakar and Marseille demonstrates that MALDI-TOF MS can be used as a first-line tool in clinical microbiology laboratories in tropical countries.

A Side by Side Comparison of Bruker Biotyper and VITEK MS: Utility of MALDI-TOF MS Technology for Microorganism Identification in a Public Health Reference Laboratory

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid, highly accurate, and cost-effective method for routine identification of a wide range of microorganisms. We carried out a side by side comparative evaluation of the performance of Bruker Biotyper versus VITEK MS for identification of a large and diverse collection of microorganisms. Most difficult and/or unusual microorganisms, as well as commonly encountered microorganisms were selected, including Gram-positive and negative bacteria, mycobacteria, actinomycetes, yeasts and filamentous fungi. Six hundred forty two strains representing 159 genera and 441 species from clinical specimens previously identified at the Laboratoire de santé publique du Québec (LSPQ) by reference methods were retrospectively chosen for the study. They included 254 Gram-positive bacteria, 167 Gram-negative bacteria, 109 mycobacteria and aerobic actinomycetes and 112 yeasts and moulds. MALDI-TOF MS analyses were performed on both systems according to the manufacturer’s instructions. Of the 642 strains tested, the name of the genus and / or species of 572 strains were referenced in the Bruker database while 406 were present in the VITEK MS IVD database. The Biotyper correctly identified 494 (86.4%) of the strains, while the VITEK MS correctly identified 362 (92.3%) of the strains (excluding 14 mycobacteria that were not tested). Of the 70 strains not present in the Bruker database at the species level, the Biotyper correctly identified 10 (14.3%) to the genus level and 2 (2.9%) to the complex/group level. For 52 (74.2%) strains, we obtained no identification, and an incorrect identification was given for 6 (8.6%) strains. Of the 178 strains not present in the VITEK MS IVD database at the species level (excluding 71 untested mycobacteria and actinomycetes), the VITEK MS correctly identified 12 (6.8%) of the strains each to the genus and to the complex/group level. For 97 (54.5%) strains, no identification was given and for 69 (38.7%) strains, an incorrect identification was obtained. Our study demonstrates that both systems gave a high level (above 85%) of correct identification for a wide range of microorganisms. However, VITEK MS gave more misidentification when the microorganism analysed was not present in the database, compared to Bruker Biotyper. This should be taken into account when this technology is used alone for microorganism identification in a public health laboratory, where isolates received are often difficult to identify and/or unusual microorganisms.

Rapid Characterization of Microalgae and Microalgae Mixtures Using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS)

Current molecular methods to characterize microalgae are time-intensive and expensive. Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) may represent a rapid and economical alternative approach. The objectives of this study were to determine whether MALDI-TOF MS can be used to: 1) differentiate microalgae at the species and strain levels and 2) characterize simple microalgal mixtures. A common protein extraction sample preparation method was used to facilitate rapid mass spectrometry-based analysis of 31 microalgae. Each yielded spectra containing between 6 and 56 peaks in the m/z 2,000 to 20,000 range. The taxonomic resolution of this approach appeared higher than that of 18S rDNA sequence analysis. For example, two strains of Scenedesmus acutus differed only by two 18S rDNA nucleotides, but yielded distinct MALDI-TOF mass spectra. Mixtures of two and three microalgae yielded relatively complex spectra that contained peaks associated with members of each mixture. Interestingly, though, mixture-specific peaks were observed at m/z 11,048 and 11,230. Our results suggest that MALDI-TOF MS affords rapid characterization of individual microalgae and simple microalgal mixtures.

Comprehensive MALDI-TOF biotyping of the non-redundant Harvard Pseudomonas aeruginosa PA14 transposon insertion mutant library

BACKGROUND

Pseudomonas aeruginosa is a gram-negative bacterium that is ubiquitously present in the aerobic biosphere. As an antibiotic-resistant facultative pathogen, it is a major cause of hospital-acquired infections. Its rapid and accurate identification is crucial in clinical and therapeutic environments.

METHODS

In a large-scale MALDI-TOF mass spectrometry-based screen of the Harvard transposon insertion mutant library of P. aeruginosa strain PA14, intact-cell proteome profile spectra of 5547 PA14 transposon mutants exhibiting a plethora of different phenotypes were acquired and analyzed.

RESULTS

Of all P. aeruginosa PA14 mutant profiles 99.7% were correctly identified as P. aeruginosa with the Biotyper software on the species level. On the strain level, 99.99% of the profiles were mapped to five different individual P. aeruginosa Biotyper database entries. A principal component analysis-based approach was used to determine the most important discriminatory mass features between these Biotyper groups. Although technical replicas were consistently categorized to specific Biotyper groups in 94.2% of the mutant profiles, biological replicas were not, indicating that the distinct proteotypes are affected by growth conditions.

CONCLUSIONS

The PA14 mutant profile collection presented here constitutes the largest coherent P. aeruginosa MALDI-TOF spectral dataset publicly available today. Transposon insertions in thousands of different P. aeruginosa genes did not affect species identification from MALDI-TOF mass spectra, clearly demonstrating the robustness of the approach. However, the assignment of the individual spectra to sub-groups proved to be non-consistent in biological replicas, indicating that the differentiation between biotyper groups in this nosocomial pathogen is unassured.