Evaluation of Autof MS 1000 and Vitek MS MALDI-TOF MS System in Identification of Closely-Related Yeasts Causing Invasive Fungal Diseases

MALDI-TOF Mass Spectrometry Characterization of Culturable Microbiota Associated with the Skin of Amphibians from the Southern Andes Mountains of Ecuador

Ecuador is recognized for having a high diversity of anuran species, which are distributed mainly south of the Andes mountains. However, due to their geographic location and accessibility, there are few studies related to the culturable microbiota of these amphibians in this region. The objective of this study was to explore the bacterial and fungal biodiversity present on the skin of wild anuran species in the southern Andes of Ecuador and to observe whether geographical barriers in the region could increase the variability of the culturable microbiota through MALDI-TOF mass spectrometry. This analysis revealed the presence of 29 bacterial taxa and 9 fungal taxa, consisting mainly of: Pseudomonas chlororaphis (28%), Acinetobacter iwoffii (14%), Pseudomonas fluorescens (14%), and Hortaea werneckii (26.4%), Fusarium solani (20.5%), Syncephalastrum spp. (20.5%), respectively. Diversity varied across the five sampling locations, with geographic location proving to be a significant driver of diversity. Some of the most abundant bacterial and fungal genera have important associations with skin diseases in wildlife and humans. This work represents a glimpse into the complex biodiversity of bacteria and fungi that inhabit the skin substrate, and further studies will be needed to better understand bacterial and fungal biodiversity with potential implications for establishing conservation strategies, along with the development of necessary animal protection measures.

Diagnosing invasive fungal infections in the laboratory today: It's all good news?

Despite the advances in medical science, invasive fungal infections (IFI) remain a diagnostic challenge. The increasing prevalence of IFI, driven by immunosuppressive therapies, advances in intensive care and emerging pathogens, underscores the need for early and accurate diagnosis. This review evaluates current laboratory methods for the diagnosis of IFI, highlighting their strengths and limitations. Conventional techniques, including fungal culture, direct microscopy, and histopathology, remain the gold standard for the diagnosis of proven IFIs. These methods allow pathogen isolation, species identification and antifungal susceptibility testing. However, these techniques have limitations in terms of sensitivity and turnaround times. Although microscopy is a rapid technique, its sensitivity and species discrimination profile are limited. Modern serological assays, such as β-d-glucan and galactomannan detection, have improved the diagnostic accuracy of probable IFI cases. Integration of these assays with clinical and radiological findings, enables earlier intervention, although this is accompanied by an increased risk of false positives and necessitates careful clinical correlation. Molecular diagnostics, particularly polymerase chain reaction (PCR), allow rapid, species-specific identification directly from clinical samples. The advent of MALDI-TOF mass spectrometry has further improved diagnostic efficiency, particularly for yeast identification, although challenges remain for filamentous fungi. Innovative techniques, such as metagenomic sequencing, lateral-flow assays, and loop-mediated isothermal amplification, offer the potential for rapid and precise detection, even in resource-limited settings. The combination of conventional and innovative methods provides a comprehensive diagnostic framework. The continuous refinement of these tools, in conjunction with multidisciplinary collaboration, is imperative to improve the early diagnostic and targeted treatment of patients with IFI.

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

OBJECTIVES

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Evaluation of Autof MS2600 and MBT Smart MALDI-TOF MS Systems for Routine Identification of Clinical Bacteria and Yeasts

The identification of microorganisms at the species level has always constituted a diagnostic challenge for clinical microbiology laboratories. The aim of the present study has been the evaluation in a real-time assay of the performance of Autobio in comparison with the Bruker mass spectrometry system for the identification of bacteria and yeasts. A total of 535 bacteria and yeast were tested in parallel with the two systems by direct smear or fast formic acid extraction for bacteria and yeasts, respectively. Discordant results were verified by 16S, ITS rRNA or specific gene sequencing. Beyond giving comparable results for bacteria with respect to the MBT smart system, Autof MS2600 mass spectrometer provided excellent accuracy for the identification of yeast species of clinical interest.

Systematic investigation of the emerging pathogen of Tsukamurella species in a Chinese tertiary teaching hospital

Tsukamurella species have been clinically regarded as rare but emerging opportunistic pathogens causing various infections in humans. Tsukamurella pneumonia has often been misdiagnosed as pulmonary tuberculosis due to its clinical presentation resembling tuberculosis-like syndromes. Tsukamurella species have also been confused in the laboratory with other phylogenetic bacteria, such as Gordonia. This study aimed to investigate the clinical, microbiological, and molecular characteristics; species distribution; and antimicrobial susceptibility of Tsukamurella species. Immunodeficiency and chronic pulmonary disease appeared to be risk factors for Tsukamurella pneumonia, and the presence of bronchiectasis and pulmonary nodules on imaging was highly correlated with this infection. The study confirmed that groEL (heat shock protein 60) and secA (the secretion ATPase) genes are reliable for identifying Tsukamurella species. Additionally, the ssrA (stable small RNA) gene showed promise as a tool for discriminating between different Tsukamurella species with the shortest sequence length. In terms of antimicrobial susceptibility, quinolones, trimethoprim/sulfamethoxazole, amikacin, minocycline, linezolid, and tigecycline demonstrated potent in vitro activity against Tsukamurella isolates in our study. The study also proposed a resistance mechanism involving a substitution (S91R) within the quinolone-resistance-determining region of the gyrA gene, which confers resistance to levofloxacin and ciprofloxacin. Furthermore, we found that disk diffusion testing is not suitable for testing the susceptibilities of Tsukamurella isolates to ciprofloxacin, imipenem, and minocycline. In conclusion, our systematic investigation may contribute to a better understanding of this rare pathogen. Tsukamurella species are rare but emerging human pathogens that share remarkable similarities with other mycolic acid-containing genera of the order Actinomycetales, especially Mycobacterium tuberculosis. Consequently, misdiagnosis and therapeutic failures can occur in clinical settings. Despite the significance of accurate identification, antimicrobial susceptibility, and understanding the resistance mechanism of this important genus, our knowledge in these areas remains fragmentary and incomplete. In this study, we aimed to address these gaps by investigating promising identification methods, the antimicrobial susceptibility patterns, and a novel quinolone resistance mechanism in Tsukamurella species, utilizing a collection of clinical isolates. The findings of our study will contribute to improve diagnosis and successful management of infections caused by Tsukamurella species, as well as establishing well-defined performance and interpretive criteria for antimicrobial susceptibility testing.

Decreased echinocandin susceptibility in Candida parapsilosis causing candidemia and emergence of a pan-echinocandin resistant case in China

Candida parapsilosis is becoming a predominant non-albicans cause of invasive candidiasis (IC). Echinocandins are the preferred choice for IC treatment and prophylaxis. Resistance to echinocandins in C. parapsilosis has emerged in several countries, but little is known about the susceptibility profile in China or about mechanisms of resistance. Here, we investigated the echinocandin susceptibilities of 2523 C. parapsilosis isolates collected from China and further explored the resistance mechanism among echinocandin-resistant isolates. Anidulafungin exhibited the highest MICs (MIC50/90, 1 and 2 µg/mL; GM, 0.948 µg/mL), while caspofungin showed better activity (0.5 and 1 µg/mL; 0.498 µg/mL). Significantly higher echinocandin MICs were observed among blood-derived isolates compared to others, especially for caspofungin (GM, 1.348 µg/mL vs 0.478 µg/mL). Isolates from ICU and surgical wards also showed higher MICs. Twenty isolates showed intermediate phenotypes for at least one echinocandin. One was resistant to all three echinocandins, fluconazole and voriconazole, which caused breakthrough IC during long-term exposure to micafungin. WGS revealed this isolate carried a mutation S656P in hotspot1 region of Fks1. Bioinformatics analyses suggested that this mutation might lead to an altered protein conformation. CRISPR Cas9-mediated introduction of this mutation into a susceptible reference C. parapsilosis strain increased MICs of all echinocandins 64-fold, with similar results found in the subspecies, C. orthopsilosis and C. metapsilosis. This is the first report of a multi-azole resistant and pan-echinocandin resistant C. parapsilosis isolate, and the identification of a FKS1S656P conferring pan-echinocandin resistance. Our study underscores the necessity of rigorous management of antifungal use and of monitoring for antifungal susceptibility.

Clinical impact of the combination of rapid species identification and antifungal stewardship intervention in adults with candidemia

BACKGROUND

Candidemia is associated with a high mortality rate. This study aimed to evaluate the clinical impact of a diagnostic intervention and antifungal stewardship in adults with candidemia, including effectiveness in facilitating appropriate antifungals and improving patient outcomes.

METHODS

A pre-post quasi-experimental study was conducted to analyze the impact of the integrated workflow of rapid species identification and antifungal stewardship intervention provided by infectious disease specialists for adults with candidemia at a medical center in southern Taiwan from March 1st, 2014 to February 29th, 2016. The primary endpoint was 30-day crude mortality, and secondary outcomes included the time to species identification, time to initial antifungal modification, and length of hospital stay.

RESULTS

Total 303 patients with candidemia were included, including 152 adults in the pre-intervention period (Mar. 1st, 2014-Feb. 28th, 2015; control group) and 151 in the intervention period (Mar. 1st, 2015-Feb. 29th, 2016; case group). Demographic and clinical characteristics of patients in two groups were similar. The case group had a shorter time to species identification (72 vs. 96 h, P < 0.001) and earlier receipt of antifungals (47 vs. 59 h, P < 0.001) than the control group. Of note, the 30-day mortality rate (27.2% vs. 39.5%, P = 0.028) was lower and the hospital stay (43.5 vs. 46.0 days, P = 0.006) was shorter in the case group.

CONCLUSION

Rapid diagnostic workflow and antifungal stewardship provided by infectious disease specialists can promote early initiation of antifungal therapy and improve outcome for adults with candidemia.

“Omic” Approaches to Bacteria and Antibiotic Resistance Identification

The quick and accurate identification of microorganisms and the study of resistance to antibiotics is crucial in the economic and industrial fields along with medicine. One of the fastest-growing identification methods is the spectrometric approach consisting in the matrix-assisted laser ionization/desorption using a time-of-flight analyzer (MALDI-TOF MS), which has many advantages over conventional methods for the determination of microorganisms presented. Thanks to the use of a multiomic approach in the MALDI-TOF MS analysis, it is possible to obtain a broad spectrum of data allowing the identification of microorganisms, understanding their interactions and the analysis of antibiotic resistance mechanisms. In addition, the literature data indicate the possibility of a significant reduction in the time of the sample preparation and analysis time, which will enable a faster initiation of the treatment of patients. However, it is still necessary to improve the process of identifying and supplementing the existing databases along with creating new ones. This review summarizes the use of “-omics” approaches in the MALDI TOF MS analysis, including in bacterial identification and antibiotic resistance mechanisms analysis.

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

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

Fungal infections diagnosis - Past, present and future

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

Microbial Identification in the Clinical Microbiology Laboratory Using MALDI-TOF-MS

MALDI-TOF mass spectrometry has been applied with huge success to the identification of cultured microorganisms in clinical microbiology laboratories where it has become the reference method because it is simple, fast, and highly reproducible. We describe the different procedures used in the routine for pathogen identification using the Bruker MALDI Biotyper^® system.

So Many Diagnostic Tests, So Little Time: Review and Preview of Candida auris Testing in Clinical and Public Health Laboratories

The recognition of a new yeast, Candida auris, in 2009 in East Asia, and its rapid global spread, was a reminder of the threats posed by multidrug-resistant fungal pathogens. C. auris had likely remained unrecognized for a long time as accurate tests were not available. The laboratory community responded to the C. auris challenge by publishing 35 new or revised diagnostic methods between 2014 and early 2021. The commercial sector also modified existing diagnostic devices. These C. auris diagnostic tests run the gamut from traditional culture-based differential and selective media, biochemical assimilations, and rapid protein profiles, as well as culture-independent DNA-based diagnostics. We provide an overview of these developments, especially the tests with validation data that were subsequently adopted for common use. We share a workflow developed in our laboratory to process over 37,000 C. auris surveillance samples and 5,000 C. auris isolates from the outbreak in the New York metropolitan area. Our preview covers new devices and diagnostic approaches on the horizon based on microfluidics, optics, and nanotechnology. Frontline laboratories need rapid, cheap, stable, and easy-to-implement tests to improve C. auris diagnosis, surveillance, patient isolation, admission screening, and environmental control. Among the urgent needs is a lateral flow assay or similar device for presumptive C. auris identification. All laboratories will benefit from devices that allow rapid antifungal susceptibility testing, including detection of mutations conferring drug resistance. Hopefully, multiplex test panels are on the horizon for synergy of C. auris testing with ongoing surveillance of other healthcare-associated infections. C. auris genome analysis has a proven role for outbreak investigations, and diagnostic laboratories need quick access to regional and national genome analysis networks.

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

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

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

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