Mass spectrometry in research laboratories and clinical diagnostic: a new era in medical mycology

Otomycosis: a systematic review and meta-analysis of prevalence and causative agents in the era of molecular diagnostics

BACKGROUND

Molecular identification of fungal agents in otomycosis can provide a more accurate diagnosis and differentiation of species compared to conventional morphological methods. Previous reviews mostly relied on studies using conventional methods to explore the prevalence and distribution of otomycosis etiologies. We aim to estimate the prevalence and distribution of causative agents in otomycosis cases confirmed with molecular methods.

METHODS

We conducted a systematic search of PubMed, Scopus, Web of Science, and Google Scholar. We selected cross-sectional studies that reported causative agents of otomycosis and used molecular methods for identification of fungi. We appraised the quality of evidence using the JBI Checklist for Prevalence Studies. Clinical and mycological data were collected, and prevalence of otomycosis was estimated by meta-analysis.

RESULTS

Twenty studies reporting 1392 fungal isolates, consisting of 46 species from 11 distinct genera, were included in this review. The prevalence of otomycosis among clinically-suspected patients was 58.3% (95% CI: 41.4-73.5%). Aspergillus (75.8%, 95% CI: 70.3-80.6%) and Candida (15.3%, 95% CI: 8.7- 25.6%) were the most common etiologies. The most frequent Aspergillus species were A. niger (n = 352, 30.9%) and A. tubingensis (n = 270, 23.7%), and the most frequent Candida species were C. parapsilosis (n = 85, 39.7%) and C. albicans (n = 66, 30.8%). The quality of evidence was assessed to be poor in all included studies.

CONCLUSIONS

Otomycosis is caused by a diverse set of species, predominantly from Aspergillus and Candida genera. Molecular identification techniques provide a more accurate understanding of the distribution of species associated with otomycosis.

CLINICAL TRIAL NUMBER

Not applicable.

Performance of the VITEK® MS system for the identification of filamentous fungi in a microbiological laboratory in Chile

Filamentous fungi are an emergent cause of severe infections in immunocompromised patients. Timely and accurate identification is crucial to initiate appropriate therapy. Traditional identification methods are time-consuming, labor-intensive, and operator-dependent. Matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry is a rapid and easy-to-perform identification method. The effectiveness of a commercial MALDI-TOF MS platform to identify filamentous fungi in a clinical laboratory was evaluated. The study included 67 fungal isolates from 35 species/species complexes, which were identified and confirmed in mycology reference laboratories; 32 derived from clinical samples, 34 from strain collections and one was an ATCC strain. The study used the VITEK® MS system (v3.2.0 database), after sample extraction by VITEK® MS Mould Kit. Results were classified as "correct species", "correct species complex", "correct genus"and "no identification". VITEK® MS correctly identified 91.0% of isolates (58.2% to species, 29.9% to species complex, and 1.5% to genus level only). In 82%, the result matched the species/species complex identified by reference methods. No misidentifications were observed. The kit was rapid and easy to use. In conclusion, the VITEK® MS system showed a high capability to accurately identify filamentous fungi in a clinical laboratory.

Enhancing ICU Candida spp. surveillance: a cost-effective approach focused on Candida auris detection

Introduction

Candida auris is an emerging pathogen that represents a worldwide health problem due to its global expansion, multidrug resistance, and difficult laboratory identification. Among the risk factors for colonization/infection by C. auris, a stay in an intensive care unit (ICU) stands out. This prospective multicenter study aimed to monitor the trend of the local epidemiology of Candida spp. and unveil the prevalence of C. auris.

Methods

From 2020 to 2022, axillar/inguinal swabs were collected from adult patients at three points: upon admission (D1) and on the fifth (D5) and eighth (D8) days of their ICU stay. We employed culture-based screening methods combined with molecular techniques to identify Candida spp. down to the species level. Specific screening for Candida auris was conducted using a real-time PCR assay in combination with an improved selective culture medium, mannitol salt agar auris (MSAA). To validate the effectiveness of MSAA, a collection of reference C. auris strains representing the four major geographical clades was used.

Results

We enrolled 675 patients, and 355 Candida isolates were retrieved from the 988 swab samples collected. From those, 185/355 (52.1%) were identified as C. albicans and 170/355 (47.9%) as non-albicans Candida (NAC). MSAA medium showed a specificity of 94.8%, albeit C. auris was not detected in this cohort. The dynamics of Candida spp. colonization by ICU were significant at the three collection points. Upon admission, C. albicans was associated with the Beatriz Ângelo Hospital ICU (p=0.003) and C. tropicalis with the general Hospital Professor Doutor Fernando Fonseca (FFH) ICU (p=0.006). C. parapsilosis and C. lusitaniae were associated with FFH ICUs, with the general ICU at D5 (p=0.047) and surgical ICU at D8 (p=0.012). The dynamics of NAC colonization by ICU were significantly different at D1 (p=0.011), D5 (p=0.047), and D8 (p=0.012).

Conclusion

We developed and implemented a screening protocol for C. auris while uncovering the colonization patterns of Candida in the ICU. Our findings contribute to the optimization of overall patient management, ensuring that ICU protocols are resilient and adaptive to emerging fungal threats.

Mechanisms of gastrointestinal toxicity in neuromyelitis optica spectrum disorder patients treated with mycophenolate mofetil: insights from a mouse model and human study

Mycophenolate mofetil (MMF) is commonly utilized for the treatment of neuromyelitis optica spectrum disorders (NMOSD). However, a subset of patients experience significant gastrointestinal (GI) adverse effects following MMF administration. The present study aims to elucidate the underlying mechanisms of MMF-induced GI toxicity in NMOSD. Utilizing a vancomycin-treated mouse model, we compiled a comprehensive data set to investigate the microbiome and metabolome in the GI tract to elucidate the mechanisms of MMF GI toxicity. Furthermore, we enrolled 17 female NMOSD patients receiving MMF, who were stratified into non-diarrhea NMOSD and diarrhea NMOSD (DNM) groups, in addition to 12 healthy controls. The gut microbiota of stool samples was analyzed using 16S rRNA gene sequencing. Vancomycin administration prevented weight loss and tissue injury caused by MMF, affecting colon metabolomes and microbiomes. Bacterial β-glucuronidase from Bacteroidetes and Firmicutes was linked to intestinal tissue damage. The DNM group showed higher alpha diversity and increased levels of Firmicutes and Proteobacteria. The β-glucuronidase produced by Firmicutes may be important in causing gastrointestinal side effects from MMF in NMOSD treatment, providing useful information for future research on MMF.

IMPORTANCE

Neuromyelitis optica spectrum disorder (NMOSD) patients frequently endure severe consequences like paralysis and blindness. Mycophenolate mofetil (MMF) effectively addresses these issues, but its usage is hindered by gastrointestinal (GI) complications. Through uncovering the intricate interplay among MMF, gut microbiota, and metabolic pathways, this study identifies specific gut bacteria responsible for metabolizing MMF into a potentially harmful form, thus contributing to GI side effects. These findings not only deepen our comprehension of MMF toxicity but also propose potential strategies, such as inhibiting these bacteria, to mitigate these adverse effects. This insight holds broader implications for minimizing complications in NMOSD patients undergoing MMF therapy.

Insights into Candida Colonization in Intensive Care Unit Patients: A Prospective Multicenter Study

The skin mycobiota plays a significant role in infection risk, pathogen transmission, and personalized medicine approaches in intensive care settings. This prospective multicenter study aimed to enhance our understanding of intensive care units' (ICUs') Candida colonization dynamics, identify modifiable risk factors, and assess their impact on survival risk. Specimens were taken from 675, 203, and 110 patients at the admission (D1), 5th (D5), and 8th (D8) days of ICU stay, respectively. The patient's demographic and clinical data were collected. Candida isolates were identified by conventional culture-based microbiology combined with molecular approaches. Overall, colonization was 184/675 (27.3%), 87/203 (42.8%), and 58/110 (52.7%) on D1, D5, and D8, respectively. Candida colonization dynamics were significantly associated with ICU type (odds ratio (OR) = 2.03, 95% CI 1.22-3.39, p = 0.007), respiratory infection (OR = 1.74, 95% CI 1.17-2.58, p = 0.006), hemodialysis (OR = 2.19, 95% CI 1.17-4.10, p = 0.014), COVID-19 (OR = 0.37, 95% CI 0.14-0.99, p = 0.048), and with a poor 3-month outcome (p = 0.008). Skin Candida spp. colonization can be an early warning tool to generate valuable insights into the epidemiology, risk factors, and survival rates of critically ill patients, and should be considered for epidemiological surveillance.