Easy analysis of bacterial whole-genome sequencing data for clinical microbiologists using open-source Galaxy platform: Characterization of ESBL-producing Enterobacterales from bloodstream infections.

OBJECTIVES: Clinical microbiologists require easy-to-use open access tools with graphical interfaces to perform bacterial whole-genome sequencing (WGS) in routine practice. This study aimed to build a bioinformatics pipeline on the open-source Galaxy platform, facilitating comprehensive and reproducible analysis of bacterial WGS data in a few steps. We then used it to characterize our local epidemiology of ESBL-producing Enterobacterales isolated from patients with bacteremia. METHODS: We built a bioinformatics pipeline consisting of the following sequential tools: Fastp (input data trimming); FastQC (read quality control); SPAdes (genome assembly); Quast (quality control of genome assembly); Prokka (gene annotation); Staramr (ResFinder database) and ABRicate (CARD database) for antimicrobial resistance (AMR) gene screening and molecular strain typing. Paired-end short read WGS data from all ESBL-producing Enterobacterales strains isolated from patients with bacteremia over one year were analysed. RESULTS: The Galaxy platform does not require command line tools. The bioinformatics pipeline was constructed within one hour. It only required uploading fastq files and facilitated systematization of de novo assembly of genomes, MLST typing, and AMR gene screening in one step. Among the 66 ESBL-producing strains analysed, the two most frequent ESBL genes were blaCTX-M-15 (62.1%) and blaCTX-M-27 (13.6%). CONCLUSIONS: The open-access Galaxy platform provides a graphical interface and easy-to-use tools suitable for routine use in clinical microbiology laboratories without bioinformatics specialists. We believe that this platform will facilitate fast and low-cost analysis of bacterial WGS data, especially in resource-limited settings.

Two cases of Francisella tularensis subspecies holartica prosthetic valve endocarditis, and review of the literature.

Francisella tularensis endocarditis is rare and difficult to diagnose, and only a few cases have been described. We report two new cases of endocarditis due to F. tularensis subsp. holarctica, with a favorable evolution after appropriate antibiotic therapy and valve replacement surgery, and review the 5 other cases reported in the literature. This rare infection may be suspected based on the local epidemiology and the patient's exposure factors. A regimen of ciprofloxacin and gentamicin, combined with surgical valve replacement if necessary, appears to be effective in treating F. tularensis endocarditis.

Tularemia in Pediatric Patients: A Case Series and Review of the Literature.

BACKGROUND: Unfamiliar to pediatricians, tularemia can lead to delays in diagnosis and hinder appropriate treatment, as its clinical presentation often shares similarities with other more prevalent causes of lymphadenopathy diseases in children. We conducted a comprehensive literature review to offer contemporary insights into the clinical manifestations and treatment strategies for tularemia infection in children. METHODS: Three cases of glandular tularemia were diagnosed in the Pediatric Robert Debré Hospital (Paris) between October 2020 and February 2022. In addition, we conducted a literature search using PubMed in December 2023 of cases of tularemia in children published in English. RESULTS: The 94 cases of the literature review highlight the large age range (from 6 weeks to 17 years) and multiple sources of infection, including diverse zoonotic transmission (86.7%) and contact with contaminated water (13.3%). Fever was a consistent symptom. Ulceroglandular (46.7%), glandular (17%) and oropharyngeal forms (18.1%) predominated. The most frequently used diagnostic method was serology (60.6%). The median time to diagnosis for tularemia was 23.5 days. Hospitalization was required in 63.2% of cases, with a median duration of 4 days. Targeted treatment was based on aminoglycosides (37.6%), fluoroquinolones (30.6%) or tetracyclines (12.9%), in accordance with WHO recommendations, with a mainly favorable outcome, although several cases of meningitis were observed. CONCLUSION: Pediatricians should be aware of the etiology of this febrile lymphadenopathy, notably when experiencing beta-lactam treatment failure, even in young infants, which could help reduce the extra costs associated with inappropriate antibiotic use and hospitalization.

Staphylococcus aureus screening and preoperative decolonisation with Mupirocin and Chlorhexidine to reduce the risk of surgical site infections in orthopaedic surgery: a pre-post study.

BACKGROUND: Nasal carriage of Staphylococcus aureus is a risk factor for surgical site infections (SSI) in orthopaedic surgery. The efficacy of decolonisation for S. aureus on reducing the risk of SSI is uncertain in this speciality. The objective was to evaluate the impact of a nasal screening strategy of S. aureus and targeted decolonisation on the risk of S. aureus SSI. METHODS: A retrospective pre-post and here-elsewhere study was conducted between January 2014 and June 2020 in 2 adult orthopaedic surgical sites (North and South) of a French university hospital. Decolonisation with Mupirocin and Chlorhexidine was conducted in S. aureus carriers starting February 2017 in the South site (intervention group). Scheduled surgical procedures for hip, knee arthroplasties, and osteosyntheses were included and monitored for one year. The rates of S. aureus SSI in the intervention group were compared to a historical control group (South site) and a North control group. The risk factors for S. aureus SSI were analysed by logistic regression. RESULTS: A total of 5,348 surgical procedures was included, 100 SSI of which 30 monomicrobial S. aureus SSI were identified. The preoperative screening result was available for 60% (1,382/2,305) of the intervention group patients. Among these screenings, 25.3% (349/1,382) were positive for S. aureus and the efficacy of the decolonisation was 91.6% (98/107). The rate of S. aureus SSI in the intervention group (0.3%, 7/2,305) was not significantly different from the historical control group (0.5%, 9/1926) but differed significantly from the North control group (1.3%, 14/1,117). After adjustment, the risk factors of S. aureus SSI occurrence were the body mass index (ORaper unit, 1.05; 95%CI, 1.0-1.1), the Charlson comorbidity index (ORaper point, 1.34; 95%CI, 1.0-1.8) and operative time (ORaper minute, 1.01; 95%CI, 1.00-1.02). Having benefited from S. aureus screening/decolonisation was a protective factor (ORa, 0.24; 95%CI, 0.08-0.73). CONCLUSIONS: Despite the low number of SSI, nasal screening and targeted decolonisation of S. aureus were associated with a reduction in S. aureus SSI.

Clinical impact and cost-consequence analysis of ePlex® blood culture identification panels for the rapid diagnosis of bloodstream infections: a single-center randomized controlled trial.

To assess clinical impact and perform cost-consequence analysis of the broadest multiplex PCR panels available for the rapid diagnosis of bloodstream infections (BSI). Single-center, randomized controlled trial conducted from June 2019 to February 2021 at a French University hospital with an institutional antimicrobial stewardship program. Primary endpoint was the percentage of patients with optimized antimicrobial treatment 12 h after transmission of positivity and Gram stain results from the first positive BC. This percentage was significantly higher in the multiplex PCR (mPCR) group (90/105 = 85.7% %, CI95% [77.5 ; 91.8] vs. 68/107 = 63.6%, CI95% [53.7 ; 72.6]; p < 10- 3) at interim analysis, resulting in the early termination of the study after the inclusion of 309 patients. For patients not optimized at baseline, the median time to obtain an optimized therapy was much shorter in the mPCR group than in the control group (6.9 h, IQR [2.9; 17.8] vs. 26.4 h, IQR [3.4; 47.5]; p = 0.001). Early optimization of antibiotic therapy resulted in a non-statistically significant decrease in mortality from 12.4 to 8.8% (p = 0.306), with a trend towards a shorter median length of stay (18 vs. 20 days; p = 0.064) and a non-significant reduction in the average cost per patient of €3,065 (p = 0.15). mPCR identified all the bacteria present in 88% of the samples. Despite its higher laboratory cost, the use of multiplex PCR for BSI diagnosis leads to early-optimised therapy, seems cost-effective and could reduce mortality and length of stay. Their impact could probably be improved if implemented 24/7.

Early picc-line infections in non-neutropenic patients are mainly due to E. coli suggesting that third-generation cephalosporin may be used as a first-line antibiotic therapy.

PURPOSE: To describe the rate of peripherally inserted central catheter (PICC) -associated bloodstream infections, and the pathogens involved. METHODS: We prospectively analyzed data collected from all adult patients with a PICC insertion in a hematology unit in a tertiary care center between January 1, 2017 and June 30, 2020. RESULTS: A total of 370 PICCs were inserted in 275 patients with hematological malignancies: 54 (15 %) confirmed cases of central-line associated bloodstream infection (CLABSI) were identified. Enterobacteria were the most frequent bacteria identified, involved in 35 % of CLABSIs. Group 1 enterobacteria bacteremia occurred a much shorter time after insertion (median time to CLABSI 16 days) than group 2 or group 3 enterobacteria (median time to CLABSI 64 days, p-value = 0.049). CONCLUSION: Among Gram-negative bacilli CLABSI among non-neutropenic patients, E. coli identification was the most frequent and occurred earlier after insertion, suggesting that third-generation cephalosporin may be used as a first-line antibiotic therapy for enterobacteria bacteremia among non-neutropenic patients.

Rapid and automated screening of carbapenemase- and ESBL-producing Gram-negative bacteria from rectal swabs using chromogenic agar media and the ScanStation device.

The ScanSation 100 device (Interscience, France) is an incubator allowing real-time detection of bacterial colony growth by frequently imaging agar plates over time, counting CFU, and detecting colony color. This study evaluated its performance for the early detection of carbapenemase-producing bacteria (CPB) and extended-spectrum ß-Lactamase-producing bacteria (ESBL-PB) from rectal swabs inoculated on CHROMagar mSuperCARBA and ESBL media, respectively. Rectal screening ESwabs collected from patients admitted to Grenoble University Hospital between January and June 2021 were analyzed. After inoculation, chromogenic media were incubated for 24 h in the automaton, with image acquisition every 30 min. ScanStation results were compared to visual observations of the plates after 24 h of incubation. In total, 501 rectal swabs were tested. ScanStation showed 100% positive percent agreement (PPA) for the detection of CPB and ESBL-PB, whereas the PPA of color categorization ranged between 45% and 100%. Negative percent agreement (NPA) ranged between 70% and 98%. Negative predictive values (NPVs) were 100% for both bacterial groups, whereas positive predictive values (PPVs) were 70.3% for CPB and 81.0% for ESBL-PB. Importantly, real-time screening allowed detection of the first suspected colony within 10-14 h of growth, on average, whereas visual observation is usually only performed once a day after 18-24 h of incubation. Our study demonstrates the potential use of early images to accelerate the detection of CPB and ESBL-PB and implement effective and timely infection control measures. IMPORTANCE The ScanStation 100 device is an incubator able to follow the real-time growth of bacterial colonies on agar plates through digital imaging, allowing users to sort plates according to the presence or absence of colonies, and to distinguish their color using four numeric color filters. Real-time screening shows that first colony detection is possible much earlier (after 10-14 h of growth, on average), whereas visual observation is usually performed only once a day after 18-24 h of incubation. The ScanStation device, combined with chromogenic agar media, is an efficient automated screening method to accelerate the detection of Gram-negative multidrug-resistant bacteria in laboratories that do not have access to larger laboratory automation systems. Our study shows that setting the image acquisition to one or two early images may allow for the detection of positive samples that were inoculated in the morning, by the end of the working day.

Evaluation of the QIAstat-Dx Meningitis/Encephalitis Panel, a multiplex PCR platform for the detection of community-acquired meningoencephalitis.

Rapid identification of the causative pathogens of central nervous system infections is essential for providing appropriate management and improving patient outcomes. The performance of QIAstat-Dx Meningitis/Encephalitis (ME) Panel-a multiplex PCR testing platform-in detecting pathogens implicated in meningitis and/or encephalitis was evaluated using BioFire FilmArray ME Panel as a comparator method. This multicenter study analyzed 585 retrospective residual cerebrospinal fluid specimens and 367 contrived specimens. The QIAstat-Dx ME Panel showed positive percent agreement (PPA) values of 100% for Neisseria meningitidis, Streptococcus agalactiae, Escherichia coli K1, Listeria monocytogenes, and Cryptococcus gattii/neoformans on clinical samples compared to the BioFire FilmArray ME Panel. The PPA values observed for Haemophilus influenzae and Streptococcus pneumoniae were 80% and 88.24%, respectively. Negative percent agreement (NPA) values were >99.0% for each of the six bacterial targets and one fungal target tested with clinical samples. One viral target, herpes simplex virus 1, exhibited a PPA value of 100.0%, while the remaining viral targets-human parechovirus, herpes simplex virus 2, human herpes virus 6, and varicella zoster virus-were >90.0%, with the exception of enterovirus, which had a PPA value of 77.8%. The QIAstat-Dx ME Panel detected five true-positive and four true-negative cases compared to BioFire FilmArray ME Panel. The NPA values for all viral pathogens were >99.0%. Overall, the QIAstat-Dx ME Panel showed comparable performance to the BioFire FilmArray ME Panel as a rapid diagnostic tool for community-acquired meningitis and encephalitis.

Carbapenem prescriptions: Compliance with guidelines in a pediatric hospital.

BACKGROUND: This study aimed to describe the use of carbapenems in a pediatric tertiary center and to assess its compliance with national and local guidelines. METHODS: This retrospective study focused on children who received at least one dose of carbapenems in a tertiary university hospital over a 1-year period (2019). The appropriateness of each prescription was assessed. RESULTS: In total, 96 prescriptions were collected for 75 patients (median age 3 years [interquartile range, IQR: 0-9]). Most prescriptions were empirical (n = 77, 80%) and mainly concerned nosocomial infections (n = 69, 72%). At least one risk factor for extended-spectrum beta-lactamases was found in 48% (n = 46) of cases. The median duration of treatment with carbapenems was 5 days and it was over 7 days in 38% (n = 36) of cases. The use of carbapenems was considered appropriate in 95% (18/19) and 70% (54/77) of cases when therapy was guided by culture results or was empirical, respectively. De-escalation of carbapenem treatment within 72 h occurred in 31% (n = 30) of cases. CONCLUSION: The use of carbapenems can be optimized in the pediatric population, even when the initial prescription for a carbapenem is considered appropriate.

Case Studies and Literature Review of Francisella tularensis-Related Prosthetic Joint Infection.

Tularemia is a zoonotic infection caused by Francisella tularensis. Its most typical manifestations in humans are ulceroglandular and glandular; infections in prosthetic joints are rare. We report 3 cases of F. tularensis subspecies holarctica-related prosthetic joint infection that occurred in France during 2016-2019. We also reviewed relevant literature and found only 5 other cases of Francisella-related prosthetic joint infections worldwide, which we summarized. Among those 8 patients, clinical symptoms appeared 7 days to 19 years after the joint placement and were nonspecific to tularemia. Although positive cultures are typically obtained in only 10% of tularemia cases, strains grew in all 8 of the patients. F. tularensis was initially identified in 2 patients by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; molecular methods were used for 6 patients. Surgical treatment in conjunction with long-term antimicrobial treatment resulted in favorable outcomes; no relapses were seen after 6 months of follow-up.

Tularemia treatment: experimental and clinical data.

Tularemia is a zoonosis caused by the Gram negative, facultative intracellular bacterium Francisella tularensis. This disease has multiple clinical presentations according to the route of infection, the virulence of the infecting bacterial strain, and the underlying medical condition of infected persons. Systemic infections (e.g., pneumonic and typhoidal form) and complications are rare but may be life threatening. Most people suffer from local infection (e.g., skin ulcer, conjunctivitis, or pharyngitis) with regional lymphadenopathy, which evolve to suppuration in about 30% of patients and a chronic course of infection. Current treatment recommendations have been established to manage acute infections in the context of a biological threat and do not consider the great variability of clinical situations. This review summarizes literature data on antibiotic efficacy against F. tularensis in vitro, in animal models, and in humans. Empirical treatment with beta-lactams, most macrolides, or anti-tuberculosis agents is usually ineffective. The aminoglycosides gentamicin and streptomycin remain the gold standard for severe infections, and the fluoroquinolones and doxycycline for infections of mild severity, although current data indicate the former are usually more effective. However, the antibiotic treatments reported in the literature are highly variable in their composition and duration depending on the clinical manifestations, the age and health status of the patient, the presence of complications, and the evolution of the disease. Many patients received several antibiotics in combination or successively. Whatever the antibiotic treatment administered, variable but high rates of treatment failures and relapses are still observed, especially in patients treated more then 2-3 weeks after disease onset. In these patients, surgical treatment is often necessary for cure, including drainage or removal of suppurative lymph nodes or other infectious foci. It is currently difficult to establish therapeutic recommendations, particularly due to lack of comparative randomized studies. However, we have attempted to summarize current knowledge through proposals for improving tularemia treatment which will have to be discussed by a group of experts. A major factor in improving the prognosis of patients with tularemia is the early administration of appropriate treatment, which requires better medical knowledge and diagnostic strategy of this disease.

Implementation of a Vancomycin Dose-Optimization Protocol in Neonates: Impact on Vancomycin Exposure, Biological Parameters, and Clinical Outcomes.

Vancomycin dosing used in neonates results frequently in insufficient concentrations. A vancomycin dose-optimization protocol consisting of an individualization of loading and maintenance doses (administered during continuous infusion) through a previously validated pharmacokinetic model was implemented in our center. This monocenter retrospective study aimed to compare vancomycin average concentration (Cavg) in the therapeutic range (15 to 25 mg/L) and biological and clinical parameters before and after implementation of this protocol. A total of 60 and 59 courses of vancomycin treatment in 45 and 49 patients were analyzed in groups before and after implementation, respectively. Initial vancomycin Cavg were more frequently in the therapeutic range in the group after implementation (74.6% versus 28.3%, P < 0.001), with 1.6-fold higher Cavg (20.3 [17.0-22.2] mg/L versus 12.9 [11.3-17.0] mg/L, P < 0.001). Considering all Cavg during longitudinal therapeutic drug monitoring (TDM), the frequency of therapeutic Cavg was higher in the group after implementation (74.8% [n = 103] versus 31% [n = 116], P < 0.001). The dose optimization protocol was also associated with a reduced time to obtain a negative blood culture (P < 0.001) and fewer antibiotic switches (P = 0.025), without increasing the frequency of nephrotoxicity. Clinical outcomes also appeared to be improved, with less periventricular leukomalacia (P = 0.021), trended toward less respiratory instability (P = 0.15) and a shorter duration of vasoactive drug use (P = 0.18) for neonates receiving personalized doses of vancomycin. This personalized vancomycin dose protocol improves vancomycin exposure in neonates, with good safety, and suggests an improvement in biological and clinical outcomes.

Dalbavancin in clinical practice: a particular place for the elderly?

We investigate dalbavancin efficiency and tolerance among elderly in Grenoble-Alpes 32 university hospital. Among the 65 patients who received dalbavancin, 51% (33) were considered as old. Patients presented mainly bones and joint infections (52%), surgical site infection 34 (31%), and infective endocarditis (IE) (8%). Clinical cure was confirmed for 79% of old 35 patients at 1, 3, and 6 months. Six adverse events (9%) were reported after 36 dalbavancin's administration, but each time in combination with other antibiotics. 37 Dalbavancin had a significant effectiveness and safety profile and represents a real 38 therapeutic option in the management of deep and complex infections of elderly patients.

Epidemiology and outcome of occult bacteremia in patients discharged from emergency departments or ambulatory units: one-year study.

Microbiological diagnosis of bloodstream infection (BSI) is made several hours after blood culture sampling. This delay could be critical in ambulatory clinics, emergency departments, and hospital day care units, as the patient may be discharged prior to blood culture positivity. Our aim was to evaluate the clinical outcome (including the number of readmissions) of patients diagnosed with BSI after discharge. We prospectively included all adult patients with positive blood culture for BSI that was confirmed after discharge from our center (Grenoble-Alpes University Hospital) in 2016. Patients were contacted about their blood culture results, and their clinical status was controlled via an external consultation or their family physician, with hospital readmission if necessary. Clinical outcome, accuracy of initial diagnosis, microbiological epidemiology, and antibiotic prescription were assessed. In 2016, 1433 episodes of positive blood culture were detected in our hospital, with 50 (3.5%) occurring after patient discharge. Clinically relevant bacteria were determined in 32/50 cases (64%), while other positive blood culture results were considered to be contaminants. Clinical reevaluation was performed in 45 patients (90%). The diagnosis was changed during the clinical reassessment of 24/49 patients (49%). Antibiotics were prescribed prior to discharge for 24/50 patients (48%), modified during follow-up for 15/45 (33%), and initiated for 13/45 (29%) at the reevaluation. Overall, 24/45 (53%) patients were readmitted to hospital units after reevaluation. The clinical follow-up of patients with positive blood culture after discharge led to diagnostic changes and hospital readmission in around half of patients.

Ulceroglandular Infection and Bacteremia Caused by Francisella salimarina in Immunocompromised Patient, France.

Although Francisella tularensis is a well-known, highly virulent bacterium that causes tularemia in humans, other Francisella species have been associated with sporadic human infections. We describe a human cutaneous infection with bacteremia caused by F. salimarina, a Francisella species recently identified from seawater and fishes, in an immunocompromised patient in France.

The Biosynthetic Pathway of Ubiquinone Contributes to Pathogenicity of Francisella novicida.

Francisella tularensis is the causative agent of tularemia. Because of its extreme infectivity and high mortality rate, this pathogen was classified as a biothreat agent. Francisella spp. are strict aerobes, and ubiquinone (UQ) has been previously identified in these bacteria. While the UQ biosynthetic pathways were extensively studied in Escherichia coli, allowing the identification of 15 Ubi proteins to date, little is known about Francisella spp. In this study, and using Francisella novicida as a surrogate organism, we first identified ubiquinone 8 (UQ8) as the major quinone found in the membranes of this bacterium. Next, we characterized the UQ biosynthetic pathway in F. novicida using a combination of bioinformatics, genetics, and biochemical approaches. Our analysis disclosed the presence in Francisella of 10 putative Ubi proteins, and we confirmed 8 of them by heterologous complementation in E. coli. The UQ biosynthetic pathways from F. novicida and E. coli share similar patterns. However, differences were highlighted: the decarboxylase remains unidentified in Francisella spp., and homologs of the Ubi proteins involved in the O2-independent UQ pathway are not present. This is in agreement with the strictly aerobic niche of this bacterium. Next, via two approaches, i.e., the use of an inhibitor (3-amino-4-hydroxybenzoic acid) and a transposon mutant, both of which strongly impair the synthesis of UQ, we demonstrated that UQ is essential for the growth of F. novicida in respiratory medium and contributes to its pathogenicity in Galleria mellonella used as an alternative animal model. IMPORTANCE Francisella tularensis is the causative bacterium of tularemia and is classified as a biothreat agent. Using multidisciplinary approaches, we investigated the ubiquinone (UQ) biosynthetic pathway that operates in F. novicida used as a surrogate. We show that UQ8 is the major quinone identified in the membranes of Francisella novicida. We identified a new competitive inhibitor that strongly decreased the biosynthesis of UQ. Our demonstration of the crucial roles of UQ for the respiratory metabolism of F. novicida and for the involvement in its pathogenicity in the Galleria mellonella model should stimulate the search for selective inhibitors of bacterial UQ biosynthesis.

Presence of Francisella tularensis subsp. holarctica DNA in the Aquatic Environment in France.

In 2018, the incidence of tularemia increased twofold in the west of France, with many pneumonic forms, suggesting environmental sources of infection. We investigated the presence of Francisellatularensis subsp. holarctica and other Francisella species DNA in the natural aquatic environment of this geographic area. Two sampling campaigns, in July 2019 and January 2020, allowed the collection of 87 water samples. Using a combination of real-time PCR assays, we tested the presence of either Francisella sp., F. tularensis/F. novicida, and F. tularensis subsp. holarctica, the latter being the only tularemia agent in Europe. Among 57 water samples of the first campaign, 15 (26.3%) were positive for Francisella sp., nine (15.8%) for F. tularensis and/or F. novicida, and four (7.0%) for F. tularensis subsp. holarctica. Ratios were 25/30 (83.3%), 24/30 (80.0%), and 4/30 (13.3%) for the second campaign. Among the thirty sites sampled during the two campaigns, nine were positive both times for Francisella sp., seven for F. tularensis and/or F. novicida, and one for F. tularensis subsp. holarctica. Altogether, our study reveals a high prevalence of Francisella sp. DNA (including the tularemia agent) in the studied aquatic environment. This aquatic environment could therefore participate in the endemicity of tularemia in the west of France.

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.