MALDI-TOF mass spectrometry in the 21st century clinical microbiology laboratory

Identification of Legionella by MALDI Biotyper through three preparation methods and an in-house library comparing phylogenetic and hierarchical cluster results

The identification and typing of bacteria are very expensive and time-consuming due to their growth times, and the expertise needed. MALDI-TOF MS represents a fast technique, reproducible with molecular approaches. This technique is still poorly applied in Legionella surveillance with estimation occurring only at the genus level. The aim of this study was to compare three sample preparation methods: direct smear (DS), extended direct smear (EDS), and full extraction (E), using MALDI Biotyper, developing an in-house library. Moreover, Hierarchical cluster analysis (HCA) was compared to mip and rpoB gene sequencing. The dataset was composed of 104 isolates belonging to six Legionella species. The isolates were identified with a sensitivity of 97.11% for DS, 98.08% for EDS, and 95.19% for E. The error rates were 2.88% for DS, 1.92% for EDS, and 4.90% for E, with no significant differences among them. The HCA confirmed the relationship among the isolates reported in the phylogenetic trees. An improvement in sensitivity was obtained using an in-house library. The results suggest the use of a fast and inexpensive DS method, combined with instrument and in-house library for routine Legionella surveillance. HCA analysis could be useful for screening isolates, before undertaking expensive and time-laborious molecular techniques.

Machine learning and matrix-assisted laser desorption/ionization time-of-flight mass spectra for antimicrobial resistance prediction: A systematic review of recent advancements and future development

BACKGROUND

The use of matrix-assisted laser desorption/ionization time-of-flight mass spectra (MALDI-TOF MS) combined with machine learning techniques has recently emerged as a method to address the public health crisis of antimicrobial resistance. This systematic review, conducted following Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, aims to evaluate the current state of the art in using machine learning for the detection and classification of antimicrobial resistance from MALDI-TOF mass spectrometry data.

METHODS

A comprehensive review of the literature on machine learning applications for antimicrobial resistance detection was performed using databases such as Web Of Science, Scopus, ScienceDirect, IEEE Xplore, and PubMed. Only original articles in English were included. Studies applying machine learning without using MALDI-TOF mass spectra were excluded.

RESULTS

Forty studies met the inclusion criteria. Staphylococcus aureus, Klebsiella pneumoniae and Escherichia coli were the most frequently cited bacteria. The antibiotics resistance most studied corresponds to methicillin for S. aureus, cephalosporins for K. pneumoniae, and aminoglycosides for E. coli. Random forest, support vector machine and logistic regression were the most employed algorithms to predict antimicrobial resistance. Additionally, seven studies reported using artificial neural networks. Most studies reported metrics such as accuracy, sensitivity, specificity, and the area under the receiver operating characteristic (AUROC) above 0.80.

CONCLUSIONS

Our study indicates that random forest, support vector machine, and logistic regression are effective for predicting antimicrobial resistance using MALDI-TOF MS data. Recent studies also highlight the potential of deep learning techniques in this area. We recommend further exploration of deep learning and multi-label supervised learning for comprehensive antibiotic resistance prediction in clinical practice.

Identification of Escherichia coli strains using MALDI-TOF MS combined with long short-term memory neural networks

The current study aims to develop a new technique for the precise identification of Escherichia coli strains, utilizing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) combined with a long short-term memory (LSTM) neural network. A total of 48 Escherichia coli strains were isolated and cultured on tryptic soy agar medium for 24 hours for the generation of MALDI-TOF MS spectra. Eight hundred MALDI-TOF MS spectra were obtained per strain, resulting in a database of 38,400 spectra. Fifty percent of the data was utilized for LSTM neural network training, with fine-tuned parameters for strain-level identification. The other half served as the test set to assess model performance. Traditional PCA dimension reduction of MALDI-TOF MS spectra indicated 47 out of 48 strains to be unclassifiable. In contrast, the LSTM neural network demonstrated remarkable efficacy. After 20 training epochs, the model achieved a loss value of 0.0524, an accuracy of 0.999, a precision of 0.985, and a recall of 0.982. When tested on the unseen data, the model attained an overall accuracy of 92.24%. The integration of MALDI-TOF MS and LSTM neural network markedly enhances the identification of Escherichia coli strains. This innovative approach offers an effective and accurate tool for MALDI-TOF MS-based strain-level identification, thus expanding the analytical capabilities of microbial diagnostics.

First report of Nocardia wallacei infection in an immunocompetent patient in Zhejiang province

Nocardiosis is an infectious disease caused by Nocardia spp., mainly affecting immunocompromised hosts. Nocardia infection is not common; especially Nocardia wallacei infection is even rarer. The patient, female, 61 years old, farmer, has been working in the field for a long time and has normal immune function. Her main clinical manifestation was persistent back pain. Chest-enhanced computed tomography showed pulmonary inflammation. Rare pathogen Nocardia wallacei was detected in alveolar lavage fluid using matrix-assisted laser destructive ionization time-of-flight mass spectrometry. She received treatment with linezolid and was discharged after her condition improved.

MSDeepAMR: antimicrobial resistance prediction based on deep neural networks and transfer learning

Introduction

Antimicrobial resistance (AMR) is a global health problem that requires early and effective treatments to prevent the indiscriminate use of antimicrobial drugs and the outcome of infections. Mass Spectrometry (MS), and more particularly MALDI-TOF, have been widely adopted by routine clinical microbiology laboratories to identify bacterial species and detect AMR. The analysis of AMR with deep learning is still recent, and most models depend on filters and preprocessing techniques manually applied on spectra.

Methods

This study propose a deep neural network, MSDeepAMR, to learn from raw mass spectra to predict AMR. MSDeepAMR model was implemented for Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus under different antibiotic resistance profiles. Additionally, a transfer learning test was performed to study the benefits of adapting the previously trained models to external data.

Results

MSDeepAMR models showed a good classification performance to detect antibiotic resistance. The AUROC of the model was above 0.83 in most cases studied, improving the results of previous investigations by over 10%. The adapted models improved the AUROC by up to 20% when compared to a model trained only with external data.

Discussion

This study demonstrate the potential of the MSDeepAMR model to predict antibiotic resistance and their use on external MS data. This allow the extrapolation of the MSDeepAMR model to de used in different laboratories that need to study AMR and do not have the capacity for an extensive sample collection.

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.

Description of new species of Mycobacterium terrae complex isolated from sewage at the São Paulo zoological park foundation in Brazil

Five mycobacterial isolates from sewage were classified as members of the genus Mycobacterium but presented inconclusive species assignments. Thus, the isolates (MYC017, MYC098, MYC101, MYC123 and MYC340) were analyzed by phenotypical, biochemical, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and genomic features to clarify their taxonomic position. Phenotypic analysis and biochemical tests did not distinguish these isolates from other non-pigmented mycobacteria. In contrast, MALDI-TOF MS analysis showed that isolates were not related to any previously described Mycobacterium species. Comparative genomic analysis showed values of ANI and dDDH between 81.59-85.56% and 24.4-28.8%, respectively, when compared to the genomes of species of this genus. In addition, two (MYC101 and MYC123) presented indistinguishable protein spectra from each other and values of ANI = 98.57% and dDDH = 97.3%, therefore being considered as belonging to the same species. Phylogenetic analysis grouped the five isolates within the Mycobacterium terrae complex (MTC) but in a specific subclade and separated from the species already described and supported by 100% bootstrap value, confirming that they are part of this complex but different from earlier described species. According to these data, we propose the description of four new species belonging to the Mycobacterium genus: (i) Mycobacterium defluvii sp. nov. strain MYC017T (= ATCC TSD-296T = JCM 35364T), (ii) Mycobacterium crassicus sp. nov. strain MYC098T (= ATCC TSD-297T = JCM 35365T), (iii) Mycobacterium zoologicum sp. nov. strain MYC101T (= ATCC TSD-298T = JCM 35366T) and MYC123 (= ATCC BAA-3216 = JCM 35367); and (iv) Mycobacterium nativiensis sp. nov. strain MYC340T (= ATCC TSD-299T = JCM 35368T).

Bloodstream Infections by Pantoea Species: Clinical and Microbiological Findings from a Retrospective Study, Italy, 2018-2023

(1) Background: The widespread use of MALDI-TOF coupled to mass spectrometry has improved diagnostic accuracy by identifying uncommon bacteria. Among Enterobacterales, Pantoea species have been seen to be implicated in several human infections, but their clinical and microbiological framework is currently based on a few anecdotal reports. (2) Methods: We conducted this five-year (2018-2023) single-center study aimed at investigating the prevalence and clinical and microbiological findings of Pantoea species bloodstream infections. (3) Results: Among the 4996 bloodstream infection Gram-negative isolates collected during the study period, Pantoea species accounted for 0.4% (n = 19) of isolates from 19 different patients, 5 of them being pediatric cases. Among Pantoea species isolates, P. agglomerans was the most frequently detected (45%; n = 9) followed by P. eucrina (30%; n = 6) and P. septica (15%; n = 3). Malignancy (35.7%) in adults and malignancy (40%) and cerebrovascular disease following meconium aspiration (40%) in pediatric patients as comorbidities and shivering and/or fever following parenteral infusion (36.8%) as a symptom/sign of Pantoea species bloodstream infection onset were the most frequently observed clinical features. Among adults, primary bloodstream infection was the most frequent (50%), whereas among pediatric patients, the most commonly identified sources of infection were catheter-related (40%) and the respiratory tract (40%). Overall, Pantoea species bloodstream infection isolates displayed high susceptibility to all the antibiotics except for ampicillin (63.2%), fosfomycin (73.7%), and piperacillin/tazobactam (84.2%). Targeted antibiotic treatment was prescribed as monotherapy for adults (71.4%) and combination therapy for pediatric patients (60%). The most prescribed antibiotic regimens were piperacillin/tazobactam (21.4%) in adults and meropenem- (40%) and aminoglycoside-containing (40%) antibiotics in pediatric patients. The overall 28-day all-cause mortality rate was 5.3% (n = 1). (4) Conclusions: The prevalence and 28-day mortality rate of Pantoea species bloodstream infections were low. The prescription of targeted therapy including broad-spectrum antibiotics could indicate an underestimation of the specific involvement of the Pantoea species in the onset of the disease, warranting further studies defining their pathogenic potential.

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.

Evaluation of a Novel Benchtop Tool for Acceleration of Sample Preparation for MALDI-TOF Mass Spectrometry

During the past decade, MALDI-TOF mass spectrometry (MS) has become a standard method for identification of bacteria and yeasts. Nonetheless, further optimization of the identification process is important to streamline workflows and save resources. This study evaluated the application of a multipurpose benchtop tool, MBT FAST Shuttle IVD, for accelerated drying of liquid assay components (matrix, formic acid, and/or sample) on a MALDI target. A total of 50 bacterial and fungal isolates were subjected to three different sample preparation procedures prior to the identification by MALDI-TOF MS: direct transfer (DT), extended direct transfer (eDT), and protein extraction (PE). Compared to conventional drying at room temperature, the preparation was performed with standardized heating of the MALDI target on the MBT FAST Shuttle. During DT, eDT, and PE, 56.7% (P < 0.001), 56.8% (P < 0.001), and 52.8% (P < 0.001) of time for matrix drying were saved by using the MBT FAST Shuttle, respectively. Applying the MBT FAST Shuttle, 57.5% (P < 0.001) of time for drying of formic acid were saved for eDT and 57.5% (P < 0.001) of time for sample drying were saved for PE. A significant improvement of the identification rates and scores was observed with MBT FAST Shuttle for eDT (P = 0.001) and PE (P = 0.008) methods, while the effect on identification quality for DT was not statistically significant (P = 0.16). In conclusion, the use of the MBT FAST Shuttle shortened the drying time of assay components by about a half for all preparation methods. Moreover, positive effect on identification success was observed.

Influence of Multiplex PCR in the Management of Antibiotic Treatment in Patients with Bacteremia

The multiplex PCR assay can be a helpful diagnostic tool for patients with bacteremia. Herein, we assessed the impact of a Blood Culture Identification Panel (BCID) on both the diagnosis and treatment of patients with bacteremia. We performed a retrospective study using laboratory and clinical data to evaluate the impact of syndromic testing using a multiplex PCR testing system (BioFire® FilmArray) for the management of patients with bloodstream infections. BCID detected the pathogen in 102 (87.9%) samples out of the 116 positive blood cultures tested. The average time from the blood culture collection to the communication of the molecular test result was 23.93 h (range: 10.67-69.27 h). The main pathogen detected was Klebsiella pneumoniae (17.6%). The antimicrobial therapy was changed in accordance with the BCID results in 28 (40.6%) out of the 69 cases, wherein the treatment could have been theoretically adjusted. This allowed the adjustment of the therapy to be performed 1305.1 h faster than it would have been possible if conventional diagnostic methods had been used; this was the case for only 35.1% of the time gained if treatment was adjusted for all patients with positive BCID. Thus, although molecular tests can make a difference in the management of bloodstream infections, there is room for improvement in the clinical application of BCID results.

A Method to Directly Identify Cronobacter sakazakii in Liquid Medium by MALDI-TOF MS

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry has been widely used as an emerging technology for the rapid identification of microorganisms. Cronobacter sakazakii (C. sakazakii) is a food-borne pathogen of particular importance to the powdered infant formula (PIF) processing environment due to its high lethality in infants. However, the traditional solid spotting detection method of pretreating samples for MALDI-TOF MS leads only to qualitative detection of C. sakazakii. We developed a new, low-cost, robust liquid spotting pretreatment method and used a response surface methodology to optimize its parameters. The applicability, accuracy, and quantitative potential were measured for different types of samples. The optimal parameters of this method were as follows: a volume of 70% formic acid of 25 μL, treatment with ultrasound at 350 W for 3 min, and a volume of acetonitrile added of 75 μL. These conditions led to the highest identification score for C. sakazakii (1926.42 ± 48.497). This method was found to detect bacteria accurately and reproducibly. When 70 strains of C. sakazakii isolates were analyzed with this method, the identification accuracy was 100%. The detection limit of C. sakazakii in environmental and PIF samples was 4.1 × 10¹ cfu/mL and 2.72 × 10³ cfu/mL, respectively.

MALDI-TOF MS Approaches for the Identification of the Susceptibility of Extended-Spectrum β-Lactamases in Escherichia coli

The increase in multidrug-resistant microorganisms that produce extended-spectrum β-lactamases (ESBLs) and carbapenemases is a serious problem worldwide. Recently, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has been used for the rapid detection of antibiotic-resistant bacteria. The objective of this study was to establish a method to detect ESBL-producing Escherichia coli by monitoring the hydrolyzation of cefotaxime (CTX) using MALDI-TOF MS. According to the ratio of the peak intensity of CTX and hydrolyzed-CTX-related compounds, the ESBL-producing strains could be clearly distinguished after 15 min of incubation. Moreover, the minimum inhibitory concentration (MIC) values for E. coli were 8 μg/mL and lower than 4 μg/mL, which could be distinguished after 30 min and 60 min of incubation, respectively. The enzymatic activity was determined using the difference in the signal intensity of the hydrolyzed CTX at 370 Da for the ESBL-producing strains incubated with or without clavulanate. The ESBL-producing strains with low enzymatic activity or bla_CTX-M genes could be detected by monitoring the hydrolyzed CTX. These results show that this method can rapidly detect high-sensitivity ESBL-producing E. coli.

Validation of a MALDI-TOF MS Method for SARS-CoV-2 Detection on the Bruker Biotyper and Nasopharyngeal Swabs: A Brazil-UK Collaborative Study

We developed a MALDI-TOF mass spectrometry method for the detection of the SARS-CoV-2 virus in saliva-gargle samples using Shimadzu MALDI-TOF mass spectrometers in the UK. This was validated in the USA to CLIA-LDT standards for asymptomatic infection detection remotely via sharing protocols, shipping key reagents, video conferencing, and data exchange. In Brazil, more so than in the UK and USA, there is a need to develop non-PCR-dependent, rapid, and affordable SARS-CoV-2 infection screening tests that also identify variant SARS-CoV-2 and other virus infections. In addition, travel restrictions necessitated remote collaboration with validation on the available clinical MALDI-TOF-the Bruker Biotyper (microflex^® LT/SH)-and on nasopharyngeal swab samples, as salivary gargle samples were not available. The Bruker Biotyper was shown to be almost log10³ more sensitive at the detection of high molecular weight spike proteins. A protocol for saline swab soaks out was developed, and duplicate swab samples collected in Brazil were analyzed by MALDI-TOF MS. The swab collected sample spectra that varied from that of saliva-gargle in three additional mass peaks in the mass region expected for IgG heavy chains and human serum albumin. A subset of clinical samples with additional high mass, probably spike-related proteins, were also found. Further, spectral data comparisons and analysis, subjected to machine learning algorithms in order to resolve RT-qPCR positive from RT-qPCR negative swab samples, showed 56-62% sensitivity, 87-91% specificity, and a 78% agreement with RT-qPCR scoring for SARS-CoV-2 infection.

The current state of laboratory mycology in Asia/Pacific: A survey from the European Confederation of Medical Mycology (ECMM) and International Society for Human and Animal Mycology (ISHAM)

INTRODUCTION

Invasive fungal infections (IFIs) in Asia/Pacific are a particular threat to patients with malignancies, uncontrolled diabetes mellitus or undiagnosed/untreated human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS). Adequate and early access to diagnostic tools and antifungals is essential for IFI clinical management and patient survival.

METHODS

Details on institution profile, self-perception on IFI, and access to microscopy, culture, serology, antigen detection, molecular testing, and therapeutic drug monitoring for IFI were collected in a survey.

RESULTS

As of June 2022, 235 centres from 40 countries/territories in Asia/Pacific answered the questionnaire. More than half the centres were from six countries: India (25%), China (17%), Thailand (5%), Indonesia, Iran, and Japan (4% each). Candida spp. (93%) and Aspergillus spp. (75%) were considered the most relevant pathogens. Most institutions had access to microscopy (98%) or culture-based approaches (97%). Furthermore, 79% of centres had access to antigen detection, 66% to molecular assays, and 63% to antibody tests. Access to antifungals varied between countries/territories. At least one triazole was available in 93% of the reporting sites (voriconazole [89%] was the most common mould-active azole), whereas 80% had at least one amphotericin B formulation, and 72% had at least one echinocandin.

CONCLUSION

According to the replies provided, the resources available for IFI diagnosis and management vary among Asia/Pacific countries/territories. Economical or geographical factors may play a key role in the incidence and clinical handling of this disease burden. Regional cooperation may be a good strategy to overcome shortcomings.

Helicobacter pylori Infection: Current Status and Future Prospects on Diagnostic, Therapeutic and Control Challenges

Helicobacter pylori (H. pylori) infection, which affects approximately half of the world's population, remains a serious public health problem. As H. pylori infection leads to a number of gastric pathologies, including inflammation, gastroduodenal ulcers, and malignancies, early detection and treatment are crucial to preventing the spread of the infection. Multiple extragastric complications, such as iron deficiency anaemia, immune thrombocytopenic purpura, vitamin B12 deficiency, diabetes mellitus, cardiovascular diseases, and certain neurological disorders, have also been linked to H. pylori infection. An awareness of H. pylori and associated health hazards is necessary to minimize or even eradicate the infection. Therefore, there is an urgent need to raise the standards for the currently employed diagnostic, eradication, alternative treatment strategies. In addition, a brief overview of traditional and cutting-edge approaches that have proven effective in identifying and managing H. pylori is needed. Based on the test and laboratory equipment available and patient clinical characteristics, the optimal diagnostic approach requires weighing several factors. The pathophysiology and pathogenic mechanisms of H. pylori should also be studied, focusing more on the infection-causing virulence factors of this bacterium. Accordingly, this review aims to demonstrate the various diagnostic, pathophysiological, therapeutic, and eradication tactics available for H. pylori, emphasizing both their advantages and disadvantages. Invasive methods (such as quick urease testing, biopsy, or culture) or noninvasive methods (such as breath tests, stool investigations, or serological tests) can be used. We also present the most recent worldwide recommendations along with scientific evidence for treating H. pylori. In addition to the current antibiotic regimens, alternative therapies may also be considered. It is imperative to eradicate the infections caused by H. pylori as soon as possible to prevent problems and the development of stomach cancer. In conclusion, significant advances have been made in identifying and treating H. pylori. To improve eradication rates, peptide mass fingerprinting can be used as a diagnostic tool, and vaccines can also eliminate the infection.

Determination of the ability of matrix-assisted laser desorption ionization time-of-flight mass spectrometry to identify high-biofilm-producing strains

Background

The traditional method for assessing the capacity of a microorganism to produce biofilm is generally a static in vitro model in a multi-well plate using the crystal violet (CV) binding assay, which takes 96 h. Furthermore, while the method is simple to perform, its reproducibility is poor.

Objective

We evaluated whether matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) could make it possible to differentiate between high-and low-biofilm-producing microorganisms on 24-h cultures of Staphylococcus aureus and Candida albicans.

Methods

We included 157 strains of S. aureus and 91 strains of C. albicans obtained from the blood cultures of patients with bacteremia/candidemia. We tested biofilm production using the CV binding assay as the gold standard to classify strains as low or high biofilm producers. We then applied MALDI-TOF MS to create a machine learning-based predictive model using 40 strains of S. aureus and C. albicans, each with extreme absorbance values, and validated this approach with the remaining 117 and 51 strains using the random forest algorithm and the support vector machine algorithm, respectively.

Results

Overall, 81.2% of the S. aureus strains (95/117) and 74.5% of the C. albicans strains (38/51) used for validation were correctly categorized, respectively, as low and high-biofilm-producing.

Conclusion

Classification based on MALDI-TOF MS protein spectra enables us to predict acceptable information about the capacity of 24-h cultures of S. aureus and C. albicans to form biofilm.

The current state of laboratory mycology and access to antifungal treatment in Europe: a European Confederation of Medical Mycology survey

Access to the appropriate tools is crucial for early diagnosis and clinical management of invasive fungal infections. This Review aims to describe the invasive fungal infection diagnostic capacity of Europe to better understand the status and the most pressing aspects that need improvement. To our knowledge, this is the first time that the mycological diagnostic capability and access to antifungal treatments of institutions has been evaluated at a pan-European level. Between Nov 1, 2021, and Jan 31, 2022, 388 institutions in Europe self-assessed their invasive fungal infection management capability. Of the 388 participating institutions from 45 countries, 383 (99%) had access to cultures, 375 (97%) to microscopy, 363 (94%) to antigen-detection assays, 329 (85%) to molecular tests (mostly PCR), and 324 (84%) to antibody tests for diagnosis and management. With the exception of microscopy, there were considerable differences in access to techniques among countries according to their gross domestic product. At least one triazole was available in 363 (94%) of the institutions, one echinocandin in 346 (89%), and liposomal amphotericin B in 301 (78%), with country gross domestic product-based differences. Differences were also observed in the access to therapeutic drug monitoring. Although Europe is well prepared to manage invasive fungal infections, some institutions do not have access to certain diagnostic tools and antifungal drugs, despite most being considered essential by WHO. These limitations need to be overcome to ensure that all patients receive the best diagnostic and therapeutic management.

Using Vitek MS v3.0 To Identify Nontuberculous Mycobacteria in Liquid Media in a Clinical Microbiology Laboratory

Recently, the incidence of diseases caused by nontuberculous mycobacteria (NTM) has been increasing worldwide, especially in immunocompromised patients and those with potential chronic lung disease. Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and reliable method for identifying mycobacteria in clinical laboratories. This study aimed to evaluate the performance of Vitek MS v3.0 by isolating NTM directly from automated liquid medium systems using patient samples. A total of 855 Mycobacterium growth indicator tube (MGIT)-positive liquid cultures were investigated. Among them, 658 (77.0%) liquid cultures were correctly identified to the species, group, or complex level, 192 (23.0%) resulted in no identification, and 5 (0.6%) were misidentified at the species level. DNA sequencing identified 855 NTM isolates from liquid cultures, comprising 316 isolates of rapidly growing mycobacteria (RGM) and 539 isolates of slow-growing mycobacteria (SGM). Using the Vitek MS system, the RGM integral identification rate (276/316 [87.34%]) was higher than the SGM rate (381/539 [70.69%]) (P < 0.01). It was also higher than the SGM rate for all MGIT report-positive periods. These results indicate that the Vitek MS v3.0 system can rapidly identify NTM species from liquid cultures. Further validation using molecular techniques is required. IMPORTANCE Rapid and accurate identification of nontuberculous mycobacteria (NTM) is essential for diagnosis, appropriate therapy, and infection control. Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and reliable method for identifying mycobacteria in clinical laboratories. This study reported a clinical validation of the Vitek MS V3.0 system for identification of NTM isolates from 855 MGIT-positive liquid cultures which contained relatively large NTM types. Vitek MS v3.0 showed a promising rate for identification NTM isolates in positive liquid cultures. Vitek MS v3.0 had a better performance with RGM than with SGM. Vitek MS v3.0 results included "unidentified" or "misidentified" NTM isolates, which would also serve as an important reference for future optimization of this system. Vitek MS v3.0 represented a valuable technique for NTM identification from positive liquid cultures.

Correlation Between Drug Resistance and Virulence of Candida Isolates from Patients with Candidiasis

Purpose

This article aims to provide a theoretical basis for new or adjuvant strategies to facilitate the early diagnosis and treatment of candidiasis and to determine if drug-resistant Candida would affect virulence.

Patients and Methods

Our strains were collected from patients diagnosed with candidiasis in our hospital. The strains were identified by MALDI-TOF system and ITS sequencing. Antifungal sensitivity testing in vitro was performed to evaluate susceptibility of these isolates to current widely used antifungal drugs. The Galleria mellonella larvae model infected by Candida spp. was used to compare the virulence of drug-resistant and susceptible Candida spp.

Results

A total of 206 Candida strains were collected from clinical specimens. Candida albicans was the most common species among them, and was predominantly isolated from male patients aged over 40 years in ICU environments suffering from pulmonary and/or cerebral conditions. The accuracy rate of MALDI TOF-MS identification was 92.72% when compared with ITS sequencing as the standard method. Most Candida species, except for C. tropicalis which showed high resistance to micafungin, showed high susceptibilities to voriconazole, itraconazole, amphotericin B and micafungin but were highly resistant to terbinafine. For each specific Candida species, the G. mellonella larvae model revealed that the virulence of drug-resistant Candida isolates did not markedly differ from that of the drug-susceptible isolates, however, the virulence was dose-dependent on inoculated fungal cells in this model.

Conclusion

The possibility of Candida infection should not be neglected in patients at critical care hospital settings and C. albicans is the most common causative agent. MALDI-TOF MS has the advantages of rapidity and high accuracy, and should be a preferred method for identification of Candida spp. in a clinical laboratory. Voriconazole, itraconazole, amphotericin B and micafungin can still be recommended as the first line antifungals to treat candidiasis.

Detection of carbapenemase-producing Enterobacterales by means of matrix-assisted laser desorption ionization time-of-flight mass spectrometry with ertapenem susceptibility-testing disks as source of carbapenem substrate

MALDI-TOF mass spectrometry has become widely used in clinical microbiology and has proved highly accurate for detection of carbapenemases in Gram-negative bacteria. However, the use of carbapenem-hydrolysis assays in routine diagnostics is hampered by the need for antibiotic substances and for making their fresh solutions each time an assay is conducted. Here, we evaluated the use of commercial antibiotic susceptibility-testing disks as source of ertapenem substrate in MALDI-TOF MS-based assay for detection of carbapenemase-producing Enterobacterales (CPE). The assay was validated on 48 CPE isolates of 8 different species expressing NDM-, VIM-, KPC- and OXA-48-type carbapenemases and exhibiting various levels of resistance to carbapenems (MIC range: 0.25- > 32 mg/l), as well as on 48 carbapenemase-non-producing isolates. The assay conditions were optimized as follows: 10-μl loopful of bacterial colonies was suspended in 150 μl 0.01 M Na-PBS buffer, pH 7.4, a 10 μg ertapenem susceptibility-testing disk was immersed in the suspension and incubated 3 h at 35°C, after which supernatant was obtained by centrifugation and applied on a target plate with alpha-cyano-4-hydroxycinnamic acid matrix. Mass spectra were analyzed between 440 and 560 m/z. Carbapenemase activity was detected in all tested CPE isolates by the appearance of m/z peaks corresponding to ertapenem hydrolysis products: [M_h + H]⁺:494.2, [M_h + Na]⁺:516.2, [M_h + 2Na]⁺:538.2, [M_h/d + H]⁺:450.2, [M_h/d + Na]⁺:472.2, and simultaneous decrease or loss of peaks of intact antibiotic: [M + H]⁺:476.2, [M + Na]⁺:498.1, [M + 2Na]⁺:520.1. No hydrolysis peaks or loss of intact ertapenem peaks were observed for carbapenemase-negative strains. We therefore report the development of a sensitive, specific and cost-effective MALDI-TOF MS-based assay for detection of CPE, which makes use of antibiotic disks readily available in most laboratories.

How MALDI-TOF Mass Spectrometry Technology Contributes to Microbial Infection Control in Healthcare Settings

Healthcare settings have been utilizing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) since 2010. MALDI-TOF MS has various benefits over the conventional method of biochemical identification, including ease of use, speed, accuracy, and low cost. This approach can solve many of the obstacles to identifying bacteria, fungi and viruses. As technology advanced, more and more databases kept track of spectra, allowing species with similar morphological, genotypic, and biochemical traits to be identified. Using MALDI-TOF MS for identification has become more accurate and quicker due to advances in sample preparation and database enrichment. Rapid sample detection and colony identification using MALDI-TOF MS have produced promising results. A key application of MALDI-TOF MS is quickly identifying highly virulent and drug-resistant diseases. Here, we present a review of the scientific literature assessing the effectiveness of MALDI-TOF MS for locating clinically relevant pathogenic bacteria, fungi, and viruses. MALDI-TOF MS is a useful strategy for locating clinical pathogens, however, it also has some drawbacks. A small number of spectra in the database and inherent similarities among organisms can make it difficult to distinguish between different species, which can result in misidentifications. The majority of the time additional testing may correct these problems, which happen very seldom. In conclusion, infectious illness diagnosis and clinical care are being revolutionized by the use of MALDI-TOF MS in the clinical microbiology laboratory.

Prosthetic Knee Joint Infection Due to Candida lusitaniae: A Diagnostic and Therapeutic Odyssey: A Case Study

Prosthetic joint infections (PJIs) caused by fungi, although relatively rare, represent a major surgery-related complication. An extremely rare fungal PJI, following revised total knee replacement (TKR) caused by Candida lusitaniae, is reported, and a meticulous review of similar cases is provided. A 74-year-old female, who underwent primary total knee arthroplasty 10 years ago and a revision surgery three weeks ago, presented with signs and symptoms of PJI. C. lusitaniae was eventually isolated from the periprosthetic tissue using the MALDI-TOF VitekMS–bioMérieux technique. Multiple strategies for managing this fungal PJI were performed, and finally, the patient was treated successfully with an intramedullary arthrodesis system and proper antifungal treatment, including fluconazole. A multidisciplinary approach is essential for the diagnosis and treatment of such severe infections. In persistent cases and in cases where revision surgery is extremely difficult to perform, arthrodesis seems to be an effective solution for the elimination of the infection. The efficacy of the therapeutic management of fungal PJIs remains unclear. Therefore, more research should be reported, focusing on proper treatment so that the optimal strategy in treating these severe infections may be established.

Systematic Characterization of Epidemiology, Antifungal Susceptibility, Risk Factors and Outcomes of Candidaemia: A Six-Year Chinese Study

Background

Candida bloodstream infection (BSI), the fourth most common nosocomial BSI, is an urgent global health challenge with the tremendous growth in antifungal resistance rate and mortality rate.

Purpose

To establish the epidemiology, species distribution, risk factors, and 30-day mortality of candidaemia among 115 patients in this 6-year surveillance study.

Materials and Methods

We retrospectively analyzed the clinical characteristics, epidemiology, antifungal susceptibility patterns, and risk factors for morbidity and mortality of 115 candidaemia cases diagnosed in one tertiary care hospital from January 2016 through December 2021.

Results

Of the 115 candidaemia cases, the most prevalent species were Candida tropicalis (33.0%), followed by Candida albicans (27.8%), Candida parapsilosis complex (19.1%), and others. The overall incidence was 0.21 cases/1000 admissions. The overall crude resistance rate of Candida spp. against azoles was 20.0% (23/115), while Candida tropicalis showed a significant increase in the resistance rate to azoles (from 1/6, 16.7% in 2017 to 6/10, 60.0% in 2021). Multivariate analyses demonstrated that hematological malignancy and neutropenia were significantly associated with Candida tropicalis BSI than Candida non-tropicalis BSI. Candida albicans BSI had a significantly higher rate of previous surgery than Candida non-albicans BSI. Candida parapsilosis BSI had a significantly higher rate of receiving total parenteral nutrition (TPN). The overall 30-day mortality rate was 27.0% (31/115). The presence of high age-adjusted Charlson comorbidity index (aCCI), neutropenia, and septic shock were factors independently associated with increased 30-day mortality.

Conclusion

Candida tropicalis are emerging as the predominant isolate in candidaemia. Of note, the unexpectedly increased resistance rate to azoles in Candida tropicalis BSI was observed. The aCCI scores, neutropenia, and septic shock were independently associated with 30-day mortality. Prompt, adequate antifungal treatment among high-risk patients may lead to a reduction in mortality.

THz-ATR Spectroscopy Integrated with Species Recognition Based on Multi-Classifier Voting for Automated Clinical Microbial Identification

The demand for rapid and accurate identification of microorganisms is growing due to considerable importance in all areas related to public health and safety. Here, we demonstrate a rapid and label-free strategy for the identification of microorganisms by integrating terahertz-attenuated total reflection (THz-ATR) spectroscopy with an automated recognition method based on multi-classifier voting. Our results show that 13 standard microbial strains can be classified into three different groups of microorganisms (Gram-positive bacteria, Gram-negative bacteria, and fungi) by THz-ATR spectroscopy. To detect clinical microbial strains with better differentiation that accounts for their greater sample heterogeneity, an automated recognition algorithm is proposed based on multi-classifier voting. It uses three types of machine learning classifiers to identify five different groups of clinical microbial strains. The results demonstrate that common microorganisms, once time-consuming to distinguish by traditional microbial identification methods, can be rapidly and accurately recognized using THz-ATR spectra in minutes. The proposed automatic recognition method is optimized by a spectroscopic feature selection algorithm designed to identify the optimal diagnostic indicator, and the combination of different machine learning classifiers with a voting scheme. The total diagnostic accuracy reaches 80.77% (as high as 99.6% for Enterococcus faecalis) for 1123 isolates from clinical samples of sputum, blood, urine, and feces. This strategy demonstrates that THz spectroscopy integrated with an automatic recognition method based on multi-classifier voting significantly improves the accuracy of spectral analysis, thereby presenting a new method for true label-free identification of clinical microorganisms with high efficiency.

Diagnosis and Treatment of Invasive Candidiasis

Candida species, belonging to commensal microbial communities in humans, cause opportunistic infections in individuals with impaired immunity. Pathogens encountered in more than 90% cases of invasive candidiasis include C. albicans, C. glabrata, C. krusei, C. tropicalis, and C. parapsilosis. The most frequently diagnosed invasive infection is candidemia. About 50% of candidemia cases result in deep-seated infection due to hematogenous spread. The sensitivity of blood cultures in autopsy-proven invasive candidiasis ranges from 21% to 71%. Non-cultural methods (beta-D-glucan, T2Candida assays), especially beta-D-glucan in combination with procalcitonin, appear promising in the exclusion of invasive candidiasis with high sensitivity (98%) and negative predictive value (95%). There is currently a clear deficiency in approved sensitive and precise diagnostic techniques. Omics technologies seem promising, though require further development and study. Therapeutic options for invasive candidiasis are generally limited to four classes of systemic antifungals (polyenes, antimetabolite 5-fluorocytosine, azoles, echinocandins) with the two latter being highly effective and well-tolerated and hence the most widely used. Principles and methods of treatment are discussed in this review. The emergence of pan-drug-resistant C. auris strains indicates an insufficient choice of available medications. Further surveillance, alongside the development of diagnostic and therapeutic methods, is essential.

Gram-Negative Rods on Inanimate Surfaces of Selected Hospital Facilities and Their Nosocomial Significance

Inanimate surfaces are often referred to as nosocomial bacterial reservoirs and represent an important vector in the process of spreading pathogens to patients. Most gram-negative rods can survive on inanimate surfaces for several months. The aim of this study is to determine the prevalence and resistance of gram-negative bacteria isolated from the inanimate surfaces of two selected hospital departments. MALDI-TOF identified gram-negative rods isolated from inanimate surfaces. Antibiotic resistance was determined using a disk diffusion method, and the phenotype of resistance was determined using an inhibitory analyzer. From the inanimate surfaces, 98 strains of gram-negative nosocomial bacteria were identified by the MALDI-TOF MS. The most frequently isolated bacterium occurring in both departments was Pseudomonas aeruginosa (n = 33), followed by Acinetobacter baumannii (n = 20) and Enterobacter cloacae (n = 14). The most common phenotypic type of resistance in both departments was ampicillin resistance—AmpC (n = 38), then production of extended-spectrum β-lactamase (ESBL) (n = 33), followed by SHV-1 (n = 11), TEM-1 (n = 11), and fluoroquinolone resistance—Qnr (n = 22). The nosocomial important enzymes capable of hydrolyzing carbapenems, OXA-48 and metallo-β-lactamases, were confirmed in 12 and 2 cases, respectively. The results of our study prove that inanimate surfaces in hospitals are a reservoir of resistant gram-negative bacteria, which directly threaten hospitalized patients.

Use of Fourier-Transform Infrared Spectroscopy With IR Biotyper® System for Legionella pneumophila Serogroups Identification

Legionella spp. are Gram-negative bacteria that inhabit freshwater environments representing a serious risk for human health. Legionella pneumophila (Lp) is the species most frequently responsible for a severe pneumonia known as Legionnaires' disease. Lp consists of 15 serogroups (Sgs), usually identified by monoclonal or polyclonal antibodies. With regard to Lp serogrouping, it is well known that phenotyping methods do not have a sufficiently high discriminating power, while genotypic methods although very effective, are expensive and laborious. Recently, mass spectrometry and infrared spectroscopy have proved to be rapid and successful approaches for the microbial identification and typing. Different biomolecules (e.g., lipopolysaccharides) adsorb infrared radiation originating from a specific microbial fingerprint. The development of a classification system based on the intra-species identification features allows a rapid and reliable typing of strains for diagnostic and epidemiological purposes. The aim of the study was the evaluation of Fourier Transform Infrared Spectroscopy using the IR Biotyper® system (Bruker Daltonik, Germany) for the identification of Lp at the serogroup (Sg) level for diagnostic purposes as well as in outbreak events. A large dataset of Lp isolates (n = 133) and ATCC reference strains representing the 15 Lp serogroups were included. The discriminatory power of the instrument's classifier, was tested by Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA). All isolates were classified as follows: 12/133 (9.0%) as Lp Sg1 and 115/133 (86.5%) as Lp Sg 2-15 (including both ATCC and environmental Lp serogroup). Moreover, a mis-classification for 2/133 (1.5%) isolates of Lp Sg 2-15 that returned as Lp Sg1 was observed, and 4/133 (3.0%) isolates were not classified. An accuracy of 95.49% and an error rate of 4.51% were calculated. IR Biotyper® is able provide a quick and cost-effective reliable Lp classification with advantages compared with agglutination tests that show ambiguous and unspecific results. Further studies including a larger number of isolates could be useful to implement the classifier obtaining a robust and reliable tool for the routine Lp serogrouping. IR Biotyper® could be a powerful and easy-to-use tool to identify Lp Sgs, especially during cluster/outbreak investigations, to trace the source of the infection and promptly adopt preventive and control strategies.

Scedosporium apiospermium keratitis: a case report

BACKGROUND

Scedosporium apiospermum, an opportunistic and filamentous fungus, is a rarely seen ocular entity that is difficult to identify and heal. We report a challenging case of S. apiospermium keratitis and discuss the treatment modalities in light of previous studies.

CASE PRESENTATION

A 30-year-old Turkish farmer with a history of contact lens misuse presented to our clinic with a painful corneal abscess and severe vision loss in his left eye. S. apiospermum was identified by spectrophotometric analysis. The patient was successfully treated with therapeutic penetrating keratoplasty, but was resistant to fluconazole and amphotericin B and susceptible but unresponsive to voriconazole.

CONCLUSION

S. apiospermum keratitis should be considered in the differential diagnosis of immunocompromised and immunocompetent patients with history of ocular trauma and contact lens use, especially those who do not respond to treatment.

Infrared pulsed fiber laser-produced silver-109-nanoparticles for laser desorption/ionization mass spectrometry of amino acids

Application of monoisotopic cationic 109Ag nanoparticles (109AgNPs) obtained by pulsed fiber laser (PFL) 2D galvo-scanner (GS) laser generated nanomaterial (LGN) for both high resolution laser desorption/ionization mass spectrometry and mass spectrometry imaging of amino acids is presented. Four amino acids, alanine, isoleucine, lysine, and phenylalanine were used as test compounds for quantification with matrix-assisted laser desorption/ionization mas (MALDI)-type mass spectrometer. Comparison of commonly made manual measurements with semiautomatic mass spectrometry imaging (MSI) was performed providing very interesting findings. Amino acids were directly tested in 1 000 000-fold concentration change conditions ranging from 1 mg/ml to 1 ng/ml, which equates to 500 ng to 500 fg of amino acid per measurement spot. Methods were also tested on samples of human blood plasma for quantification of endogenous amino acids.

Risk Stratifying and Prognostic Analysis of Subclinical Cardiac Implantable Electronic Devices Infection: Insight From Traditional Bacterial Culture

Background

Subclinical infection of cardiac implantable electronic devices (CIEDs) is a common condition and increases the risk of clinical infection. However, there are limited studies focused on risk stratifying and prognostic analysis of subclinical CIED infection.

Methods and Results

Data from 418 consecutive patients undergoing CIED replacement or upgrade between January 2011 and December 2019 were used in the analysis. Among the patients included, 50 (12.0%) were detected as positive by bacterial culture of pocket tissues. The most frequently isolated bacteria were coagulase‐negative staphylococci (76.9%). Compared with the noninfection group, more patients in the subclinical infection group were taking immunosuppressive agents, received electrode replacement, or received CIED upgrade and temporary pacing. Patients in the subclinical infection group had a higher PADIT (Prevention of Arrhythmia Device Infection Trial) score. Univariable and multivariable logistic regression analysis found that use of immunosuppressive agents (odds ratio [OR], 6.95 [95% CI, 1.44–33.51]; P=0.02) and electrode replacement or CIED upgrade (OR, 6.73 [95% CI, 2.23–20.38]; P=0.001) were significantly associated with subclinical CIED infection. Meanwhile, compared with the low‐risk group, patients in the intermediate/high‐risk group had a higher risk of subclinical CIED infection (OR, 3.43 [95% CI, 1.58–7.41]; P=0.002). After a median follow‐up time of 36.5 months, the end points between the subclinical infection group and noninfection group were as follows: composite events (58.0% versus 41.8%, P=0.03), rehospitalization (54.0% versus 32.1%, P=0.002), cardiovascular rehospitalization (32.0% versus 13.9%, P=0.001), CIED infection (2.0% versus 0.5%, P=0.32), all‐cause mortality (28.0% versus 21.5%, P=0.30), and cardiovascular mortality (10.0% versus 7.6%, P=0.57).

Conclusions

Subclinical CIED infection was a common phenomenon. The PADIT score had significant value for stratifying patients at high risk of subclinical CIED infection. Subclinical CIED infection was associated with increased risks of composite events, rehospitalization, and cardiovascular rehospitalization.

Invited review: Stress resistance of Cronobacter spp. affecting control of its growth during food production

Members of the Cronobacter genus include food-borne pathogens that can cause infections in infants, with a mortality rate as high as 40 to 80%. The high fatality rate of Cronobacter and its isolation from numerous types of food, especially from powdered infant formula, demonstrate the serious nature of this organism. The source tracking of Cronobacter spp. and the analysis of high-frequency species from different sources are helpful for a more targeted control. Furthermore, the persistence during food processing and storage may be attributed to strong resistance of Cronobacter spp. to environment stresses such as heat, pH, and desiccation. There are many factors that support the survival of Cronobacter spp. in harsh environments, such as some genes, regulatory systems, and biofilms. Advanced detection technology is helpful for the strict monitoring of Cronobacter spp. In addition to the traditional heat treatment, many new control techniques have been developed, and the ability to control Cronobacter spp. has been demonstrated. The control of this bacteria is required not only during manufacture, but also through the selection of packaging methods to reduce postprocessing contamination. At the same time, the effect of inactivation methods on product quality and safety must be considered. This review considers the advances in our understanding of environmental stress response in Cronobacter spp. with special emphasis on its implications in food processing.

MALDI-TOF mass spectrometry for antimicrobial susceptibility testing

The advent of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in clinical microbiology has dramatically improved the accuracy and speed of diagnostics. However, this progress has mainly been limited to the identification of microorganisms, whereas the practical improvement of antimicrobial susceptibility testing (AST) still lags behind. MALDI-TOF MS-based approaches include the detection of selected resistance mechanisms and the universal phenotypic AST. This minireview focuses on the discussion of those MALDI-TOF MS methods that allow universal growth-based phenotypic AST. The method of minimal profile change concentrations (MPCC) is based on detecting proteome modification in presence of an antimicrobial. Using stable-isotope labeling, characteristic mass shifts in the presence of an antimicrobial indicate the incorporation of the isotopic labels, and, thus, the viability and resistance of the microorganism. For MALDI Biotyper antibiotic susceptibility test rapid assay (MBT-ASTRA), microorganisms are incubated with or without an antimicrobial, followed by cell lysis, protein extraction, and transfer of the cell lysate onto a MALDI target plate. Using the internal standard, peak intensities are correlated to the amount of microbial proteins, and the relative microbial growth is calculated. Most recent development in the field is the direct-on-target microdroplet growth assay (DOT-MGA). Here, incubation of microorganisms with antimicrobials takes place directly on spots of a MALDI target in form of microdroplets. After incubation, nutrient medium is removed by dabbing with absorptive material. Resistant microorganisms grow despite the presence of antimicrobial, and their amplified biomass is detected by MALDI-TOF MS. Finally, an outlook is provided for further assay improvements.

Identification of Fungi Isolated from Oral Cavity of Patients with HIV Using MALDI-TOF MS

BACKGROUND

A growing incidence of invasive fungal infections, especially among immunocompromised patients, has given increased significance to microbiological diagnostics of yeast-like fungi. More accurate and faster fungi identification methods that can compete with classical methods are being searched for. In this paper, classical microbiological methods are compared to MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry).

METHODS

The diagnostic material was collected from buccal mucosa from 98 adults, including 69 with HIV. Only positive cultures were included in the study.

RESULTS

Matching results were obtained in 45 samples, and there were nonmatching results in 35 samples, with the majority of these in the study group, constituting 50% of identifications within this group. A particularly common mistake resulting from the use of classical methods is the false identification of C. dubliniensis as C. albicans. Additionally, C. tropicalis proves to be difficult to identify.

CONCLUSIONS

Our results and literature data suggest that MALDI-TOF MS should be considered an effective alternative to classical methods in terms of fungi identification, especially among HIV-positive patients, due to the different morphology of fungal colonies.

Isolation, comparison of identification methods and antibiotic resistance of Cronobacter spp. in infant foods

Cronobacter spp. are opportunistic pathogens that cause serious infections, especially in infants, elderly, and immunocompromised people. Dehydrated infant foods are the main vehicle associated with infections caused by these bacteria. Thus, this study aims to investigate the occurrence of Cronobacter spp. in 152 commercial samples of dehydrated infant formulas (77 samples) and dehydrated infant cereals (75 samples), as well as characterize the isolates. Polymerase Chain Reaction (PCR) and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF/MS) methods for isolate identification were used, and their results compared. Furthermore, the susceptibility to 11 antibiotics was tested, and DNA sequencing of one isolate with multi-drug resistance was analyzed. No contamination in the infant formula samples was found, whereas 17.33% (13/75) of the infant cereal samples presented contamination with Cronobacter sakazakii. The identification results by PCR and MALDI-TOF/MS were divergent for some isolates. The antimicrobial resistance results showed a high incidence of resistance to cefazolin (94.4%) besides resistance to amoxicillin (9.45%), cefpodoxime (5.55%), streptomycin (1.35%), and trimethoprim/sulfamethoxazole (1.35%). Whole genome sequencing of one multi-drug resistant isolate showed six genes associated with antimicrobial resistance and an 82% possibility of being a human pathogen based on the presence of virulence factors. The presence of Cronobacter spp. in infant foods represents a risk for the infant's health. Moreover, the presence of a pathogenic multi-drug resistant isolate in infant's food reinforces the necessity of improving food safety policies to protect young children.