Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology

Artificial intelligence in bacterial diagnostics and antimicrobial susceptibility testing: Current advances and future prospects

Recently, artificial intelligence (AI) has emerged as a transformative tool, enhancing the speed, accuracy, and scalability of bacterial diagnostics. This review explores the role of AI in revolutionizing bacterial detection and antimicrobial susceptibility testing (AST) by leveraging machine learning models, including Random Forest, Support Vector Machines (SVM), and deep learning architectures such as Convolutional Neural Networks (CNNs) and transformers. The integration of AI into these methods promises to address the current limitations of traditional techniques, offering a path toward more efficient, accessible, and reliable diagnostic solutions. In particular, AI-based approaches have demonstrated significant potential in resource-limited settings by enabling cost-effective and portable diagnostic solutions, reducing dependency on specialized infrastructure, and facilitating remote bacterial detection through smartphone-integrated platforms and telemedicine applications. This review highlights AI's transformative role in automating data analysis, minimizing human error, and delivering real-time diagnostic results, ultimately improving patient outcomes and optimizing healthcare efficiency. In addition, we not only examine the current advances in machine learning and deep learning but also review their applications in plate counting, mass spectrometry, morphology-based and motion-based microscopic detection, holographic microscopy, colorimetric and fluorescence detection, electrochemical sensors, Raman and Surface-Enhanced Raman Spectroscopy (SERS), and Atomic Force Microscopy (AFM) for bacterial diagnostics and AST. Finally, we discuss the future directions and potential advancements in AI-driven bacterial diagnostics.

Healthcare-Associated Infections: The Role of Microbial and Environmental Factors in Infection Control-A Narrative Review

Healthcare-associated infections (HAIs), previously known as nosocomial infections, represent a significant threat to healthcare systems worldwide, prolonging patient hospital stays and the duration of antimicrobial therapy. One of the most serious consequences of HAIs is the increase in the rate of antibiotic resistance (AR) generated by the prolonged, frequent, and sometimes incorrect use of antibiotics, which leads to the selection of resistant bacteria, making treatment difficult and expensive, with direct consequences for the safety of patients and healthcare personnel. Therefore, timely and accurate diagnosis of HAIs is mandatory to develop appropriate infection prevention and control practices (IPC) and new therapeutic strategies. This review aimed to present the prevalence, risk factors, current diagnosis, including artificial intelligence (AI) and machine learning approaches, future perspectives in combating HAIs causative bacteria (phage therapy, microbiome-based interventions, and vaccination), and HAIs surveillance strategies. Also, we discussed the latest findings regarding the relationships of AR with climate change and environmental pollution in the context of the One Health approach. Phage therapy is an emerging option that can offer an alternative to ineffective antibiotic treatments for antibiotic-resistant bacteria causing HAIs. Clinical trials dealing with vaccine development for resistant bacteria have yielded conflicting results. Two promising strategies, fecal microbiota transplantation and probiotic therapy, proved highly effective against recurrent Clostridium difficile infections and have been shown to reduce HAI incidence in hospitalized patients undergoing antibiotic therapy. Artificial intelligence and machine learning systems offer promising predictive capabilities in processing large volumes of clinical, microbiological, and patient data but require robust data integration. Our paper argues that HAIs are still a global challenge, requiring stringent IPC policies, computer vision, and AI-powered tools. Despite promising avenues like integrated One Health approaches, optimized phage therapy, microbiome-based interventions, and targeted vaccine development, several knowledge gaps in clinical efficacy, standardization, and pathogen complexity remain to be answered.

The fungus Escovopsis (Ascomycota: Hypocreales): a critical review of its biology and parasitism of attine ant colonies

Two biological phenomena that contribute to increasing complexity in biological systems are mutualistic symbiotic interactions and the evolution of sociality. These two phenomena are also of fundamental importance to our understanding of the natural world. An organism that poses a threat to one or both of these is therefore also of great interest as it represents a challenge that mutualistic symbioses and social organisms have to overcome. This is the case with the fungus Escovopsis (Ascomycota: Hypocreales), which attacks the fungus garden of attine ants (Formicidae: Attina) such as the leaf cutters. This parasite has attracted much high-profile scientific interest for considerable time, and its study has been fruitful in understanding evolutionary, ecological and behavioural processes. Despite this, much of the biology and ecology of this organism remains unknown. Here we discuss this fungus and three sister genera (Escovopsioides, Luteomyces and Sympodiorosea) that until recently were considered as a single group. We first describe its position as the most highly specialised microbial symbiont in this system other than the mutualistic fungal cultivar itself and as that of greatest scientific interest. We then review the taxonomic history of the group and its macroevolution and biogeography. We examine what we know of its life cycle in the field - surprisingly little is known of how it is transmitted between colonies, but we explain what is known to date. We then review how it interacts with its host(s), first at the level of its direct interaction with the basidiomycete host fungi wherein we show the evidence for it being a mycoparasite; then at the colony level where empirical evidence points towards it being a parasite with a very low virulence or even merely a opportunist. Finally, we offer directions for future research.

Primary Axillary Actinomycosis: A Case Report on the Integration of Culture and Molecular Diagnostics for Accurate Diagnosis of Polymicrobial Infections

Actinomycosis is a chronic suppurative granulomatous disease caused by Actinomyces spp. Although cutaneous actinomycosis is rare, dermatologists must consider it due to its potential coexistence with other pathogens, often as part of polymicrobial infections. We present a rare case of primary axillary cutaneous actinomycosis in a young woman, likely triggered by cosmetic axillary hair removal and home shaving practices. Histological examination revealed characteristics of actinomycosis, including sulfur granules and Gram-positive filamentous structures. Bacterial cultures failed to isolate Actinomyces, but identified Staphylococcus epidermidis, S. aureus (MRSA), and Corynebacterium simulans, suggesting a polymicrobial infection contributing to the inflammatory response. Molecular analysis of DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue yielded a 675 bp PCR product using Actinomyces-specific primers. BLAST analysis confirmed the species as A. gerencseriae, establishing the diagnosis of actinomycosis. However, a 1000 bp PCR product obtained using universal 16S rDNA primers could not be sequenced successfully, likely due to the presence of multiple bacterial species. Notably, Actinomyces was detected only through molecular methods, while bacterial cultures identified the aforementioned bacteria. This discrepancy between FFPE-PCR results and bacterial culture findings demonstrates a key challenge in the microbiological diagnosis of polymicrobial infections. This case highlights the importance of integrating histopathological, microbiological, and molecular techniques for accurate pathogen identification in polymicrobial infections. The failure to detect Actinomyces in bacterial cultures, despite its presence in FFPE-PCR, suggests that conventional culture methods alone may be insufficient for diagnosing such infections. Extended culture durations, selective anaerobic culture techniques, and molecular diagnostic methods are essential for a comprehensive evaluation. Recognizing Actinomyces as more than a contaminant is important for timely diagnosis and effective treatment. Increased awareness of its potential involvement in polymicrobial infection should improve clinical outcomes.

Pseudopeptides of Marine Vibrio spp. from Taiwan and Their Combined Treatment Effects with Commercial Antibiotics

Vibrio strains, identified by 16S rDNA, were isolated from the marine environment surrounding Taiwan, revealing diverse bioactive effects, such as iron-chelating and antimicrobial activities. Notably, the hierarchical clustering dendrogram of mass spectrum profiles of the Vibrio strains using matrix-assisted laser desorption ionization time-of-flight, in contrast to the phylogenetic tree based on 16S rDNA sequencing analysis, exhibited a strong correlation with their observed bioactivities. Within this set, global natural products social molecular network analysis by LC-HRMS/MS highlighted that three strains, Vibrio tubiashii DJW05 - 1, Vibrio japonicus DJW05 - 8, and Vibrio fortis DJW21 - 4, shared similar bioactive pseudopeptides in the same cluster. Subsequent chromatographical isolation and purification yielded an unprecedented unsaturated diketopiperazine, (Z)-3-(2-methylpropylidene)-2,3-dihydropyrrolo[1,2-a]pyrazine-1,4-dione (1: ), along with a series of diketopiperazines, and a potential new annotated pseudopeptide (2: ), as well as three pseudopeptides, including andrimid (10: ), moiramide B (11: ), and moiramide C (12: ), and several alkaloids from V. tubiashii DJW05 - 1. Further investigation into the combined applications of the major antimicrobial compound and commercial antibiotics revealed that andrimid (10: ) displayed significant inhibitory effects against gram-positive Staphylococcus aureus, and gram-negative Escherichia coli, Salmonella typhimurium, and Acinetobacter baumannii, but not Pseudomonas aeruginosa. Nevertheless, the potential for synergistic and additive effects of andrimid (10: ) with certain antibiotics remains, presenting valuable prospects for medicinal applications.

Analysis of the Culturable Skin Microbiome of Horses from Southern Germany

Horses have close interactions with humans and are important as working animals and livestock. In contrast to smaller companion animals like cats and dogs, there is only little information available about their skin microbiome. The objective of this study was to identify and characterize the culturable cutaneous microbiome of healthy horses. Samples were taken from 14 horses from Southern Germany which were randomly enrolled in this study. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used as a method to detect the culturable microorganisms of horse skin. The most abundant culturable species of horse skin identified in this study include Bacillus cereus, Bacillus pumilus, Carnobacterium inhibens, Exiguobacterium sibiricum, Macrococcus carouselicus, Macrococcus goetzii and Staphylococcus equorum. Analyses of the bacteria across different body regions indicated the specific preferences of species for certain skin areas. In addition, our data hinted to an influence of the age of the horses tested and an influence between the four stables studied.

Impact of rapid identification by MALDI-TOF MS from positive blood cultures in Enterococcus spp. bloodstream infections

PURPOSE

Regarding bloodstream infections (BSI) Enterococcus spp. rank among the top five most common organisms. Due to enterococci intrinsic resistance, empiric antibiotic therapy is often inappropriate and early identification becomes crucial. Our objective was to assess the clinical impact of MALDI-TOF identification directly from positive blood cultures (BC) in Enterococcus spp. BSI (E-BSI).

METHODS

A retrospective cohort study included all adult patients with E-BSI from 2010 to 2017 in a tertiary hospital. ID consultation within 48 h and MALDI-TOF identification directly from BC within 24 h were inclusion criteria. The primary outcome was antimicrobial treatment change following MALDI-TOF and secondary outcomes included 30-day and 1-year mortality, length of stay (LOS) and antimicrobial de-escalation.

RESULTS

Among 267 BSI episodes, E. faecalis was isolated in 130 episodes (48.7%), E. faecium in 122 (45.7%), and 104 (39%) were polymicrobial. Empiric antibiotic therapy was inappropriate in 60.3% of patients. The LOS was 36 (IQR 20-64) days, 30-day and 1-year mortality were 16.1% and 43.4%, respectively. Enterococci identification with MALDI-TOF at the species level was possible in 66.3% cases and in 73% of monomicrobial cases. Antibiotics were changed in 85.3% of the former vs. 63.3% in remaining patients (p < 10- 4), and de-escalation occurred in 35% of subjects (vs. 12.2%,p = 10- 4). Changing antibiotics after correct identification was associated with a shorter LOS. In multivariate analysis, appropriate antibiotic therapy before MALDI-TOF was protective against 30-day mortality (aOR 0.40(0.08-1.96)), and appropriate antibiotic therapy afterwards against 1-year mortality (aOR 0.21(0.05-0.84)).

CONCLUSION

In E-BSI, direct MALDI-TOF identification from positive BC has a significant clinical impact due to a more frequent antibiotic spectrum correction and de-escalation. This may improve patient outcomes, reducing LOS and potentially mortality.

CLINICAL TRIAL NUMBER

Not applicable.

Comparison of Raman spectroscopy with mass spectrometry for sequence typing of Acinetobacter baumannii strains: a single-center study

The rapid sequence typing (ST) of bacterial strains is crucial for effective nosocomial infection control and mitigating the spread of nosocomial pathogens, e.g., Acinetobacter baumannii. While accurate in identifying A. baumannii strains, current typing methods are often impractical in clinical settings due to their time-consuming nature. This study developed a novel approach, combining surface-enhanced Raman spectroscopy (SERS) with machine-learning (ML) algorithms, to construct predictive models for A. baumannii sequence typing based on SERS spectra. The objective was to assess the feasibility of this integrated method for efficient sequence typing of A. baumannii strains. Clinically isolated A. baumannii strains (N = 267) were collected from a single hospital between 2013 and 2023. Based on multilocus sequence typing, 39 STs of A. baumannii were identified. Then, a SERS spectral database for all these strains was constructed, and predictive models based on eight ML algorithms were developed to predict SERS signals to determine their STs, among which the support vector machine (SVM) model had the best performance (fivefold cross-validation = 99.74%). The typing capacity of the SERS-SVM method was compared with that of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) for A. baumannii sequence typing, confirming the superiority of SERS-SVM over MALDI-TOF mass spectrometer. This pilot study lays the groundwork for employing the SERS-ML method to rapidly identify A. baumannii strain types in clinical laboratories, aiding in controlling bacterial pathogen transmission. Further studies are warranted to evaluate its potential in nosocomial surveillance systems, especially for rapidly identifying outbreaks within hospitals.

IMPORTANCE

The rapid and accurate sequence typing (ST) of bacterial pathogens is pivotal in controlling transmission within healthcare settings. Acinetobacter baumannii infection, known for its high transmissibility and drug resistance, presents a major challenge in nosocomial infection control. In this study, surface-enhanced Raman spectroscopy (SERS) was used to differentiate A. baumannii strains with distinct STs based on unique Raman spectral profiles. We then constructed and compared eight machine-learning models on SERS spectra to quickly identify bacterial STs. The results showed that the support vector machine model outperformed matrix-assisted laser desorption/ionization time-of-flight mass spectrometer in determining A. baumannii STs. This approach enables rapid identification of A. baumannii variants with different STs, supporting the early detection and control of nosocomial infections by this multidrug-resistant pathogen.

The performance of nanopore sequencing in rapid detection of pathogens and antimicrobial resistance genes in blood cultures

Rapid identification of causative microbes and their resistance is essential for effective monitoring, treating, and controlling of infectious diseases. Oxford Nanopore Technologies (ONT) is capable of generating and analyzing data in real time, its potential in clinically detecting pathogens and antimicrobial resistance (AMR) genes and subsequently predicting resistance phenotypes needs to be evaluated. In this study, positive blood cultures from 67 patients with bloodstream infection were collected for matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), ONT next generation sequencing (NGS) with a sequencing time limit of 1 h, and Illumina NGS. Antimicrobial susceptibility test was also performed. ONT NGS achieved 100 % coincidence rate (67/67) with MALDI-TOF-MS and Illumina NGS in pathogen identification, the sensitivity reached 100 %. Both ONT and Illumina NGS detected a high number of AMR genes (584 and 585, respectively). The consistent rate of ONT NGS against Illumina NGS for AMR genes detection reached 91.79 % (537/585). When considering antimicrobial susceptibility test results as the standard to evaluate the prediction value of ONT NGS in detecting AMR genes, ONT NGS showed competitive sensitivity (77.4 % vs 77.3 %), specificity (83.3 % vs 83.7 %), and accuracy (80.4 % vs 80.4 %) with Illumina NGS. Furthermore, the average time cost of ONT NGS (3.5 h) was significantly shorter than Illumina NGS (50.5 h) and MALDI-TOF-MS + antimicrobial susceptibility test (66-96 h). These findings highlight the potential of ONT NGS in rapidly and accurately detecting pathogens and AMR genes in clinical practices, which can assist in predicting resistance phenotypes and subsequently improving the diagnosis and treatment of infectious diseases.

Rapid identification of pathogenic bacteria from clinical positive blood cultures via virus-like magnetic bead enrichment and MALDI-TOF MS profiling

Reducing the time required for the detection of bacteria in blood samples is a critical area of investigation in the field of clinical diagnosis. Positive blood culture samples often require a plate culture stage due to the interference of blood cells and proteins, which can result in significant delays before the isolation of single colonies suitable for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. In this study, we developed a non-specific enrichment strategy based on SiO2-encapsulated Fe3O4 nanoparticles combined with MALDI-TOF MS for direct identification of bacteria from aqueous environments or positive blood culture samples. Three distinct types of Fe3O4@SiO2 magnetic nanoparticles (MNPs) with unique surface morphologies were developed: spherical MNPs with smooth surfaces (Fe3O4@SN), mesoporous silica coated MNPs (Fe3O4@MSN), and MNPs exhibiting a viral spiked structure (Fe3O4@VSN). These MNPs exhibited excellent binding affinity towards both Staphylococcus aureus and Klebsiella pneumoniae in PBS and artificial saliva solutions. Furthermore, the strategy of using Fe3O4@VSN, which involves non-specific interactions between bacterial cells and the virus-like surface, resulted in a dramatic reduction in the minimum detectable concentrations of target pathogens by up to 1000-fold compared to conventional methods. Our results demonstrate that the use of Fe3O4@VSN has the potential to significantly reduce the processing time required after blood culture and may be useful for enrichment and identification of microorganisms in complex clinical samples.

Capnocytophaga ochracea detected in cerebrospinal fluid of a meningioma patient: a case report

Capnocytophaga ochracea (C. ochracea) is a species of Gram-negative and facultative anaerobic bacterium. It was first reported in 1979 and isolated from both healthy and diseased sites in the oral flora. The bacteria can cause septicemia, endocarditis, endometritis, blepharoconjunctivitis and other infections. Herein, we present the first cerebrospinal fluid (CSF) infection case caused by C. ochracea in humans. Gram-negative fusiform, non-spore forming rods were detected in an anaerobic bottle of CSF culture obtained from a 50-year-old man who had been hospitalized for meningioma in Tianjin Huanhu Hospital. Although the organism could not be identified using a conventional method, it was finally identified as C. ochracea based on the results of metagenomics next generation sequencing, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and 16 S rDNA sequencing analysis. Subsequently, Streptococcus oralis was also detected in the CSF of the patient. The patient was treated with meropenem and vancomycin, and the infection was well controlled. The clinically rare C. ochracea can be pathogenic in central nervous system of humans.

Genomically-supported Redefinition of an Outbreak in a Pediatric Unit Caused by blaVIM -harboring Klebsiella michiganensis

BACKGROUND

Klebsiella michiganensis , a member of the Klebsiella oxytoca complex, is an emerging nosocomial pathogen known to frequently carry plasmids with antibiotic-resistance genes, including carbapenemases. Using genomics, this study redefined an outbreak alert of K. michiganensis carrying a blaVIM carbapenemase in a pediatric ward in a Spanish hospital.

METHODS

A total of 31 isolates of Verona integron-encoded metallo-β-lactamase (VIM)-carbapenemase K. oxytoca from suspected outbreak cases and unrelated controls from 2015 to 2022 were analyzed. Whole-genome sequencing (both short and long reads) was applied to determine phylogenetic relationships based on single-nucleotide polymorphisms (SNPs) and identify plasmids and antimicrobial resistance genes.

RESULTS

The sequences from 12 isolates identified in 2021 showed pairwise SNP distances ranging from 0 to 16 SNPs, confirming the outbreak. Examination of isolates before and after the study period revealed 7 additional cases, 2 in 2020 and 5 in 2022. The outbreak comprised 18 isolates from 17 patients in 3 different pediatric wards, together with 1 environmental sample. In all outbreak isolates, the blaVIM-1 gene was located within a gene cassette carried by a class 1 integron on an IncFIB(pQil) plasmid. A genomic network based on SNPs revealed 5 unsampled intermediate nodes, suggesting additional subclones that may have involved healthcare staff, patient relatives or environmental reservoirs. Blood and rectal isolates obtained from the same patient were positioned on separate branches of the network, making a direct evolutionary pathway between them unlikely.

CONCLUSIONS

Our study redefined the full extent of this K. michiganensis -VIM outbreak and highlights the critical importance of genomic analysis in accurately understanding outbreaks in healthcare settings.

Identification of Challenging Dermatophyte Species Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a widely adopted technique for bacterial and yeast identification in clinical laboratories but is less frequently applied to filamentous fungi due to inconsistent performance, limitations of commercial libraries, and variability of preparation methods. This study aimed to validate the efficiency of MALDI-TOF MS-based dermatophyte identification using the Bruker Biotyper system. Focusing on species from the Trichophyton, Nannizzia, Microsporum, and Epidermophyton genera, an in-house reference library was established and evaluated with clinical isolates. The expanded library, which combined the in-house and Bruker libraries, achieved significantly higher accuracy than the Bruker library alone, correctly identifying 90.7% (107/118) of isolates at the species level compared to 16.1% (19/118) by the Bruker library. This study presents an efficient, standardized MALDI-TOF MS protocol for routine dermatophyte identification and provides a review of the current status and influencing factors in MALDI-TOF MS-based dermatophyte identification strategies.

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

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

Identification of Southeast Asian Anopheles mosquito species with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using a cross-correlation approach

BACKGROUND

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is proposed for mosquito species identification. The absence of public repositories sharing mass spectra and open-source data analysis pipelines for fingerprint matching to mosquito species limits the widespread use of this technology. The objective of this study was to develop a free open-source data analysis pipeline for Anopheles species identification with MALDI-TOF MS.

METHODS

Anopheles mosquitoes were captured in 33 villages in Karen (Kayin) state in Myanmar. A subset of 403 specimens was selected for inclusion in either the reference or the test panel (270 and 133 specimens, respectively). Three hundred fifty-nine specimens could be identified with DNA barcodes and were assigned to 21 sensu stricto species and five sibling species pairs or complexes. A total of 3584 mass spectra of the head of these specimens identified with DNA barcoding were acquired and the similarity between mass spectra was quantified using a cross-correlation approach adapted from the published literature. A reference mass spectra database was created using all spectra of the PCR-identified specimens assigned to the reference panel. A simulation experiment was carried out by querying the reference database with the spectra of the test panel to evaluate the performance of species identification with MALDI-TOF MS at varying thresholds of the cross-correlation index for the algorithm to output an identification result and with varying numbers of technical replicates for the tested specimens, considering PCR identification results as the reference.

RESULTS

With one spot and a threshold value of -14 for the cross-correlation index on the log scale, the sensitivity was 0.99 [95% credible interval (CrI): 0.98-1.00], the predictive positive value was 0.99 (95% CrI: 0.98-0.99), and the accuracy was 0.98 (95% CrI: 0.97-0.99). It was not possible to directly estimate the sensitivity and negative predictive value because there was no true negative (i.e., queries of species not referenced in the database) in the assessment.

CONCLUSIONS

The cross-correlation approach can be used to match mass spectral fingerprints to predefined taxa. MALDI-TOF MS is a valuable tool for rapid, accurate, and affordable identification of Anopheles species.

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.

Characterizing Antimicrobial Effects of Radiation and Antibiotic Interactions on Staphylococcus aureus and Escherichia coli Using MALDI-TOF MS

Background/Objectives: Antibiotic-resistant bacteria are becoming a major challenge in human and veterinary medicine, as well as in food processing. Methods: In this study, the protein diversity in antibiotic-sensitive and -resistant strains of Staphylococcus aureus and Escherichia coli was investigated by exposing them to varying doses of gamma irradiation, with and without antibiotic presence. Changes in bacterial protein profiles were characterized using MALDI-TOF MS to reveal dose-dependent adaptations and potentiation effects under combined irradiation and antibiotic treatments. Results: The results indicate that MALDI-TOF MS effectively differentiates between sensitive and resistant strains, particularly at lower radiation doses (0, 0.2, and 0.4 kGy), with distinct separation in protein spectra. However, at 0.6 kGy, protein profiles plateaued, suggesting a potential threshold effect in radiation response. In 24-h cultures from irradiated Staphylococcus aureus, significant differences emerged in the resistant strain at 0.6 kGy in the presence of antibiotics, with further generational divergence dependent on initial antibiotic exposure. In the case of the sensitive strain, profiles were notably distinct at the 0.4 and 0.6 kGy doses, revealing dose- and treatment-specific responses. For Escherichia coli, generational differences between resistant and sensitive strains were apparent, though antibiotic effects on protein profiles were limited to the 0.6 kGy dose. Conclusions: The results underscore a potentiation interaction between irradiation and antibiotic exposure, affecting protein diversity and adaptation. Sensitive strains displayed heightened proteomic responses to minor treatment variations, while resistant strains exhibited more stable profiles across conditions. The findings highlight MALDI-TOF MS as a valuable tool in detecting proteomic biomarkers linked to bacterial resistance and stress adaptation.

I-dOne: A diagnostic tool in the field of identification of clinically relevant microbial strains

This study evaluates the performance of I-dOne, the first CE-IVD marked software for microbial species identification based on Attenuated Total Reflection Fourier Transform Infrared Spectroscopy (ATR-FTIR) and compares its results with MALDI-TOF MS technology (Vitek MS, bioMérieux). A total of 410 clinical isolates were analyzed, spanning 45 species and 24 genera. I-dOne demonstrated a high agreement rate (97.3 %) with the Vitek MS, meeting CLSI standard for microbial identification accuracy. Additionally, this study explored the development of a novel algorithm within I-dOne to discriminate between Bacteroides fragilis and Bacteroides ovatus strains, overcoming the current limitations in species-level differentiation. Finally, the influence of ageing under prolonged aerobic exposure on ATR-FTIR profiles was investigated, highlighting no significant spectral changes in Bacteroides fragilis strains under prolonged aerobic exposure. These findings underscore the accuracy of I-dOne software in microbial identification, offering a reliable alternative to conventional methods.

Actinomyces Species As Emerging Pathogens: An Observational Study of Clinical Infections and Microbiological Implications

INTRODUCTION

 Actinomyces species, Gram-positive filamentous anaerobic microaerophilic organisms, are commensals of the human oropharynx, gastrointestinal, and urogenital tracts. Actinomycosis is rare and occurs when tissue integrity is compromised, typically in a polymicrobial fashion. There is an emerging rise in Actinomyces species-associated infections, with attendant therapeutic challenges.

AIM

We evaluated the pattern, presentation, and risk factors for Actinomyces species-associated infections.

MATERIAL AND METHODS

Blood culture, tissue, fluids, bone, and swab samples with isolated Actinomyces species were evaluated between July 2016 and April 2021. The antibiotic susceptibility of the isolated Actinomyces was obtained as per the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Electronic medical records were retrospectively evaluated for demographic and clinicopathological data relating to the patients.

RESULTS

A total of 145 patients were evaluated, comprising 63 males and 82 females; the mean age was 49 years. About 52.4% and 59.3% of comorbidities and risk factors for Actinomyces species infection susceptibility, respectively. The most common presentations were infected sebaceous cysts (25.5%) and pilonidal abscesses (13.8%). Actinomyces species were isolated from swabs (78), pus (32), blood cultures (26), body fluids (6), soft tissues (2), and bone fragments (1). Eleven different Actinomyces species were isolated, and commonly isolated species were Actinomyces neuii (24.8%), Actinomyces turicensis (22.8%), and Actinomyces europaeus (13.8%). About 57.2% of the samples had mixed microorganisms isolated; 26 of 29 blood culture samples yielded Actinomyces, and 6 of 29 yielded mixed microbial agents. A majority (78.6%) of the patients received empirical antibiotics, and 79% of the antibiotic choice was appropriate. Conclusion​​​​​: Actinomyces species isolates and infections are increasingly reported, potentially attributed to improved culture techniques. We recommend epidemiology and resistance surveillance in Actinomyces species-associated infections.

Multiple introductions of NRCS-A Staphylococcus capitis to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey

Background. The Staphylococcus capitis NRCS-A strain has emerged as a global cause of late-onset sepsis associated with outbreaks in neonatal intensive care units (NICUs) whose transmission is incompletely understood.Methods. Demographic and clinical data for 45 neonates with S. capitis and 90 with other coagulase-negative staphylococci (CoNS) isolated from sterile sites were reviewed, and clinical significance was determined. S. capitis isolated from 27 neonates at 2 hospitals between 2017 and 2022 underwent long-read (ONT) (n=27) and short-read (Illumina) sequencing (n=18). These sequences were compared with S. capitis sequenced from blood culture isolates from other adult and paediatric patients in the same hospitals (n=6), S. capitis isolated from surface swabs (found in 5/150 samples), rectal swabs (in 2/69 samples) in NICU patients and NICU environmental samples (in 5/114 samples). Reads from all samples were mapped to a hybrid assembly of a local sterile site strain, forming a complete UK NRCS-A reference genome, for outbreak analysis and comparison with 826 other S. capitis from the UK and Germany.Results. S. capitis bacteraemia was associated with increased length of NICU stay at sampling (median day 22 vs day 12 for other CoNS isolated; P=0.05). A phylogeny of sequenced S. capitis revealed a cluster comprised of 25/27 neonatal sterile site isolates and 3/5 superficial, 2/2 rectal and 1/5 environmental isolates. No isolates from other wards belonged to this cluster. Phylogenetic comparison with published sequences confirmed that the cluster was NRCS-A outbreak strain but found a relatively high genomic diversity (mean pairwise distance of 84.9 SNPs) and an estimated NRCS-A S. capitis molecular clock of 5.1 SNPs/genome/year (95% credibility interval 4.3-5.9). The presence of S. capitis in superficial cultures did not correlate with neonatal bacteraemia, but both neonates with rectal NRCS-A S. capitis carriage identified also experienced S. capitis bacteraemia.Conclusions. S. capitis bacteraemia occurred in patients with longer NICU admission than other CoNS. Genomic analysis confirms clinically significant infections with the NRCS-A S. capitis strain, distinct from non-NICU clinical samples. Multiple introductions of S. capitis, rather than prolonged environmental persistence, were seen over 5 years of infections.

Invasive Streptococcus pseudopneumoniae infection in an adult patient with acute community-acquired meningitis: a case report

Rapid identification of pathogens in acute meningitis is critical for timely treatment. However, traditional methods often face limitations in differentiating closely related species such as Streptococcus pneumoniae and Streptococcus pseudopneumoniae. We report a case of community-acquired meningitis caused by S. pseudopneumoniae secondary to a cerebrospinal fluid fistula, highlighting the microbiological diagnostic challenges.

Detection of methicillin resistance of Staphylococcus aureus in vitreous humor using MALDI-TOF MS and Fc-MBL@Fe3O4 enrichment

Endophthalmitis is a serious infectious eye disease that causes permanent vision loss. This study developed a method for rapid identification and drug resistance analysis of pathogens in vitreous humor. After short-term rapid culture, 30 Staphylococcus aureus isolates were enriched and purified from the vitreous humor using Fc-MBL@Fe3O4, and then identified by MALDI-TOF MS. The bacterial solution was adjusted to 106 CFU/mL and mixed with CAMHB containing cefoxitin (4 µg/mL) at the same volume. After culture, it was enriched by Fc-MBL@Fe3O4 and identified by MALDI-TOF MS. MRSA was judged according to whether the bacteria could successfully be identified. The enrichment efficiency of Fc-MBL@Fe3O4 for S. aureus in CAMHB was 88.1%. The detection rate of S. aureus reached 100% after 8 h of vitreous humor culture. The best test performance was achieved with Fc-MBL@Fe3O4 enrichment after a 3 h incubation. At this time point, 96.7% validity, 100% sensitivity, and 100% specificity were achieved. Thus, the identification and drug resistance analysis of S. aureus (51-110 CFU) in vitreous humor was completed within 11 h. This study provides a new method for rapid clinical diagnosis of endophthalmitis and precise treatment with antibiotics.

Splash Basins in the Operating Room: Clean or Contaminated? A Study on Bacterial Contamination in Splash Basins Used to Rinse Surgical Instruments During Surgery

Background: Preventing postoperative infection and promoting patient safety are essential responsibilities of the operating room nurse. In some hospitals, splash basins are used to rinse instruments during surgery, although previous studies emphasise the risk of bacterial contamination. A recent systematic review calls for further investigation into surgical teams' use of splash basins. Objectives: Our objective was to investigate bacterial contamination in splash basins and to identify the variables that may have an influence on this contamination. Methods: This prospective observational pilot study involved collecting, cultivating, and analysing water samples obtained from splash basins during operations performed in the thoracic and neurosurgical departments. The ventilation systems, length of surgery, number of instruments in the splash basin, number of persons present in the operating room, frequency of door openings during surgery, and type of bacteria were observed. Results: Bacterial growth was found in 44% of the final water samples: 41% from the thoracic surgical department, which had laminar airflow ventilation systems/unidirectional airflow ventilation, and 47% from the neurosurgical department, which had conventional ventilation systems/turbulent mixing ventilation. However, the binary logistic regression analysis revealed no significant correlation between bacterial growth and the ventilation systems, length of surgery, number of instruments in the splash basin, number of people in the operating room, or frequency of door openings. The most common types of bacteria found were coagulase-negative staphylococci and Micrococcus luteus. Conclusions: Splash basins become contaminated with bacteria during surgery. Therefore, using splash basins with sterile water is not recommended. Further research is needed to determine the best evidence-based practice for rinsing instruments perioperatively.

Tsukamurella conjunctivitidis peritonitis diagnosed by 16S rRNA gene sequencing in a patient undergoing peritoneal dialysis

Peritoneal dialysis (PD)-associated peritonitis remains a serious and life-threatening complication in patients undergoing PD. Majority of peritonitis cases are caused by bacteria, with coagulase-negative Staphylococcus being the most common cause. Tsukamurella species are obligate aerobic gram-positive bacilli found in various environments; however, peritonitis caused by Tsukamurella species in association with PD is rare, with few reports of infections caused by T. conjunctivitidis, including PD-associated peritonitis. We describe a rare case of peritonitis caused by T. conjunctivitidis in a patient undergoing PD. A 62-year-old man undergoing PD was referred to our hospital for fever and abdominal pain lasting for 4 days and was diagnosed with PD-associated peritonitis based on abdominal pain, cloudy effluent, elevated white blood cell count in the peritoneal fluid, and presence of gram-positive rods in the effluent culture. Yellow-grayish, dry, membrane-like colonies were observed on a blood agar plate. The isolated strain was identified as T. conjunctivitidis through 16S rRNA gene sequencing. Because the PD-associated peritonitis was refractory to antibiotics, the PD catheter was removed, and the patient was switched to hemodialysis on day 21 of admission. Clinicians should consider peritonitis caused by T. conjunctivitidis as a differential diagnosis in cases where diagnosis using routine examination is challenging. Notably, 16S rRNA gene sequencing is a useful diagnostic tool for identifying T. conjunctivitidis. Further analyses of similar cases are required to understand the characteristics of such infections and establish adequate diagnostic methods and treatment regimens.

Porin expression in clinical isolates of Klebsiella pneumoniae: a comparison of SDS-PAGE and MALDI-TOF/MS and limitations of whole genome sequencing analysis

BACKGROUND

The permeability of the outer membrane barrier modulates the susceptibility of microorganisms to antimicrobial agents. Loss or structural alterations of porins contribute to decreased antibiotic concentration of multiple antimicrobial agents. Precise definition of porin profiles is of critical importance to understand the role of porins in antimicrobial resistance. The objectives of this study are to compare the expression patterns of major outer membrane proteins (OMP) of clinical isolates of Klebsiella pneumoniae obtained with Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF/MS), with those obtained with sodium-dodecyl-sulphate polyacrylamide gel electrophoresis (SDS-PAGE), and to correlate porin expression patterns with the sequences of porins genes defined with whole genome sequencing (WGS).

METHODS

The OMP profiles of 26 clinical isolates of K. pneumoniae and of strain ATCC 13883 (wild-type) and ATCC 700603 (producing SHV-18) have been determined using both SDS-PAGE and MALDI-TOF/MS. SDS-PAGE was performed using both homemade and commercial gels, and protein bands were identified by liquid chromatography coupled to mass spectrometry. A rapid extraction method was used to analyse OMPs by MALDI-TOF/MS. The sequences of porin genes were obtained by WGS and mutations were defined by BLAST.

RESULTS

Same results were obtained for all strains either using SDS-PAGE or MALDI-TOF/MS. SDS-PAGE showed protein bands of ~ 35, ~36, and ~ 37 kDa, identified as OmpA, OmpK36 and OmpK35, respectively. By MALDI-TOF/MS, peaks at ~ 35,700 (OmpA), ~ 37,000 (OmpK35), and ~ 38,000 (OmpK36) m/z were detected. ompK35 was intact in nine wild-type isolates and was truncated in 13 isolates, but OmpK35 was not observed in 3 isolates without mutations in ompK35. One point mutation was detected in another isolate and multiple mutations were detected in the remaining isolate. ompK36 was truncated in two isolates lacking this protein and presented one point mutation (n = 1) or multiple mutations in the remaining isolates.

CONCLUSION

MALDI-TOF/MS was reliable for porin detection, but because of the complex regulation of porin genes, WGS cannot always anticipate protein expression, as observed with SDS-PAGE and MALDI-TOF/MS.

Characterization of middle ear microbiome in otitis media with effusion in Hungarian children: Alloiococcus otitidis may potentially hamper the microbial diversity

Introduction

Although otitis media with effusion (OME) is a common cause of hearing impairment in children, little is known about its microbiological background. We aimed to analyse the microbiome of the middle ear fluid (MEF) in OME to identify microbiological, demographic and environmental factors that may potentially influence the middle ear microbiome. In addition, we aimed to compare the results of conventional culture techniques and PCR-based methods.

Methods

39 samples from children with OME were investigated using conventional culture and 16S rRNA sequencing. Bioinformatic analyses were carried out to assess the microbial communities and their association with clinical data.

Results

By conventional culture technique bacteria could be cultured in 33 % of the MEF samples; the most frequent bacterium was Haemophilus influenzae, followed by Staphylococcus species, Cutibacterium acne, and Streptococcus species. The 16S rRNA analysis showed that Alloiococcus was the most abundant bacterium, followed by Haemophilus, Streptococcus. and Sphingobium.A "High Alloiococcus group" with significantly lower and a "Low Alloiococcus group" with significantly higher alpha and beta diversity could be defined. Children born by Caesarean sections had lower beta and Shannon diversity than patients born by natural birth. Breastfeeding for at least six months showed a negative correlation with alpha diversity. Age, previous antibiotic treatment, parental smoking, duration of symptoms, existence of siblings, did not alter the significantly bacterial composition of MEF samples and there were no significant differences in regard to alpha or beta diversity.

Conclusion

The conventional culture technique and 16S rRNA results were not congruent. Remarkably, Alloiococcus could not be cultured at all, even by 16S rRNA analysis the presence of Alloiococcus seems to be important. Based on our results, A. otitidis possibly impacts the diversity of middle ear microbiome in children with OME. However, further studies are required to determine the role of A. otidis in middle ear pathologies.

Investigation of Carriers of Salmonella and Other Hydrogen Sulphide-Positive Bacteria in the Digestive Content of Fish from the Atlantic Area of Macaronesia: A Comparative Study of Identification by API Gallery and MALDI-TOF MS

Salmonella spp. are known pathogens in fish, with their presence potentially resulting from the contamination of the aquatic environment or improper handling. Accurate bacterial identification is crucial across various fields, including medicine, microbiology, and the food industry, and thus a range of techniques are available for this purpose. In this study, Salmonella spp. and other hydrogen sulphide-positive bacteria were investigated in the digestive contents of fish destined for consumption from the Atlantic area of Macaronesia. Two identification techniques were compared: the traditional API method and the MALDI-TOF MS technique. For the identification of Salmonella spp. carriers, 59 samples were processed following ISO 6579-1:2017. A total of 47 strains of Gram-negative bacilli were obtained. No Salmonella spp. isolates were detected. The most frequent genus was Enterobacter (76.50%), followed by Shewanella (10.63%). The MALDI-TOF MS technique showed a high concordance with the API technique, with 72.34% concordance at the species level. Both techniques demonstrated a high degree of concordance in the identification of Enterobacter cloacae, with 87.23% genus-level concordance and 12.76% non-concordant identifications. This study highlights the limitations of the API technique and the speed and precision of MALDI-TOF MS. The identified bacteria could pose a health risk to humans.

Rapid and accurate identification of yeast subspecies by MALDI-MS combined with a cell membrane disruption reagent

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been widely used for microbial analysis. However, due to the impenetrable shell of fungi the direct identification of fungi remains challenges. Targeting on this problem, the yeast Saccharomyces cerevisiae (S. cerevisiae) was selected as a model fungus, and a new fungal cell membrane disruption reagent C18-G1 was used before MALDI-MS detection. As a result, much more intensive peaks which distributed in wider m/z range of S. cerevisiae have been identified in comparison with the use of traditional fungal pretreatment methods. Furthermore, a differential peak at m/z 4993 between two subspecies of S. cerevisiae has been identified. The corresponding protein with exclusive sequence of the specific peak was obtained based on MS/MS fragments and database searching. In addition, the method was successfully applied for the discrimination of four commercial yeasts.

The impact of optimizing microbial diagnosis processes on clinical and healthcare economic outcomes in hospitalized patients with bloodstream infections

PURPOSE

Bloodstream infections (BSIs) are associated with significant morbidity, mortality and costs, while prolonged blood culture (BC) diagnosis may delay the initiation of targeted therapy. This study evaluates the impact of an optimized microbiology laboratory process on turnaround times, antibiotic use, clinical outcomes and economics for hospitalized BSI patients.

METHODS

A pre-post study was conducted in a Chinese hospital in which BSI derived BC results before (Oct. 2020- Sep. 2021) and after (Oct. 2021- Sep. 2022) newly implemented microbiology diagnostics and workflow changes were analyzed. Turnaround times, antibiotic initiation, length of stay and in-hospital costs were compared.

RESULTS

From 213 included patients, 134 were pre-optimization (pre-op) and 79 were post-optimization (post-op) cases. The median time from blood sample collection (BSC) to pathogen identification (ID) decreased from 70.12 to 47.43 h post-op (P < 0.001). The median time from BSC to the first ID report related initiation of pathogen-directed antibiotic use decreased from 88.48 to 47.85 h post-op (P < 0.001). The average hospital stay decreased from 19.54 to 16.79 days and 30-day readmissions declined from 18.7 to 13.9%, while the mean total antimicrobial drug usage costs decreased by 3,889 CNY per patient (P = 0.022) after optimization.

CONCLUSIONS

Implementing new diagnostics technologies and optimizing laboratory workflows significantly reduced antimicrobial drug usage costs, shortened the time to ID results and improved the timeliness of appropriate antibiotic choices to treat BSIs. Investments in faster testing and process improvements were clearly beneficial for patient outcomes and healthcare economics.

Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens

Phage therapy is gaining increasing interest in the fight against critically antibiotic-resistant nosocomial pathogens. However, the narrow host range of bacteriophages hampers the development of broadly effective phage therapeutics and demands precision approaches. Here, we combine large-scale phylogeographic analysis with high-throughput phage typing to guide the development of precision phage cocktails targeting carbapenem-resistant Acinetobacter baumannii, a top-priority pathogen. Our analysis reveals that a few strain types dominate infections in each world region, with their geographical distribution remaining stable within 6 years. As we demonstrate in Eastern Europe, this spatiotemporal distribution enables preemptive preparation of region-specific phage collections that target most local infections. Finally, we showcase the efficacy of phage cocktails against prevalent strain types using in vitro and animal infection models. Ultimately, genomic surveillance identifies patients benefiting from the same phages across geographical scales, thus providing a scalable framework for precision phage therapy.

Diagnostic performance of an automated robot for MALDI target preparation in microbial identification

The MBT Pathfinder is an automated colony-picking robot designed for efficient sample preparation in matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. This article presents results from three key experiments evaluating the instrument's performance in conjunction with MALDI Biotyper instrument. The method comparison experiment assessed its clinical performance, demonstrating comparable results with gram-positive, gram-negative, and anaerobic bacteria (scores larger than 2.00) and superior performance over simple direct yeast transfer (score: 1.80) when compared to samples prepared manually. The repeatability experiment confirmed consistent performance over multiple days and labs (average log score: 2.12, std. deviation: 0.59). The challenge panel experiment showcased its consistent and accurate performance across various samples and settings, yielding average scores between 1.76 and 2.19. These findings underline the MBT Pathfinder as a reliable and efficient tool for MALDI-TOF mass spectrometry sample preparation in clinical and research applications.

Discovery of clinical isolation of drug-resistant Klebsiella pneumoniae with overexpression of OqxB efflux pump as the decisive drug resistance factor

Background emergence of multidrug-resistant (MDR) bacterial strains is a public health concern that threatens global and regional security. Efflux pump-overexpressing MDR strains from clinical isolates are the best subjects for studying the mechanisms of MDR caused by bacterial efflux pumps. A Klebsiella pneumoniae strain overexpressing the OqxB-only efflux pump was screened from a clinical strain library to explore reverse OqxB-mediated bacterial resistance strategies. We identified non-repetitive clinical isolated K. pneumoniae strains using a matrix-assisted laser desorption/ionization time-of-flight (TOF) mass spectrometry clinical TOF-II (Clin-TOF-II) and susceptibility test screening against levofloxacin and ciprofloxacin. And the polymorphism analysis was conducted using pulsed-field gel electrophoresis. Efflux pump function of resistant strains is obtained by combined drug sensitivity test of phenylalanine-arginine beta-naphthylamide (PaβN, an efflux pump inhibitor) and detection with ethidium bromide as an indicator. The quantitative reverse transcription PCR was performed to assess whether the oqxB gene was overexpressed in K. pneumoniae isolates. Additional analyses assessed whether the oqxB gene was overexpressed in K. pneumoniae isolates and gene knockout and complementation strains were constructed. The binding mode of PaβN with OqxB was determined using molecular docking modeling. Among the clinical quinolone-resistant K. pneumoniae strains, one mediates resistance almost exclusively through the overexpression of the resistance-nodulation-division efflux pump, OqxB. Crystal structure of OqxB has been reported recently by N. Bharatham, P. Bhowmik, M. Aoki, U. Okada et al. (Nat Commun 12:5400, 2021, https://doi.org/10.1038/s41467-021-25679-0). The discovery of this strain will contribute to a better understanding of the role of the OqxB transporter in K. pneumoniae and builds on the foundation for addressing the threat posed by quinolone resistance.IMPORTANCEThe emergence of antimicrobial resistance is a growing and significant health concern, particularly in the context of K. pneumoniae infections. The upregulation of efflux pump systems is a key factor that contributes to this resistance. Our results indicated that the K. pneumoniae strain GN 172867 exhibited a higher oqxB gene expression compared to the reference strain ATCC 43816. Deletion of oqxB led a decrease in the minimum inhibitory concentration of levofloxacin. Complementation with oqxB rescued antibiotic resistance in the oqxB mutant strain. We demonstrated that the overexpression of the OqxB efflux pump plays an important role in quinolone resistance. The discovery of strain GN 172867 will contribute to a better understanding of the role of the OqxB transporter in K. pneumoniae and promotes further study of antimicrobial resistance.

Atypical Periprosthetic Joint Infection Post-Total Knee Arthroplasty: A Case of Actinomyces europaeus

Periprosthetic joint infection (PJI) is a significant complication following total knee arthroplasty (TKA), representing a substantial challenge due to the difficulty in diagnosis and management. The main causes are predominantly common bacteria, but rare pathogens such as Actinomyces europaeus can complicate diagnosis and treatment. We report a unique case of a 75-year-old Caucasian patient with a history of multiple comorbidities including obesity, arterial hypertension, total thyroidectomy, rheumatoid arthritis, and prior venous thrombosis. The patient presented with pain, functional impairment, and signs of inflammation in the left knee seven months post-TKA. An active fistula was also noted. Initial management with broad-spectrum antibiotics did not halt the progression of infection, prompting further diagnostic evaluation. Actinomyces europaeus was identified as the causative agent through cultures and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A two-stage surgical intervention was necessitated, involving removal of the infected prosthesis followed by reimplantation with an antibiotic-impregnated spacer. This case highlights the importance of considering rare organisms like Actinomyces europaeus in atypical PJI. It underscores the necessity of advanced diagnostic tools and susceptibility testing in managing infections effectively. Timely intervention, tailored antimicrobial therapy, and appropriate surgical strategies are crucial for successful outcomes in infections involving uncommon pathogens.

Advancements in rapid diagnostics and genotyping of Piscirickettsia salmonis using Loop-mediated Isothermal Amplification

Introduction

Piscirickettsia salmonis, the causative agent of Piscirickettsiosis, poses a significant threat to the Chilean aquaculture industry, resulting in substantial economic losses annually. The pathogen, first identified as specie in 1992, this pathogen was divided into two genogroups: LF-89 and EM-90, associated with different phenotypic mortality and pathogenicity. Traditional genotyping methods, such as multiplex PCR, are effective but limited by their cost, equipment requirements, and the need for specialized expertise.

Methods

This study validates Loop-mediated Isothermal Amplification (LAMP) as a rapid and specific alternative for diagnosing P. salmonis infections. We developed the first qPCR and LAMP assay targeting the species-conserved tonB receptor gene (tonB-r, WP_016210144.1) for the specific species-level identification of P. salmonis. Additionally, we designed two genotyping LAMP assays to differentiate between the LF-89 and EM-90 genogroups, utilizing the unique coding sequences Nitronate monooxygenase (WP_144420689.1) for LF-89 and Acid phosphatase (WP_016210154.1) for EM-90.

Results

The LAMP assays demonstrated sensitivity and specificity comparable to real-time PCR, with additional benefits including rapid results, lower costs, and simplified operation, making them particularly suitable for field use. Specificity was confirmed by testing against other salmonid pathogens, such as Renibacterium salmoninarum, Vibrio ordalii, Flavobacterium psychrophilum, Tenacibaculum maritimum, and Aeromonas salmonicida, with no cross-reactivity observed.

Discussion

The visual detection method and precise differentiation between genogroups underscore LAMP's potential as a robust diagnostic tool for aquaculture. This advancement in the specie detection (qPCR and LAMP) and genotyping of P. salmonis represents a significant step forward in disease management within the aquaculture industry. The implementation of LAMP promises enhanced disease surveillance, early detection, and improved management strategies, ultimately benefiting the salmonid aquaculture sector.

Occurrence, Molecular Serogroups, Antimicrobial Susceptibility and Identification by MALDI-TOF MS of Listeria monocytogenes Isolated from RTE Meat Products in Southern Poland

L. monocytogenes is considered one of the most dangerous foodborne pathogens. This study aimed to determine the occurrence of L. monocytogenes in RTE meat products from southern Poland, including serogroups and antimicrobial susceptibility, and to assess the usefulness of MALDI-TOF MS as a tool for identifying L. monocytogenes. A total of 848 production batches of RTE meat products were analyzed for L. monocytogenes. All L. monocytogenes isolates were serotyped using the multiplex PCR method, tested for antimicrobial susceptibility using the disk diffusion method and identified using the MALDI-TOF MS method. L. monocytogenes was detected in 52/848 batches of RTE meat products (6.13%). The isolates belonged to four serogroups: 17/52 (33%) isolates to IVb; 15/52 (29%) isolates to IIa; 10/52 (19%) isolates to IIc and 10/52 (19%) isolates to IIb. All isolates (52/52) showed susceptibility to the tested antimicrobials. Using MALDI-TOF MS, 10/52 isolates (19.2%) were identified at the level of secure genus identification, probable species identification; 37/52 isolates (71.2%) were identified at the level of probable genus identification; 3/52 isolates (5.8%) were incorrectly identified as L. innocua; and 2/52 isolates (3.8%) were not identified. The occurrence of L. monocytogenes in RTE meat products was low. Almost half of the analyzed isolates were L. monocytogenes of serogroups, which are most often associated with listeriosis in humans in Poland. All isolates showed susceptibility to five commonly used antimicrobials for treating listeriosis. The use of MALDI-TOF MS as a tool for the identification of L. monocytogenes indicated its limitations related to the insufficient representation of the pathogen in the reference database.

Recent Development in Detection and Control of Psychrotrophic Bacteria in Dairy Production: Ensuring Milk Quality

Milk is an ideal environment for the growth of microorganisms, especially psychrotrophic bacteria, which can survive under cold conditions and produce heat-resistant enzymes. Psychrotrophic bacteria create the great problem of spoiling milk quality and safety. Several ways that milk might get contaminated by psychrotrophic bacteria include animal health, cowshed hygiene, water quality, feeding strategy, as well as milk collection, processing, etc. Maintaining the quality of raw milk is critically essential in dairy processing, and the dairy sector is still affected by the premature milk deterioration of market-processed products. This review focused on the recent detection and control strategies of psychrotrophic bacteria and emphasizes the significance of advanced sensing methods for early detection. It highlights the ongoing challenges in the dairy industry caused by these microorganisms and discusses future perspectives in enhancing milk quality through innovative rapid detection methods and stringent processing controls. This review advocates for a shift towards more sophisticated on-farm detection technologies and improved control practices to prevent spoilage and economic losses in the dairy sector.

Evaluation of MALDI-TOF mass spectrometry coupled with ClinProTools as a rapid tool for toxin-producing Clostridioides difficile

INTRODUCTION

The performance of MALDI-TOF MS combined with analysis platform for identification of toxin-producing Clostridiodes difficile is yet to be known.

METHODS

Between August 2018 and September 2020, 61 isolates from stool specimens of patients with C. difficile-associated diarrhea were analyzed using the MALDI Biotyper system. A C. difficile toxin-producer detection model was developed using ClinProTools. The model was validated using 28 known strains that differed from the isolates used to develop the model.

RESULTS

The sensitivity and specificity of the Genetic Algorithm (GA) model using isolates grown on Brucella with hemin and vitamin K (BHK) agar plates were 91.7% and 44.4%, respectively. When isolates grown on cycloserine-cefoxitin mannitol agar were analyzed by the model, sensitivity and specificity were 6.3% and 100%, respectively. The GA model using BHK medium showed the highest discriminatory performance in detection of toxin-producing C. difficile. However, a discrepancy in detection of toxin-producing C. difficile was observed in the results generated when the model was being developed and when the model was validated which suggests that incubation conditions may have affected the results.

CONCLUSION

MALDI-TOF analysis using ClinProTools has a potential to be a cost-effective tool for rapid diagnosis and contribute to antimicrobial stewardship by differentiating toxin-producing C. difficile from non-producers.

Applying MALDI-TOF MS to resolve morphologic and genetic similarities between two Dermacentor tick species of public health importance

Hard ticks (Acari: Ixodidae) have been historically identified by morphological methods which require highly specialized expertise and more recently by DNA-based molecular assays that involve high costs. Although both approaches provide complementary data for tick identification, each method has limitations which restrict their use on large-scale settings such as regional or national tick surveillance programs. To overcome those obstacles, the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been introduced as a cost-efficient method for the identification of various organisms, as it balances performance, speed, and high data output. Here we describe the use of this technology to validate the distinction of two closely related Dermacentor tick species based on the development of the first nationwide MALDI-TOF MS reference database described to date. The dataset obtained from this protein-based approach confirms that tick specimens collected from United States regions west of the Rocky Mountains and identified previously as Dermacentor variabilis are the recently described species, Dermacentor similis. Therefore, we propose that this integrative taxonomic tool can facilitate vector and vector-borne pathogen surveillance programs in the United States and elsewhere.

Bacterial Pesticides: Mechanism of Action, Possibility of Food Contamination, and Residue Analysis Using MS

As Sustainable Development Goals (SDGs) and the realities of climate change become widely accepted around the world, the next-generation of integrated pest management will become even more important for establishing a sustainable food production system. To meet the current challenge of food security and climate change, biological control has been developed as one sustainable crop protection technology. However, most registered bacteria are ubiquitous soil-borne bacteria that are closely related to food poisoning and spoilage bacteria. Therefore, this review outlined (1) the mechanism of action of bacterial pesticides, (2) potential concerns about secondary contamination sources associated with past food contamination, and, as a prospective solution, focused on (3) principles and methods of bacterial identification, and (4) the possibility of identifying residual bacteria based on mass spectrometry.

Mass spectrometry imaging as a promising analytical technique for herbal medicines: an updated review

Herbal medicines (HMs) have long played a pivotal role in preventing and treating various human diseases and have been studied widely. However, the complexities present in HM metabolites and their unclear mechanisms of action have posed significant challenges in the modernization of traditional Chinese medicine (TCM). Over the past two decades, mass spectrometry imaging (MSI) has garnered increasing attention as a robust analytical technique that enables the simultaneous execution of qualitative, quantitative, and localization analyses without complex sample pretreatment. With advances in technical solutions, MSI has been extensively applied in the field of HMs. MSI, a label-free ion imaging technique can comprehensively map the spatial distribution of HM metabolites in plant native tissues, thereby facilitating the effective quality control of HMs. Furthermore, the spatial dimension information of small molecule endogenous metabolites within animal tissues provided by MSI can also serve as a supplement to uncover pharmacological and toxicological mechanisms of HMs. In the review, we provide an overview of the three most common MSI techniques. In addition, representative applications in HM are highlighted. Finally, we discuss the current challenges and propose several potential solutions. We hope that the summary of recent findings will contribute to the application of MSI in exploring metabolites and mechanisms of action of HMs.

Straightforward Creation of Multishell Hollow Hybrids for an Integrated Metabolic Monitoring System in Disease Management

Multidimensional metabolic analysis has become a new trend in establishing efficient disease monitoring systems, as the constraints associated with relying solely on a single dimension in refined monitoring are increasingly pronounced. Here, coordination polymers are employed as derivative precursors to create multishell hollow hybrids, developing an integrated metabolic monitoring system. Briefly, metabolic fingerprints are extracted from hundreds of serum samples and urine samples, encompassing not only membranous nephropathy but also related diseases, using high-throughput mass spectrometry. With optimized algorithm and initial feature selection, the established combined panel demonstrates enhanced accuracy in both subtype differentiation (over 98.1%) and prognostic monitoring (over 95.6%), even during double blind test. This surpasses the serum biomarker panel (≈90.7% for subtyping, ≈89.7% for prognosis) and urine biomarker panel (≈94.4% for subtyping, ≈76.5% for prognosis). Moreover, after attempting to further refine the marker panel, the blind test maintains equal sensitivity, specificity, and accuracy, showcasing a comprehensive improvement over the single-fluid approach. This underscores the remarkable effectiveness and superiority of the integrated strategy in discriminating between MN and other groups. This work has the potential to significantly advance diagnostic medicine, leading to the establishment of more effective strategies for patient management.

A narrative review of wastewater surveillance: pathogens of concern, applications, detection methods, and challenges

Introduction

The emergence and resurgence of pathogens have led to significant global health challenges. Wastewater surveillance has historically been used to track water-borne or fecal-orally transmitted pathogens, providing a sensitive means of monitoring pathogens within a community. This technique offers a comprehensive, real-time, and cost-effective approach to disease surveillance, especially for diseases that are difficult to monitor through individual clinical screenings.

Methods

This narrative review examines the current state of knowledge on wastewater surveillance, emphasizing important findings and techniques used to detect potential pathogens from wastewater. It includes a review of literature on the detection methods, the pathogens of concern, and the challenges faced in the surveillance process.

Results

Wastewater surveillance has proven to be a powerful tool for early warning and timely intervention of infectious diseases. It can detect pathogens shed by asymptomatic and pre-symptomatic individuals, providing an accurate population-level view of disease transmission. The review highlights the applications of wastewater surveillance in tracking key pathogens of concern, such as gastrointestinal pathogens, respiratory pathogens, and viruses like SARS-CoV-2.

Discussion

The review discusses the benefits of wastewater surveillance in public health, particularly its role in enhancing existing systems for infectious disease surveillance. It also addresses the challenges faced, such as the need for improved detection methods and the management of antimicrobial resistance. The potential for wastewater surveillance to inform public health mitigation strategies and outbreak response protocols is emphasized.

Conclusion

Wastewater surveillance is a valuable tool in the fight against infectious diseases. It offers a unique perspective on the spread and evolution of pathogens, aiding in the prevention and control of disease epidemics. This review underscores the importance of continued research and development in this field to overcome current challenges and maximize the potential of wastewater surveillance in public health.

Intact cell lipidomics using the Bruker MBT lipid Xtract assay allows the rapid detection of glycosyl-inositol-phospho-ceramides from Aspergillus fumigatus

Glycosyl-inositol-phospho-ceramides (GIPCs) or glycosylphosphatidylinositol-anchored fungal polysaccharides are major lipids in plant and fungal plasma membranes and play an important role in stress adaption. However, their analysis remains challenging due to the multiple steps involved in their extraction and purification prior to mass spectrometry analysis. To address this challenge, we report here a novel simplified method to identify GIPCs from Aspergillus fumigatus using the new Bruker MBT lipid Xtract assay. A. fumigatus reference strains and clinical isolates were cultured, harvested, heat-inactivated and suspended in double-distilled water. A fraction of this fungal preparation was then dried in a microtube, mixed with an MBT lipid Xtract matrix (Bruker Daltonik, Germany) and loaded onto a MALDI target plate. Analysis was performed using a Bruker MALDI Biotyper Sirius system in the linear negative ion mode. Mass spectra were scanned from m/z 700 to m/z 2 000. MALDI-TOF MS analysis of cultured fungi showed a clear signature of GIPCs in Aspergillus fumigatus reference strains and clinical isolates. Here, we have demonstrated that routine MALDI-TOF in the linear negative ion mode combined with the MBT lipid Xtract is able to detect Aspergillus fumigatus GIPCs.

Challenges for ticks and tick-borne diseases research in Southeast Asia: Insight from the first international symposium in Cambodia

BACKGROUND

Ticks, as critical vectors of a variety of pathogens, pose a significant public health challenge globally. In Southeast Asia (SEA), ticks are responsible for transmitting a diverse array of pathogens affecting humans and animals. The geographical and ecological diversity of SEA provides a unique environment that supports a wide range of tick species, which complicates the management and study of tick-borne diseases (TBDs).

METHODOLOGY/PRINCIPAL FINDINGS

This article synthesizes findings from the first international symposium on ticks and TBDs in Southeast Asia, held in Phnom Penh on June 22 and 23, 2023. It highlights regional efforts to understand tick ecology and pathogen transmission. This paper proposes to present a summary of the various presentations given during the symposium following 3 main parts. The first one is devoted to the state of knowledge regarding ticks and TBDs in SEA countries, with presentations from 6 different countries, namely Cambodia, Indonesia, Laos, Malaysia, Thailand, and Vietnam. The second part focuses on the development of new research approaches on tick-borne pathogens (TBPs) and TBDs. The last part is a summary of the round table discussion held on the final day, with the aim of defining the most important challenges and recommendations for researches on TBP and TBD in the SEA region.

CONCLUSIONS/SIGNIFICANCE

Key topics discussed include advancements in diagnostic tools, such as MALDI-TOF MS and proteomics, and the development of sustainable strategies for tick management and disease prevention. The symposium facilitated the exchange of knowledge and collaborative networks among experts from various disciplines, promoting a unified approach to tackling TBDs in the region. The symposium underscored the need for enhanced surveillance, diagnostics, and inter-regional cooperation to manage the threat of TBDs effectively. Recommendations include the establishment of a regional database for tick identification and the expansion of vector competence studies. These initiatives are crucial for developing targeted interventions and understanding the broader implications of climate change and urbanization on the prevalence of TBDs.

Multidimensional mass profiles increase confidence in bacterial identification when using low-resolution mass spectrometers

Field-forward analytical technologies, such as portable mass spectrometry (MS), enable essential capabilities for real-time monitoring and point-of-care diagnostic applications. Significant and recent investments improving the features of miniaturized mass spectrometers enable various new applications outside of small molecule detection. Most notably, the addition of tandem mass spectrometry scans (MS/MS) allows the instrument to isolate and fragment ions and increase the analytical specificity by measuring unique chemical signatures for ions of interest. Notwithstanding these technological advancements, low-cost, portable systems still struggle to confidently identify clinically significant organisms of interest, such as bacteria, viruses, and proteinaceous toxins, due to the limitations in resolving power. To overcome these limitations, we developed a novel multidimensional mass fingerprinting technique that uses tandem mass spectrometry to increase the chemical specificity for low-resolution mass spectral profiles. We demonstrated the method's capabilities for differentiating four different bacteria, including attentuated strains of Yersinia pestis. This approach allowed for the accurate (>92%) identification of each organism at the strain level using de-resolved matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data to mimic the performance characteristics of miniaturized mass spectrometers. This work demonstrates that low-resolution mass spectrometers, equipped with tandem MS acquisition modes, can accurately identify clinically relevant bacteria. These findings support the future application of these technologies for field-forward and point-of-care applications where high-performance mass spectrometers would be cost-prohibitive or otherwise impractical.

Antibiotic resistance profiles of sentinel bacteria isolated from aquaculture in Cambodia

The misuse of antibiotics and the emergence of antimicrobial resistance (AMR) is a concern in the aquaculture industry because it contributes to global health risks and impacts the environment. This study analyzed the AMR of sentinel bacteria associated with striped catfish (Pangasisanodon hypophthalmus) and giant snakehead (Channa micropeltes), the two main fish species reared in the pond culture in Cambodia. Phenotypic and genotypic characterization of the recovered isolates from fish, water, and sediment samples revealed the presence of bacteria, such as 22 species belonging to families Aeromonadaceae, Enterobacteriaceae, and Pseudomonadaceae. Among 48 isolates, Aeromonas caviae (n = 2), Aeromonas hydrophila (n = 2), Aeromonas ichthiosmia (n = 1), Aeromonas salmonicida (n = 4) were detected. A. salmonicida and A. hydrophilla are known as fish pathogens that occur worldwide in both fresh and marine water aquaculture. Antibiotic susceptibility testing revealed antibiotic resistance patterns of 24 (50 %) isolates among 48 isolates with higher multiple antibiotic resistance index (> 0.2). All the isolates of Enterobacteriaceae were susceptible to ciprofloxacin. Ciprofloxacin is a frontline antibiotic that is not recommended to use in aquaculture. Therefore, its use has to be strictly controlled. This study expands our knowledge of the AMR status in aquaculture farms which is very limited in Cambodia.

Contribution of MALDI-TOF mass spectrometry and machine learning including deep learning techniques for the detection of virulence factors of Clostridioides difficile strains

Clostridioides difficile (CD) infections are defined by toxins A (TcdA) and B (TcdB) along with the binary toxin (CDT). The emergence of the 'hypervirulent' (Hv) strain PR 027, along with PR 176 and 181, two decades ago, reshaped CD infection epidemiology in Europe. This study assessed MALDI-TOF mass spectrometry (MALDI-TOF MS) combined with machine learning (ML) and Deep Learning (DL) to identify toxigenic strains (producing TcdA, TcdB with or without CDT) and Hv strains. In total, 201 CD strains were analysed, comprising 151 toxigenic (24 ToxA+B+CDT+, 22 ToxA+B+CDT+ Hv+ and 105 ToxA+B+CDT-) and 50 non-toxigenic (ToxA-B-) strains. The DL-based classifier exhibited a 0.95 negative predictive value for excluding ToxA-B- strains, showcasing accuracy in identifying this strain category. Sensitivity in correctly identifying ToxA+B+CDT- strains ranged from 0.68 to 0.91. Additionally, all classifiers consistently demonstrated high specificity (>0.96) in detecting ToxA+B+CDT+ strains. The classifiers' performances for Hv strain detection were linked to high specificity (≥0.96). This study highlights MALDI-TOF MS enhanced by ML techniques as a rapid and cost-effective tool for identifying CD strain virulence factors. Our results brought a proof-of-concept concerning the ability of MALDI-TOF MS coupled with ML techniques to detect virulence factor and potentially improve the outbreak's management.

Carbapenem and colistin-resistant hypervirulent Klebsiella pneumoniae: An emerging threat transcending the egyptian food chain

BACKGROUND

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a great public health problem and is associated with many disease outbreaks and high mortality rates. Alarmingly, K. pneumoniae has been isolated from food in several recent studies. This study aimed to investigate the prevalence and characteristics of CRKP in food samples from Egypt.

METHODS

A total of 311 food samples (including 116 minced meat, 92 chicken meat, 75 diced meat, and 28 mutton) were collected from local markets in Egypt and were screened for CRKP with the determination of their antimicrobial resistance profiles. The whole genome sequence was done for 23 CRKP isolates to clarify the relationship between CRKP from food and human cases in Egypt using the SNP core genome. The conjugation probability of the blaNDM-5 harboring plasmid was identified using oriTfinder RESULTS: CRKP was isolated from 11% (35/311) of the samples, with 45.71% (16/35) of them showing resistance to colistin, one of the last-resort options for treating CRKP-mediated infections. In addition to the carbapenem and colistin resistance, the CRKP isolates frequently exhibited resistance to multiple antimicrobials including β-lactams, fluoroquinolones, aminoglycosides, tetracyclines, and chloramphenicol. In addition, most of the CRKP were potentially hypervirulent K. pneumoniae (HvKP) identified as phylogroup Kp1 and of high-risk groups as detected in STs reported in many human outbreaks globally, such as ST383 and ST147. The core-genome phylogeny showed similarities between the isolates from this study and those previously isolated from clinical human samples in Egypt. In addition, analysis of the plasmid on which blaNDM is encoded revealed that several antimicrobial resistance genes such as blaOXA-9, blaCTX-M-15, aac(6')-Ib, qnrS1, and several virulence genes are encoded on the same plasmid.

CONCLUSIONS

This study is significant for food safety and public health and is important to further identify the change in the epidemiology of CRKP infections, especially the consumption of contaminated food products.

Nigrospora oryzae causing human corneal keratitis: A case report

Purpose

We report a rare case of microbial keratitis caused by Nigrospora oryzae.

Observations

A 72-year-old Japanese woman was injured by plant debris and developed oval corneal ulcers and hypopyon in the anterior chamber. After 5 days, she complained of pain, redness, and vision loss in her left eye and was treated with antibacterial eye drops and an ointment (1.5 % levofloxacin hydrate, cefmenoxime hydrochloride, and sterilization and disinfection eye drops; SAN-IODE and ofloxacin ophthalmic ointment). Examination revealed a worsening oval corneal ulcer with Descemet's folds and a faint hypopyon. Considering the infection from soil or plants and the poor response to intensive antibacterial eye drops, topical antifungal eye drops, i.e., 1 % voriconazole eye drops, and 1 % natamycin ointment were applied. Direct microscopy of the corneal scraping with Gram staining was performed and the result was negative. Cultures from corneal scrapings showed the growth of dark colonies after several days. The colony was identified as Nigrospora oryzae by sequencing of the fungal internal transcribed spacer region. Pain and vision loss improved with improvement in corneal ulcers. The antifungal treatment was administered for 37 days. Discontinuation of the eye drops after 1 month did not result in keratitis recurrence. At the final follow-up at 70 days, the best-corrected visual acuity was 20/25, with persistent small corneal opacity.

Conclusions and importance

Here, we report a case of fungal keratitis caused by Nigrospora oryzae. Microbiological identification of the causes of rare infections is difficult in clinical laboratories, necessitating the use of advanced molecular techniques based on amplification and sequencing of appropriate phylogenetic markers. Nigrospora oryzae responds to topical voriconazole and natamycin.

Applicability of selected reaction monitoring for precise screening tests

INTRODUCTION

The proactive identification of diseases through screening tests has long been endorsed as a means to preempt symptomatic onset. However, such screening endeavors are fraught with complications, such as diagnostic inaccuracies, procedural risks, and patient unease during examinations. These challenges are amplified when screenings for multiple diseases are administered concurrently. Selected Reaction Monitoring (SRM) offers a unique advantage, allowing for the high-throughput quantification of hundreds of analytes with minimal interferences.

AREAS COVERED

Our research posits that SRM-based assays, traditionally tailored for single-disease biomarker profiling, can be repurposed for multi-disease screening. This innovative approach has the potential to substantially alleviate time, labor, and cost demands on healthcare systems and patients alike. Nonetheless, there are formidable methodological hurdles to overcome. These include difficulties in detecting low-abundance proteins and the risk of model overfitting due to the multiple functionalities of single proteins across different disease spectrums - issues especially pertinent in blood-based assays where detection sensitivity is constrained. As we move forward, technological strides in sample preparation, online extraction, throughput, and automation are expected to ameliorate these limitations.

EXPERT OPINION

The maturation of mass spectrometry's integration into clinical laboratories appears imminent, positioning it as an invaluable asset for delivering highly sensitive, reproducible, and precise diagnostic results.