Search Results (388)

Microbiological contamination of food remains a critical global public health concern, contributing to millions of foodborne illness cases each year. Traditional diagnostic methods, particularly culture-based techniques, have been widely employed but are often limited by low sensitivity, insufficient specificity, and lengthy turnaround times. Recent advances in molecular biology, biosensor technology, and analytical chemistry have enabled the development of more rapid and precise diagnostic tools. Among these, Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has emerged as a transformative method for microbial identification. This review provides a comprehensive overview of the current applications of MALDI-TOF MS in the diagnosis of microbiological contamination in food. The method offers rapid, accurate, and cost-effective identification of microorganisms and is increasingly used in food safety laboratories for the detection of foodborne pathogens, ensuring the safety and quality of food products. We highlight the fundamental principles of MALDI-TOF MS, discuss its methodologies, and examine its advantages, limitations, and future prospects in food microbiology and quality assurance. Full article

Background: The oral microbiome differs in obese patients compared to normal-weight subjects. Microbiologic shifts very often appear after surgical interventions such as bariatric surgery (BS) and in immunocompromised patients. However, the oral microbiome composition and load in subjects after bariatric surgery are unclear. Aim: The aim of this review is to summarize the current state of the art related to the oral microbiome shift induced by bariatric surgery and to discuss its implications on oral cavity health. Methods: Electronic databases: PubMed/Medline, Web of Science, and Cochrane Library were searched for articles published up to March 30, 2025, describing prospective studies focused on changes in the oral microbiota of patients who underwent bariatric surgery. Results: Eight studies measuring the oral microbiome with different approaches—16S ribosomal RNA (16S rRNA) sequencing, polymerase chain reaction (PCR), culture, and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI TOF MS)—were included in this review. The following bariatric techniques were used: sleeve gastrectomy, Roux-en-Y gastric bypass, Omega loop gastric bypass, and laparoscopic gastric plication. The follow-up period ranged from 3 to 12 months. The results of microbiologic studies were unequivocal. There was an increment in Streptococcus mutans reported, high levels of Candida species, and increased rates of some periodontitis-associated bacteria (Porphyromonas gingivalis) in the post-bariatric surgery period, though some studies suggested a shift towards non-pathogenic composition of the oral microbiome in prospective observations. Conclusions: The local oral microbial homeostasis becomes strongly impacted by the bariatric surgical treatment itself as well as its consequences in the further post-operative period. Therefore, obese patients undergoing BS require very careful dental observation. Full article

Background: Rheumatoid arthritis (RA) is a chronic autoimmune disorder that predominantly affects synovial joints, leading to inflammation, pain, and progressive joint damage. Despite therapeutic advancements, the molecular basis of established RA remains poorly defined. Methods: In this study, we conducted an untargeted plasma proteomic analysis using two-dimensional differential gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in samples from RA patients and healthy controls in the discovery phase. Results: Significantly (ANOVA, p ≤ 0.05, fold change > 1.5) differentially abundant proteins (DAPs) were identified. Notably, upregulated proteins included mitochondrial dicarboxylate carrier, hemopexin, and 28S ribosomal protein S18c, while CCDC124, osteocalcin, apolipoproteins A-I and A-IV, and haptoglobin were downregulated. Receiver operating characteristic (ROC) analysis identified CCDC124, osteocalcin, and metallothionein-2 with high diagnostic potential (AUC = 0.98). Proteins with the highest selected frequency were quantitatively verified by multiple reaction monitoring (MRM) analysis in the validation cohort. Bioinformatic analysis using Ingenuity Pathway Analysis (IPA) revealed the underlying molecular pathways and key interaction networks involved STAT1, TNF, and CD40. These central nodes were associated with immune regulation, cell-to-cell signaling, and hematological system development. Conclusions: Our combined proteomic and bioinformatic approaches underscore the involvement of dysregulated immune pathways in RA pathogenesis and highlight potential diagnostic biomarkers. The utility of these markers needs to be evaluated in further studies and in a larger cohort of patients. Full article

Copper nanoparticles (CuNPs) are increasingly used in agriculture either alone or in combination with pesticides. Recognizing the potential hazards of CuNPs in soil environments, our study evaluated their effects on the metabolic activity of Nitrobacter winogradskyi ATCC 2539, a chemolithoautotrophic bacterium crucial for the nitrification process, which involves the oxidation of nitrite to nitrate in soil ecosystems. This study evaluated the effects of concentration ranges of CuNPs (2.5 to 162.7 mg L⁻¹), CuONPs (3.2 to 203.6 mg L⁻¹), and various pesticides (iprodione, carbendazim, and 2,4-D) and their derivatives (3,5-dichloroaniline, catechol, and 2,4-dichlorophenol) at concentrations ranging from 0.04 to 2.56 mM. CuSO₄ was also used as a control for comparative purposes. Our findings indicated that the CuNPs significantly inhibited the metabolic activity of N. winogradskyi, resulting in a reduction of up to 95% at concentrations of ≥2.5 mg L⁻¹. The CuONPs were less toxic, while the pesticides and their derivatives generally showed lower toxicity. Notably, combinations of CuNPs with pesticides or their derivatives maintained high toxicity levels comparable to those of the CuNPs alone. According to the Loewe additivity model, these effects were largely additive and primarily associated with CuNPs or CuONPs. Protein profiling using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF)/TOF mass spectrometry (MS) revealed that carbendazim induced noticeable changes in protein profiles. These findings underscore the detrimental impacts of CuNPs and CuONPs on the metabolic activity of N. winogradskyi, posing a considerable risk to the health of agricultural soils. Overall, this research provides crucial insights into the risks associated with using CuNPs in agriculture, particularly regarding their potential threat to nitrifying microorganisms in soils. Full article

With the global rise in antimicrobial resistance (AMR), rapid and reliable microbial diagnostics have become more critical than ever. Traditional culture-based and molecular diagnostic techniques often fall short in terms of speed, cost-efficiency, or scalability, particularly in resource-limited settings. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF MS) has emerged as a transformative tool in clinical microbiology. Its unparalleled speed and accuracy in microbial identification, along with expanding applications in AMR profiling, make it a leading candidate for next-generation diagnostic workflows. This review aims to provide a comprehensive update on recent advances in MALDI–TOF MS, focusing on its technological evolution, clinical applications, and future potential in microbial diagnostics and resistance detection. We conducted a critical synthesis of peer-reviewed literature published over the last decade, with emphasis on innovations in sample preparation, instrumentation, data interpretation, and clinical integration. Key developments in AMR detection, including growth-based assays, resistance biomarker profiling, and machine learning-driven spectral analysis, are discussed. MALDI–TOF MS is increasingly deployed not only in clinical laboratories but also in environmental surveillance, food safety, and military biodefense. Despite challenges such as database variability and limited access in low-income regions, it remains a cornerstone of modern microbial diagnostics and holds promise for future integration into global AMR surveillance systems. Full article

Candida auris (C. auris) is an emerging multidrug-resistant fungal pathogen recognized by the World Health Organization (WHO) as a critical global health threat. Its rapid transmission, high mortality rate, and frequent misidentification in clinical laboratories present significant challenges for diagnosis and infection control. This review provides a comprehensive overview of current and emerging diagnostic methods for C. auris detection, including culture-based techniques, biochemical assays, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and molecular diagnostics such as PCR and loop-mediated isothermal amplification (LAMP). We evaluate each method’s sensitivity, specificity, turnaround time, and feasibility in clinical and surveillance settings. While culture remains the diagnostic gold standard, it is limited by slow turnaround and phenotypic overlap with related species. Updated biochemical platforms and MALDI-TOF MS with expanded databases have improved identification accuracy. Molecular assays offer rapid, culture-independent detection. Antifungal susceptibility testing (AFST), primarily using broth microdilution, is essential for guiding treatment, although standardized breakpoints remain lacking. This review proposes an integrated diagnostic workflow and discusses key innovations and gaps in current practice. Our findings aim to support clinicians, microbiologists, and public health professionals in improving early detection, containment, and management of C. auris infections. Full article

The identification of filamentous fungi by matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI–TOF MS) represents a challenge due to their complex taxonomy and the lack of comprehensive databases. The aim of this study was to evaluate the current status of available MALDI–TOF MS databases for the identification of dermatophytes, including commercial, in-house, and web-based databases. We collected 289 dermatophyte strains from different centers and analyzed them using four databases and a combination of them. The combination of commercial and in-house databases was shown to improve the identification rate and accuracy at the species level. For Trichophyton rubrum, the concordance among all databases was above 90.0%. For the T. mentagrophytes group, correct identification at the species level ranged from 30.0 to 78.9%, depending on the database, and showed very low agreement among them. The addition of the novel species T. japonicum to our in-house database resulted in the successful identification of this species. On the other hand, T. interdigitale and T. tonsurans were the species most frequently misidentified by MALDI–TOF MS. Through deep spectra analysis of both species, up to 29 protein peaks were found to be suitable for their differentiation, demonstrating the potential of peak analysis in differentiating closely related species. In conclusion, improvements of the databases with new strains resulted in increased identification accuracy at the species level. This, combined with peak analysis, could improve the overall identification of dermatophytes by MALDI–TOF MS in clinical laboratories. Full article

Milk’s biological origin determination, including its adulteration and authenticity, presents serious limitations, highlighting the need for innovative advanced solutions. The utilisation of proteomic technologies combined with personalised algorithms creates great potential for a more comprehensive approach to analysing milk samples effectively. The current study presents an innovative approach utilising proteomics and neural networks to classify and distinguish bovine, ovine and caprine milk samples by employing advanced machine learning techniques; we developed a precise and reliable model capable of distinguishing the unique mass spectral signatures associated with each species. Our dataset includes a diverse range of mass spectra collected from milk samples after MALDI-TOF MS (Matrix-assisted laser desorption/ionization-time of flight mass spectrometry) analysis, which were used to train, validate, and test the neural network model. The results indicate a high level of accuracy in species identification, underscoring the model’s potential applications in dairy product authentication, quality assurance, and food safety. The current research offers a significant contribution to agricultural science, providing a cutting-edge method for species-specific classification through mass spectrometry. The dataset comprises 648, 1554, and 2392 spectra, represented by 16,018, 38,394, and 55,055 eight-dimensional vectors from bovine, caprine, and ovine milk, respectively. Full article

Background. Blastocystis spp. is a common protozoan found in the gastrointestinal tract, typically existing as a non-pathogenic organism in humans and other animals. However, it can become pathogenic when the immune system is compromised due to bacterial, viral, fungal, or other parasitic infections, as well as systemic conditions, leading to symptomatic blastocystosis. Methods. Fecal samples were collected from patients at the University Hospital of Campania “Luigi Vanvitelli” and Cotugno Hospital in Naples. Among these samples, those that tested positive for Blastocystis spp. and were associated with other microbial infections were further analyzed. Bacterial co-infections were identified using immunochromatographic tests (ICTs) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Viral infections were detected using chemiluminescent immunoassay (CLIA), while fungal infections were diagnosed through microscopic examination and molecular biology techniques. Additionally, co-infections with other parasites were identified through microscopic analysis after Ridley’s concentration and Giemsa staining (O&P). Results. Out of the 2050 stool samples collected, 121 were positive for Blastocystis spp., of which 75 were associated with other infections. We identified the vacuolar form in patients co-infected with bacteria (n = 22), viruses (n = 30), fungi (n = 3), and other parasites (n = 20). Conclusions. Our findings indicated a higher incidence of the vacuolar form of Blastocystis spp. in symptomatic and immunocompromised patients, suggesting that a weakened immune system may increase the risk of contracting Blastocystis and other microbial infections. Full article

Objectives: The aim of this scoping review was to delineate the current role and possible applications of proteomics in personalized breast cancer diagnostic evaluation and treatment. Methods: A comprehensive search in PubMed/MEDLINE and Scopus/EMBASE was conducted, according to the PRISMA–ScR guidelines. Inclusion criteria: proteomic studies of specimens from breast cancer patients, clinically relevant studies and clinical studies. Exclusion criteria: in silico, in vitro and studies in animal models, review articles, case reports, case series, comments, editorials, and articles in language other than English. The study protocol was registered in the Open Science Framework. Results: In total, 1093 records were identified, 170 papers were retrieved and 140 studies were selected for data extraction. Data analysis and synthesis of evidence showed that most proteomic analyses were conducted in breast tumor specimens (n = 77), followed by blood samples (n = 48), and less frequently in other biologic material taken from breast cancer patients (n = 19). The most commonly used methods were liquid chromatography–tandem mass spectrometry (LC–MS/MS), followed by Matrix-assisted laser desorption/ionization-time of flight (MALDI–TOF), Surface-Enhanced Laser Desorption/Ionization Time-of-Flight (SELDI–TOF) and Reverse Phase Protein Arrays (RPPA). Conclusions: The present review provides a thorough map of the published literature reporting clinically relevant results yielded from proteomic studies in various biological samples from different subgroups of breast cancer patients. This analysis shows that, although proteomic methods are not currently used in everyday practice to guide clinical decision-making, nevertheless numerous proteins identified by proteomics could be used as biomarkers for personalized diagnostic evaluation and treatment of breast cancer patients. Full article

Background: Superficial candidiasis (SC) is widespread in humans worldwide. This study aimed to evaluate species distribution patterns and antifungal susceptibility through cluster analysis. Methods: A total of 180 Candida strains isolated from skin and nail samples of 1593 examined patients with suspected superficial fungal infection were identified by Matrix-assisted laser desorption in ionization-time of flight mass spectrometry (MALDI-TOF MS; Zybio EXS2600, China). Antifungal susceptibility was assessed using the commercial Integral System YEASTS Plus test (ISYPT; Liofilchem^®, Italy). Agglomerative hierarchical cluster analysis was used to analyze species distribution and susceptibility. Results: Candida parapsilosis (44.4%) and C. albicans (40%) were the most prevalent causative agents of SC. Cluster analysis established two defined clusters. Cluster 1 (121 isolates) showed a statistically significant difference compared to Cluster 2 (54 isolates) in species distribution (C. albicans was dominant in the first and C. parapsilosis in the second cluster) as well as in susceptibility to ECN (p ≤ 0.001), KCA (p = 0.030), CLO (p ≤ 0.001), MCZ (p ≤ 0.001), ITZ (p ≤ 0.001), and FLU (p ≤ 0.006). Conclusion: The fact that one-third of isolates exhibited low sensitivity to antifungals highlights the need for a new approach in SC treatment, emphasizing the importance of mycological analyses, including in vitro testing of antifungal effectiveness. Full article

Identification of mycobacterial infections for both Mycobacterium tuberculosis and non-tuberculosis mycobacteria is important for effective patient care. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a promising tool that is used in many clinical laboratories for the identification of bacteria and yeast. This study evaluates the impact of growth media on the performance of the MALDI Biotyper^® MBT smart MS for mycobacteria identification. Increased rates of identification, particularly in non-rapid growers and pigment producers, and higher confidence scores were generated in mycobacteria isolated from solid agar, rather than liquid broth. Testing each isolate in triplicate can increase yield of detection. Using the Bruker MBT Mycobacteria Kit to process our samples for testing on the Bruker MALDI Biotyper^® instrument generated precise and accurate mycobacteria identification. These findings emphasize the importance of optimizing mycobacterial specimen processing workflows to include appropriate culture media, which can enhance mycobacterial identification and improve diagnostic accuracy. Full article

Ensuring the authenticity of Mozzarella di Bufala Campana (MdBC), a Protected Designation of Origin (PDO) cheese, is essential for regulatory enforcement and consumer protection. This study evaluates a multi-technology analytical platform developed to detect adulteration due to the addition of non-buffalo milk or non-PDO buffalo milk in PDO dairy buffalo products. Peripheral laboratories use gel electrophoresis combined with polyclonal antipeptide antibodies for initial screening, enabling the detection of foreign caseins, including those originating outside the PDO-designated regions. For more precise identification, Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) differentiates species by detecting proteotypic peptides. In cases requiring confirmation, nano-liquid chromatography coupled to electrospray tandem mass spectrometry (nano-LC-ESI-MS/MS) is used in central state laboratories for the highly sensitive detection of extraneous milk proteins in PDO buffalo MdBC cheese. On the other hand, analysis of the pH 4.6 soluble fraction from buffalo blue cheese identified 2828 buffalo-derived peptides and several bovine specific peptides, confirming milk adulteration. Despite a lower detection extent in the pH 4.6 insoluble fraction following tryptic hydrolysis, the presence of bovine peptides was still sufficient to verify fraud. This integrated proteomic approach, which combines electrophoresis and mass spectrometry technologies, significantly improves milk adulteration detection, providing a robust tool to face increasingly sophisticated fraudulent practices. Full article

The human milk (HM) microbiome is variable and depends on maternal, perinatal, and cultural–environmental factors. The diversity of the HM microbiome is crucial in the development of the child. The aim of the study was to assess the prevalence of bacteria (using culture-based methods) of Polish women with normal BMI, giving birth on time through vaginal delivery. Methods: The research material consisted of human milk and swabs from the areola and nipple, before and after breastfeeding, derived from Polish women (n = 86). Classic culture methods were used to obtain multiple bacteria. Species identification of the grown colonies was performed using MALDI TOF MS (Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry). Results: 120 species of bacteria were isolated, mainly from the genus Streptococcus and Staphylococcus. Species specific only to human milk were identified (belonging to the following genera: Microbacterium, Shewanella, Psychrobacter, Aeromonas, Serratia, Buttiauxella, Lactobacillus, Bifidobacterium) as well as species specific only to areola and nipple swabs after breastfeeding (Acinetobacter lactucae, Moraxella catarrhalis, Corynebacterium pseudodiphtheriticum, Corynebacterium propinquim). It was confirmed that most species were present in all tested materials collected from one patient. Conclusions: The analysis carried out showed the presence of bacteria in the human milk of Polish women, including strains of lactic acid bacteria. The human milk microbiota may significantly influence the formation of the infant’s intestinal microbiota, including some key genera, i.e., Lactobacillus, Bifidobacterium, and Limosilactobacillus, which were also isolated from the tested samples. The data presented here provide new data on culturable bacterial species isolated from breast milk from Polish women giving birth via vaginal delivery and potential routes of transmission from the neonate’s oral cavity. Full article

Glioblastoma is the most common and aggressive brain tumor in adults. However, due to the limitations of conventional treatments, as well as their side effects, there is a need to develop more effective and less harmful therapy strategies. There is evidence that plants endemic to northern Mexico possess biological activities that positively impact human health, particularly against cancer. Echinocereus engelmannii and Echinocereus pectinatus are cacti from the north of Mexico that produce bioactive compounds with antitumor activity. We obtained methanol extracts from previously isolated and fermented microorganisms associated with these cacti. Cell lines of extracts with cytotoxicity against glioblastoma cells U87, neuroblastoma cells SH-S5Y5, and Schwann neuronal cells (healthy control) were evaluated, using a colorimetric 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazole bromide (MTT) reduction technique. The selective cytotoxicity extracts were analyzed using liquid chromatography tandem mass spectrometry (LC/MS²). We isolated 19 endophytic and soil-associated microorganisms from both cacti. Two of them were selected for their high percentages of tumor growth inhibition. The microorganism ES4 possessed the best activity with an IC₅₀ of 17.31 ± 1.70 µg/mL and a selectivity index of 3.11. We identified the bacterium Stenotrophomonas maltophilia by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) from the most active microorganisms against tumor growth. LC/MS² characterized the HS4 extract, and the most abundant group (50.0%) identified included carboxylic acids and derivatives, particularly bisgerayafolin A, Cyclo (Pro-Leu), maculosin, and tryptophan. In conclusion S. maltophilia extract inhibit the growth of glioma cells, showing greater sensitivity in the U87 cell line. Full article