Sign in to use this feature.

Years

Between: -

Subjects

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Journals

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Article Types

Countries / Regions

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Search Results (1,245)

Search Parameters:
Keywords = MALDI-TOF MS

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
18 pages, 2528 KB  
Article
Characterization of a Boron-Tolerant Nocardia niigatensis Isolated from Boron-Rich Soils: Physiological, Enzymatic, and Genomic Insights
by Kerem Özdemir
Microorganisms 2026, 14(2), 306; https://doi.org/10.3390/microorganisms14020306 - 28 Jan 2026
Abstract
In this study, a Nocardia niigatensis strain was isolated from boron-rich mining soils in the Bigadiç region of Türkiye and comprehensively characterized. The primary aim of this study was to isolate boron-tolerant Nocardia species and evaluate their physiological, enzymatic, and biochemical profiles. Selective [...] Read more.
In this study, a Nocardia niigatensis strain was isolated from boron-rich mining soils in the Bigadiç region of Türkiye and comprehensively characterized. The primary aim of this study was to isolate boron-tolerant Nocardia species and evaluate their physiological, enzymatic, and biochemical profiles. Selective isolation techniques were employed to obtain Nocardia isolates, and species-level identification was achieved using both 16S rRNA gene sequencing and MALDI-TOF MS analysis, which consistently confirmed the isolate as N. niigatensis. In addition to molecular identification, the morphological, physiological, and biochemical characteristics of the strain were extensively investigated. The strain demonstrated notable boron tolerance, exhibiting robust growth at concentrations up to 50 mM, highlighting its potential applicability in the bioremediation of boron-contaminated environments. Physiological assays further revealed moderate halotolerance and a mesophilic growth profile, with optimal growth observed at 27–37 °C. Enzymatic screening indicated positive L-glutaminase activity, an enzyme of considerable industrial relevance. Moreover, API ZYM profiling revealed a broad enzymatic spectrum, including esterases, arylamidases, phosphatases, and glucosidases, suggesting substantial metabolic versatility. Antibiotic susceptibility testing showed sensitivity to doxycycline, tobramycin, and erythromycin, whereas resistance was observed against imipenem and several β-lactam antibiotics. Metagenomic analysis of boron-rich soils from two distinct mining sites revealed marked differences in microbial community composition, with variations in Actinobacteria abundance associated with mineral type. Overall, these findings emphasize the adaptive capacity and biotechnological potential of environmental Nocardia strains inhabiting chemically stressful ecosystems, warranting further genomic and metabolomic investigations. Full article
(This article belongs to the Collection Feature Papers in Environmental Microbiology)
Show Figures

Figure 1

31 pages, 1311 KB  
Article
Mapping Escherichia coli in Women with Simple Urinary Tract Infections: Phenotypic ESBL/AmpC Screening and Whole-Genome Insights from Oman
by Aisha Al-Mufarji, Meher Rizvi, Nawal Al-Kindi, Nada Al-Tamtami and Zaaima Al-Jabri
Antibiotics 2026, 15(2), 124; https://doi.org/10.3390/antibiotics15020124 - 27 Jan 2026
Abstract
Background/Objectives: Simple urinary tract infections (sUTIs) are common in women and increasingly affected by multidrug-resistant (MDR) Escherichia coli. Extended-spectrum β-lactamase (ESBL) and AmpC producers restrict oral treatment options and promote carbapenem use. This study aimed to (i) describe the etiology and antimicrobial [...] Read more.
Background/Objectives: Simple urinary tract infections (sUTIs) are common in women and increasingly affected by multidrug-resistant (MDR) Escherichia coli. Extended-spectrum β-lactamase (ESBL) and AmpC producers restrict oral treatment options and promote carbapenem use. This study aimed to (i) describe the etiology and antimicrobial susceptibility of sUTIs in women of reproductive age in Oman, (ii) determine the prevalence of ESBL/AmpC-producing E. coli, (iii) evaluate nitroxoline, fosfomycin, mecillinam, and temocillin against ESBL and non-ESBL E. coli, and (iv) characterize circulating clones and resistance/virulence determinants using whole-genome sequencing (WGS). Methods: In this multicentric study (September 2022–August 2023), 795 uropathogens from 762 women (15–50 years) with sUTI were collected from four Omani hospitals. Identification and susceptibility testing of E. coli (n = 489) and Klebsiella pneumoniae (n = 140) using BD Phoenix and MALDI-TOF MS was performed (CLSI 2022). Thirty ESBL-producing and 82 non-ESBL E. coli underwent phenotypic ESBL/AmpC testing and evaluation of mecillinam, temocillin, nitroxoline, and fosfomycin. WGS was performed on 26 isolates (23 ESBL, 3 wild type) and analyzed for MLST, and SNP phylogeny using ResFinder, CARD, PlasmidFinder, VirulenceFinder. Statistical significance was set at p < 0.05. Results: E. coli (62%) and K. pneumoniae (18%) were the predominant pathogens. E. coli showed high susceptibility to nitrofurantoin (~97%), carbapenems, aminoglycosides, and piperacillin–tazobactam, but reduced susceptibility to cephalosporins, fluoroquinolones, cotrimoxazole, and ampicillin. ESBL prevalence ranged from 38–51%; AmpC producers were rare (4.6%). Mecillinam, nitroxoline, and fosfomycin exhibited 100% activity against both ESBL and non-ESBL isolates; temocillin showed 89.3% activity in ESBL strains. WGS identified 15 sequence types dominated by ST-131, ST-1193, ST-73, and ST-174, with blaCTX-M-15 as the major ESBL genotype. Conclusions: sUTIs in Oman show a high burden of ESBL-producing E. coli. Nitrofurantoin, mecillinam, fosfomycin, temocillin, and nitroxoline would be effective carbapenem-sparing oral options. Continuous phenotypic and genomic surveillance are crucial to guide antimicrobial therapy and stewardship. Full article
Show Figures

Figure 1

14 pages, 856 KB  
Article
Phenotypic and Whole-Genome Sequencing-Based Profiling of Antimicrobial Resistance and Virulence in Pseudomonas aeruginosa Isolated from Patients with Ventilator-Associated Pneumonia and Ventilator-Associated Tracheobronchitis in a Croatian Intensive Care Unit
by Marija Cavka, Marija Kvesic Ivankovic, Ana Maravic, Mia Dzelalija, Jelena Marinovic, Ivana Goic-Barisic, Marija Tonkic and Anita Novak
Genes 2026, 17(2), 130; https://doi.org/10.3390/genes17020130 - 26 Jan 2026
Viewed by 44
Abstract
Background/Objectives: Pseudomonas aeruginosa is one of the leading causes of ventilator-associated pneumonia (VAP) and ventilator-associated tracheobronchitis (VAT), with a worldwide spread of difficult-to-treat high-risk clones. This study aimed to investigate the virulence potential and to characterize phenotypic and genotypic antimicrobial resistance (AMR) in [...] Read more.
Background/Objectives: Pseudomonas aeruginosa is one of the leading causes of ventilator-associated pneumonia (VAP) and ventilator-associated tracheobronchitis (VAT), with a worldwide spread of difficult-to-treat high-risk clones. This study aimed to investigate the virulence potential and to characterize phenotypic and genotypic antimicrobial resistance (AMR) in P. aeruginosa causing VAP/VAT in the Intensive Care Unit (ICU), University Hospital of Split, Croatia. Methods: The study included P. aeruginosa isolates obtained from ICU patients who met the criteria for VAP or VAT, between January 2023 and January 2024. Isolates were identified using MALDI-TOF MS and tested for antimicrobial susceptibility (AST). A subset of phenotypically multidrug-resistant (MDR) isolates was further analyzed using whole-genome sequencing (WGS) and multilocus sequence typing. Results: A high rate of resistance was detected to ceftazidime (23.4%), imipenem (39.6%), and meropenem (43.8%). WGS confirmed the presence of multiple AMR genes, including the blaVIM-2 gene, whose genetic environment highlights a complex MDR locus integrating multiple AMR determinants and mobile genetic elements. All tested isolates possessed genes for class C (blaPDC34, blaPDC374 or blaPDC16) and class D (blaOXA-2, blaOXA-10 or blaOXA-50) β-lactamases, fosA, aph(3′)-IIb and crpP genes. Additionally, WGS analysis revealed the presence of numerous virulence genes including those for adherence (Type IV pili and Fap protein production), motility (such as flgF), biofilm formation (e.g., algE and mucE), quorum sensing (lasI, lasR, rhlI and rhlR), exotoxin (toxA and plcH) and exoenzyme activity (exoU, exoT, exoS, exoY, pcrV, hcp1 and lasA). The isolates belonged to four different sequence types: ST235, ST446, the high-risk ST253 and the widely distributed ST395. Phylogenomic comparison demonstrated that the isolates from this study do not originate from a single clonal source, but instead represent multiple globally distributed high-risk P. aeruginosa lineages introduced into the clinical setting. Conclusions: Due to the emergence of high-risk clones with broad AMR and strong virulence potential, ineffectiveness of standard empirical therapy may be anticipated, highlighting the urgent need for new therapeutic approaches (including those targeting major virulence factors). Full article
Show Figures

Figure 1

13 pages, 771 KB  
Article
Microbiological Assessment and Production of Ochratoxin A by Fungi Isolated from Brazilian Dry-Cured Loin (Socol)
by Felipe Coser Chow, Gustavo Lucas Costa Valente, Viviana Patrícia Fraga Santos, Mariana Rodrigues Wenzel, Kelly Moura Keller, Carla Ferreira Soares, Henrique César Pereira Figueiredo, Marcelo Resende Souza, Silvana de Vasconcelos Cançado and Tadeu Chaves Figueiredo
Foods 2026, 15(3), 433; https://doi.org/10.3390/foods15030433 - 24 Jan 2026
Viewed by 158
Abstract
This study aimed to evaluate the microbiological quality of Brazilian dry-cured loin (Socol), as well as the presence of ochratoxin A (OTA) and its synthesis by the isolated Aspergillus ochraceus complex under different conditions (culture media, temperature, and time of incubation). Nine bacterial [...] Read more.
This study aimed to evaluate the microbiological quality of Brazilian dry-cured loin (Socol), as well as the presence of ochratoxin A (OTA) and its synthesis by the isolated Aspergillus ochraceus complex under different conditions (culture media, temperature, and time of incubation). Nine bacterial genera were isolated and identified by Matrix Assisted Laser Desorption Ionization—Time Of Flight/Mass Spectrometry (MALDI-TOF/MS), including Serratia spp. (32.4%), Citrobacter spp. (20.9%), Enterobacter spp. (13.6%), and Staphylococcus spp. (6.3%), among others. Salmonella spp. was not observed, and counts of thermotolerant coliforms and coagulase-positive Staphylococcus were below the confidence level. Fifteen fungal strains were isolated and identified as Aspergillus spp. (n = 5), Cladosporium sp. (n = 1), and Penicillium spp. (n = 9). OTA was quantified in Socol samples, and the enumeration of fungi showed a correlation (r = 0.77) with the mycotoxin detection. A. ochraceus complex produced OTA in Czapek Yeast Autolyzed (CYA) and Yeast Extract Sucrose (YES) agars at different times and temperatures. It was concluded that the microbiota of Socol is complex, encompassing spoilage bacteria. Undesirable fungi are also present, including those belonging to the A. ochraceus complex that produce OTA. Full article
(This article belongs to the Section Food Quality and Safety)
Show Figures

Figure 1

18 pages, 2151 KB  
Article
Silent Waterborne Carriers of Carbapenem-Resistant Gram-Negative Bacilli and Antimicrobial Resistance Genes in Rio de Janeiro’s Aquatic Ecosystems
by Laura Brandão Martins, Marcos Tavares Carneiro, Kéren Vieira-Alcântara, Thiago Pavoni Gomes Chagas and Viviane Zahner
Antibiotics 2026, 15(2), 115; https://doi.org/10.3390/antibiotics15020115 - 23 Jan 2026
Viewed by 153
Abstract
Background/Objectives: Water pollution caused by human activities disrupts ecosystems and promotes the spread of antimicrobial resistance genes (ARGs), posing a public health threat. This study investigated the presence of resistant Gram-negative bacteria and resistance genes in water from two sites occasionally exposed [...] Read more.
Background/Objectives: Water pollution caused by human activities disrupts ecosystems and promotes the spread of antimicrobial resistance genes (ARGs), posing a public health threat. This study investigated the presence of resistant Gram-negative bacteria and resistance genes in water from two sites occasionally exposed to domestic and hospital effluents, the Carioca River (CR) and Rodrigo de Freitas Lagoon (RFL), both used for recreation. Methods: Physicochemical parameters and coliform levels were measured. Bacterial isolates were identified by Matrix-Assisted Laser Desorption Ionization–Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and tested for antimicrobial susceptibility using disk diffusion. The Minimum Inhibitory Concentration (MIC) was determined using the E-test® and broth microdilution methods. PCR was used to detect carbapenem resistance and other ARGs from the DNA of bacterial isolates obtained from water samples. Results: CR presented signs of environmental degradation, with low dissolved oxygen and high coliform counts. One Citrobacter braakii isolate showed resistance to all tested antimicrobials, raising concern for untreatable infections. Carbapenem-resistant isolates accounted for 49.4% of the total, harboring blaKPC (20%), blaTEM (5%), blaVIM (5%), and blaSPM (5%). The intl1 gene was found in 10% of isolates, indicating potential horizontal gene transfer. Conclusions: The findings from a one-day sampling reveal the presence of multidrug-resistant bacteria that carry antimicrobial resistance genes in polluted aquatic systems. These highlight the connection between water contamination and antimicrobial resistance. The evidence underscores the urgent need for environmental monitoring and effective management strategies to reduce public health risks. Full article
Show Figures

Figure 1

16 pages, 14226 KB  
Article
Preparation of a Magnetic Ti-IMAC Material Based on Thiol-Ene Click Reaction and the Application in Intact Phosphoprotein Enrichment
by Yan Lu, Sen Zhang, Hong-Yan Ge, Han-Yue Yang, Feng Zhang, Yi-Fan Pan and Hong-Zhen Lian
Molecules 2026, 31(3), 396; https://doi.org/10.3390/molecules31030396 - 23 Jan 2026
Viewed by 212
Abstract
Protein phosphorylation is a crucial post-translational modification that regulates protein activity, cellular signaling, transcriptional regulation, and cell cycle control. However, the analysis of phosphoproteins in biological samples is often compromised by complex sample matrices and interference from high-abundance proteins. While the top-down phosphoproteomics [...] Read more.
Protein phosphorylation is a crucial post-translational modification that regulates protein activity, cellular signaling, transcriptional regulation, and cell cycle control. However, the analysis of phosphoproteins in biological samples is often compromised by complex sample matrices and interference from high-abundance proteins. While the top-down phosphoproteomics strategy enables comprehensive analysis of post-translational modifications based on intact proteins, its requirement for higher protein purity due to low protein ionization efficiency poses stern challenges. Consequently, developing appropriate enrichment methods for phosphoproteins in practical samples becomes essential. Immobilized metal ion affinity chromatography (IMAC) represents a common strategy for phosphorylated protein separation and enrichment. Among metal ions, Ti4+ has gained widespread application as IMAC chelating ligands due to its capacity to form multiple coordination networks and its high selectivity for phosphorylated protein enrichment, leveraging the strong chelating ability of phosphate groups toward metal ions. This paper presents the design and preparation of a novel magnetic Ti-IMAC nanocomposite, MNP@MPTMS–VPA–Ti(IV). The material is modified with phosphate groups via facile thiol-ene click chemistry and then immobilizes Ti4+, enabling selective enrichment of intact phosphoproteins through IMAC affinity. The efficiency of enrichment was evaluated using subsequent matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for detection and analysis. This Ti-IMAC material-based magnetic solid-phase extraction (MSPE)-MALDI-TOF MS protocol has been successfully applied to enrich intact phosphoproteins in milk and eel mucus with high selectivity, sensitivity, and suitability. Full article
(This article belongs to the Section Analytical Chemistry)
Show Figures

Figure 1

19 pages, 4468 KB  
Article
Natural Bio-Sourced Additives for Bread Technology Improvement and Highly Nutritive Products
by Nicoleta Platon, Oana Cristina Pârvulescu, Vasilica Alisa Aruș, Ana Maria Georgescu, Mihaela Silion, Anca Miron, Gabriela Muntianu, Ana Maria Roșu, Petrica Iancu and Abdelkrim Azzouz
Foods 2026, 15(3), 413; https://doi.org/10.3390/foods15030413 - 23 Jan 2026
Viewed by 141
Abstract
Hydrolyzed collagen (HC) and konjac glucomannan (KGM) were used as additives in non-frozen and frozen doughs (NFDs and FDs). Both additives were characterized using specific techniques, i.e., SEM-EDX, MALDI-TOF MS, TGA, and DSC analyses. Rheological analysis of NFD samples was performed using a [...] Read more.
Hydrolyzed collagen (HC) and konjac glucomannan (KGM) were used as additives in non-frozen and frozen doughs (NFDs and FDs). Both additives were characterized using specific techniques, i.e., SEM-EDX, MALDI-TOF MS, TGA, and DSC analyses. Rheological analysis of NFD samples was performed using a Chopin Mixolab Profiler. According to a central composite design (CCD), two sets of twelve experiments were conducted to evaluate the influence of percentages of HC and KGM in the mixture of flour and both additives (cHC = 0.79–2.21% and cKGM = 0.79–2.21%) on the porosity (PO = 58.96–78.76%), humidity (HU = 42.51–45.60%), electrical conductivity (EC = 2.06–2.29 μS/cm), and pH (pH = 5.5–5.9) of bread samples prepared from NFD and FD. The freezing led to a significant decrease in PO and pH, as well as a significant increase in HU, whereas its effect on EC was not statistically significant. The highest values of response variables that were significantly affected by the process factors, i.e., POFD = 70.8%, pHFD = 5.6, and pHNFD = 5.9, were obtained in the center point runs (cHC = cKGM = 1.50%). For bread samples prepared from FD, the mold development process began approximately four days later than for those prepared from NFD. Bread samples produced from FD and NFD samples in the center point runs showed a low rate of mold formation. Full article
(This article belongs to the Section Grain)
Show Figures

Figure 1

19 pages, 2230 KB  
Article
Prevalence of Biofilm-Forming and Antibiotic-Resistant Coagulase-Negative Staphylococci Isolated from Hospitalized Patients in an Orthopedic Clinic
by Tatiana Szabóová, Gabriela Gregová, Ján Király, Nikola Dančová, Vanda Hajdučková, Patrícia Hudecová, Simona Hisirová, Peter Polan and Viera Lovayová
Pathogens 2026, 15(1), 120; https://doi.org/10.3390/pathogens15010120 - 21 Jan 2026
Viewed by 111
Abstract
Methicillin-resistant coagulase-negative staphylococci (MRCoNS) are a major cause of infectious diseases, owing to their ability to form biofilms and colonize community and hospital environments. MRCoNS strains were identified using biochemical tests, an MALDI-TOF MS analyzer, and PCR-based 16S rRNA gene confirmation. This study [...] Read more.
Methicillin-resistant coagulase-negative staphylococci (MRCoNS) are a major cause of infectious diseases, owing to their ability to form biofilms and colonize community and hospital environments. MRCoNS strains were identified using biochemical tests, an MALDI-TOF MS analyzer, and PCR-based 16S rRNA gene confirmation. This study was designed to assess antibiotic resistance and biofilm-forming capacity and to determine the presence of the mecA, mecC, agrA, srtA, icaABCD, bap, fnbAB, and clfAB genes in MRCoNS isolates. From patients undergoing random screening during hospitalization in the Orthopedics Clinic in Slovakia, 28 strains of MRCoNS were identified: S. epidermidis (n = 10), S. hominis (n = 8), S. haemolyticus (n = 4), S. lugdunensis (n = 3), while S. simulans, S. pasteuri, and S. warneri were detected only once. The highest rates of resistance were observed for ampicillin, oxacillin, rifampicin, trimethoprim (100%), and erythromycin (62%). The mecA gene was detected in 12 analyzed isolates. In 12 isolates, MDR, strong efflux pump activity, and strong or moderate biofilm formation were simultaneously detected. Our findings highlight the problems posed by biofilm-forming, resistant CoNS in hospitalized patients and the importance of diagnostics, separation, rapid treatment, and proper hospital hygiene. Full article
Show Figures

Figure 1

15 pages, 1411 KB  
Article
Utilizing MALDI-TOF MS for Legionella pneumophila Subspecies Typing and Classification
by Lana Madagi, Shimon Edelstein, Hila Ben-Amram and Yehonatan Sharaby
Water 2026, 18(2), 269; https://doi.org/10.3390/w18020269 - 21 Jan 2026
Viewed by 118
Abstract
Legionella pneumophila (L. pneumophila), the primary causative agent of Legionnaires’ disease, is a waterborne bacterial pathogen that poses significant public health concern. This opportunistic pathogen commonly inhabits both natural and man-made water systems, particularly drinking water distribution systems (DWDSs), where it [...] Read more.
Legionella pneumophila (L. pneumophila), the primary causative agent of Legionnaires’ disease, is a waterborne bacterial pathogen that poses significant public health concern. This opportunistic pathogen commonly inhabits both natural and man-made water systems, particularly drinking water distribution systems (DWDSs), where it can proliferate and pose a risk to human health. In this study, we evaluated the potential of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for rapid and accurate subtyping of L. pneumophila. Our analysis included 70 L. pneumophila strains collected from the Middle East, representing one of the largest and most comprehensive MALDI-TOF MS-based subtyping of strains from this geographically underrepresented region. These strains, representing three Multi-Locus Variable Number Tandem Repeat Analysis (MLVA-8) genotypic groups (GT4, GT6, and GT15), have been extensively characterized in previous studies for their virulence traits, cytotoxicity patterns, and antimicrobial susceptibility profiles. Our findings revealed distinct genotype-associated spectral signatures with 30 discriminatory m/z peaks (p ≤ 0.005). These markers enabled accurate genotype-level classification, achieving over 85% classification accuracy with a Random Forest model and over 71% accuracy using a Decision Tree algorithm. Importantly, the m/z peak at 5358 was uniquely present in the GT15 strains, whereas m/z 5353 was consistently detected in both GT4 and GT6 isolates, demonstrating the potential of specific mass peaks to serve as reliable genotype markers. Furthermore, GT15 strains consistently formed a separate cluster in both Principal Component Analysis (PCA) and hierarchical analyses, whereas GT4 and GT6 exhibited partial overlap, reflecting their exceptionally high genomic similarity. Full article
(This article belongs to the Section Water and One Health)
Show Figures

Figure 1

22 pages, 1289 KB  
Article
Evaluating the Quality of Selected Commercial Probiotic Products, Both Dietary Supplements and Foods for Special Medical Purposes
by Anna Zawistowska-Rojek, Justyna Rybak, Paulina Smoleń, Agnieszka Kociszewska, Paweł Rudnicki-Velasquez, Karolina Węgrzyńska, Tomasz Zaręba, Stefan Tyski and Anna Baraniak
Foods 2026, 15(2), 373; https://doi.org/10.3390/foods15020373 - 20 Jan 2026
Viewed by 267
Abstract
Probiotics are live microorganisms that provide health benefits when administered in adequate amounts. Due to the increasing popularity of probiotic supplements, concerns have arisen regarding their quality, microbial composition, and safety. This study aimed to evaluate the quantitative and qualitative characteristics of the [...] Read more.
Probiotics are live microorganisms that provide health benefits when administered in adequate amounts. Due to the increasing popularity of probiotic supplements, concerns have arisen regarding their quality, microbial composition, and safety. This study aimed to evaluate the quantitative and qualitative characteristics of the selected probiotics available on the Polish market, including both dietary supplements and foods for special medical purposes, and to compare the obtained results with the information provided on the product labels. Fifteen commercial probiotic products were analysed. Viable microorganism counts were determined using the traditional culture-based plate count method and by flow cytometry for selected products. Species identification was performed using MALDI-TOF MS and qPCR, whereas microbiological purity testing was conducted to confirm the absence of pathogenic bacteria. Significant differences were observed between the declared and experimentally determined numbers of viable microorganisms. Only a few products maintained bacterial counts consistent with label claims, while most contained considerably low viable cells. Flow cytometry revealed higher viable cell counts than plate counting, indicating the presence of viable but non-culturable bacteria. The declared species composition of the strains was mostly confirmed, although in several cases, undeclared probiotic microorganisms were identified. All tested products were free from pathogens. The study indicates significant discrepancies in the quality of probiotic supplements available on the Polish market. From a consumer perspective, these findings highlight the importance of verifying probiotic quality and suggest that not all commercial products may guarantee the full range of claimed health benefits. The implementation of standardised analytical procedures and enhanced quality control measures is therefore essential to ensure the product safety, strain authenticity, and reliability of health-related claims. Full article
(This article belongs to the Section Food Microbiology)
Show Figures

Figure 1

21 pages, 1234 KB  
Article
ReShuffle-MS: Region-Guided Data Augmentation Improves Artificial Intelligence-Based Resistance Prediction in Escherichia coli from MALDI-TOF Mass Spectrometry
by Dongbo Dai, Chenyang Huang, Junjie Li, Xiao Wei, Shengzhou Li, Qiong Wu and Huiran Zhang
Microorganisms 2026, 14(1), 177; https://doi.org/10.3390/microorganisms14010177 - 13 Jan 2026
Viewed by 206
Abstract
Rapid antimicrobial resistance (AMR) prediction from MALDI-TOF mass spectrometry (MS) remains challenging, particularly when training artificial intelligence (AI) models under small-sample constraints. Performance is often hampered by the high dimensionality of spectral data and the subtle nature of resistance-related signals: full-spectrum approaches risk [...] Read more.
Rapid antimicrobial resistance (AMR) prediction from MALDI-TOF mass spectrometry (MS) remains challenging, particularly when training artificial intelligence (AI) models under small-sample constraints. Performance is often hampered by the high dimensionality of spectral data and the subtle nature of resistance-related signals: full-spectrum approaches risk overfitting to high-dimensional noise, whereas peak-selection strategies risk discarding structurally informative, low-intensity signals. Here, we propose ReShuffle-MS, a region-guided data augmentation framework for MS data. Each spectrum is partitioned into a Main Discriminative Region (MDR) and a Peripheral Peak Region (PPR). By recombining signals within the PPR across samples of the same class while keeping the MDR intact, ReShuffle-MS generates structure-preserving augmented samples. On a clinical dataset for Escherichia coli (E. coli) levofloxacin resistance prediction, ReShuffle-MS delivered significant and consistent performance gains. It improved the average accuracy of classical machine learning models by 3.7% and enabled a one-dimensional convolutional neural network (CNN) to achieve 83.25% accuracy and 97.28% recall. Visualization using Grad-CAM revealed a shift from sparse, peak-dependent attention toward broader and more meaningful spectral patterns. Validation on the external DRIAMS-C dataset for ceftriaxone resistance further demonstrated that the method generalizes to a distinct laboratory setting and a different antibiotic target. These findings suggest that ReShuffle-MS can enhance the robustness and clinical utility of AI-based AMR prediction from routinely acquired MALDI-TOF spectra. Full article
Show Figures

Figure 1

18 pages, 1325 KB  
Article
Clinical Significance of cfiA Positivity Detected by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry in Bacteroides fragilis Infections
by Wing-Man Chik, Lam-Kwong Lee, Jason Chi-Ka Cheng, Suk-Han Yuen, Rocky Shum, Gilman Kit-Hang Siu and Sandy Ka-Yee Chau
Microorganisms 2026, 14(1), 168; https://doi.org/10.3390/microorganisms14010168 - 12 Jan 2026
Viewed by 216
Abstract
The MALDI-TOF MS Bruker Biotyper MBT subtyping IVD module enables the early detection of cfiA-positive Bacteroides fragilis (cfiA+ BF) during bacterial identification. However, the relationship between genetic positivity, phenotypic resistance, and clinical outcomes has not been fully elucidated. This retrospective [...] Read more.
The MALDI-TOF MS Bruker Biotyper MBT subtyping IVD module enables the early detection of cfiA-positive Bacteroides fragilis (cfiA+ BF) during bacterial identification. However, the relationship between genetic positivity, phenotypic resistance, and clinical outcomes has not been fully elucidated. This retrospective study analyzed B. fragilis isolates from three Hong Kong hospitals between 2021 and 2025 to examine their prevalence and the clinical utility of MALDI-TOF MS in rapid cfiA detection. Antibiotic susceptibility testing, cfiA gene detection using MALDI-TOF MS, and Oxford Nanopore sequencing were performed. Medical records were reviewed, and univariate analyses and multivariate logistic regression were used to identify factors associated with cfiA positivity and 30-day all-cause mortality. Overall, B. fragilis exhibited a high rate of antibiotic resistance. Concomitant resistance to carbapenems and metronidazole was identified in three isolates. Among the 166 isolates, 40 (24.1%) were cfiA-positive. cfiA detection by MALDI-TOF MS showed 100% concordance with the gene sequencing results and correlated strongly with phenotypic carbapenem resistance (Φ = 0.82, p < 0.001 for meropenem; Φ = 0.70, p < 0.001 for ertapenem; Φ = 0.63, p < 0.001 for imipenem). Phylogenetic analysis revealed two distinct clusters corresponding to cfiA status, each exhibiting genetic diversity based on multi-locus sequence typing (MLST). The cfiA+ BF isolates demonstrated high-level phenotypic carbapenem resistance in the presence of upstream insertion sequences. The predominant sequence type (ST) among cfiA+ BF isolates was ST157, and 70% of ST157 isolates harbored IS1187 in the upstream region of cfiA. Gene sequencing also identified other emerging beta-lactamase genes blaOXA-347 and blaMUN. The 30-day all-cause mortality following B. fragilis infection was 13.3%, with independent predictors including a high Charlson Comorbidity Index (OR = 1.30; p = 0.02) and the absence of early source control (OR = 4.84; p = 0.03). This study highlights the widespread occurrence of cfiA+ BF in Hong Kong and the clinical significance of rapid cfiA detection. Continuous surveillance is essential to monitor the ongoing threat of antibiotic resistance in B. fragilis. Full article
(This article belongs to the Special Issue Advances in Clinical Infections and Antimicrobial Resistance)
Show Figures

Figure 1

17 pages, 665 KB  
Article
Respiratory and Pleural Pathogens in Octogenarians Hospitalized with COVID-19: Impact of Secondary Bacterial Pneumonia on Day-5 SOFA and Mortality
by Petrinela Daliu, Felix Bratosin, Ovidiu Rosca, Monica Licker, Elena Hogea, Livia Stanga, Camelia Vidita Gurban and Delia Muntean
Microorganisms 2026, 14(1), 164; https://doi.org/10.3390/microorganisms14010164 - 12 Jan 2026
Viewed by 145
Abstract
Background and Objectives: Secondary bacterial infection drives poor outcomes in older adults with COVID-19, but age-specific microbiology and its interaction with severity scores are not well defined. We characterized respiratory and pleural pathogens, resistance profiles, and their impact on day-5 SOFA/APACHE II in [...] Read more.
Background and Objectives: Secondary bacterial infection drives poor outcomes in older adults with COVID-19, but age-specific microbiology and its interaction with severity scores are not well defined. We characterized respiratory and pleural pathogens, resistance profiles, and their impact on day-5 SOFA/APACHE II in octogenarians versus younger adults. Methods: We performed a retrospective cohort study of adults with RT-PCR-confirmed coronavirus disease 2019 (COVID-19) at a tertiary infectious diseases center (≥80 years, n = 152; <65 years, n = 327). Respiratory and pleural samples were processed according to EUCAST standards. Identification employed matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Pathogen distributions, susceptibilities, and rates of superimposed pneumonia, empyema, and bacteremia were compared by age, and associations between secondary pneumonia, day-5 SOFA/APACHE II, and 28-day mortality were analyzed. Results: Sputum was obtained in 67.1% of older and 65.7% of younger adults, with numerically higher culture positivity in older patients (73.5% vs. 65.1%). Pathogen spectra were similar, dominated by Streptococcus pneumoniae (24.0% vs. 24.3%), methicillin-susceptible Staphylococcus aureus (MSSA) (18.7% vs. 20.7%), methicillin-resistant Staphylococcus aureus (MRSA) (9.3% vs. 6.4%), and Klebsiella pneumoniae, including extended-spectrum β-lactamase (ESBL)-producing strains. Empyema was more frequent in octogenarians (7.9% vs. 3.1%), and pleural cultures were usually positive. Meropenem retained 100% activity against ESBL-producing K. pneumoniae and Pseudomonas in both strata. In ≥80-year-olds, superimposed pneumonia was associated with higher day-5 SOFA (6.6 vs. 5.5) and APACHE II (24.3 vs. 21.0) scores and markedly increased 28-day mortality (37.5% vs. 9.8%). Conclusions: In octogenarians with COVID-19, secondary bacterial pneumonia and empyema are frequent, microbiologically similar to younger adults, and strongly amplify organ dysfunction and mortality even with largely preserved carbapenem susceptibility. Full article
(This article belongs to the Section Medical Microbiology)
Show Figures

Figure 1

14 pages, 255 KB  
Article
Predictors of Multidrug-Resistant Urinary Tract Infections in Women: A Large Retrospective Cohort Study in a Romanian University Hospital
by Corina-Ioana Anton, Cristian Sorin Sima, Ștefan Ion and Viorel Jinga
Microorganisms 2026, 14(1), 157; https://doi.org/10.3390/microorganisms14010157 - 10 Jan 2026
Viewed by 191
Abstract
Urinary tract infections (UTIs) represent a major cause of morbidity among adult women, with a disproportionate burden among postmenopausal patients. Limited data exist from Eastern Europe regarding pathogen distribution, antimicrobial resistance, and treatment patterns in hospitalized women. We conducted a retrospective cohort study [...] Read more.
Urinary tract infections (UTIs) represent a major cause of morbidity among adult women, with a disproportionate burden among postmenopausal patients. Limited data exist from Eastern Europe regarding pathogen distribution, antimicrobial resistance, and treatment patterns in hospitalized women. We conducted a retrospective cohort study of 948 adult female patients hospitalized with symptomatic UTIs between January 2021 and December 2023 in a Romanian multidisciplinary hospital. Demographic, clinical, and microbiological parameters were analyzed. Pathogen identification was performed by MALDI-TOF MS, and antimicrobial susceptibility testing followed EUCAST 2024 standards. Empiric treatment strategies and subsequent therapy modifications were assessed. Postmenopausal women accounted for 78.4% of cases and exhibited higher rates of recurrent UTIs, frailty, diabetes, urinary catheterization, and prior antibiotic exposure. Escherichia coli remained the predominant pathogen (52.6%), followed by Klebsiella spp. (18.4%) and Enterococcus spp. (12.1%). ESBL-producing organisms were found in 21.4% of E. coli and 38.7% of Klebsiella isolates. Pathogen distribution differed by age: younger women had a higher proportion of E. coli, whereas postmenopausal women showed a relative increase in opportunistic/healthcare-associated pathogens, particularly Klebsiella spp. and Enterococcus spp., consistent with higher catheter exposure and comorbidity burden. Carbapenem resistance was rare but present in a small subset of Klebsiella isolates with phenotypes compatible with OXA-48-like carbapenemase production. Empiric therapy most frequently included ceftriaxone or fluoroquinolones, but 27.8% of regimens required adjustment after susceptibility results. Independent predictors of prolonged hospitalization included age > 65 years, recurrent UTI, MDR infection, urinary catheterization, and delayed targeted therapy. UTIs among hospitalized adult women—especially postmenopausal patients—are strongly influenced by comorbidity burden and antimicrobial resistance. Local resistance patterns highlight the need for evidence-based empiric treatment and rapid therapy optimization. Strengthening stewardship and preventive interventions in elderly women is essential. Full article
16 pages, 1035 KB  
Article
Proteomic and Functional Characterization of Antimicrobial Peptides Derived from Fisheries Bycatch via Enzymatic Hydrolysis
by Vicky Balesteros S. Blumen Galendi, Guilherme Rabelo Coelho, Letícia Murback, Wagner C. Valenti, Tavani Rocha Camargo, Marcia Regina Franzolin, Daniel Carvalho Pimenta and Rui Seabra Ferreira
Mar. Drugs 2026, 24(1), 36; https://doi.org/10.3390/md24010036 - 10 Jan 2026
Viewed by 224
Abstract
Fisheries bycatch, while representing a major ecological concern due to the incidental capture of non-target species, also constitutes an underexplored source of marine biomass with biotechnological potential. This study aimed to generate and characterize bioactive peptides from the muscle tissue of three common [...] Read more.
Fisheries bycatch, while representing a major ecological concern due to the incidental capture of non-target species, also constitutes an underexplored source of marine biomass with biotechnological potential. This study aimed to generate and characterize bioactive peptides from the muscle tissue of three common bycatch species from the Brazilian coast: Paralonchurus brasiliensis, Micropogonias furnieri, and Hepatus pudibundus. Muscle homogenates were hydrolyzed using either Alcalase or Protamex to produce peptide-rich hydrolysates, which were analyzed through SDS-PAGE, HPLC-UV, MALDI-TOF, and LC-MS/MS. De novo sequencing and bioinformatic analyses predicted bioactivities that were subsequently validated by in vitro assays. The results demonstrated that enzyme selection strongly influenced both peptide profiles and bioactivity. The Protamex hydrolysate of P. brasiliensis (PBP) exhibited potent antifungal activity, inhibiting Candida albicans growth by 81%, whereas the Alcalase hydrolysate (PBA) showed moderate inhibition of Staphylococcus aureus (29%). No significant effect was observed against Escherichia coli. Overall, this study highlights a sustainable strategy for the valorization of fisheries bycatch through the production of bioactive marine peptides and identifies P. brasiliensis hydrolyzed with Protamex as a promising source of anti-Candida peptides for pharmaceutical and nutraceutical applications. Full article
Show Figures

Graphical abstract

Back to TopTop