Search Results (89)

Protein profiling generated by MALDI-TOF (matrix-assisted laser desorption ionization-time-of-flight) was used to distinguish meat from different livestock species and identify meat species. Meat proteins from fresh beef (n = 12), pork (n = 7), chicken (n = 5) and tilapia fish (n = 3) were extracted and analyzed in a MALDI Biotyper mass spectrometer (Bruker Daltonics, Bremen, Germany) with alpha-cyano-4-hydroxycinnamic acid as the matrix. Mass spectra allowed the distinction of meat species, including between Nellore and Angus bovine breeds, and PCA classification revealed possible biomarkers for meat types. Our results corroborate MALDI-TOF mass spectrometry as an interesting tool for meat identification, which is useful for quality control and the certification of meat products. Full article

High-amylose Lueang Patew Chumphon (LPC) rice, a Thai geographical indication variety, represents an underutilized resource for functional food development. This study investigated sweet fermented LPC rice (SFLPC) compared to conventional sweet fermented glutinous rice (SFGR) through comprehensive microbial, chemical, and nutritional characterization. Starter cakes contained Aspergillus sp., Rhizopus stolonifer, and Pediococcus pentosaceus (>99% similarity by ITS/16S rRNA sequencing and MALDI Biotyper). Both varieties demonstrated comparable fermentation with pH reductions to ~3.5 and lactic acid production (~6 g/L). GC-MS analysis with mass spectral library matching and Linear Retention Index (LRI) comparison tentatively annotated twelve volatile compounds. Absolute peak area analysis revealed distinct variety-specific profiles: SFGR was characterized by significantly higher ethyl palmitate (75.89 ± 19.30 vs. 16.80 ± 7.21 × 10⁶, p = 0.008) and isobutyl alcohol (33.09 ± 3.56 vs. 23.53 ± 1.71 × 10⁶, p = 0.014), exclusive ethyl dodecanoate (44.87 ± 20.60 × 10⁶), and exclusive 2,4-di-tert-butylphenol, while SFLPC showed exclusive ethyl acetate formation. Isoamyl alcohol was the dominant volatile in both varieties, with comparable absolute peak areas (273.91 ± 22.65 vs. 267.54 ± 28.78 × 10⁶, ns). SFLPC demonstrated superior mineral retention (2.1-fold phosphorus, 1.9-fold potassium and magnesium) and enhanced antioxidant capacity (IC₅₀: 3.30 vs. 5.20 μg/mL, representing 36% improvement). Degree of gelatinization analysis validated comparable starch gelatinization (32.5–40.1%) despite different cooking methods, confirming volatile differences arose from rice variety rather than processing. These findings demonstrate high-amylose LPC rice as a promising fermented food substrate offering enhanced nutritional properties and volatile compound profiles through traditional fermentation. Full article

Background/Objectives: Hospital outbreaks of Pseudomonas aeruginosa are difficult to control due to the pathogen’s extensive repertoire, including its ability to form biofilms, adapt and persist in diverse environments, and develop multidrug resistance, all of which contribute to prolonged outbreaks. This study integrates the phenotypic, proteomic, and genomic characterization of a nosocomial outbreak comprising 38 clinical isolates and one environmental isolate recovered from the intensive care unit (ICU) of Hospital IESS Quito Sur. Methods: Clinical data were collected, antimicrobial susceptibility was assessed by minimum inhibitory concentration (MIC), carbapenemase genes were detected by multiple PCR and immunochromatographic assays, and the biofilm formation index (BFI) was determined. In addition, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used for species identification and clustering based on spectral similarity. Twelve representative isolates underwent whole genome sequencing (WGS) to characterize the resistome and virulome and to compare phylogenetic relationships with proteomic clustering defined by MALDI Biotyper Compass Explorer software. Results: All isolates were identified as P. aeruginosa, and phenotypic antimicrobial susceptibility classified most isolates as multidrug resistant, including 32 CRPA strains. The bla_VIM gene was detected in 22 isolates, while BFI analysis showed that all isolates formed moderate to strong biofilms. Genomic analysis revealed that most isolates belonged to ST111 and ST253, and both conserved and heterogeneous resistome and virulome profiles, with a broad distribution of determinants related to biofilm formation, stress tolerance, and persistence. Comparison between MALDI-TOF MS and WGS showed predominant concordance in clustering, mainly within subclusters but disagreement at the cluster level. Conclusions: The detection of carbapenemases, biofilm-forming ability, and virulence determinants associated with prolonged persistence highlights the need for integrated molecular tools, such as MALDI-TOF MS with MALDI Biotyper Compass Explorer software, to support epidemiological surveillance and to inform strategies aimed at mitigating prolonged hospital outbreaks caused by P. aeruginosa. Full article

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 bla_OXA-347 and bla_MUN. 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

Yeasts of the Candida genus are part of the normal human microbiota but can cause infections (candidiasis) under certain conditions. While Candida albicans remains the most common etiological agent, the prevalence of non-albicans Candida species—such as C. glabrata, C. tropicalis, C. krusei, C. parapsilosis, C. kefyr, C. lusitaniae, and the emerging multidrug-resistant C. auris—has been increasing. Effective treatment of candidiasis requires rapid and accurate identification of the causative species, particularly due to species-specific antifungal agent resistance patterns. The aim of this study was to evaluate the usefulness of five chromogenic media for the differentiation of Candida species: BD CHROMagar Candida (Becton Dickinson), CHROM ID Candida (bioMérieux), CHROMAgar Candida Plus (CHROMAgar France, Biomaxima), CHROMAgar Candida Plus (GRASO Biotech), and Brilliance Candida Agar (OXOID). A total of 175 strains from the following species were tested: C. albicans, C. parapsilosis, C. dubliniensis, C. lusitaniae, C. tropicalis, C. glabrata, C. kefyr, C. krusei, and C. auris. Species identification was confirmed by MALDI-TOF mass spectrometry using the MALDI Biotyper system (Bruker). Colony morphology, especially color characteristics, was assessed on each medium. The morphological features of most Candida species were consistent with the manufacturer’s descriptions and allowed for presumptive species-level identification. However, some species showed reproducible but previously undescribed morphological traits, including variations in colony shade. Notably, C. auris could not be reliably identified using BD, bioMérieux, or OXOID media. In conclusion, while chromogenic media are a helpful preliminary diagnostic tool, subtle differences in colony coloration can complicate interpretation. Diagnostic caution is recommended, and confirmatory methods such as MALDI-TOF remain essential for reliable identification, especially for emerging or less common Candida species. Full article

Rapid and accurate serotyping of Salmonella (S.) enterica subsp. enterica serovars is essential for effective public health surveillance, outbreak control, and food safety management. Traditional serotyping, although considered the gold standard, is time-consuming, technically demanding, and costly. This study aimed to evaluate the applicability of artificial intelligence (AI)-enhanced Fourier-transform infrared (FT-IR) spectroscopy using an IR Biotyper (Bruker Daltonics, Bremen, Germany) for the rapid and accurate serotyping of Salmonella enterica subsp. enterica isolates in Croatia. Materials and Methods: A total of 143 isolates representing different S. enterica serovars of human and food origin were analysed using the IR Biotyper. Each strain was tested in three biological and at least three technical replicates. The obtained results were compared with traditional serotyping according to the Kauffmann–White–Le Minor scheme. Isolate identification at the genus level was further confirmed by MALDI-TOF mass spectrometry. Results: The IR Biotyper demonstrated high reproducibility and complete concordance with standard serotyping methods, enabling accurate differentiation of the most prevalent S. enterica serovars in Croatia. Conclusions: Our findings demonstrate the applicability of FT-IR in routine laboratory work, with the potential to reduce typing time, reduce the number of strains, and lower overall costs required for epidemiological surveillance within the One Health approach. Full article

The demand for wild animal meat, popularly called “bushmeat”, serves as a driving force behind the emergence of infectious diseases, potentially transmitting a variety of pathogenic bacteria to humans through handling and consumption. This study investigated the microbial load and bacterial diversity in bushmeat sourced from a prominent bushmeat market in Kumasi, Ghana. Carcasses of 61 wild animals, including rodents (44), antelopes (14), and African civets (3), were sampled for microbiological analysis. These samples encompassed meat, intestines, and anal and oral swabs. The total aerobic bacteria plate count (TPC), Enterobacteriaceae count (EBC), and fungal counts were determined. Bacterial identification was conducted using MALDI-TOF biotyping. Fungal counts were the highest across all animal groups, with African civets having 11.8 ± 0.3 log₁₀ CFU/g and 11.9 ± 0.2 log₁₀ CFU/g in intestinal and meat samples, respectively. The highest total plate count (TPC) was observed in rodents, both in their intestines (10.9 ± 1.0 log₁₀ CFU/g) and meat (10.9 ± 1.9 log₁₀ CFU/g). In contrast, antelopes exhibited the lowest counts across all categories, particularly in EBC from intestinal samples (6.1 ± 1.5 log₁₀ CFU/g) and meat samples (5.6 ± 1.2 log₁₀ CFU/g). A comprehensive analysis yielded 524 bacterial isolates belonging to 20 genera, with Escherichia coli (18.1%) and Klebsiella spp. (15.5%) representing the most prevalent species. Notably, the detection of substantial microbial contamination in bushmeat underscores the imperative for a holistic One Health approach to enhance product quality and mitigate risks associated with its handling and consumption. Full article

Milk is frequently susceptible to contamination by potential pathogens, posing risks to both food safety and public health. Cheesemaking often relies on raw milk, where microbial communities—including Staphylococcus xylosus—can play a dual role: (i) contributing to fermentation and (ii) acting as opportunistic pathogens that can be often present in subclinical mastitis and be subjected to carry over in dairy products. In this study, Staphylococcus xylosus was isolated from raw bovine milk (preclinical mastitis) and identified via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (Biotyper scores: 1.87–2.19). Its susceptibility to erythromycin and to an essential oil blend composed of Myrtus communis, Salvia officinalis, and Cistus ladanifer was evaluated. The essential oil blend produced inhibition zones ranging from 9 mm to 13.3 mm, indicating moderate antibacterial activity. Further Minimum Inhibitory Concentration analysis revealed that Myrtus communis, Salvia officinalis, and the essential oil blend inhibited Staphylococcus xylosus growth at concentrations between 0.5 and 0.25 percent, while Cistus ladanifer required higher levels (1 to 0.5 percent). These findings suggest that selected essential oils—especially in combination—hold promise as complementary antimicrobial agents in food safety and antimicrobial resistance mitigation efforts. Full article

The emergence of antimicrobial resistance and the increasing demand for a healthier lifestyle have set new goals for science and industry. In the search for new, more effective, and environmentally friendly antimicrobial agents, special attention is being paid to natural resources. In this regard, essential oils derived from plants, which are widely used in the cosmetic, food, and pharmaceutical industries, are one of the solutions. In view of the above, this study aims to investigate the biological effects of Abies alba essential oil (AAEO). The chemical profile of AAEO was evaluated by GC/MS analysis, which revealed a high abundance of limonene (52.2%) and α-pinene (36.2%). Antioxidant activity evaluation showed a higher potential of AAEO in scavenging ABTS radical species with an IC₅₀ value of 1.18 ± 0.05 mg/mL. In vitro antimicrobial activity was determined by disc diffusion and minimum inhibitory concentration assays and showed that AAEO was more efficient in inhibiting the growth of G⁺ bacterial species. On contrary, in situ evaluations of antimicrobial effects of AAEO on different food models (strawberry, kiwi, white radish, and beetroot) resulted in more efficient suppression of G⁻ bacterial species. Although AAEO showed low effects on yeasts determined by in vitro methods, in situ investigations showed its higher potential in eradication of Candida yeast. The antibiofilm properties of the AAEO matrix were determined by means of crystal violet assay and MALDI-TOF MS Biotyper analysis against biofilm-forming Salmonella enterica. The analysis performed led to the conclusion that AAEO, when applied prior to biofilm formation, may contribute to the removal of planktonic cells and alter the abiotic surface, thereby reducing the suitability of Salmonella enterica for microbial attachment. Full article

Background/Objectives: The present study was aimed at documenting S. maltophilia occurrence in dogs with skin ailments, investigating its virulence, biofilm-forming ability, antimicrobial susceptibility, and zoonotic potential to inform preventive and therapeutic strategies against multidrug resistant S. maltophilia infections. Methods: Skin swabs (n = 300) were collected from dogs with dermatological ailments. Isolation was performed using selective media and confirmed with molecular methods, validated by MALDI Biotyper. Antimicrobial susceptibility testing and efflux activity assessment were conducted. Resistance genes related to sulfonamides, quinolones, and β-lactams were screened. Virulence was assessed by biofilm formation, motility, and virulence gene profiling. Results: In total, 15 S. maltophilia (5%) isolates were identified. All 15 isolates were susceptible to trimethoprim-sulfamethoxazole, enrofloxacin, gatifloxacin, levofloxacin, minocycline, and tigecycline, but resistant to cefpodoxime and aztreonam. The following resistance genes qnr (93.3%), bla_OXA-48 (46.7%), bla_KPC (33.3%), bla_NDM (33.3%), bla_CTX-M (20%), bla_SHV (20%), and bla_TEM (6.7%) were detected. All 15 isolates displayed high efflux activity. Overall, 9 isolates (60%) were strong biofilm producers, and 6 (40%) were moderate. Virulence genes such as virB, motA, rmlA, and fliC were present in all 15 isolates, with others varying in frequency. All isolates exhibited swimming motility. Heat map clustering showed diverse profiles, with no identical isolate patterns. Correlation analysis indicated positive associations between several antimicrobial resistance and virulence genes. Conclusions: This study underscores the zoonotic potential of S. maltophilia from dogs, advocating for a One Health approach to mitigate infection risks and limit the spread of virulent multidrug resistant pathogens. 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

The goal of the present study was to analyze Acinetobacter baumannii strains isolated from hospitalized patients in the period of the COVID-19 pandemic by phenotypic and molecular methods and evaluate their antimicrobial resistance patterns and biofilm production. Forty-seven strains were isolated in 2021–2022 from a hospital in Brazil, and were identified by VITEK^®2, MALDI-TOF/MS (VITEK MS^® and MALDI Biotyper^®), and 16S rRNA sequencing. Fourier-transform infrared (FTIR) spectroscopy was applied for typing and antimicrobial susceptibility testing (AST). In addition, biofilm formation and disinfectant tolerance tests were used. All methods accurately identified all the A. baumannii strains. FTIR typing identified 23 different profiles and 11 clusters, as well as differentiated between the strains from patients with and without COVID-19. Most strains exhibited resistance to the drugs tested, 91.5% of the strains were classified as XDR, 6.4% of the strains were MDR and only 1 strain was classified as non-MDR. Over half of the strains (n = 27, 57.4%) produced biofilms on polystyrene. Sodium hypochlorite (1.0%/15 min) was the best option for effective disinfection. Overall, this study will lay the foundation for further research on effective cleaning protocols for the eradication of A. baumannii biofilms, as well as the use of FTIR for pathogen surveillance in healthcare settings. Full article

Escherichia albertii is a lactose-negative Escherichia that causes gastritis and enteritis in humans. An analysis of possible sources of infection points out that poultry may be a significant reservoir for this pathogen. The question of whether E. albertii can cause infections in poultry is still unanswered. Our article describes the isolation of E. albertii, for the first time in Russia, from the intestines of birds on a quail farm and a characterization of obtained cultures. We isolated different bacteria from pathological poultry material using bacteriological methods and ruled them out as probable causes for enteritis. The biochemical identification of E. albertii and antibiotic sensitivity were performed using a Vitek-2 Compact instrument. Bacterial identification was carried out using the MALDI-TOF Biotyper instrument. E. albertii-specific genes, virulence factor genes, and microcin genes were detected by real-time PCR. It was concluded that E. albertii isolated from sites of intestinal inflammation are a potential cause of enteritis and high poultry mortality—up to 15% of total livestock for 10- to 20-day-old quails. One of the E. albertii culture differed from the main group of Escherichia by its biochemical properties, and subsequent PCR analysis showed a lack of the intimin gene (eae). We describe the first occasion of infection caused by E. albertii in industrial quails. During the study, it was found that, according to the molecular–genetic and phenotypic properties of isolated strains in quails, there were at least two clonal groups of E. albertii differing in antibiotic resistance, biochemical indices, and presence of the eae (intimin) gene. Full article

European hedgehogs are an important reservoir for many pathogens of health interest. Since hedgehogs live in close contact with humans, potential zoonotic fungi raise significant public health concerns, especially in areas with a high hedgehog density. From 2020 to 2023, 134 hedgehogs were surveyed for potential zoonotic fungi. Non-invasive methods were used, such as brushing live animals with a sterile toothbrush and taking oral and rectal swabs from deceased ones (86 animals). Dermatophytes were cultured on Dermasel agar and identified using molecular tools, while yeasts were isolated on Sabouraud agar with chloramphenicol and determined using Candida Chromogenic agar (MicroBiolDiagnostici^®, Cagliari, Italy) and MALDI-TOF (Microflex LT Smart Biotyper with FlexControlBiotyper 3.4 software, Bruker Daltonics, Bremen, Germany). Minimum inhibitory concentrations (MICs) were determined for Candida albicans isolates. Dermatophytes were found in just one hedgehog (0.8%, 95% C.I.: 0–0.04), identified as Paraphyton mirabile. Yeasts were detected in 22 of 86 hedgehogs (25.6%, 95% C.I.: 16.4–34.8), with 25 isolates obtained, including 21 Candida albicans, 2 Yarrowia lipolytica, 1 Rhodotorula mucilaginosa, and 1 Meyerozyma guilliermondii. All C. albicans isolates showed a high susceptibility to the antimycotic panel tested. Monitoring zoonotic fungi harbored by European hedgehogs, as well as raising public awareness on the topic, is of great importance for public health. Full article

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. Full article