ABSTRACT
Vibrio vulnificus is a halophilic gram-negative bacillus that can cause fulminant septicaemia in immunocompromised patients. A 67-year-old man who was immunosuppressed as a result of cytotoxic chemotherapy presented with a brief history of fever, lethargy, myalgia, and reduced oral intake. He had recently travelled to the beach to consume seafood. His blood pressure was 81/47 mm Hg, necessitating fluid resuscitation followed by inotropic support and admission to the intensive care unit. His blood culture was positive for curved gram-negative bacilli. The isolate was oxidase-positive and produced an acid butt with an alkaline slant in triple sugar iron agar. Matrix-assisted laser desorption ionization-time of flight mass spectrometry conclusively identified the isolate as V. vulnificus. Intravenous ceftazidime plus ciprofloxacin were administered, and by the fifth day of admission, he was successfully transferred out to the general ward. In total, the patient completed a 14-day course of antibiotic therapy.
Subject(s)
Anti-Bacterial Agents , Sepsis , Vibrio Infections , Vibrio vulnificus , Humans , Male , Aged , Vibrio vulnificus/isolation & purification , Anti-Bacterial Agents/therapeutic use , Sepsis/microbiology , Immunocompromised Host , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Ciprofloxacin/therapeutic use , Ceftazidime/therapeutic useABSTRACT
Globally, Campylobacter spp. are responsible for most cases of bacterial gastrointestinal infections in humans and although rare, extraintestinal Campylobacter infections have been described. A 2-yearold neutropenic girl with underlying precursor B-cell acute lymphoblastic leukemia presented with a 3-day history of diarrhea. Her stool culture yielded no enteric bacterial pathogens. However, when her blood culture was flagged as positive for bacterial growth, no colonies could be observed on routine bacteriological isolation media. Nonetheless, gram-negative bacilli with seagull and spiral morphologies were seen when the surface of the isolation media used to subculture her blood was Gram-stained. Bacterial colonies were only visible when a subculture was attempted on a Campylobacter blood-free selective agar medium. The organism was identified as Campylobacter jejuni by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Since the organism was erythromycin-resistant and the patient's age precluded the use of tetracycline and ciprofloxacin, an antibiotic regimen consisting of piperacillin-tazobactam and gentamicin was commenced. Her C. jejuni bacteremia resolved following eight days of antibiotic therapy.
Subject(s)
Anti-Bacterial Agents , Bacteremia , Campylobacter Infections , Campylobacter jejuni , Humans , Female , Bacteremia/microbiology , Bacteremia/drug therapy , Bacteremia/diagnosis , Campylobacter jejuni/isolation & purification , Campylobacter Infections/drug therapy , Campylobacter Infections/microbiology , Campylobacter Infections/diagnosis , Anti-Bacterial Agents/therapeutic use , Child, Preschool , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/diagnosis , Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/drug therapyABSTRACT
Traumatic brain injury (TBI) is an alteration of brain function caused by a sudden transmission of an external force to the head. The biomechanical impact induces acute and chronic metabolic changes that highly contribute to injury evolution and outcome. TBI heterogeneity calls for approaches allowing the mapping of regional molecular and metabolic changes underpinning disease progression, with mass spectrometry imaging (MSI) as an efficient tool to study the spatial distribution of small metabolites. In this study, we applied an innovative targeted atmospheric pressure-MALDI mass spectrometry imaging (AP-MALDI MSI) approach, starting from an extensive list of metabolites, representative of different metabolic pathways, individually validated on the tissue under analysis with original standards using 2,5-dihydroxybenzoic acid (DHB), to characterize the impact of TBI on regional changes to small metabolites in the brain. Brains from sham and TBI mice obtained 21 days post-injury were analyzed to examine the spatial metabolic profile of small metabolites belonging to different metabolic pathways. By a whole brain analysis, we identified four metabolites (alanine, lysine, histidine, and inosine) with higher abundance in TBI than sham mice. Within the TBI group, lysine, histidine, and inosine were higher in the hemisphere ipsilateral to the biomechanical impact vs. the contralateral one. Images showed a major involvement of the ipsilateral thalamus characterized by the increase of arginine, lysine, histidine, and inosine and a significant reduction of glutamic acid, and N-acetylaspartic acid compared to the contralateral thalamus. These findings indicate high-resolution imaging mass spectrometry as a powerful tool to identify region-specific changes after a TBI to understand the metabolic changes underlying brain injury evolution.
Subject(s)
Brain Injuries, Traumatic , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Brain Injuries, Traumatic/metabolism , Animals , Mice , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Male , Mice, Inbred C57BL , Brain/metabolismABSTRACT
Antimicrobial susceptibility testing (AST) plays a critical role in assessing the resistance of individual microbial isolates and determining appropriate antimicrobial therapeutics in a timely manner. However, conventional AST normally takes up to 72 h for obtaining the results. In healthcare facilities, the global distribution of vancomycin-resistant Enterococcus fecium (VRE) infections underscores the importance of rapidly determining VRE isolates. Here, we developed an integrated antimicrobial resistance (AMR) screening strategy by combining matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) with machine learning to rapidly predict VRE from clinical samples. Over 400 VRE and vancomycin-susceptible E. faecium (VSE) isolates were analyzed using MALDI-MS at different culture times, and a comprehensive dataset comprising 2388 mass spectra was generated. Algorithms including the support vector machine (SVM), SVM with L1-norm, logistic regression, and multilayer perceptron (MLP) were utilized to train the classification model. Validation on a panel of clinical samples (external patients) resulted in a prediction accuracy of 78.07%, 80.26%, 78.95%, and 80.54% for each algorithm, respectively, all with an AUROC above 0.80. Furthermore, a total of 33 mass regions were recognized as influential features and elucidated, contributing to the differences between VRE and VSE through the Shapley value and accuracy, while tandem mass spectrometry was employed to identify the specific peaks among them. Certain ribosomal proteins, such as A0A133N352 and R2Q455, were tentatively identified. Overall, the integration of machine learning with MALDI-MS has enabled the rapid determination of bacterial antibiotic resistance, greatly expediting the usage of appropriate antibiotics.
Subject(s)
Anti-Bacterial Agents , Machine Learning , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Humans , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/analysis , Microbial Sensitivity Tests , Enterococcus faecium/drug effects , Enterococcus faecium/isolation & purification , Vancomycin-Resistant Enterococci/drug effects , Vancomycin-Resistant Enterococci/isolation & purification , Support Vector Machine , Drug Resistance, BacterialABSTRACT
Application of stable isotopically labelled (SIL) molecules in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) over a series of time points allows the temporal and spatial dynamics of biochemical reactions to be tracked in a biological system. However, these large kinetic MSI datasets and the inherent variability of biological replicates presents significant challenges to the rapid analysis of the data. In addition, manual annotation of downstream SIL metabolites involves human input to carefully analyse the data based on prior knowledge and personal expertise. To overcome these challenges to the analysis of spatiotemporal MALDI-MSI data and improve the efficiency of SIL metabolite identification, a bioinformatics pipeline has been developed and demonstrated by analysing normal bovine lens glucose metabolism as a model system. The pipeline consists of spatial alignment to mitigate the impact of sample variability and ensure spatial comparability of the temporal data, dimensionality reduction to rapidly map regional metabolic distinctions within the tissue, and metabolite annotation coupled with pathway enrichment modules to summarise and display the metabolic pathways induced by the treatment. This pipeline will be valuable for the spatial metabolomics community to analyse kinetic MALDI-MSI datasets, enabling rapid characterisation of spatio-temporal metabolic patterns from tissues of interest.
Subject(s)
Glucose , Lens, Crystalline , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Animals , Cattle , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Lens, Crystalline/metabolism , Glucose/metabolism , Isotope Labeling/methods , Workflow , Metabolomics/methods , Data Analysis , Metabolic Networks and PathwaysABSTRACT
To evaluate the diagnostic accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry based on nucleotide (nucleotide MALDI-TOF MS) on bronchoalveolar lavage fluid (BALF) from suspected pulmonary tuberculosis (PTB) patients. A retrospective study was conducted on suspected PTB patients (total of 960) admitted to Chongqing Public Health Medical Center between May 2021 and January 2022. The sensitivity, specificity, positive predictive value, negative predictive value (NPV) and area under the curve values of nucleotide MALDI-TOF MS as well as smear microscopy, Mycobacterium Growth Indicator Tube 960 culture (MGIT culture), and Xpert MTB/RIF were calculated and compared. Total of 343 presumed PTB cases were enrolled. Overall, using the clinical diagnosis as reference, the sensitivity and NPV of nucleotide MALDI-TOF MS was 71.5% and 43.1%, respectively, significantly higher than smear microscopy (22.6%, 23.2%), MGIT culture (40.6%, 18.9%), Xpert MTB/RIF (40.8%, 27.9%). Furthermore, nucleotide MALDI-TOF MS also outperformed over Xpert MTB/RIF and MGIT culture on smear-negative BALFs. Approximately 50% and 30% of patients benefited from nucleotide MALDI-TOF MS compared with smear and MGIT culture or Xpert MTB/RIF, respectively. This study demonstrated that the analysis of BALF with nucleotide MALDI-TOF MS provided an accurate and promising tool for the early diagnosis of PTB.
Subject(s)
Bronchoalveolar Lavage Fluid , Mycobacterium tuberculosis , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Tuberculosis, Pulmonary , Humans , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Bronchoalveolar Lavage Fluid/microbiology , Bronchoalveolar Lavage Fluid/chemistry , Retrospective Studies , Tuberculosis, Pulmonary/diagnosis , Tuberculosis, Pulmonary/microbiology , Female , Male , Middle Aged , Adult , Mycobacterium tuberculosis/isolation & purification , Sensitivity and Specificity , Nucleotides/analysis , AgedABSTRACT
BACKGROUND: Several diagnostic environments in Uganda lack real-time, robust and high-throughput technologies for comprehensive typing of microbes, which is a setback to infectious disease surveillance. This study combined various wet laboratory diagnostics to understand the epidemiology of pathogenic staphylococci isolated from animals in Uganda and the implications for global health security priorities. METHODS: A retrospective study was conducted employing records and pathogenic staphylococci (from animals) archived at the Central Diagnostic Laboratory (CDL), Makerere University, Uganda, between January 2012 and December 2019. The bacteria were speciated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and tested for virulence factors [beta lactamases, lecithinase, deoxyribonuclease (DNase), haemolysins] and resistance to ten antimicrobials of clinical and veterinary relevance. Tetracycline and methicillin resistance genes were also tested. RESULTS: The prevalent diseases were mastitis in cattle and skin infections in dogs. Of the 111 staphylococci tested by MALDI-TOF MS, 79 (71.2%) were Staphylococcus aureus, 27 (24.3%) were Staphylococcus pseudintermedius and 5 (4.5%) were Staphylococcus schleiferi. All these strains expressed haemolysins. The prevalence of strains with lecithinase, penicillinase, cephalosporinase and DNase was 35.9% (14/39), 89.7% (35/39), 0.0% (0/39) and 87.2% (34/39), respectively. Staphylococci were primarily resistant to early penicillins (over 80%), tetracycline (57.7%), and chloramphenicol (46.2%). Minimal resistance was noted with cloxacillin (0.0%), ciprofloxacin (9.6%), and cefoxitin (3.8%). The prevalence of multidrug resistance (MDR) was 78.8% for general staphylococci, 82.2% for S. aureus, 73.1% for S. pseudintermedius, and 60.0% for S. schleiferi. Multidrug resistant staphylococci were significantly more prevalent in the cattle isolates than in the dog isolates (P < 0.05). The prevalence of methicillin-resistant staphylococci (MRS) tested by resistance to cefoxitin and mecA carriage was 3.8%. These four strains were all isolated from dog skin infections. The tetK gene was the most predominant (35.4%), followed by tetM (25.0%). CONCLUSION: In resource-constrained settings, the approach of integrated diagnostics promises sustainable disease surveillance and the addressing of current capacity gaps. The emergence of MRS (zoonotic bacteria) in companion animals creates a likelihood of reduced treatment options for related human infections, a threat to global health.
Subject(s)
Staphylococcal Infections , Staphylococcus , Animals , Uganda/epidemiology , Staphylococcal Infections/microbiology , Staphylococcal Infections/veterinary , Staphylococcal Infections/epidemiology , Cattle , Retrospective Studies , Staphylococcus/genetics , Staphylococcus/drug effects , Staphylococcus/isolation & purification , Staphylococcus/classification , Dogs , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Anti-Bacterial Agents/pharmacology , Virulence Factors/genetics , Female , Dog Diseases/microbiology , Dog Diseases/epidemiology , Dog Diseases/diagnosis , Cattle Diseases/microbiology , Cattle Diseases/epidemiology , Cattle Diseases/diagnosis , Microbial Sensitivity TestsABSTRACT
Multiple myeloma (MM) is the second most prevalent hematological malignancy, characterized by infiltration of the bone marrow by malignant plasma cells. Extramedullary disease (EMD) represents a more aggressive condition involving the migration of a subclone of plasma cells to paraskeletal or extraskeletal sites. Liquid biopsies could improve and speed diagnosis, as they can better capture the disease heterogeneity while lowering patients' discomfort due to minimal invasiveness. Recent studies have confirmed alterations in the proteome across various malignancies, suggesting specific changes in protein classes. In this study, we show that MALDI-TOF mass spectrometry fingerprinting of peripheral blood can differentiate between MM and primary EMD patients. We constructed a predictive model using a supervised learning method, partial least squares-discriminant analysis (PLS-DA) and evaluated its generalization performance on a test dataset. The outcome of this analysis is a method that predicts specifically primary EMD with high sensitivity (86.4%), accuracy (78.4%), and specificity (72.4%). Given the simplicity of this approach and its minimally invasive character, this method provides rapid identification of primary EMD and could prove helpful in clinical practice.
Subject(s)
Multiple Myeloma , Humans , Multiple Myeloma/blood , Multiple Myeloma/diagnosis , Liquid Biopsy/methods , Male , Female , Middle Aged , Aged , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Biomarkers, Tumor/bloodABSTRACT
The recent advances in pigeon pea genomics, including high-quality whole genome and chloroplast genome sequence information helped develop improved varieties. However, a comprehensive Cajanus proteome, including the organelle proteome, is yet to be fully mapped. The spatial delineation of pigeon pea proteins at sub-cellular levels and inter-organelle communication could offer valuable insights into its defense mechanism against various stresses. However, the major bottleneck in the proteomic study is the lack of a suitable method of protein extraction and sample preparation compatible with two-dimensional gel electrophoresis (2D-PAGE), liquid chromatography-mass spectrometry (LCMS), or matrix-assisted laser desorption ionization-time of flight (MALDi-ToF). Our study introduces two efficient methods, one for isolating total proteins and another for organelle (chloroplast) proteins from various Cajanus spp. For total protein extraction, we have optimized a protocol using phenol in combination with a reducing agent (DTT) and protease inhibitor cocktail, also washing (6-7 times) with ice-cold acetone after overnight protein precipitation of total proteins. Our modified extraction method using phenol for total leaf protein yielded approximately 2-fold more proteins than the previously reported protocols from C. cajan (3.18 ± 0.11 mg/gm) and C. scarabaeoides (2.06 ± 0.08 mg/gm). We have also optimized a protocol for plastid protein extraction, which yielded 1.33 ± 0.25 mg/10 gm plastid proteins from C. cajan and 0.88 ± 0.19 mg/10 gm plastid proteins from C. scarabaeoides. The 2D-PAGE analysis revealed 678 ± 08 reproducible total protein spots from C. cajan and 597 ± 22 protein spots from C. scarabaeoides. Similarly, we found 566 ± 10 and 486 ± 14 reproducible chloroplast protein spots in C. cajan and C. scarabaeoides, respectively. We confirmed the plastid protein fractions through immunoblot analysis using antibodies against LHCb1/LHCâ ¡ type â protein. We found both methods suitable for 2D-PAGE and mass spectrometry (MS). This is the first report on developing protocols for total and chloroplastic protein extraction of Cajanus spp. suitable for advanced proteomics research.
Subject(s)
Cajanus , Chloroplast Proteins , Electrophoresis, Gel, Two-Dimensional , Electrophoresis, Gel, Two-Dimensional/methods , Cajanus/chemistry , Chloroplast Proteins/metabolism , Chloroplasts/metabolism , Chloroplasts/chemistry , Proteomics/methods , Plant Proteins/isolation & purification , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Proteome , Mass Spectrometry/methodsABSTRACT
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that oxidatively cleave recalcitrant polysaccharides such as cellulose. Several studies have reported LPMO action in synergy with other carbohydrate-active enzymes (CAZymes) for the degradation of lignocellulosic biomass but direct LPMO action at the plant tissue level remains challenging to investigate. Here, we have developed a MALDI-MS imaging workflow to detect oxidised oligosaccharides released by a cellulose-active LPMO at cellular level on maize tissues. Using this workflow, we imaged LPMO action and gained insight into the spatial variation and relative abundance of oxidised and non-oxidised oligosaccharides. We reveal a targeted action of the LPMO related to the composition and organisation of plant cell walls.
Subject(s)
Mixed Function Oxygenases , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Zea mays , Zea mays/chemistry , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/chemistry , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Cellulose/chemistry , Cellulose/metabolism , Cell Wall/chemistry , Cell Wall/metabolism , Oligosaccharides/chemistry , Oligosaccharides/metabolism , Lignin/chemistry , Lignin/metabolism , Oxidation-Reduction , Polysaccharides/chemistry , Polysaccharides/metabolism , Plant Proteins/chemistry , Plant Proteins/metabolismABSTRACT
Azoospermia, the absence of sperm cells in semen, affects around 15% of infertile males. Sertoli cell-only syndrome (SCOS) is the most common pathological lesion in the background of non-obstructive azoospermia and is characterised by the complete absence of germinal epithelium, with Sertoli cells exclusively present in the seminiferous tubules. Studies have shown a correlation between successful spermatogenesis and male fertility with lipid composition of spermatozoa, semen, seminal plasma or testis. The aim of this research was to discover the correlation between the Johnsen scoring system and phospholipid expressions in testicular cryosections of SCOS patients. MALDI imaging mass spectrometry is used to determine spatial distributions of molecular species, such as phospholipids. Phosphatidylcholines (PCs), phosphatidylethanolamines (PEs) and sphingomyelins (SMs) are the most abundant phospholipids in mammalian cells and testis. SMs, the structural components of plasma membranes, are crucial for spermatogenesis and sperm function. Plasmalogens, are unique PCs in testis with strong antioxidative properties. This study, using imaging mass spectrometry, demonstrates the local distribution of phospholipids, particularly SMs, PCs, plasmalogens and PEs in human testicular samples with SCOS for the first time. This study found a strong relationship between the Johnsen scoring system and phospholipid expression levels in human testicular tissues. Future findings could enable routine diagnostic techniques during microTESE procedures for successful sperm extraction.
Subject(s)
Sertoli Cell-Only Syndrome , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Testis , Male , Humans , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Testis/metabolism , Testis/pathology , Sertoli Cell-Only Syndrome/metabolism , Sertoli Cell-Only Syndrome/pathology , Phospholipids/metabolism , Spermatogenesis , Azoospermia/metabolism , Azoospermia/pathology , Sphingomyelins/metabolism , Lipids/analysis , Adult , Spermatozoa/metabolism , Spermatozoa/pathologyABSTRACT
Strain Lactiplantibacillus plantarum D1 with bacteriocin producing ability was found in the intestine of Gambusia affinis. The bacteriocin was found to have high inhibitory activity against multiple Streptococcus species and several other Gram-positive and Gram-negative bacteria. Bacteriocin was purified from culture supernatant by ion-exchange chromatography, Sep-Pak C18 cartridge, and reverse-phase high-performance liquid chromatography (RP-HPLC). Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectral analysis determined that purified bacteriocin has a molecular mass of 2,731 Da. A partial N-terminal sequence KRKKHKXQIYNNGM was obtained from the Edman analysis. The N-terminal sequence was employed to search against a translation of the draft genome of strain D1. The translated full amino acid sequence of the mature peptide is as follows: NH2- KRKKHKCQIYNNGMPTGQYRWC, which has a molecular weight of 2738 Da. A BLAST search revealed that this bacteriocin was most similar to bactofencin A but differed from it with three amino acid residues. No identical peptide or protein has been previously reported, and this peptide, termed bactofencin YH, was therefore considered to be a new bacteriocin produced by Lactiplantibacillus plantarum D1.
Subject(s)
Amino Acid Sequence , Anti-Bacterial Agents , Bacteriocins , Molecular Weight , Streptococcus , Bacteriocins/pharmacology , Bacteriocins/chemistry , Bacteriocins/isolation & purification , Bacteriocins/metabolism , Streptococcus/drug effects , Streptococcus/genetics , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/isolation & purification , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Microbial Sensitivity Tests , Animals , Chromatography, High Pressure Liquid , Gram-Negative Bacteria/drug effects , Gram-Positive Bacteria/drug effectsABSTRACT
BACKGROUND: The increased resistance rate of Salmonella to third-generation cephalosporins represented by ceftriaxone (CRO) may result in the failure of the empirical use of third-generation cephalosporins for the treatment of Salmonella infection in children. The present study was conducted to evaluate a novel method for the rapid detection of CRO-resistant Salmonella (CRS). METHODS: We introduced the concept of the ratio of optical density (ROD) with and without CRO and combined it with matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) to establish a new protocol for the rapid detection of CRS. RESULTS: The optimal incubation time and CRO concentration determined by the model strain test were 2 h and 8 µg/ml, respectively. We then conducted confirmatory tests on 120 clinical strains. According to the receiver operating characteristic curve analysis, the ROD cutoff value for distinguishing CRS and non-CRS strains was 0.818 [area under the curve: 1.000; 95% confidence interval: 0.970-1.000; sensitivity: 100.00%; specificity: 100%; P < 10- 3]. CONCLUSIONS: In conclusion, the protocol for the combined ROD and MALDI-TOF MS represents a rapid, accurate, and economical method for the detection of CRS.
Subject(s)
Anti-Bacterial Agents , Ceftriaxone , Microbial Sensitivity Tests , Salmonella Infections , Salmonella , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Ceftriaxone/pharmacology , Humans , Anti-Bacterial Agents/pharmacology , Salmonella/drug effects , Salmonella Infections/microbiology , Microbial Sensitivity Tests/methods , Drug Resistance, Bacterial , Sensitivity and Specificity , ROC CurveABSTRACT
In this study, 80 carbapenem-resistant Klebsiella pneumoniae (CR-KP) and 160 carbapenem-susceptible Klebsiella pneumoniae (CS-KP) strains detected in the clinic were selected and their matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) peaks were collected. K-means clustering was performed on the MS peak data to obtain the best "feature peaks", and four different machine learning models were built to compare the area under the ROC curve, specificity, sensitivity, test set score, and ten-fold cross-validation score of the models. By adjusting the model parameters, the test efficacy of the model is increased on the basis of reducing model overfitting. The area under the ROC curve of the Random Forest, Support Vector Machine, Logistic Regression, and Xgboost models used in this study are 0.99, 0.97, 0.96, and 0.97, respectively; the model scores on the test set are 0.94, 0.91, 0.90, and 0.93, respectively; and the results of the ten-fold cross-validation are 0.84, 0.81, 0.81, and 0.85, respectively. Based on the machine learning algorithms and MALDI-TOF MS assay data can realize rapid detection of CR-KP, shorten the in-laboratory reporting time, and provide fast and reliable identification results of CR-KP and CS-KP.
Subject(s)
Bacterial Proteins , Klebsiella Infections , Klebsiella pneumoniae , Machine Learning , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , beta-Lactamases , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Klebsiella pneumoniae/drug effects , Humans , Klebsiella Infections/microbiology , Klebsiella Infections/diagnosis , Bacterial Proteins/analysis , beta-Lactamases/analysis , Sensitivity and Specificity , Carbapenem-Resistant Enterobacteriaceae/isolation & purification , Carbapenem-Resistant Enterobacteriaceae/drug effects , ROC Curve , Anti-Bacterial Agents/pharmacology , Microbial Sensitivity Tests/methodsABSTRACT
The intricate composition of microalgal pigments plays a crucial role in various biological processes, from photosynthesis to biomarker identification. Traditional pigment analysis methods involve complex extraction techniques, posing challenges in maintaining analyte integrity. In this study, we employ Electron Transfer Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (ET-MALDI-MS) to compare the pigmentary profiles of Chlorella vulgaris intact cells, chloroplasts, and solvent extracts. We aim to obtain comprehensive extracts rich in polar and non-polar compounds using ultrasound-assisted and supercritical fluid extraction methods. Additionally, intact chloroplasts are isolated using a lysis buffer and sucrose density gradient centrifugation. Our ET-MALDI-MS analysis reveals distinct compositional differences, highlighting the impact of extraction protocols on microalgal pigment identification. We observe prominent signals corresponding to radical cations of key pigments, including chlorophylls and carotenoids, which are crucial for C. vulgaris identification. Furthermore, ET-MALDI-MS facilitates the identification of specific lipids within chloroplast membranes and other organelles. This study underscores the rapid and precise nature of ET-MALDI-MS in microalgal biomarker analysis, providing valuable insights into phytoplankton dynamics, trophic levels, and environmental processes. C. vulgaris emerges as a promising model for studying pigment composition and membrane lipid diversity, enhancing our understanding of microalgal ecosystems.
Subject(s)
Chlorella vulgaris , Chloroplasts , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Chlorella vulgaris/chemistry , Chlorella vulgaris/metabolism , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Chloroplasts/chemistry , Chloroplasts/metabolism , Carotenoids/analysis , Carotenoids/chemistry , Chlorophyll/analysis , Chlorophyll/chemistry , Pigments, Biological/analysis , Pigments, Biological/chemistryABSTRACT
The purpose of this study was to conduct a comparative analysis of the composition of the dominant groups of vaginal microorganisms in healthy pregnant women and pregnant women infected with HPV using a microbiological culture-based method. The MALDI TOF MS method and 16S rRNA gene fragment sequencing were used to identify microorganisms isolated from healthy pregnant women (n=32) and pregnant women infected with HPV (n=24). It was found that vaginal secretion samples from both groups contained bacteria of 4 phyla: Bacillota, Actinomycetota, Pseudomonadota, Bacteroidota, and Ascomycota fungi. The most common microbial community in healthy pregnant women being CST I (p=0.0007), and CST V in pregnant women infected with HPV (p=0.0001). At the genus level, a total of 25 taxa were found in all samples, with Lactobacillus being the dominant genus overall. Escherichia (p<0.0001) and Prevotella (p=0.0001) concentrations were higher in HPV infected patients. When calculating the Pearson correlation coefficient for the phyla, it was found that Bacillota correlated negatively with HPV genotypes 16 and 51 (p≤0.05), but positively with HPV genotype 59 (p≤0.05), just like Actinomycetota (p≤0.05). Bacteroidota correlated positively with HPV genotype 56 (0.001
Subject(s)
Bacteria , Microbiota , Papillomavirus Infections , RNA, Ribosomal, 16S , Vagina , Humans , Female , Vagina/microbiology , Vagina/virology , Pregnancy , Papillomavirus Infections/virology , Papillomavirus Infections/microbiology , Microbiota/genetics , Adult , RNA, Ribosomal, 16S/genetics , Bacteria/classification , Bacteria/isolation & purification , Bacteria/genetics , Papillomaviridae/genetics , Papillomaviridae/isolation & purification , Papillomaviridae/classification , Young Adult , Pregnancy Complications, Infectious/microbiology , Pregnancy Complications, Infectious/virology , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Sequence Analysis, DNAABSTRACT
A one-step, on-tissue chemical derivatisation method for MALDI mass spectrometry imaging was found to improve the detectability of aldehydes and ketones by charge-tagging. The developed reactive matrices, containing a UV-chromophore, ionisable moiety and hydrazide group, showed an equal or higher detection efficiency than Girard's reagent P, enabling improved imaging of brain metabolites without the need for additional co-matrices.
Subject(s)
Aldehydes , Hydrazines , Ketones , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Aldehydes/chemistry , Aldehydes/analysis , Ketones/chemistry , Ketones/analysis , Hydrazines/chemistry , Hydrazines/analysis , Animals , Brain/diagnostic imaging , Brain/metabolism , MiceABSTRACT
The goal of the present study was to establish a rapid, simple method for simultaneous allergy testing of sera from multiple fish-allergic patients. Sera from fish-allergic patients were pooled and used for capturing allergens in fish muscle of crucian carp (Carassius auratus), which was studied as a fish model. Sarcoplasmic proteins of crucian carp (Carassius auratus) were extracted for the analysis of allergens. Anti-human IgE antibody-functionalized magnetic beads were utilized to collect IgE antibodies from human pooled sera. The isolation of allergenic proteins was immunomagnetically performed in microfluidic channels, and the elution of the captured allergenic proteins was done with 5% (v/v) acetic acid aqueous solution. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and peptide mass fingerprinting were used for the analysis of tryptic digests of eluted proteins. Ten potential allergenic proteins were identified from crucian carp (Carassius auratus). The present protocol provides a rapid, efficient, and simple method for simultaneous detection of multiple allergens, based on multitargeted antibodies from pooled sera of allergic patients. The constructed multiple antibody-modified MBs can be applied for the deallergenicity of food matrices. The efficiency of allergen detection can be greatly improved, with promising application in allergen discovery and filtration for other muscle-based foods.
Subject(s)
Allergens , Fish Proteins , Food Hypersensitivity , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Animals , Allergens/immunology , Allergens/chemistry , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Fish Proteins/immunology , Fish Proteins/chemistry , Food Hypersensitivity/immunology , Food Hypersensitivity/veterinary , Humans , Carps/immunology , Immunoglobulin E/immunology , Immunoglobulin E/blood , Goldfish/immunologyABSTRACT
Sand flies are vectors of great public health importance, since they constitute a group of hematophagous insects responsible for etiological agents transmission of zoonotic diseases such a visceral leishmaniasis. In face of the expansion of these diseases, efficient control strategies are needed which depend on comprehending the sand fly eco-epidemiology. In this regard, MALDI-TOF mass spectrometry has been used for bacteria, fungi and yeast detection studies through peptide/protein profiles. However, little is known about interference of biological factors associated with vector ecology, such as blood meal preferences and even sand fly age on the peptide/protein profiles. Thus, the present study aimed to evaluate the differences in peptide/protein profiles of the sand fly Lutzomyia longipalpis, by means of MALDI-TOF, due to the sand fly's age, sex, blood meal source and Leishmania infantum infection. Sample preparation was made removing both head and last abdomen segments keeping the thorax, its appendices and the rest of the abdomen. Five specimens per pool were used to obtain peptide/protein extract of which 1 µL solution was deposited over 1 µL MALDI matrix dried. Characteristic spectra were analyzed using principal coordinate analysis as well as indicator species analysis to discriminate differences in sand flies's peptide/protein profile by sex, age, blood meal source and L. infantum infection. The results show that the evaluated variables produced distinct peptide/protein profiles, demonstrated by the identification of specific diagnostic ions. It was found that the interference of biological factors should be taken into account when using the MALDI-TOF analysis of sand fly species identification and eco-epidemiological applications in field studies. Based on our results, we believe that it is possible to identify infected specimens and the source of blood meal in a collection of wild sand flies, serving to measure infectivity and understand the dynamics of the vector's transmission chain. Our results may be useful for epidemiological studies that look at the ecology of sand flies and leishmaniasis, as well as for raising awareness of biological characteristics' impact on peptide/protein profiles in sand fly species identification.
Subject(s)
Psychodidae , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Animals , Psychodidae/parasitology , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Female , Male , Peptides/analysis , Insect Proteins/analysis , Insect Vectors/parasitology , Leishmania infantum/isolation & purification , Leishmaniasis, Visceral/transmissionABSTRACT
Protein citrullination is an irreversible post-translational modification process regulated by peptidylarginine deiminases (PADs) in the presence of Ca2+. This process is closely related to the occurrence and development of autoimmune diseases, cancers, neurological disorders, cardiovascular and cerebrovascular diseases, and other major diseases. The analysis of protein citrullination by biomass spectrometry confronts great challenges owing to its low abundance, lack of affinity tags, small mass-to-charge ratio change, and susceptibility to isotopic and deamidation interferences. The methods commonly used to study the protein citrullination mainly involve the chemical derivatization of the urea group of the guanine side chain of the peptide to increase the mass-to-charge ratio difference of the citrullinated peptide. Affinity-enriched labels are then introduced to effectively improve the sensitivity and accuracy of protein citrullination by mass spectrometry. 2,3-Butanedione or phenylglyoxal compounds are often used as derivatization reagents to increase the mass-to-charge ratio difference of the citrullinated peptide, and the resulting derivatives have been observed to contain α-dicarbonyl structures. To date, however, no relevant studies on the reactivity of dicarbonyl compounds with citrullinated peptides have been reported. In this study, we determined whether six α-dicarbonyl and two ß-dicarbonyl compounds undergo derivatization reactions with standard citrullinated peptides using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Among the α-dicarbonyl compounds, 2,3-butanedione and glyoxal reacted efficiently with several standard citrullinated peptides, but yielded a series of by-products. Phenylglyoxal, methylglyoxal, 1,2-cyclohexanedione, and 1,10-phenanthroline-5,6-dione also derivated efficiently with standard citrullinated peptides, generating a single derivative. Thus, a new derivatization method that could yield a single derivative was identified. Among the ß-dicarbonyl compounds, 1,3-cyclohexanedione and 2,4-pentanedione successfully reacted with the standard citrullinated peptides, and generated a single derivative. However, their reaction efficiency was very low, indicating that the ß-dicarbonyl compounds are unsuitable for the chemical derivatization of citrullinated peptides. The above results indicate that the α-dicarbonyl structure is necessary for realizing the efficient and specific chemical derivatization of citrullinated peptides. Moreover, the side chains of the α-dicarbonyl structure determine the structure of the derivatives, derivatization efficiency, and generation (or otherwise) of by-products. Therefore, the specific enrichment and precise identification of citrullinated peptides can be achieved by synthesizing α-dicarbonyl structured compounds containing affinity tags. The proposed method enables the identification of citrullinated proteins and their modified sites by MS, thereby providing a better understanding of the distribution of citrullinated proteins in different tissues. The findings will be beneficial for studies on the mechanism of action of citrullinated proteins in a variety of diseases.