Matrix-Assisted Laser Desorption/Ionization Time-of-Flight: The Revolution in Progress

Activity and potential mechanisms of action of persimmon tannins according to their structures: A review

One distinguishing feature of the persimmon, that differentiates it from other fruits, is its high proanthocyanidins content, known as persimmon tannin (PT). Despite the poor absorption of PT in the small intestine, results from animal studies demonstrate that PT has many health benefits. Our goal in this review is to summarize the literature that elucidates the relationship between PT structure and activity. In addition, we also summarize the potential mechanisms underlying the health benefits that result from PT consumption; this includes the hypolipidemic, hypoglycemic, antioxidant, anti-inflammatory, antiradiation, antibacterial and antiviral, detoxification effects on snake venom, and the absorption of heavy metals and dyes. Studies show that PT is a structurally distinct proanthocyanidins that exhibits a high degree of polymerization. It is galloylation-rich and possesses unique A-type interflavan linkages in addition to the more common B-type interflavan bonds. Thus, PT is converted into oligomeric proanthocyanidins by depolymerization strategies, including the nucleophilic substitution reaction, acid hydrolysis, and hydrogenolysis. In addition, multiple health benefits exerted by PT mainly involve the inactivation of lipogenic and intracellular inflammatory signaling pathways, activation of the fatty acid oxidation signaling pathway, regulation of gut microbiota, and highly absorptive properties.

Sample preparation and culture condition effects on MALDI-TOF MS identification of bacteria: A review

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an excellent tool for bacterial identification. It allows high throughput, sensitive and specific applications in clinical diagnostics and environmental research. Currently, there is no optimal standardized protocol for sample preparation and culture conditions to profile bacteria. The performance of MALDI-TOF MS is affected by several variables, such as sample preparation, culture media and culture conditions, incubation time/growth stage, incubation temperature, high salt content, blood in the culture media, and others. This review thus aims to clarify why a uniformed protocol is not plausible, to assess the effects these factors have on MALDI-TOF MS identification score, and discuss possible optimizations for its methodology, in relation to specific bacterial representatives and strain requirements.

Optimization of a lysis method to isolate periplasmic proteins from Gram-negative bacteria for clinical mass spectrometry

PURPOSE

Clinical mass spectrometry requires a simple step process for sample preparation. This study aims to optimize the method for isolating periplasmic protein from Gram-negative bacteria and apply to clinical mass spectrometry.

EXPERIMENTAL DESIGN

The Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli standard cells were used for optimizing the osmotic shock (OS) lysis method. The supernatant from OS lysis was analysed by LC-MS/MS and MALDI-TOF MS. The effectiveness of the OS lysis method for KPC-2-producing Enterobacteriaceae clinical isolates were then confirmed by MALDI-TOF MS.

RESULTS

The optimized OS lysis using KPC-2 producing E. coli standard cells showed a high yield of KPC-2 protein and enriches periplasmic proteins. Compared with other lysis methods, the detection sensitivity of KPC-2 protein significantly increased in MALDI-TOF MS analysis. Nineteen clinical isolates were validated by MALDI-TOF MS using the OS method, which also showed higher detection sensitivity compared to other lysis method (e.g., 1.5% n-octyl-β-D-glucopyranoside) (p < 0.001).

CONCLUSIONS AND CLINICAL RELEVANCE

This study provides a straightforward, rapid, affordable, and detergent-free method for the analysis of periplasmic proteins from Enterobacteriaceae clinical isolates. This approach may contribute to MS-based clinical diagnostics.

Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.

Detection of Species-Specific Lipids by Routine MALDI TOF Mass Spectrometry to Unlock the Challenges of Microbial Identification and Antimicrobial Susceptibility Testing

MALDI-TOF mass spectrometry has revolutionized clinical microbiology diagnostics by delivering accurate, fast, and reliable identification of microorganisms. It is conventionally based on the detection of intracellular molecules, mainly ribosomal proteins, for identification at the species-level and/or genus-level. Nevertheless, for some microorganisms (e.g., for mycobacteria) extensive protocols are necessary in order to extract intracellular proteins, and in some cases a protein-based approach cannot provide sufficient evidence to accurately identify the microorganisms within the same genus (e.g., Shigella sp. vs E. coli and the species of the M. tuberculosis complex). Consequently lipids, along with proteins are also molecules of interest. Lipids are ubiquitous, but their structural diversity delivers complementary information to the conventional protein-based clinical microbiology matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) based approaches currently used. Lipid modifications, such as the ones found on lipid A related to polymyxin resistance in Gram-negative pathogens (e.g., phosphoethanolamine and aminoarabinose), not only play a role in the detection of microorganisms by routine MALDI-TOF mass spectrometry but can also be used as a read-out of drug susceptibility. In this review, we will demonstrate that in combination with proteins, lipids are a game-changer in both the rapid detection of pathogens and the determination of their drug susceptibility using routine MALDI-TOF mass spectrometry systems.

Helix Matrix Transformation Combined With Convolutional Neural Network Algorithm for Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry-Based Bacterial Identification

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis is a rapid and reliable method for bacterial identification. Classification algorithms, as a critical part of the MALDI-TOF MS analysis approach, have been developed using both traditional algorithms and machine learning algorithms. In this study, a method that combined helix matrix transformation with a convolutional neural network (CNN) algorithm was presented for bacterial identification. A total of 14 bacterial species including 58 strains were selected to create an in-house MALDI-TOF MS spectrum dataset. The 1D array-type MALDI-TOF MS spectrum data were transformed through a helix matrix transformation into matrix-type data, which was fitted during the CNN training. Through the parameter optimization, the threshold for binarization was set as 16 and the final size of a matrix-type data was set as 25 × 25 to obtain a clean dataset with a small size. A CNN model with three convolutional layers was well trained using the dataset to predict bacterial species. The filter sizes for the three convolutional layers were 4, 8, and 16. The kernel size was three and the activation function was the rectified linear unit (ReLU). A back propagation neural network (BPNN) model was created without helix matrix transformation and a convolution layer to demonstrate whether the helix matrix transformation combined with CNN algorithm works better. The areas under the receiver operating characteristic (ROC) curve of the CNN and BPNN models were 0.98 and 0.87, respectively. The accuracies of the CNN and BPNN models were 97.78 ± 0.08 and 86.50 ± 0.01, respectively, with a significant statistical difference (p < 0.001). The results suggested that helix matrix transformation combined with the CNN algorithm enabled the feature extraction of the bacterial MALDI-TOF MS spectrum, which might be a proposed solution to identify bacterial species.

Actinotignum schaalii and Aerococcus urinae as Etiology of Infected Kidney Cyst: A Diagnostic Challenge

The case presented here illustrates a sometimes complex disease presentation where interdisciplinary teamwork is essential. A 74-years-old woman with stable chronic obstructive pulmonary lung disease and a composite graft aortic valve implant was admitted to hospital with an episode of acute lower back pain combined with long-term fever. The final diagnoses of a left-sided, infected and radiologically evident kidney cyst caused by the urinary tract pathogens Actinotignum schaalii and Aerococcus urinae was established by the use of partial 16S/18S rRNA gene sequence analysis on kidney cyst drainage material taken after four weeks of relevant antibiotic therapy.

The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update

The evolution of resistance to antimicrobial agents in gram-negatives has challenged the role of the clinical microbiology laboratory to implement new methods for their timely detection. Recent development has enabled the use of novel methods for more rapid pathogen identification, antimicrobial susceptibility testing, and detection of resistance markers. Commonly used methods improve the rapidity of resistance detection from both cultured bacteria and specimens. This review focuses on the commercially available systems available together with their technical performance and possible clinical impact.

Ceftolozane/Tazobactam and Ceftazidime/Avibactam for Multidrug-Resistant Gram-Negative Infections in Immunocompetent Patients: A Single-Center Retrospective Study

Complicated infections from multidrug-resistant Gram-negative bacteria (MDR-GNB) represent a serious problem presenting many challenges. Resistance to many classes of antibiotics reduces the probability of an adequate empirical treatment, with unfavorable consequences, increasing morbidity and mortality. Readily available patient medical history and updated information about the local microbiological epidemiology remain critical for defining the baseline risk of MDR-GNB infections and guiding empirical treatment choices, with the aim of avoiding both undertreatment and overtreatment. There are few literature data that report real-life experiences in the use of ceftolozane/tazobactam and ceftazidime/avibactam, with particular reference to microbiological cure. Some studies reported experiences for the treatment of MDR-GNB infections in patients with hematological malignancies or specifically in Pseudomonas aeruginosa infections. We report our clinical single-center experience regarding the real-life use of ceftolozane/tazobactam and ceftazidime/avibactam to treat serious and complicated infections due to MDR-GNB and carbapenem-resistant Enterobacterales (CRE), with particular regard given to intra-abdominal and urinary tract infections and sepsis.

After another decade: LC-MS/MS became routine in clinical diagnostics

Tandem mass spectrometry - especially in combination with liquid chromatography (LC-MS/MS) - is applied in a multitude of important diagnostic niches of laboratory medicine. It is unquestioned in its routine use and is often unreplaceable by alternative technologies. This overview illustrates the development in the past decade (2009-2019) and intends to provide insight into the current standing and future directions of the field. The instrumentation matured significantly, the applications are well understood, and the in vitro diagnostics (IVD) industry is shaping the market by providing assay kits, certified instruments, and the first laboratory automated LC-MS/MS instruments as an analytical core. In many settings the application of LC-MS/MS is still burdensome with locally lab developed test (LDT) designs relying on highly specialized staff. The current routine applications cover a wide range of analytes in therapeutic drug monitoring, endocrinology including newborn screening, and toxicology. The tasks that remain to be mastered are, for example, the quantification of proteins by means of LC-MS/MS and the transition from targeted to untargeted omics approaches relying on pattern recognition/pattern discrimination as a key technology for the establishment of diagnostic decisions.