Bacterial Identification and Susceptibility Testing

Comparative Evaluation of Commercial Gradient Diffusion and Disk Diffusion Tests for Aztreonam-Avibactam Susceptibility Testing

This study compares four commercial AZA susceptibility testing methods for carbapenem-resistant Enterobacterales, finding acceptable performance with minor errors mainly in breakpoint-adjacent isolates.

Identification by MALDI-TOF MS of Coleopteran insect pests collected in the field

This study evaluates MALDI-TOF MS for identifying Coleopteran pests, finding it effective for laboratory-reared specimens but with limitations for field-collected samples due to DNA degradation and low peak diversity.

A synthetic MALDI-TOF MS atlas for microbial classification across hospitals

The paper creates a synthetic MALDI-TOF MS atlas to improve microbial classification across hospitals by addressing dataset fragmentation and variability.

Droplet-array culture enables single-cell isolation of bacteria directly from blood

This paper introduces a method to isolate and expand single bacteria from blood using droplet arrays, achieving faster detection than conventional blood culture.

Branch-Wise Regularization for Heterogeneous GNN-Based MALDI-TOF AMR Prediction with Biomarker-Consensus Edges

This paper evaluates a heterogeneous GNN for AMR prediction from MALDI-TOF spectra, showing it performs better than MLP only at high spectral similarity.

Rapid Phenotypic Antibiotic Susceptibility Determination Direct From Spiked Urine Samples Shows Strong Correlation with Gold Standard for Urinary Tract Infection

This study demonstrates a rapid AST method using spiked urine samples achieving 98% categorical agreement with gold standard culture results for UTI pathogens.

Benchmarking nanopore-based strategies for antimicrobial resistance prediction

This study benchmarks in silico AMR prediction tools using nanopore data, finding that assembly strategy and data volume impact accuracy, but no tool perfectly matches lab-based AST results.

Resolution of MALDI-TOF MS Compared to Whole Genome Sequencing for the Identification of Vibrio parahaemolyticus Strains Isolated from Oysters

This study compares MALDI-TOF MS and whole-genome sequencing for identifying Vibrio parahaemolyticus strains from oysters, finding MALDI-TOF MS provides comparable resolution to WGS for strain tracking.

Optimisation of Solid-Phase Antimicrobial Susceptibility Testing for Hydrophobic Antibiotics Using an Agarose-Based MIC Assay

The paper develops an agarose-based MIC assay to improve the accuracy of antimicrobial susceptibility testing for hydrophobic antibiotics.

J-AST: a web-based analysis platform for antimicrobial susceptibility testing

J-AST is a web-based platform for analyzing antimicrobial susceptibility tests, providing automated annotation and MIC detection with high agreement with manual methods.

IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry.

IDBac provides a centralized database and platform for bacterial identification via MALDI-TOF MS, enabling spectral comparison and analysis of bacterial isolates.

From culture to clarity in four hours: accelerating clinical management of bloodstream infections using metagenomics

This paper develops and evaluates a method for rapid metagenomic sequencing of blood cultures to identify pathogens and antimicrobial resistance in bloodstream infections within 4 hours.

Machine learning-guided discovery of a conserved plasmid proteomic signature enables MALDI-TOF MS detection of pOXA-48-carrying Enterobacterales

The paper develops a machine learning model to detect pOXA-48-carrying Enterobacterales using MALDI-TOF MS spectra, achieving high accuracy across different cohorts.

Performance of pathogen identification and resistance gene expression tests using ASTar(R) remnant bacterial suspension in Gram-negative contrived positive blood cultures

This paper evaluates a rapid pathogen identification and resistance detection method using ASTar remnant bacterial suspensions in Gram-negative blood cultures, showing high accuracy and cost savings.

A Dual-Phase Strategy to Integrate the VITEK MS RUO Database into Routine Clinical Practice: From Validation of Analytical Performance to Implementation of an Automated Workflow

This paper validates and implements an automated workflow integrating the VITEK MS RUO database into clinical practice, improving identification rates and efficiency.

Label-free Pathogen Identification with Microscopy Imaging and Deep Learning

This paper develops a label-free imaging and deep learning approach to rapidly identify pathogens, achieving high accuracy in clinical samples and reducing diagnosis time.

Precision culturomics enabled by unlabeled single-cell morphology and Raman spectra

This paper introduces a precision culturomics method using single-cell morphology and Raman spectra to sort and analyze microbial cells, revealing antibiotic-driven resistance and mutations in gut commensals.

Rapid Identification of Infections Directly from Isolates and Clinical Specimens with the MasSpec Pen Technology

This study demonstrates that MasSpec Pen technology can rapidly identify bacterial species in clinical isolates and specimens with high accuracy using molecular profiles of metabolites and lipids.

Rapid identification of microbial pathogens and antimicrobial resistance from bloodstream infections using long-read sequencing

This paper presents a workflow using long-read sequencing to rapidly identify microbial pathogens and antimicrobial resistance in bloodstream infections, achieving faster results than conventional methods.

Pairing Data Independent Acquisition and High-Resolution Full Scan for Fast Urinary Tract Infection Diagnosis

This paper presents a method combining DIA MS/MS and MS1-only spectra for rapid UTI pathogen identification, achieving high accuracy in both controlled and clinical samples.

Early antifungal resistance prediction based on MALDI-TOF mass spectrometry and machine learning

The paper develops a machine learning pipeline using MALDI-TOF mass spectrometry data to predict antifungal resistance and identify biomarkers, achieving high performance across multiple yeast species and drug combinations.

Up-to-date MALDI-TOF MS based identification of the complete Corynebacterium diphtheriae species complex for improved diagnostics

This paper expands a MALDI-TOF MS database to accurately identify all species in the Corynebacterium diphtheriae species complex according to updated taxonomy and validates the results using a formal procedure.

MicrobeMS - A MATLAB Toolbox for Microbial Identification Based on Mass Spectrometry

MicrobeMS is a MATLAB toolbox for microbial identification using MALDI-ToF MS, enabling database compilation, spectrum analysis, and identification tasks.

Amplification-Free Detection of Antibiotic Resistance in Enterococcus faecium using PNA-FISH

This paper develops a PNA-FISH method to detect antibiotic resistance in Enterococcus faecium without amplification, showing specificity for vanA and vanB genes in individual cells.

Machine Learning applied to MALDI-TOF data in a clinical setting: a systematic review

This review evaluates ML applications for MALDI-TOF MS in clinical microbiology, identifying trends and challenges in bacterial identification, resistance prediction, and strain typing.

A low-cost rpoB-based multiplex MAMA PCR for differentiation of the Klebsiella pneumoniae species complex

This paper develops a low-cost MAMA PCR assay for accurately differentiating members of the Klebsiella pneumoniae species complex using rpoB SNPs, achieving 100% sensitivity and specificity compared to WGS.

Ion Mobility-Enhanced Liquid Chromatography Coupled with Mass Spectrometry (LC-MS) Enables Reliable Detection of OXA-48-Like Carbapenemases Beyond Conventional Activity-Based Assays

This paper introduces an ion mobility-enhanced LC-MS method for detecting and classifying carbapenemases, showing it reliably identifies OXA-48-like enzymes that conventional methods miss.

ONETest PathoGenome: A Multi-Cohort Evaluation of an Optimized NGS Assay for Detection of Lower Respiratory Pathogens in Bronchoalveolar Lavage

This paper evaluates ONETest Pathogenome, a metagenomic assay, for detecting lower respiratory pathogens in bronchoalveolar lavage, showing improved sensitivity and specificity compared to traditional methods.

Sequential Dual-Ion MALDI Glycotyping Enables Rapid Phenotypic O-Antigen Typing of Escherichia coli and Shigella

This paper introduces a MALDI glycotyping method for rapid O-antigen phenotyping of E. coli and Shigella, detecting structural variations and correcting serotype discrepancies in a strain panel.

Early detection of ampicillin susceptibility in Enterococcus faecium with MALDI-TOF MS and machine learning

This paper uses machine learning on MALDI-TOF mass spectrometry data to detect ampicillin susceptibility in Enterococcus faecium, achieving high accuracy across datasets.