Bacterial Identification and Susceptibility Testing

Performance of shotgun metagenomic sequencing for detection of fungi and parasites across clinical sample types: a multicenter retrospective study.

This study evaluates shotgun metagenomic sequencing for detecting fungi and parasites in clinical samples, finding it performs well with sample-specific thresholds.

Poloxamer dilution as an on-demand alternative to agar dilution-based antimicrobial susceptibility testing

This paper introduces poloxamer dilution as an on-demand alternative to agar dilution for antimicrobial susceptibility testing, showing comparable performance for fosfomycin against gram-negative pathogens.

A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing

This paper introduces s5PSeq, a streamlined protocol for rapid antimicrobial sensitivity testing using 5P mRNA degradation intermediates, demonstrating its clinical utility in identifying resistant Clostridioides difficile isolates.

A rapid ionic liquid-based DNA extraction method for molecular diagnostics of urinary tract infections

This paper introduces an ionic liquid-based DNA extraction method (IL-DEx) for urine samples, achieving comparable performance to commercial kits while being faster, simpler, and safer.

Comparative Performance of Portable DNA Extraction Protocols and Bioinformatics Workflows for Rapid Detection of Pathogens and Antimicrobial Resistance Using Oxford Nanopore Sequencing.

This study compares DNA extraction protocols and bioinformatics workflows for Oxford Nanopore sequencing of bacterial pathogens, finding that extraction method significantly impacts workflow success and genomic resolution.

Antibiotic resistance detection and concomitant species identification of ESKAPE pathogens by proteomics

This study evaluates proteomics for rapid detection of antibiotic resistance and species identification of ESKAPE pathogens from clinical isolates, achieving high specificity and sensitivity.

Development of Surface Enhanced Raman Spectra coupled with Machine Learning Analysis for Differentiation of Closely Related Species within Enterobacter cloacae Complex

This study develops a SERS and machine learning approach to accurately identify closely related species within the Enterobacter cloacae complex.

Non-targeted screening method for detecting temporal shifts in spectral patterns of Methicillin Resistance Staphylococcus aureus and post-hoc description of peak features

The paper presents a method to detect temporal shifts in MALDI-TOF MS spectral patterns of MRSA/MSSA using CNNs and statistical methods, with GradCam for feature analysis.

Low-Cost In-House Re-formulated Brain Heart Infusion Medium for Effective Planktonic Growth and Early Detection of Bloodstream Bacterial Pathogens

The paper develops a low-cost in-house culture medium for faster and more accessible detection of bloodstream bacterial pathogens compared to commercial systems.

Primer Blind Spots: Underrepresentation of ESKAPE Pathogens from Developing Regions in 16S rRNA Targeted Sequencing

This study identifies underrepresentation of ESKAPE pathogens from developing regions in 16S rRNA sequencing due to primer bias.

Evaluating Seqstant LiveGene Analysis in Real-Time Assessment of Metagenomic Next-Generation Sequencing (mNGS) Data from Respiratory Samples

This study evaluates real-time metagenomic next-generation sequencing (rt-mNGS) for pathogen detection in respiratory samples, showing non-inferiority to culture methods with higher sensitivity and timely results.

Optimizing Antimicrobial Susceptibility Testing: Cost and Environmental Benefits of MIC Volume Reduction

This study shows that reducing MIC assay volumes in antimicrobial testing maintains accuracy while lowering costs and environmental impact, except for micafungin.

Outbreak Investigation of Phytobacter diazotrophicus Using Fourier Transform Infrared Spectroscopy compared to cgMLST

This study compares Fourier Transform Infrared Spectroscopy (FT-IR) using IR Biotyper with cgMLST for clonal typing of Phytobacter diazotrophicus outbreak isolates, finding strong agreement between the methods.

Rapid label-free identification of seven bacterial species using microfluidics, single-cell time-lapse phase-contrast microscopy, and deep learning-based image and video classification

This study uses microfluidics, time-lapse microscopy, and deep learning to rapidly identify seven bacterial species with high accuracy in one hour.

Automatic Culture-free Detection of Bacteria from Blood for Rapid Sepsis Diagnostics

This paper develops a method to rapidly detect bacteria in blood using smart centrifugation, microfluidic trapping, and deep learning for sepsis diagnostics.

A Simple, Low-Cost, and Efficient Protocol for Rapid Isolation of Pathogenic Bacteria from Human Blood

This paper presents a rapid, low-cost protocol for isolating pathogenic bacteria from human blood, achieving over 70% efficiency within 30 minutes.

Polyphasic discrimination of Shewanella seohaensis from closely related species and a whole-genome multilocus (wgMLST) scheme for the evaluation of diversity within this Shewanella clade

This paper develops a whole-genome multilocus sequence typing (wgMLST) scheme to accurately discriminate Shewanella seohaensis from closely related species and assess their diversity.

Development and optimization of the host DNA depletion in blood cultures using a saponin and SAN nucleases-based method

This paper develops and optimizes a method using saponin and SAN nucleases to deplete host DNA from blood cultures, improving bacterial DNA extraction for sepsis diagnosis.

Surface-enhanced Raman spectroscopy on the membranes for antimicrobial resistance testing

This paper describes a rapid antimicrobial resistance test using surface-enhanced Raman spectroscopy and MTT assay to detect low-titer bacterial samples within 1.5 hours.

MSclassifR: an R package for supervised classification of mass spectra with machine learning methods

MSclassifR is an R package that improves mass spectra classification using machine learning, achieving high accuracy on real datasets and outperforming commercial software.

Stability of four carbapenem antibiotics in discs used for antimicrobial susceptibility testing

This study tests the stability of four carbapenem antibiotics in discs under unfavorable storage conditions and finds imipenem discs from Oxoid and Becton Dickinson to be the most stable.

MARISMa: a routine MALDI-TOF MS database from 2018 to 2024 from Spain

The paper introduces a large MALDI-TOF MS dataset from Spain to support AI-driven clinical microbiology research and improve antimicrobial resistance detection.

Real-time identification of carbapenemase-producing Klebsiella pneumoniae lineages and outbreak detection using FT-IR ATR

This paper evaluates a real-time FT-IR ATR workflow for typing carbapenemase-producing Klebsiella pneumoniae isolates, showing high accuracy and enabling rapid outbreak detection.

Characterization of a nosocomial outbreak caused by VIM-1 Klebsiella michiganensis using Fourier-Transform Infrared (FT-IR) Spectroscopy

This study uses FT-IR spectroscopy to rapidly characterize a nosocomial outbreak of VIM-1-producing K. oxytoca, showing high concordance with whole-genome sequencing.

Phenotypic Antibiotic Susceptibility Testing at the limit of one bacterial cell

This study evaluates if phenotypic antibiotic susceptibility testing can be performed on single bacterial cells by monitoring phenotypic changes over time, finding that single-cell responses are heterogeneous and require sequential antibiotic exposure for accurate resistance classification.

Impact of media brand on cefiderocol disk diffusion results

This paper evaluates the impact of different Mueller-Hinton agar brands on cefiderocol disk diffusion results, finding significant variability and discrepancies in antimicrobial susceptibility testing.

Establishment and Thorough External Validation of a FTIR Spectroscopy Classifier for Salmonella Serogroup Differentiation

This paper develops and validates an FTIR spectroscopy classifier for Salmonella serogroup differentiation, achieving >99% inclusivity for key serogroups.

Rapid Automated Isolation and Concentration of Bacteria from Blood Samples

This paper introduces a centrifuge-based device that rapidly isolates and concentrates bacteria from blood samples, improving detection and identification for sepsis diagnosis.

GenomicGapID: Leveraging Spatial Distribution of Conserved Genomic Sites for Broad-Spectrum Microbial Identification

GenomicGapID uses conserved genomic site spacing to create universal primers for broad microbial identification, achieving high coverage with few primer sets.

Analytical Assessment of Metagenomic Workflows for Pathogen Detection with NIST RM 8376 and Two Sample Matrices

The paper evaluates metagenomic workflows for pathogen detection using NIST RM 8376 in CSF and stool samples, finding workflow-dependent strain discrimination and sample-agnostic detection responses.