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Journal Club: clinical, page 4

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16S-Based Metagenomic NGS Improves Detection of Pathogens

Evaluation of 16S-Based Metagenomic NGS
16SAssay ValidationNext Generation Sequencing (NGS)
27 Dec 2025 Lora Benoit Ph.D
Targeted 16S metagenomic Next-Generation Sequencing (Next-Generation Sequencing) identifies pathogens in ~74% of culture-negative clinical samples, improving diagnostic yield over conventional methods and revealing diverse bacterial species, including fastidious and anaerobic organisms.
Clinical & Veterinary

Pharmaceutical Contamination Remains a Quality Challenge

Contamination of medicinal products is an ongoing industry issue
EndotoxinSterility Testing
19 Dec 2025 Lora Benoit Ph.D
Despite stringent regulations and pharmacopoeial standards, contamination of both sterile and non-sterile products continues to be an issue, with documented incidents and outbreaks linked to bacteria, fungi, as well as endotoxin exposures, highlighting ongoing manufacturing challenges. 
Clinical & Veterinary

Importance of Validating Recombinant Endotoxin Reagents

Validation Needed When Replacing LAL With rFC Endotoxin Tests
Assay ValidationEndotoxinKinetic Colorimetric Assay (KCA)
19 Dec 2025 Lora Benoit Ph.D
Recombinant endotoxin reagents offer sustainable, animal-free endotoxin testing alternatives, but manufacturers must validate them against autochthonous or indigenous microbial flora from their own environments to ensure accurate detection.
Clinical & Veterinary

Automated AST by Colibri and WASP Matches Manual Accuracy

Fully automated AST testing for the clinical microbiology laboratory
Antibiotic SensitivityAssay ValidationAutomation
19 Dec 2025 Lora Benoit Ph.D
Automated bacterial suspension preparation with Colibri® combined with plate streaking by WASP® demonstrates high categorical agreement with manual methods for antibiotic disk diffusion susceptibility testing, supporting its use in total laboratory automation.
Clinical & Veterinary

Improving ESBL Recovery in Healthcare Environmental Samples

Improved recovery of ESBL-producing bacteria using chromogenic agar
Antibiotic ResistanceCarbapenemase-Resistant Enterobacterales (CRE)Chromogenic Media
19 Dec 2025 Lora Benoit Ph.D
Recovery of ESBL-producing E. coli and K. pneumoniae from healthcare environmental samples is optimized by 18-hour pre-enrichment in buffered peptone water followed by plating on cefotaxime-supplemented Membrane Lactose Glucuronide Agar.
Clinical & Veterinary

Flow Cytometry Reveals Hidden Microbes in Dialysis Water

VBNC Bacteria in Dialysis Water Detected by Flow Cytometry
Flow CytometryViable But Not Culturable (VBNC)
13 Dec 2025 Lora Benoit Ph.D
A direct comparison of flow cytometry and heterotrophic plate count methods shows that culture-based testing substantially underestimates microbial contamination in dialysis water.
Clinical & Veterinary

Shedding Light on 'Low Endotoxin Recovery' in LAL Assays

Low Endotoxin Recovery in LAL Assays
Clinical TrialsEndotoxinPyrogen Free Labware
04 Dec 2025 Lora Benoit Ph.D
Excipients used in pharmaceutical formulations can induce endotoxin masking, causing the Limulus Amebocyte Lysate (LAL) assay to underestimate true endotoxin levels. Gorman et al. show that masking arises from excipient-driven alterations in endotoxin structure and aggregate size.
Clinical & Veterinary Assay Development

Human Transmission of Invasive Nontyphoidal Salmonella

Human Transmission of Invasive Nontyphoidal Salmonella
Microbial controlSalmonella EnteritidisSalmonella/Shigella
04 Dec 2025 Lora Benoit Ph.D
Phylogenomic and epidemiological analyses of invasive non-typhoidal Salmonella (iNTS) indicate that >50% of infections - historically considered foodborne or zoonotic - arise from human-to-human transmission, with diarrheal patients acting as intermediaries. 
Clinical & Veterinary

Did Vaccine Change Cause Global Spread of AMR Pertussis?

Link Between Less Antigenic Vaccines and AMR Bordetella pertussis
BordatellaVaccine Development
20 Nov 2025 Lora Benoit Ph.D
A possible link between a less antigenic form of the whooping cough vaccine and global transmission of antimicrobial resistant B. pertussis is explored by Xu et al., 2025 in their analysis of 1,774 genomes isolated from China, Japan, US, and France. 
Clinical & Veterinary

Rapid Point-of-Care Detection of STIs CT/NG/MG

Study Supports Shift Toward POC Molecular Diagnostics for STIs
ChlamydiaMycoplasma genitaliumNeisseria
20 Nov 2025 Lora Benoit Ph.D
The Cobas Liat molecular POC assay delivers rapid results in 20 min and specificities >97% for Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycoplasma genitalium (MG), and sensitivities ≥92% regardless of symptomatic status.
Clinical & Veterinary

Syndromic Respiratory Pathogen Panel Multicenter Evaluation

Study on LIAISON PLEX Respiratory Flex Assay
BordatellaDiagnostic SystemsInfluenza
20 Nov 2025 Lora Benoit Ph.D
A multicenter evaluation confirms that the LIAISON PLEX Respiratory Flex Assay delivers robust, clinically reliable detection of up to 19 respiratory pathogens, supporting its integration into routine diagnostic use.
Clinical & Veterinary

Spray-on Biocide Durability Claims a Bust in the Real World

Study on Effects of Spray-on Biocide
SanitizersSurface Monitoring
18 Nov 2025 Lora Benoit Ph.D
Commercially available spray-on surface biocide (SAQAS) showed no significant antimicrobial effect at either 5- or 30-day post-application under real world conditions. 
Food & Beverage Clinical & Veterinary

Microbiome-informed Diagnostic for Clostridioides difficile Infection

Clostridioides difficile
Clostridioides difficle
17 Nov 2025 Lora Benoit Ph.D
Gut microbiome profiles can be used to distinguish C. difficile colonized patients with diarrhea from those with true CDI infections. 
Clinical & Veterinary

Multiplex PCR Detects Resistance Genes from Blood Cultures

Detection of Resistance Genes in Blood Cultures by Multiplex PCR
Antibiotic ResistanceBlood CultureJournal Club
17 Nov 2025 Lora Benoit Ph.D
Marxreiter et al. (2025) benchmarked a rapid multiplex PCR assay against microdilution susceptibility testing, demonstrating how effectively molecular detection of resistance genes mirrors phenotypic resistance in Gram-negative pathogens.
Clinical & Veterinary

Comparison of Three Rapid Antimicrobial-Susceptibility-Testing Systems

Comparison of Rapid AST Systems like VITEK REVEAL
Antibiotic ResistanceAntimicrobial Susceptibility TestingJournal Club
17 Nov 2025 Lora Benoit Ph.D
Squitieri et al. (2025) have conducted a head-to-head comparison of 3 rapid antimicrobial-susceptibility-testing (AST) systems applied directly to Gram-negative blood cultures in a clinical microbiology setting.
Clinical & Veterinary

Rapid Serotyping of Salmonella via MALDI-TOF and Machine Learning

Serotyping Salmonella Using MALDI-TOF and AI
Artifical IntelligenceJournal ClubMALDI-TOF
05 Nov 2025 Lora Benoit Ph.D
Study shows that combining MALDI-TOF MS with machine learning (XGBoost) can accurately identify Salmonella serotypes. This combined approach might soon provide diagnostic labs with a rapid and cost-effective approach to resolving Salmonella serotypes.
Food & Beverage Clinical & Veterinary

What Microbiology Labs Need to Know About Updates to Antimicrobial Resistance Testing in CLSI M100

Antimicrobial Resistance Testing in CLSI M100
Antibiotic ResistanceJournal Club
15 Oct 2025 Lora Benoit Ph.D
In the new CLSI M100 edition, major updates were introduced - including restructured tables, new breakpoints, and a tiered approach to reporting. 
Clinical & Veterinary

Everything You Need to Know About Equipment Validation for Sterility Testing

Sterility Testing of Cell and Gene Therapy Products
ATMP - Advanced Therapeutic Medicinal ProductsCell and Gene TherapiesJournal Club
14 Oct 2025 Lora Benoit Ph.D
As novel biologics and cell therapies advance, sterility testing is becoming increasingly complex and subject to cGMP scrutiny. Gebo et al. outline how clinical microbiology labs - traditionally CLIA/CAP-regulated - can align with FDA, USP, and ISO expectations.
Clinical & Veterinary Pharmaceutical

How Klebsiella pneumoniae Evolves and Persists in the Clinical Setting

How K pneumoniae Evolves and Persists in Clinical Setting
Journal ClubKlebsiella pneumoniae carbapenemase (KPC)
13 Oct 2025 Lora Benoit Ph.D
Study on Klebsiella pneumoniae clone that evolved within patients over a 5-year hospital outbreak: virulence, capsule, iron scavenging, and biofilms shifted independently across hosts - highlighting how multidrug-resistant pathogens rapidly adapt and persist under clinical pressures.
Clinical & Veterinary

Tracing 20 Years of Salmonella Dublin Evolution: Human, Animal, Environmental Sources

Salmonella Spread Risk From Livestock
Journal ClubSalmonella
04 Nov 2025 Lora Benoit Ph.D
In one of the most comprehensive studies of its kind, a genomic analysis of 2,150 Salmonella Dublin isolates collected in the U.S. over 20 years reveals strong genetic similarity among  isolates from human, cattle, and environmental reservoirs. 
Clinical & Veterinary

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