Journal Club

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Journal Club

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Journal Club - 15 Jan to 30 Jan 2026

Journal Club

Antibiotic Resistance Blood Culture Microbiome

05 Feb 2026

Peer-reviewed studies on high-throughput DNA barcoding, postbiotics and next-gen nutrition, mNGS transforming meningitis diagnosis, Illumina vs Oxford Nanopore Tech comparison, fecal transplants for dermatitis, pandemic-risk viruses, microbial contamination risks during PRP, and more
Food & Beverage Clinical & Veterinary Microbiome

How to Distinguish Contaminants from Pathogens in Blood Cultures

A practical approach to reducing false positive blood cultures

Blood Culture

30 Jan 2026 Lora Benoit Ph.D

Analysis of 38,216 peripheral blood culture sets indicates that discordant versus concordant bottle positivity provides a practical and effective means of differentiating contamination from true bacteremia.
Clinical & Veterinary

Effective Control Measures of Carbapenemase Producing Enterobacterales (CPE)

Integrated approach to reducing CPE transmission in the healthcare setting

Antibiotic Resistance Carbapenemase-Resistant Enterobacterales (CRE)Hygiene Monitoring

30 Jan 2026 Lora Benoit Ph.D

Hospital water systems can act as persistent reservoirs for Carbapenemase Producing Enterobacterales (CPE). This scoping review synthesizes recent evidence from 22 studies (2014–2024) on disinfection and environmental control strategies targeting CPE in hospitals.
Clinical & Veterinary

Eliminating Microbial Risks in Platelet-Rich Therapies (PRP): Comparison of Rapid Testing Options

Analysis of Platelet-Rich Plasma Therapy Microbial Risks

Sterility Testing

29 Jan 2026 Lora Benoit Ph.D

This study investigates microbial contamination risks during Platelet-Rich Plasma preparation and evaluates rapid microbial detection methods to determine sterility in the clinical setting.
Clinical & Veterinary

Novel Targets for Viruses of Pandemic Concern

Targeting host factors to block viruses with pandemic risk

Corona Virus Influenza

22 Jan 2026 Lora Benoit Ph.D

A meta-analysis of 62 genomics studies reveals conserved cellular pathways exploited by pandemic-risk viruses, highlighting host targets with broad-spectrum antiviral potential.
Clinical & Veterinary

Microbiome-based Therapeutics: Washed Fecal Microbiota Transplants for Atopic Dermatitis

Washed fecal microbiota transplants improve atopic dermatitis

Microbiome

22 Jan 2026 Lora Benoit Ph.D

Washed fecal transplantation significantly improved atopic dermatitis severity in adult participants by reshaping both the gut and skin microbiomes, suggesting that targeting the gut–skin axis is a viable therapeutic strategy.
Clinical & Veterinary Microbiome

Illumina WGS vs Oxford Nanopore WGS Platforms in Clinical Microbiology

WGS platform benchmarking in the clinical lab setting

Assay Validation Whole Genome Sequencing

22 Jan 2026 Lora Benoit Ph.D

Comparative benchmarking of Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms demonstrates platform-specific strengths and limitations for bacterial whole-genome sequencing (WGS), with implications for clinical microbiology applications.
Clinical & Veterinary

Journal Club - Week 2: 7 Jan to 14 Jan 2026

rapidmicrobiology Journal Club

Avian Influenza Bacillus cereus Streptococcus pneumoniae

14 Jan 2026

At a glance summaries of studies on rapid sterility testing for ATMPs, pathogenic Avian flu testing, incidence of B. cereus in infant formula, accurate serotyping of S. pneumoniae.
Food & Beverage Clinical & Veterinary Pharmaceutical

Metagenomic Next-Gen Sequencing Can Transform Meningitis and Encephalitis Diagnosis

Metagenomic Sequencing Predictis CNS Issues

Next Generation Sequencing (NGS)

20 Jan 2026 Lora Benoit Ph.D

Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid offers an unbiased, broad-spectrum approach to identify infectious and autoimmune causes of meningitis and encephalitis.
Clinical & Veterinary

The Age of Postbiotics and Next-Generation Nutrition

The Postbiotic Advantage for Functional Foods

Microbiome Probiotics

20 Jan 2026 Lora Benoit Ph.D

A review of 35 current publications on postbiotics, addresses their sources, mechanisms, health benefits, formulation strategies, and regulatory considerations.
Food & Beverage

High-Throughput DNA Barcoding Increases Accuracy and Taxonomic Resolution of Yeast Species

High-throughput DNA barcoding for yeast ID

Metagenomics Next Generation Sequencing (NGS)Yeasts and Moulds

14 Jan 2026 Lora Benoit Ph.D

By generating high-quality DNA barcode sequences from a curated yeast culture collection, researchers expanded reference databases and improved the performance of metabarcoding-based and sequence-based identification pipelines, increasing accuracy and taxonomic resolution for yeast species.
Clinical & Veterinary

Accurate Serotyping of Streptococcus pneumoniae Using nCATSerotyping

Molecular serotyping using Cas9-targeting of capsular locus

Assay Validation Streptococcus pneumoniae

10 Jan 2026 Lora Benoit Ph.D

A novel Cas9-targeted nanopore sequencing platform (nCATSerotyping) achieves accurate serotype identification of S. pneumoniae that outperforms conventional serotyping.
Clinical & Veterinary

Novel Test Strategy for Highly Pathogenic Avian Influenza A

Testing for Bird Flu using combined molecular approach

Assay Development Assay Validation Avian Influenza

10 Jan 2026 Lora Benoit Ph.D

By combining FDA-authorized clinical and research-developed RT-PCR assays, researchers enabled adaptable, cost-effective diagnostics and large-scale surveillance for highly pathogenic avian influenza A H5.
Clinical & Veterinary Assay Development

New Enrichment Broth Finds B.cereus in Half of Powdered Infant Foods Sampled

Improved Recovery of B cereus From Infant Formulas

Assay Validation Bacillus cereus Toxins

09 Jan 2026 Lora Benoit Ph.D

Using a novel enrichment (R & F® Bacillus cereus Group Enrichment Broth) and detection scheme, researchers found B.cereus group species in 50 per cent of PIF and infant cereal samples. WGS and cytotoxicity assays confirmed the presence of potentially virulent strains.
Food & Beverage Assay Development

BACTEC Validated for Sterility Testing of ATMP Suspensions

BACTEC can be used for sterility testing of ATMP Suspensions

ATMP - Advanced Therapeutic Medicinal Products Cell and Gene Therapies Sterility Testing

02 Jan 2026 Lora Benoit Ph.D

The BACTEC automated microbial detection system reliably detects low-level contamination (≥ 5 CFU) in stem cell products suspended in Ringer’s Lactate, demonstrating full concordance with pharmacopeial sterility testing while delivering significantly faster results.
Assay Development

2-Day Sterility Testing for Cell-Based Therapeutics

Rapid and reliable sterility testing of ATMP

ATMP - Advanced Therapeutic Medicinal Products Cell and Gene Therapies Sterility Testing

02 Jan 2026 Lora Benoit Ph.D

Using an automated blood culture system, researchers demonstrated that mesenchymal stem cell (MSC) therapeutic preparations can be reliably screened for microbial contamination within 48 hr, supporting substantially faster product release compared with conventional 14-day sterility testing.
Pharmaceutical

Prevalence of Salmonella in Lymphatic Tissues of US Pigs

Lymphatic tissue is a significant Salmonella reservoir in US hogs

Salmonella Smarter Food Safety

02 Jan 2026 Lora Benoit Ph.D

A study of 6 US cull hog processing facilities found Salmonella in tonsils and mesenteric lymph nodes of boars, sows, and gilts, with >59% of carcasses positive in at least one lymphatic tissue, highlighting internal tissues as a key contamination reservoir.
Food & Beverage

Metagenomic Next Generation Sequencing (mNGS) Outperforms Culture in Detecting Lung Pathogens

Using mNGS for difficult to culture lung pathogens

Metagenomics Next Generation Sequencing (NGS)

27 Dec 2025 Lora Benoit Ph.D

In clinical lower respiratory tract infection samples, metagenomic NGS demonstrates higher overall detection rates and superior identification of co-infections compared with conventional culture, while agreeing closely with Sanger sequencing results.
Clinical & Veterinary

Antibiotics Shape Upper Respiratory Tract (URT) Microbiome in Recurrent Otitis Media

Antibiotics and age influence the microbiome in recurrent ear infections

16S Antibiotic Stewardship Microbiome

27 Dec 2025 Lora Benoit Ph.D

Study highlights the dynamic interplay between host age, antibiotic exposure, and the upper respiratory microbiome in children prone to recurrent acute otitis media.
Clinical & Veterinary Microbiome

16S-Based Metagenomic NGS Improves Detection of Pathogens

Evaluation of 16S-Based Metagenomic NGS

16S Assay Validation Next 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

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