Journal Club: clinical

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Journal Club: clinical

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Advances in SARS-CoV-2 Wastewater Genomic Surveillance (WWGS)

Advances in Wastewater Genomic Surveillance of SARS-CoV-2

SARS in Wastewater SARS-CoV-2

21 Feb 2026 Lora Benoit Ph.D

This comprehensive review evaluates Wastewater Genomic Surveillance (WWGS) methods for SARS-CoV-2, detailing sampling and sequencing approaches, analytical challenges, and opportunities to improve outbreak detection, variant tracking, and public health responses.
Clinical & Veterinary

Point-of-Care Fingerstick Test Shows High Agreement With Reference PCR

HBV POC testing is a valid alternative to lab testing

Assay Validation Hepatitis

21 Feb 2026 Lora Benoit Ph.D

A diagnostic accuracy study evaluated the Xpert HBV Viral Load POC assay against a laboratory-based quantitative HBV DNA reference standard, demonstrating good concordance and potential for real-time therapeutic decision-making, particularly in resource-limited settings.
Clinical & Veterinary

Standardizing Mpox Metadata to Enhance Genomic Surveillance

Standardized metadata is key for pandemic preparedness

Mpox Virus

21 Feb 2026 Lora Benoit Ph.D

The Mpox contextual data specification package presents a structured metadata standard and accompanying curation toolkit designed to harmonize contextual data accompanying mpox virus genome sequences.
Clinical & Veterinary

Journal Club - 1 Feb to 13 Feb 2026

Journal Club Highlights

Cleanroom Hospital Acquired Infection (HAI)Rhinovirus

17 Feb 2026 Lora Benoit Ph.D

Latest from our Journal Club covering: targeted, risk-based sampling to maintain cleanroom compliance, importance of antimicrobial therapy and robust infection control in postoperative care, plus how the severity of rhinovirus disease may be due to inadequate early antiviral signalling.
Clinical & Veterinary Pharmaceutical

Why Some Colds Hit Harder: Rhinovirus vs Innate Immunity

Innate immune functions dictate the severity of cold symptoms

Rhinovirus

10 Feb 2026 Lora Benoit Ph.D

Rhinovirus infection can trigger robust interferon responses at the level of the epithelium, which are protective; in their absence, inflammatory signaling arises which can lead to severe cold symptoms.
Clinical & Veterinary Pharmaceutical

Microbiological Assessment of Surgical Site Infections

Surgical site infections following laparotomy or neurosurgery

E. coli Hospital Acquired Infection (HAI)Staphylococcus aureus

12 Feb 2026 Lora Benoit Ph.D

This prospective observational study evaluated the microbiological spectrum and antimicrobial susceptibility of surgical site infections. The findings emphasize the importance of targeted empirical therapy and robust infection control in postoperative care.
Clinical & Veterinary

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

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

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

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