Journal Club

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Journal Club

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Journal Club - 11 March to 20 March 2026

Journal Club

Hospital Acquired Infection (HAI)Mycobacterium Next Generation Sequencing (NGS)

23 Mar 2026

Latest from our Journal Club: Community- and hospital-acquired septic shock, timing of Metagenomic NGS-guided antibiotic adjustment (mNGS), and nanopore-based targeted next-generation sequencing to detect M. tuberculosis.
Clinical & Veterinary

Key Differences Between Community- and Hospital-Acquired Septic Shock

Key differences between Community- and Hospital-Acquired Septic Shock

Hospital Acquired Infection (HAI)Sepsis

20 Mar 2026 Lora Benoit Ph.D

New study compares community- and hospital-acquired septic shock, demonstrating that acquisition setting shapes pathogen profiles, host immune responses, and treatment outcomes, with important implications for diagnosis, therapy, and prognosis.
Clinical & Veterinary

mNGS-Guided Antibiotic Adjustments Improve Survival in Severe Pneumonia

NGS-guided antimicrobial adjustments improve outcomes for patients with severe pneumonia

Next Generation Sequencing (NGS)Sepsis

19 Mar 2026 Lora Benoit Ph.D

This retrospective multicenter study evaluated how timing of Metagenomic NGS-guided antibiotic adjustment (mNGS) impacts patient mortality in ICU patients with severe community-acquired pneumonia.
Clinical & Veterinary

Rapid TB Detection, AMR Profiling from Non-Sputum Samples

Rapid TB Detection AMR Profiling using nanopore tNGS

Mycobacterium Mycobacterium tuberculosis Next Generation Sequencing (NGS)

19 Mar 2026 Lora Benoit Ph.D

This multicenter prospective study evaluated nanopore-based targeted next-generation sequencing to detecting M. tuberculosis and drug resistance directly from non-sputum specimens.
Clinical & Veterinary

Journal Club - 3 March to 10 March 2026

Journal Club

Antibiotic Sensitivity Blood Culture Phenotyping

10 Mar 2026

Latest from our Journal Club: comparing rapid phenotypic AST platforms, approaches to resolving genotype–phenotype discordance, and proposed breakpoint adjustments to improve reliability of disk-diffusion.
Clinical & Veterinary

Comparison of VITEK MS PRIME vs MALDI Biotyper Sirius

MALDI-TOF Systems for Microbial ID

Identification MALDI-TOF

09 Mar 2026 Lora Benoit Ph.D

New study compares the VITEK MS PRIME and the MALDI Biotyper Sirius for microbial ID accuracy and laboratory workflow efficiency across 927 isolates: both systems showed high identification accuracy, but VITEK MS PRIME achieved higher identification rates and shorter turnaround times.
Clinical & Veterinary

Faster AST Reporting Improves Bloodstream Infection (BSI) Outcomes and Reduces Costs

Faster AST reporting equals better outcomes

Antibiotic Sensitivity Antibiotic Stewardship Blood Culture

09 Mar 2026 Lora Benoit Ph.D

Evidence shows that faster AST reporting enables earlier optimization of antibiotic therapy, improved carbapenem stewardship, and reduced hospital length of stay and healthcare costs for patients with bloodstream infections.
Clinical & Veterinary

Culture vs. Culture-Free Identification of Mycobacteria

Culture-free ID of Mycobacteria in clinical samples

Mycobacterium Mycobacterium paratuberculosis

09 Mar 2026 Lora Benoit Ph.D

This prospective study compares conventional culture with a culture-free target capture sequencing method for identifying mycobacteria directly from clinical samples. The sequencing approach enabled species- and subspecies-level identification without requiring growth.
Clinical & Veterinary

Challenges and Solutions for Identifying Breakpoints Using Disk Diffusion

Antimicrobial Susceptibility Testing Challenges of Anaerobes

Antibiotic Sensitivity

05 Mar 2026 Lora Benoit Ph.D

This study re-analyzed a large panel of anaerobes to assess how disk-diffusion methods classify susceptibility under CLSI, CA-SFM, and EUCAST breakpoints. The authors identified discrepancies and proposed breakpoint adjustments to improve reliability, highlighting challenges for anaerobic bacteria.
Clinical & Veterinary

How to Resolve Genotype–Phenotype AST Discordance in a MRSA+ Blood Culture

A case of resolving genotype phenotype AST discordance

Antibiotic Sensitivity

05 Mar 2026 Lora Benoit Ph.D

This report describes a case of S. aureus bacteremia where rapid genotypic testing detected methicillin resistance while initial phenotypic AST indicated susceptibility. The authors demonstrate a practical approach to resolving genotype–phenotype discordance.
Clinical & Veterinary

Comparison of Rapid Phenotypic AST Platforms Directly from Positive Blood Cultures

Comparison of Rapid Phenotypic AST Platforms Direct from Blood Cultures

Antibiotic Sensitivity Blood Culture Phenotyping

05 Mar 2026 Lora Benoit Ph.D

New study compares the VITEK REVEAL AST System and the Accelerate Pheno System for rapid AST directly from Gram-negative positive blood cultures. Across 128 specimens and 1,410 organism–drug pairs, both systems demonstrated high agreement and delivered actionable results in under 8 hours.
Clinical & Veterinary

Journal Club - 22 Feb to 2 March 2026

Journal Club

Air Sampling Aspergillus Identification

02 Mar 2026

Latest from our Journal Club: Measles cases are resurging globally, FDA reports the most common microorganisms in pharmaceuticals, and DNA metabarcoding of air samples from waste sorting plants enhances microbial risk assessment.
Clinical & Veterinary Other Pharmaceutical

Global Measles Resurgence Linked to Declining Vaccination

Increased global measle outbreaks due to reduced vaccination

Respiratory Viruses

25 Feb 2026 Lora Benoit Ph.D

Measles cases are resurging globally as routine immunization falls below protective thresholds, reversing elimination gains. Widespread outbreaks - including in previously measles-free countries - reflect immunity gaps driven by pandemic disruptions and vaccine hesitancy.
Clinical & Veterinary Other

Review of FDA Enforcement: Microbial Contaminants in Sterile and Non-sterile Pharmaceuticals

Review of FDA enforcement reports demonstrates patterns of microbial contamination

Aspergillus Burkholderia cepacia complex (BCC)Identification

25 Feb 2026 Lora Benoit Ph.D

FDA enforcement reports (2004–2025) were analyzed to define microbial contamination events driving recalls of drugs. The most common microorganisms detected were Aspergillus penicilloides, followed by Burkholderia cepacia complex (BCC).
Pharmaceutical

DNA Metabarcoding: Identification of Airborne Pathogens in Waste Sorting Plants

DNA metabarcoding IDs complex microorganism populations in Air Samples

Air Sampling Identification

25 Feb 2026 Lora Benoit Ph.D

Using DNA metabarcoding in air samples from waste sorting plants can substantially improve microbial risk assessment by capturing both culturable and non-culturable organisms with species-level precision. This facilitates the identification of hazardous taxa that conventional methods overlook.
Clinical & Veterinary Other

Journal Club - 14 Feb to 21 Feb

Journal Club

Assay Validation Mpox Virus SARS in Wastewater

24 Feb 2026

Latest from our Journal Club: Wastewater Genomic Surveillance methods for SARS-CoV-2, Xpert HBV Viral Load POC assay versus laboratory-based quantitative HBV DNA reference standard, and a formalized metadata specification package tailored to Mpox virus surveillance.
Clinical & Veterinary

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

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Test for Flu and COVID with Puritan UniTranz RT

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Bio-rad Supporting the Science of Food Safety

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Bacillus cereus and Cereulide Toxin What do you need to know

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