Optimized Method for Bacterial Nucleic Acid Extraction from Positive Blood Culture Broth for Whole-Genome Sequencing, Resistance Phenotype Prediction, and Downstream Molecular Applications

Review Microbiology

Klebsiella oxytoca Complex: Update on Taxonomy, Antimicrobial Resistance, and Virulence

Jing Yang et al.

Summary: Klebsiella oxytoca is a complex of nine species that can cause various infections and is increasingly becoming resistant to antibiotics, posing a potential threat to human health.

CLINICAL MICROBIOLOGY REVIEWS (2022)

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Review Infectious Diseases

Strengths and caveats of identifying resistance genes from whole genome sequencing data

Brian M. Forde et al.

Summary: The use of whole-genome sequencing for antimicrobial resistance prediction presents an exciting opportunity to enhance our understanding of infectious pathogens and improve patient outcomes. Collaborative efforts across various disciplines will be critical to fully realize the potential of this approach.

EXPERT REVIEW OF ANTI-INFECTIVE THERAPY (2022)

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Article Microbiology

MALDI-TOF MS Using a Custom-Made Database, Biomarker Assignment, or Mathematical Classifiers Does Not Differentiate Shigella spp. and Escherichia coli

Maaike J. C. van den Beld et al.

Summary: Three alternative approaches using MALDI-TOF MS were explored to identify and distinguish Shigella spp., E. coli, and EIEC, but none of them were suitable for clinical diagnostics. Other tests should be used for the identification of this complex.

MICROORGANISMS (2022)

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Article Genetics & Heredity

nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning

Sabrina Krakau et al.

Summary: The study presents the nf-core/mag pipeline for metagenome assembly, binning, and taxonomic classification. The pipeline is characterized by its ease of installation, portability, and reproducibility, and it utilizes sample-wise group information to enhance assembly continuity.

NAR GENOMICS AND BIOINFORMATICS (2022)

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Article Genetics & Heredity

Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing

Menglan Zhou et al.

Summary: Bloodstream infection is a major global health concern, and MinION nanopore sequencing has shown promising results in accelerating pathogen diagnosis, resistance, and virulence gene prediction in simulated blood samples and cultures, achieving comprehensive results within 2 hours.

FRONTIERS IN GENETICS (2021)

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Article Multidisciplinary Sciences

AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

Michael Feldgarden et al.

Summary: With the advancement of technology, in silico approaches to assessing AMR gene content have become possible. NCBI has developed a comprehensive AMR gene database and AMR gene detection tool, expanding the Reference Gene Catalog and releasing AMRFinderPlus to provide a more accurate means of identifying AMR genes and determining their relationship with phenotypes.

SCIENTIFIC REPORTS (2021)

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Article Genetics & Heredity

Recovery of small plasmid sequences via Oxford Nanopore sequencing

Ryan R. Wick et al.

Summary: This study compared the ligation and rapid approaches for bacterial whole-genome sequencing by Oxford Nanopore Technologies, finding that the rapid library preparation method is preferable for recovering small plasmid sequences. Sequencing DNA from seven plasmid-rich bacterial isolates using Illumina as a reference, it was observed that small plasmids were underrepresented in ligation read sets but not in rapid read sets. The results also showed lower rates of chimaeric reads in the rapid read sets compared to ligation read sets.

MICROBIAL GENOMICS (2021)

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Article Biochemistry & Molecular Biology

Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids

Wei Gu et al.

Summary: The developed mNGS test using cell-free DNA from body fluids demonstrates high sensitivity and specificity for identifying pathogens, showing potential clinical utility. This method shows promise in rapid pathogen detection and may accelerate clinical decisions by providing high-specificity, unbiased detection from diverse body fluids using metagenomic sequencing.

NATURE MEDICINE (2021)

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Article Biochemical Research Methods