F. M. Aarestrup

Time-series sewage metagenomics can separate the seasonal, human-derived and environmental microbial communities, holding promise for source-attributed surveillance

This study uses sewage metagenomics to distinguish seasonal, human-derived, and environmental microbial communities, offering potential for improved AMR surveillance.

Large-scale phenotypic and genomic characterization of Listeria monocytogenes susceptibility to quaternary ammonium compounds

This study characterizes QAC susceptibility in 1,671 L. monocytogenes isolates, identifies genetic markers linked to tolerance, and examines global prevalence across 37,897 genomes.

West Nile Virus spread in Europe - phylogeographic pattern analysis and key drivers

This study analyzes the phylogeographic patterns of West Nile Virus in Europe, identifying key drivers like agriculture and lineage diversity.

Detection of Parasites in Microbiomes using Metagenomics

This study detects parasites in microbiomes using metagenomics, finding Blastocystis sp. and Eimeria in livestock and various subtypes in humans, with prevalence patterns linked to income level and age.

Global distribution and diversity of prevalent sewage water plasmidomes

This study analyzes global sewage plasmidomes to identify antimicrobial resistance genes and their distribution across bacterial hosts.

Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome

The paper detects specific uncultured bacteriophages in pig microbiomes using modified phageFISH and PCR, revealing their life cycle stages and demonstrating the first in vivo detection of jumbophages without culturing.

Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes

This study shows that library preparation and sequencing platforms introduce systematic biases in metagenomic microbiome analysis, emphasizing the need for standardization.

Standard Sample Storage Conditions Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns

This study evaluates how storage conditions affect microbiome composition and antimicrobial resistance in metagenomics data, finding significant effects from temperature, time, and freeze-thaw cycles.

A Peek into the Plasmidome of Global Sewage

This study analyzes the plasmidome of global sewage samples to identify plasmid-encoded traits, revealing novel plasmids and AMR gene distribution.

Feature matrix normalization, transformation and calculation of beta-diversity in metagenomics: Theoretical and applied perspectives on your decisions

The paper discusses normalization, transformation, and beta-diversity calculation methods in metagenomics and provides a framework for evaluating their impact on data analysis.

Specific Gut Microbiome Members are Associated with Distinct Immune Markers in Allogeneic Hematopoietic Stem Cell Transplantation

The paper identifies associations between gut microbiome taxa and immune markers in HSCT patients, linking specific microbial profiles to clinical outcomes like aGvHD and mortality.

Proficiency of WHO Global Foodborne Infections Network External Quality Assurance System participants in the identification and susceptibility testing of thermo-tolerant Campylobacter spp. from 2003-2012.

The paper assesses the proficiency of WHO GFN EQAS participants in identifying and testing susceptibility of thermo-tolerant Campylobacter spp. from 2003-2012, finding improvements in AST but persistent gaps in identification, especially in African labs.

Megaphage infect Prevotella and variants are widespread in gut microbiomes

The paper identifies large phage (Lak phage) in gut microbiomes that infect Prevotella and are widespread, especially in developing-world individuals.

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid

This study develops a genomics-based approach to identify microorganisms in human ocular body fluids, showing high concordance with traditional methods.

Abundance and diversity of the fecal resistome in slaughter pigs and broilers in nine European countries

The paper quantifies and compares the resistomes of slaughter pigs and broilers across nine European countries, finding differences in AMR gene abundance and diversity linked to country-specific antimicrobial usage.