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The livestock reservoir for antimicrobial resistance: a personal view on changing patterns of risks, effects of interventions and the way forward

Philosophical transactions of the Royal Society of London. Series B. Biological sciences, 2015-06, Vol.370 (1670), p.20140085

Aarestrup, Frank M

2015

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Solving the problem of comparing whole bacterial genomes across different sequencing platforms

PloS one, 2014-08, Vol.9 (8), p.e104984-e104984

2014

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Rapid and precise alignment of raw reads against redundant databases with KMA

BMC bioinformatics, 2018-08, Vol.19 (1), p.307-307, Article 307

2018

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Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli

Journal of clinical microbiology, 2014-05, Vol.52 (5), p.1501-1510

2014

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Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica

PloS one, 2014-02, Vol.9 (2), p.e87991-e87991

2014

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ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes

Microbial genomics, 2022-01, Vol.8 (1)

2022

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Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing

PloS one, 2017-01, Vol.12 (1), p.e0170199-e0170199

2017

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The Role of Outer Membrane Proteins and Lipopolysaccharides for the Sensitivity of Escherichia coli to Antimicrobial Peptides

Frontiers in microbiology, 2018-09, Vol.9, p.2153-2153

2018

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Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand

PloS one, 2017-01, Vol.12 (1), p.e0169324-e0169324

2017

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A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome

PLoS biology, 2022-09, Vol.20 (9), p.e3001792-e3001792

2022

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Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

Emerging infectious diseases, 2021-05, Vol.27 (5), p.1405-1415

2021

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Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

Journal of Clinical Microbiology, 2012-04, Vol.50 (4), p.1355-1361

2012

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Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

Journal of Clinical Microbiology, 2014-01, Vol.52 (1), p.139-146

2014

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A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more

PloS one, 2020-12, Vol.15 (12), p.e0242987-e0242987

2020

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

PloS one, 2023-03, Vol.18 (3), p.e0283676-e0283676

2023

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Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015

Euro surveillance : bulletin européen sur les maladies transmissibles, 2015-12, Vol.20 (49), p.1

2015

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Benchmarking of methods for genomic taxonomy

Journal of clinical microbiology, 2014-05, Vol.52 (5), p.1529-1539

2014

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Using Genomics to Track Global Antimicrobial Resistance

Frontiers in public health, 2019-09, Vol.7, p.242

2019

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Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world

PloS one, 2023-10, Vol.18 (10), p.e0293169-e0293169

2023

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Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

BMC genomics, 2012-10, Vol.13 (1), p.577-577

2012

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Modelling the effectiveness of surveillance based on metagenomics in detecting, monitoring, and forecasting antimicrobial resistance in livestock production under economic constraints

Scientific reports, 2023-11, Vol.13 (1), p.20410-20410, Article 20410

2023

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Metagenomic analysis of sewage for surveillance of bacterial pathogens: A release experiment to determine sensitivity

PloS one, 2024-05, Vol.19 (5), p.e0300733-e0300733

2024

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World Health Organization Ranking of Antimicrobials According to Their Importance in Human Medicine: A Critical Step for Developing Risk Management Strategies for the Use of Antimicrobials in Food Production Animals

Clinical infectious diseases, 2009-07, Vol.49 (1), p.132-141

2009

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Livestock-Associated Methicillin Resistant and Methicillin Susceptible Staphylococcus aureus Sequence Type (CC)1 in European Farmed Animals: High Genetic Relatedness of Isolates from Italian Cattle Herds and Humans

PloS one, 2015-08, Vol.10 (8), p.e0137143-e0137143

2015

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Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage

Scientific reports, 2021-01, Vol.11 (1), p.1600-1600, Article 1600

2021

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The livestock reservoir for antimicrobial resistance: a personal view on changing patterns of risks, effects of interventions and the way forward

Solving the problem of comparing whole bacterial genomes across different sequencing platforms

Rapid and precise alignment of raw reads against redundant databases with KMA

Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli

Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica

ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing

The Role of Outer Membrane Proteins and Lipopolysaccharides for the Sensitivity of Escherichia coli to Antimicrobial Peptides

Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand

A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome

Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more

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

Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015

Benchmarking of methods for genomic taxonomy

Using Genomics to Track Global Antimicrobial Resistance

Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

Modelling the effectiveness of surveillance based on metagenomics in detecting, monitoring, and forecasting antimicrobial resistance in livestock production under economic constraints

Metagenomic analysis of sewage for surveillance of bacterial pathogens: A release experiment to determine sensitivity

World Health Organization Ranking of Antimicrobials According to Their Importance in Human Medicine: A Critical Step for Developing Risk Management Strategies for the Use of Antimicrobials in Food Production Animals

Livestock-Associated Methicillin Resistant and Methicillin Susceptible Staphylococcus aureus Sequence Type (CC)1 in European Farmed Animals: High Genetic Relatedness of Isolates from Italian Cattle Herds and Humans

Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage

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