Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

1. 5.

   Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities · 2015

2. 28.

   Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing · 2014

3. 29.

   A New Perspective on Listeria monocytogenes Evolution · 2008

4. 32.

   Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations · 2008

5. 39.

   Tracing the Source of Campylobacteriosis · 2008

6. 48.

   High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak · 2010

7. 52.
   Corrected

   Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica · 2012

8. 54.

   Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica · 2011

9. 66.

   Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps · 2014

10. 71.

    SRST2: Rapid genomic surveillance for public health and hospital microbiology labs · 2014

11. 74.

    Reagent and laboratory contamination can critically impact sequence-based microbiome analyses · 2014

12. 79.

    Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis · 2016

13. 86.

    Identification of Salmonella for public health surveillance using whole genome sequencing · 2016

14. 90.

    Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes · 2016

15. 92.

    In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages · 2016

16. 98.

    The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies · 2016

17. 114.

    Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak · 2016

18. 119.

    IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses · 2016

19. 124.

    In-depth resistome analysis by targeted metagenomics · 2018

20. 138.

    PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance · 2017

21. 154.
    Corrected

    The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle · 2017

22. 159.
    Corrected

    Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes · 2018

23. 160.

    Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen · 2018

24. 166.

    Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak · 2018

25. 170.

    Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal Salmonella enterica · 2018

26. 172.

    A genomic overview of the population structure of Salmonella · 2018

27. 178.
    Corrected

    The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain · 2018

28. 187.

    MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies · 2018

29. 197.

    Genome-Based Prediction of Bacterial Antibiotic Resistance · 2019

30. 208.

    Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle · 2019

31. 213.

    Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage · 2019

32. 214.

    New insights from uncultivated genomes of the global human gut microbiome · 2019

33. 216.

    Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence · 2019

34. 219.

    Statistical Analysis of Metagenomics Data · 2019

35. 221.

    Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing · 2019

36. 226.
    Corrected

    Hypervirulent Listeria monocytogenes clones’ adaption to mammalian gut accounts for their association with dairy products · 2019

37. 227.

    Fast and flexible bacterial genomic epidemiology with PopPUNK · 2019

38. 228.

    Fast hierarchical Bayesian analysis of population structure · 2019

39. 229.

    Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition · 2016

40. 233.

    Using Genomics to Track Global Antimicrobial Resistance · 2019

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