Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water

Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations

(2020) Brittany Suttner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream

(2020) Andrea Ottesen et al.   BMC INFECTIOUS DISEASES

Preliminary Incidence and Trends of Infections with Pathogens Transmitted Commonly Through Food — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2016–2019

(2020) Danielle M. Tack et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

The Mandate for a Global “One Health” Approach to Antimicrobial Resistance Surveillance

(2019) Siddhartha Thakur et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Ultra-deep, long-read nanopore sequencing of mock microbial community standards

(2019) Samuel M Nicholls et al.   GigaScience

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

(2019) Denis Bertrand et al.   NATURE BIOTECHNOLOGY

Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli

(2019) Narjol González-Escalona et al.   PLoS One

Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017

(2019) Narjol González-Escalona et al.   PLoS One

Fishing in the Soup – Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing

(2019) Josephine Grützke et al.   Frontiers in Microbiology

Tree Lab: Portable genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa

(2019) Boykin et al.   Genes

Microbiome convergence following sanitizer treatment and identification of sanitizer resistant species from spinach and lettuce rinse water

(2019) Ganyu Gu et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Genomics of foodborne pathogens for microbial food safety

(2018) Marc W Allard et al.   CURRENT OPINION IN BIOTECHNOLOGY

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients

(2018) Federica Gigliucci et al.   Frontiers in Cellular and Infection Microbiology

The evolution of FDA's policy on Listeria monocytogenes in ready-to-eat foods in the United States

(2018) Douglas L .Archer   Current Opinion in Food Science

Unraveling the Role of Vegetables in Spreading Antimicrobial-Resistant Bacteria: A Need for Quantitative Risk Assessment

(2018) Christina Susanne Hölzel et al.   Foodborne Pathogens and Disease

National Antimicrobial Resistance Monitoring System: Two Decades of Advancing Public Health Through Integrated Surveillance of Antimicrobial Resistance

(2017) Beth E. Karp et al.   Foodborne Pathogens and Disease

Precision food safety: A systems approach to food safety facilitated by genomics tools

(2017) Jasna Kovac et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance

(2017) Robert M Cooper et al.   eLife

High Throughput Sequencing for Detection of Foodborne Pathogens

(2017) Camilla Sekse et al.   Frontiers in Microbiology

Virulence Gene Profiles and Clonal Relationships of Escherichia coli O26:H11 Isolates from Feedlot Cattle as Determined by Whole-Genome Sequencing

(2016) Narjol Gonzalez-Escalona et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Strain-Level Discrimination of Shiga Toxin-Producing Escherichia coli in Spinach Using Metagenomic Sequencing

(2016) Susan R. Leonard et al.   PLoS One

Application of Metagenomic Sequencing to Food Safety: Detection of Shiga Toxin-Producing Escherichia coli on Fresh Bagged Spinach

(2015) Susan R. Leonard et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Tracing Origins of theSalmonellaBareilly Strain Causing a Food-borne Outbreak in the United States

(2015) Maria Hoffmann et al.   JOURNAL OF INFECTIOUS DISEASES

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Irrigation Water Quality for Leafy Crops: A Perspective of Risks and Potential Solutions

(2015) Ana Allende et al.   International Journal of Environmental Research and Public Health

Omics approaches in food safety: fulfilling the promise?

(2014) Teresa M. Bergholz et al.   TRENDS IN MICROBIOLOGY

Factors influencing the microbial safety of fresh produce: A review

(2012) Amin N. Olaimat et al.   FOOD MICROBIOLOGY

Presence and survival of Escherichia coli O157:H7 on lettuce leaves and in soil treated with contaminated compost and irrigation water

(2012) M. Oliveira et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Distribution and decline of human pathogenic bacteria in soil after application in irrigation water and the potential for soil-splash-mediated dispersal onto fresh produce

(2012) J.M. Monaghan et al.   JOURNAL OF APPLIED MICROBIOLOGY

Outbreak of Shiga Toxin–Producing Escherichia coli (STEC) O104:H4 Infection in Germany Causes a Paradigm Shift with Regard to Human Pathogenicity of STEC Strains

(2012) LOTHAR BEUTIN et al.   JOURNAL OF FOOD PROTECTION