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

Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology

(2018) J.W.A. Rossen et al.   CLINICAL MICROBIOLOGY AND INFECTION

Genomics of foodborne pathogens for microbial food safety

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

Novel insights into the microbiology of fermented dairy foods

(2018) Guerrino Macori et al.   CURRENT OPINION IN BIOTECHNOLOGY

Use of whole-genome sequencing for Campylobacter surveillance from NARMS retail poultry in the United States in 2015

(2018) Chris A. Whitehouse et al.   FOOD MICROBIOLOGY

Early transmissible ampicillin resistance in zoonotic Salmonella enterica serotype Typhimurium in the late 1950s: a retrospective, whole-genome sequencing study

(2018) Alicia Tran-Dien et al.   LANCET INFECTIOUS DISEASES

Comparative genome analysis and characterization of the Salmonella Typhimurium strain CCRJ_26 isolated from swine carcasses using whole-genome sequencing approach

(2018) P.H.N. Panzenhagen et al.   LETTERS IN APPLIED MICROBIOLOGY

Antibiotic-Resistance Genes in Waste Water

(2018) Antti Karkman et al.   TRENDS IN MICROBIOLOGY

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

(2018) Robert D. Stewart et al.   Nature Communications

Poultry hatcheries as potential reservoirs for antimicrobial-resistant Escherichia coli: A risk to public health and food safety

(2018) Kamelia M. Osman et al.   Scientific Reports

Genome Sequencing of Extended-Spectrum β-Lactamase (ESBL)-Producing Klebsiella pneumoniae Isolated from Pigs and Abattoir Workers in Cameroon

(2018) Luria L. Founou et al.   Frontiers in Microbiology

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

(2018) Saskia Neuert et al.   Frontiers in Microbiology

Whole-genome sequencing based characterization of antimicrobial resistance in Enterococcus

(2018) Gregory H Tyson et al.   Pathogens and Disease

Phenotypic and Genotypic Analysis of Antimicrobial Resistance among Listeria monocytogenes Isolated from Australian Food Production Chains

(2018) et al.   Genes

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data

(2018) Gustavo Arango-Argoty et al.   Microbiome

Characterization of multiple antibiotic resistance of culturable microorganisms and metagenomic analysis of total microbial diversity of marine fish sold in retail shops in Mumbai, India

(2017) Onkar A. Naik et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Whole genome sequencing (WGS) for food-borne pathogen surveillance and control – taking the pulse

(2017) Jacob Moran-Gilad   Eurosurveillance

MRSA and multidrug-resistant Staphylococcus aureus in U.S. retail meats, 2010–2011

(2017) Beilei Ge et al.   FOOD MICROBIOLOGY

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Detection and molecular characterization of Livestock-Associated MRSA in raw meat on retail sale in North West England

(2017) A. Fox et al.   LETTERS IN APPLIED MICROBIOLOGY

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Towards standards for human fecal sample processing in metagenomic studies

(2017) Paul I Costea et al.   NATURE BIOTECHNOLOGY

Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States

(2017) Yi Chen et al.   PLoS One

Characterization of NDM-5-positive extensively resistant Escherichia coli isolates from dairy cows

(2017) Tao He et al.   VETERINARY MICROBIOLOGY

Translating Omics to Food Microbiology

(2017) Aaron M. Walsh et al.   Annual Review of Food Science and Technology

An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli

(2017) Roderick M. Card et al.   mBio

Antibiotic resistance, serogroups, virulence genes, and phylogenetic groups of Escherichia coli isolated from yaks with diarrhea in Qinghai Plateau, China

(2017) Mujeeb Ur Rehman et al.   Gut Pathogens

Molecular Epidemiology of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus in the Ovine Dairy Chain and in Farm-Related Humans

(2017) Guerrino Macori et al.   Toxins

Extensive horizontal gene transfer in cheese-associated bacteria

(2017) Kevin S Bonham et al.   eLife

High Throughput Sequencing for Detection of Foodborne Pathogens

(2017) Camilla Sekse et al.   Frontiers in Microbiology

A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria

(2017) Ana B. Flórez et al.   Frontiers in Microbiology

Risk of Transmission of Antimicrobial Resistant Escherichia coli from Commercial Broiler and Free-Range Retail Chicken in India

(2017) Arif Hussain et al.   Frontiers in Microbiology

Epidemiology of Danish Aeromonas salmonicida subsp. salmonicida in Fish Farms Using Whole Genome Sequencing

(2017) Simona Bartkova et al.   Frontiers in Microbiology

Whole Genome Sequencing for Surveillance of Antimicrobial Resistance in Actinobacillus pleuropneumoniae

(2017) Janine T. Bossé et al.   Frontiers in Microbiology

Metagenomics: The Next Culture-Independent Game Changer

(2017) Jessica D. Forbes et al.   Frontiers in Microbiology

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access

(2017) Eduardo N. Taboada et al.   Frontiers in Microbiology

Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission

(2017) Daniel R. Knight et al.   Frontiers in Microbiology

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer

(2017) Alfonso Benítez-Páez et al.   GigaScience

Antibiotic resistance in the food supply chain: where can sequencing and metagenomics aid risk assessment?

(2017) Johan Bengtsson-Palme   Current Opinion in Food Science

Genotypic and phenotypic characterization of multidrug resistant Salmonella Typhimurium and Salmonella Kentucky strains recovered from chicken carcasses

(2017) Rizwana Tasmin et al.   PLoS One

Characterization of SXT/R391 Integrative and Conjugative Elements in Proteus mirabilis Isolates from Food-Producing Animals in China

(2016) Chang-Wei Lei et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella

(2016) Patrick F. McDermott et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Establishing Genotypic Cutoff Values To Measure Antimicrobial Resistance in Salmonella

(2016) Gregory H. Tyson et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Various Sequence Types of Escherichia coli Isolates Coharboring bla NDM-5 and mcr-1 Genes from a Commercial Swine Farm in China

(2016) Ling-Han Kong et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain

(2016) Xiang Yang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods

(2016) Andrew D. Huang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2016) Andrea Ottesen et al.   BMC MICROBIOLOGY

Multidrug resistance and ESBL-producing Salmonella spp. isolated from broiler processing plants

(2016) Rosangela Estel Ziech et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota

(2016) Alejandra Escobar-Zepeda et al.   FOOD MICROBIOLOGY

Metagenomic Evidence of the Prevalence and Distribution Patterns of Antimicrobial Resistance Genes in Dairy Agroecosystems

(2016) Dipti W. Pitta et al.   Foodborne Pathogens and Disease

Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening

(2016) Oylum Erkus et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Whole genome sequence-based serogrouping of Listeria monocytogenes isolates

(2016) Patrick Hyden et al.   JOURNAL OF BIOTECHNOLOGY

The Future of Whole-Genome Sequencing for Public Health and the Clinic

(2016) Marc W. Allard   JOURNAL OF CLINICAL MICROBIOLOGY

Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database

(2016) Marc W. Allard et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Dynamics of Listeria monocytogenes colonisation in a newly-opened meat processing facility

(2016) Andrei Sorin Bolocan et al.   MEAT SCIENCE

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Whole genome sequencing of diverse Shiga toxin-producing and non-producing Escherichia coli strains reveals a variety of virulence and novel antibiotic resistance plasmids

(2016) Liliana Losada et al.   PLASMID

Advances in DNA typing in the agro-food supply chain

(2016) Giandomenico Corrado   TRENDS IN FOOD SCIENCE & TECHNOLOGY

Identification of a Plasmid-Mediated Quinolone Resistance Gene in Salmonella Isolates from Texas Dairy Farm Environmental Samples

(2016) K. J. Cummings et al.   Zoonoses and Public Health

Resistome diversity in cattle and the environment decreases during beef production

(2016) Noelle R Noyes et al.   eLife

Predominance of CTX-M-15 among ESBL Producers from Environment and Fish Gut from the Shores of Lake Victoria in Mwanza, Tanzania

(2016) Nyambura Moremi et al.   Frontiers in Microbiology

Livestock-Associated Methicillin Resistant Staphylococcus aureus (LA-MRSA) Clonal Complex (CC) 398 Isolated from UK Animals belong to European Lineages

(2016) Meenaxi Sharma et al.   Frontiers in Microbiology

Thermus and the Pink Discoloration Defect in Cheese

(2016) Lisa Quigley et al.   mSystems

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

(2016) Aaron M. Walsh et al.   mSystems

Colonization of a Newly Constructed Commercial Chicken Further Processing Plant with Listeria monocytogenes

(2016) MARK E. BERRANG et al.   JOURNAL OF FOOD PROTECTION

Carbapenem-Resistant Bacteria Recovered from Faeces of Dairy Cattle in the High Plains Region of the USA

(2016) Hattie E. Webb et al.   PLoS One

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

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

Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems

(2016) Noelle R. Noyes et al.   Scientific Reports

Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine

(2016) Xutao Hong et al.   Scientific Reports

Bacteriophages Isolated from Chicken Meat and the Horizontal Transfer of Antimicrobial Resistance Genes

(2015) Amira Shousha et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Helicobacter pullorum Isolated from Fresh Chicken Meat: Antibiotic Resistance and Genomic Traits of an Emerging Foodborne Pathogen

(2015) Vítor Borges et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

The Connection between Persistent, Disinfectant-Resistant Listeria monocytogenes Strains from Two Geographically Separate Iberian Pork Processing Plants: Evidence from Comparative Genome Analysis

(2015) Sagrario Ortiz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

(2015) S. Zhao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing

(2015) Karen G. Jarvis et al.   BMC MICROBIOLOGY

Importance of sigma factor mutations in increased triclosan resistance in Salmonella Typhimurium

(2015) Mette Rørbæk Gantzhorn et al.   BMC MICROBIOLOGY

IntermingledKlebsiella pneumoniaePopulations Between Retail Meats and Human Urinary Tract Infections

(2015) Gregg S. Davis et al.   CLINICAL INFECTIOUS DISEASES

Whole-Genome Sequencing for National Surveillance of Shiga Toxin–ProducingEscherichia coliO157

(2015) Timothy J. Dallman et al.   CLINICAL INFECTIOUS DISEASES

Characterization of a multidrug resistant C. difficile meat isolate

(2015) Shankumar Mooyottu et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Validated predictive modelling of the environmental resistome

(2015) Gregory CA Amos et al.   ISME Journal

Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes

(2015) Jason C. Kwong et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data

(2015) Shaokang Zhang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

Tackling antibiotic resistance: the environmental framework

(2015) Thomas U. Berendonk et al.   NATURE REVIEWS MICROBIOLOGY

Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses

(2015) Eric Dugat-Bony et al.   PLoS One

Emergence of a Clonal Lineage of Multidrug-Resistant ESBL-Producing Salmonella Infantis Transmitted from Broilers and Broiler Meat to Humans in Italy between 2011 and 2014

(2015) Alessia Franco et al.   PLoS One

Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011–2013

(2014) D. Schmid et al.   CLINICAL MICROBIOLOGY AND INFECTION

Metagenomic analysis of the microbial community in kefir grains

(2014) Ufuk Nalbantoglu et al.   FOOD MICROBIOLOGY

Comparative Genomic Analysis and Virulence Differences in Closely Related Salmonella enterica Serotype Heidelberg Isolates from Humans, Retail Meats, and Animals

(2014) Maria Hoffmann et al.   Genome Biology and Evolution

Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing

(2014) N. C. Gordon et al.   JOURNAL OF CLINICAL MICROBIOLOGY

What is a resistance gene? Ranking risk in resistomes

(2014) José L. Martínez et al.   NATURE REVIEWS MICROBIOLOGY

Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution

(2014) Narender Kumar et al.   NUCLEIC ACIDS RESEARCH

A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures

(2014) Francesca De Filippis et al.   PLoS One

Whole-genome sequencing to control antimicrobial resistance

(2014) Claudio U. Köser et al.   TRENDS IN GENETICS

Functional Screening of Antibiotic Resistance Genes from a Representative Metagenomic Library of Food Fermenting Microbiota

(2014) Chiara Devirgiliis et al.   Biomed Research International

Whole-Genome Sequencing of Gentamicin-Resistant Campylobacter coli Isolated from U.S. Retail Meats Reveals Novel Plasmid-Mediated Aminoglycoside Resistance Genes

(2013) Yuansha Chen et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Identification of novel antimicrobial resistance genes from microbiota on retail spinach

(2013) Hillary F Berman et al.   BMC MICROBIOLOGY

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere

(2013) Andrea R. Ottesen et al.   PLoS One

PNAS Plus: From the Cover: Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

(2013) N. A. Bokulich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of a Novel Genomic Island Conferring Resistance to Multiple Aminoglycoside Antibiotics in Campylobacter coli

(2012) Shangshang Qin et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Novel Aminoglycoside 2″-Phosphotransferase Identified in a Gram-Negative Pathogen

(2012) Marta Toth et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach

(2012) Marc W Allard et al.   BMC GENOMICS

Antibiotic-Resistant Bacteria: A Challenge for the Food Industry

(2012) Rosa Capita et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Milk microbiome signatures of subclinical mastitis-affected cattle analysed by shotgun sequencing

(2012) V.D. Bhatt et al.   JOURNAL OF APPLIED MICROBIOLOGY

Diversity of Multidrug-ResistantSalmonella entericaStrains Associated with Cattle at Harvest in the United States

(2011) Dayna M. Brichta-Harhay et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food

(2011) Ji Young Jung et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study

(2011) Laura García-Álvarez et al.   LANCET INFECTIOUS DISEASES

Identification of a Salmonellosis Outbreak by Means of Molecular Sequencing

(2011) E. Kurt Lienau et al.   NEW ENGLAND JOURNAL OF MEDICINE

Metagenomic Analysis of the Viral Communities in Fermented Foods

(2010) Eun-Jin Park et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A 3-Year Surveillance of the Genetic Diversity and Persistence of Listeria monocytogenes in an Iberian Pig Slaughterhouse and Processing Plant

(2010) Sagrario Ortiz et al.   Foodborne Pathogens and Disease