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2026
Probiotic strain identification and safety assessment of unlabeled bacteria in infant products
International Journal of Food Microbiology
2026
An investigation of an outbreak of Salmonella Typhimurium infections linked to alfalfa sprouts – United States, 2022
Food Control
2025
Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches
Frontiers in Microbiology
2025
dTOURS: Dense-region tagging for outbreak detection using ratio statistics
PLOS One
2025
Streptococcus equi subsp. zooepidemicus: Epidemiological and Genomic Findings of an Emerging Pathogen in Central Italy
Animals
2025
Occurrence of Selected Foodborne Pathogens on Frozen Berries Collected at Retail Level in Switzerland
Journal of Food Protection
2025
Emergence of Salmonella enterica carrying blaOXA-181 carbapenemase gene, Italy, 2021 to 2024
Eurosurveillance
2025
Urinary tract infection in a cat and cholangiohepatitis in a dog caused by the same strain of CTX-M-14 extended-spectrum beta-lactamase-producing Escherichia coli ST162 in a household: case report
ASM Case Reports
2025
Transformer-based models for uncovering genetic mutations in cancerous and non-cancerous genomes
Gene
2025
Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection
BMC Genomics
2025
Multistate Outbreak of Salmonella Thompson Infections Linked to Diced Onions—2023
Foodborne Pathogens and Disease
2025
A novel virulent core genome multilocus sequence type CT 11424 of Listeria monocytogenes isolate causing stillbirth in Bangladesh
BMC Microbiology
2025
A two-year study of Salmonella in four natural watersheds highlights the need for increased environmental Salmonella surveillance to close the One Health loop
Applied and Environmental Microbiology
2025
Prevalence and Levels of Shiga Toxin–producing Escherichia coli and Salmonella in California Raw Almond Kernels From the 2021 Harvest Compared With Data From Harvests Between 2001 and 2013
Journal of Food Protection
2025
Outbreak of carbapenem resistant Klebsiella pneumoniae in a neurorehabilitation unit: Genomic epidemiology reveals complex transmission pattern in a tertiary care hospital
Journal of Global Antimicrobial Resistance
2025
Pseudomonas aeruginosa investigation in water samples of Campania region, Southern Italy
American Journal of Infection Control
2025
Outbreak of Salmonella enterica subsp. enterica Serovar Napoli on a Dairy Cow Farm
Animals
2025
Emergence and Clonal Spread of Extended-Spectrum β-Lactamase-Producing Salmonella Infantis Carrying pESI Megaplasmids in Korean Retail Poultry Meat
Antibiotics
2025
Whole-genome sequencing surveillance of vancomycin-resistant Enterococcus faecium (VRE) detects hospital outbreaks and identifies the postanesthesia care unit as a transmission locus
Infection Control & Hospital Epidemiology
2025
A Binational Sample-Initiated Retrospective Outbreak Investigation of Listeria monocytogenes Infections in the United States and Canada Linked to Enoki Mushrooms Imported from China 2022–2023
Journal of Food Protection
2025
Genomic tracing and resolution of environmental Klebsiella pneumoniae ST307 CTX-M-15 linked to a nosocomial urinary tract infection in a cat: a veterinary teaching hospital case study
BMC Veterinary Research
2025
Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens
Nature Communications
2025
Salmonella enterica serovar Braenderup shows clade-specific source associations and a high proportion of molecular epidemiological clustering
Applied and Environmental Microbiology
2025
Bathing seawater and sand as reservoirs of clinically relevant and antimicrobial resistant Klebsiella pneumoniae strains
Science of The Total Environment
2025
Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest
Microbiology Spectrum
2025
A foodborne outbreak caused by atypical enteropathogenic Escherichia coli O45:H15 in the Kinki region of Japan
Applied and Environmental Microbiology
2025
Comparative genomic analysis reveals the emergence and dissemination of different Salmonella enterica serovar Gallinarum biovar Gallinarum lineages in Brazil
Avian Pathology
2025
Occurrence of <i>Salmonella</i> and presumptive <i>Bacillus cereus</i> in sesame products from Swiss retail stores
Italian Journal of Food Safety
2025
Prospective whole genome sequencing to aid the identification and control of methicillin-susceptible Staphylococcus aureus transmissions in a neonatal ICU
Journal of Infection
2025
Exploring the genomic and antimicrobial resistance tapestry: comparative insights into Salmonella enterica serotypes Agona, Braenderup, Muenchen, and Panama in Latin American surface waters
Microbiology Spectrum
2025
Molecular Characterization and Antimicrobial Resistance Evaluation of Listeria monocytogenes Strains from Food and Human Samples
Pathogens
2025
An Investigation of an Outbreak of Salmonella Newport Infections Linked to Melons from Southwest Indiana—United States, 2023
Foodborne Pathogens and Disease
2025
An International Outbreak Investigation of Salmonella Enteritidis Infections in the United States and Canada Linked to Peaches – 2020
Journal of Food Protection
2025
Genomic characterization of Klebsiella spp. from bovine mastitis: dissemination of a conserved, highly transmissible lac acq + fec + plasmid drives burden of disease
Applied and Environmental Microbiology
2024
Tracing carriage, acquisition, and transmission of ESBL-producing Escherichia coli over two years in a tertiary care hospital
Genome Medicine
2024
Genomic analysis of Listeria monocytogenes CC7 associated with clinical infections and persistence in the food industry
International Journal of Food Microbiology
2024
vSNP: a SNP pipeline for the generation of transparent SNP matrices and phylogenetic trees from whole genome sequencing data sets
BMC Genomics
2024
SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models
Bioinformatics
2024
Inside Mycobacterium bovis SB0120 spoligotype circulating in Italy: analysis of the most frequent genotypes by whole genome sequencing
Frontiers in Microbiology
2024
Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes
PLOS Computational Biology
2024
Multistate outbreak of Salmonella Oranienburg infections linked to bulb onions imported from Mexico – United States, 2021
Food Control
2024
Genomic analysis of a cAmpC (CMY-41)-producing Citrobacter freundii ST64 isolated from patient
Letters in Applied Microbiology
2024
Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates
BMC Genomics
2024
Antimicrobial resistance and phylogenetic relatedness of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli in peridomestic rats (Rattus norvegicus and Rattus tanezumi) linked to city areas and animal farms in Hong Kong
Environmental Research
2024
Emergence and genomic characteristics of multi-drug-resistant Salmonella in pet turtles and children with diarrhoea
Microbial Genomics
2024
Does strain-level persistence of lactobacilli in long-term back-slopped sourdoughs inform on domestication of food-fermenting lactic acid bacteria?
Applied and Environmental Microbiology
2024
Genomic epidemiology of hypervirulent Listeria monocytogenes CC619: Population structure, phylodynamics and virulence
Microbiological Research
2024
DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era
GigaScience
2024
Genetic relatedness and virulence potential of Salmonella Schwarzengrund strains with or without an IncFIB-IncFIC(FII) fusion plasmid isolated from food and clinical sources
Frontiers in Microbiology
2024
An Outbreak Investigation of Salmonella Weltevreden Illnesses in the United States Linked to Frozen Precooked Shrimp Imported from India – 2021
Journal of Food Protection
2024
Utilizing whole-genome sequencing to characterize Listeria spp. persistence and transmission patterns in a farmstead dairy processing facility and its associated farm environment
Journal of Dairy Science
2024
Role of Whole Genome Sequencing in Assessing Resident and Transient Listeria monocytogenes in a Produce Packinghouse
Journal of Food Protection
2024
Molecular Medical Microbiology
2024
Microbiological survey and genomic analysis of Cronobacter sakazakii strains isolated from US households and retail foods
Applied and Environmental Microbiology
2024
Intensive Environmental Sampling and Whole Genome Sequence-based Characterization of Listeria in Small- and Medium-sized Dairy Facilities Reveal Opportunities for Simplified and Size-appropriate Environmental Monitoring Strategies
Journal of Food Protection
2024
Genotypic and Phenotypic Analyses Show Ralstonia solanacearum Cool Virulence Is a Quantitative Trait Not Restricted to “Race 3 Biovar 2”
Phytopathology®
2024
Complete genome sequence of the linezolid-resistant clinical Enterococcus faecalis N23-3408 linked to a livestock lineage in Switzerland
Microbiology Resource Announcements
2024
Unveiling the genomic landscape ofSalmonella entericaserotypes Typhimurium, Newport, and Infantis in Latin American surface waters: a comparative analysis
Microbiology Spectrum
2024
Exploring the occurrence of Listeria in biofilms and deciphering the bacterial community in a frozen vegetable producing environment
Frontiers in Microbiology
2024
Genetic diversity and antimicrobial susceptibility of Streptococcus suis from diseased Swiss pigs collected between 2019 – 2022
Veterinary Microbiology
2024
Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens
Journal of Clinical Microbiology
2024
Comparison of the performance of multiple whole-genome sequence-based tools for the identification of Bacillus cereus sensu stricto biovar Thuringiensis
Applied and Environmental Microbiology
2024
Application of Environmental Monitoring Programs and Root Cause Analysis to Identify and Implement Interventions to Reduce or Eliminate Listeria Populations in Apple Packinghouses
Journal of Food Protection
2023
PRAWNS: compact pan-genomic features for whole-genome population genomics
Bioinformatics
2023
An Outbreak Investigation of Vibrio parahaemolyticus Infections in the United States Linked to Crabmeat Imported from Venezuela: 2018
Foodborne Pathogens and Disease
2023
Identification of the Novel Streptococcus equi subsp. zooepidemicus Sequence Type 525 in Donkeys of Abruzzo Region, Italy
Pathogens
2023
Dissemination of ESBL-producing E. coli ST131 through wastewater and environmental water in Switzerland
Environmental Pollution
2023
Soil Collected from a Single Great Smoky Mountains Trail Contains a Diversity of Listeria monocytogenes andListeriaspp.
Microbiology Spectrum
2023
Severe Streptococcus equi Subspecies zooepidemicus Outbreak from Unpasteurized Dairy Product Consumption, Italy
Emerging Infectious Diseases
2023
Surveillance of carbapenem-resistant organisms using next-generation sequencing
Frontiers in Public Health
2023
Phylogeny and Genomic Characterization of Clinical Salmonella enterica Serovar Newport Collected in Tennessee
Microbiology Spectrum
2023
Prospective Genomic Surveillance Reveals Cryptic MRSA Outbreaks with Local to International Origins among NICU Patients
Journal of Clinical Microbiology
2023
Genetic diversity of Salmonella enterica isolated over 13 years from raw California almonds and from an almond orchard
PLOS ONE
2023
Listeria monocytogenes Transmission from Donated Blood to Platelet Transfusion Recipient, Italy
Emerging Infectious Diseases
2023
Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation
BMC Genomics
2023
Characterizing the Genetic Diversity of Salmonella Isolated from U.S. Raw Inshell Pistachios Using Whole Genome Sequencing
Journal of Food Protection
2023
ClinMicroNow
2023
bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting
Frontiers in Microbiology
2023
The Slaughterhouse as Hotspot of CC1 and CC6 Listeria monocytogenes Strains with Hypervirulent Profiles in an Integrated Poultry Chain of Italy
Microorganisms
2023
Diversity of antimicrobial resistance, stress resistance, and virulence factors of Salmonella, Shiga toxin-producing Escherichia coli, and Listeria monocytogenes from produce, spices, and tree nuts by whole genome sequencing
Frontiers in Sustainable Food Systems
2023
Genomic and phylogenetic analysis of Salmonella enterica serovar Enteritidis strains linked to multiple outbreaks in Brazil
Letters in Applied Microbiology
2023
An investigation of an outbreak of Salmonella Newport infections linked to melons – United States, 2020
Food Control
2023
Multi-approach methods to predict cryptic carbapenem resistance mechanisms in Klebsiella pneumoniae detected in Central Italy
Frontiers in Microbiology
2023
Investigation of a Multistate Outbreak of Listeria monocytogenes Infections Linked to Frozen Vegetables Produced at Individually Quick-Frozen Vegetable Manufacturing Facilities
Journal of Food Protection
2023
Validating the Utility of Multilocus Variable Number Tandem-repeat Analysis (MLVA) as a Subtyping Strategy to Monitor Listeria monocytogenes In-built Food Processing Environments
Journal of Food Protection
2023
Ciprofloxacin‐resistantST198SalmonellaKentucky in a hospitalized American black bear (Ursus americanus), with evidence of subsequent nosocomial transmission
Zoonoses and Public Health
2023
Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications
Microbial Genomics
2023
Tetracycline resistance in Listeria monocytogenes and L. innocua from wild black bears ( Ursus americanus ) in the United States is mediated by novel transposable elements
Applied and Environmental Microbiology
2023
Deep Learning Framework for Complex Disease Risk Prediction Using Genomic Variations
Sensors
2023
Evolution and genomic profile of Salmonella enterica serovar Gallinarum biovar Pullorum isolates from Brazil
Avian Diseases
2023
Whole genome characterization of thermophilic Campylobacter species isolated from dairy manure in small specialty crop farms of Northeast Ohio
Frontiers in Microbiology
2023
Population genomics meets the taxonomy of cyanobacteria
Algal Research
2023
Prevalence of ciprofloxacin resistance and associated genetic determinants differed among Campylobacter isolated from human and poultry meat sources in Pennsylvania
Food Microbiology
2023
Evaluation of 10 Different Pipelines for Bacterial Single-Nucleotide Variant Detection
Infectious Microbes and Diseases
2023
Challenges Associated with Investigating Salmonella Enteritidis with Low Genomic Diversity in New York State: The Impact of Adjusting Analytical Methods and Correlation with Epidemiological Data
Foodborne Pathogens and Disease
2022
Epidemiological links and antimicrobial resistance of clinical Salmonella enterica ST198 isolates: a nationwide microbial population genomic study in Switzerland
Microbial Genomics
2022
Discovery and characterization of a new genotype of Salmonella enterica serovar Bareilly isolated from diarrhea patients of food-borne outbreaks
Frontiers in Microbiology
2022
Whole Genome Sequencing Reveals Biopesticidal Origin of Bacillus thuringiensis in Foods
Frontiers in Microbiology
2022
Genomic analysis of Listeria monocytogenes from US food processing environments reveals a high prevalence of QAC efflux genes but limited evidence of their contribution to environmental persistence
BMC Genomics
2022
Nonsynonymous Mutations in fepR Are Associated with Adaptation of Listeria monocytogenes and Other Listeria spp. to Low Concentrations of Benzalkonium Chloride but Do Not Increase Survival of L. monocytogenes and Other Listeria spp. after Exposure to Benzalkonium Chloride Concentrations Recommended for Use in Food Processing Environments
Applied and Environmental Microbiology
2022
Genomic Analysis of Clostridioides difficile in 2 Regions of the United States Reveals a Diversity of Strains and Limited Transmission
The Journal of Infectious Diseases
2022
Bacterial typing methods from past to present: A comprehensive overview
Gene Reports
2022
Microbiological Risk Assessment Associated with the Food Processing and Distribution Chain
2022
Nosocomial Pluralibacter gergoviae Isolates Expressing NDM and KPC Carbapenemases Characterized Using Whole-Genome Sequencing
Antimicrobial Agents and Chemotherapy
2022
Massive Spread of OXA-48 Carbapenemase-Producing Enterobacteriaceae in the Environment of a Swiss Companion Animal Clinic
Antibiotics
2022
Recent paradigm shifts in the perception of the role of Bacillus thuringiensis in foodborne disease
Food Microbiology
2022
Occurrence and Characteristics of Escherichia albertii in Wild Birds and Poultry Flocks in Switzerland
Microorganisms
2022
Pervasive Listeria monocytogenes Is Common in the Norwegian Food System and Is Associated with Increased Prevalence of Stress Survival and Resistance Determinants
Applied and Environmental Microbiology
2022
Using Evolutionary Analyses to Refine Whole-Genome Sequence Match Criteria
Frontiers in Microbiology
2022
Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States
Journal of Food Protection
2022
Genomic analysis of Salmonella Typhimurium from humans and food sources accurately predicts phenotypic multi-drug resistance
Food Microbiology
2022
Characterization and Genetic Diversity of Bacillus cereus Strains Isolated from Baby Wipes
Microorganisms
2022
Subtyping Evaluation of Salmonella Enteritidis Using Single Nucleotide Polymorphism and Core Genome Multilocus Sequence Typing with Nanopore Reads
Applied and Environmental Microbiology
2022
Whole-Genome Sequencing-Based Characterization of Listeria Isolates from Produce Packinghouses and Fresh-Cut Facilities Suggests Both Persistence and Reintroduction of Fully Virulent L. monocytogenes
Applied and Environmental Microbiology
2022
A case report of Salmonella enterica serovar Corvallis from environmental isolates from Cambodia and clinical isolates in the UK
Access Microbiology
2022
Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria
Microbial Genomics
2022
Toward the Adoption of Loop-Mediated Isothermal Amplification for Salmonella Screening at the National Antimicrobial Resistance Monitoring System's Retail Meat Sites
Foodborne Pathogens and Disease
2021
Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil
Applied and Environmental Microbiology
2021
SALMONELLA ISOLATED FROM CENTRAL NEW YORK WILDLIFE ADMITTED TO A VETERINARY MEDICAL TEACHING HOSPITAL
Journal of Wildlife Diseases
2021
Household acquisition and transmission of extended-spectrum β-lactamase (ESBL) -producing Enterobacteriaceae after hospital discharge of ESBL-positive index patients
Clinical Microbiology and Infection
2021
Determination of Genomic Epidemiology of Historical Clostridium perfringens Outbreaks in New York State by Use of Two Web-Based Platforms: National Center for Biotechnology Information Pathogen Detection and FDA GalaxyTrakr
Journal of Clinical Microbiology
2021
Comprehensive Foodomics
2021
Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products
Foods
2021
Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel
Microbial Genomics
2021
GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians
BMC Genomics
2021
Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads
BMC Genomics
2021
Large diversity of linezolid-resistant isolates discovered in food-producing animals through linezolid selective monitoring in Belgium in 2019
Journal of Antimicrobial Chemotherapy
2021
Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks
PeerJ
2021
Comprehensive Foodomics
2021
Genomic diversity of Listeria monocytogenes isolates from seafood, horticulture and factory environments in New Zealand
International Journal of Food Microbiology
2021
Identification of Closely Related Listeria monocytogenes Isolates with No Apparent Evidence for a Common Source or Location: A Retrospective Whole Genome Sequencing Analysis
Journal of Food Protection
2021
Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania
Microorganisms
2021
inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains
Nature Biotechnology
2021
Identification and Characterization of a Novel Genomic Island Harboring Cadmium and Arsenic Resistance Genes in Listeria welshimeri
Biomolecules
2021
A Series of Papaya-Associated Salmonella Illness Outbreak Investigations in 2017 and 2019: A Focus on Traceback, Laboratory, and Collaborative Efforts
Journal of Food Protection
2021
Salmonella Genomics in Public Health and Food Safety
EcoSal Plus
2021
Microbial source tracking using metagenomics and other new technologies
Journal of Microbiology
2021
Molecular Epidemiology of Salmonellosis in Florida, USA, 2017–2018
Frontiers in Medicine
2021
Whole-Genome Sequencing Analysis of Salmonella Enterica Serotype Enteritidis Isolated from Poultry Sources in South Korea, 2010–2017
Pathogens
2021
Evaluation of nanopore sequencing technology to identify Salmonella enterica Choleraesuis var. Kunzendorf and Orion var. 15+, 34+
International Journal of Food Microbiology
2021
Whole-Genome Assessment of Clinical Acinetobacter baumannii Isolates Uncovers Potentially Novel Factors Influencing Carbapenem Resistance
Frontiers in Microbiology
2021
Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak
Frontiers in Microbiology
2021
Retrospective whole-genome comparison of Salmonella enterica serovar Enteritidis from foodborne outbreaks in Southern Brazil
Brazilian Journal of Microbiology
2021
Comprehensive and accurate genetic variant identification from contaminated and low-coverage Mycobacterium tuberculosis whole genome sequencing data
Microbial Genomics
2021
Survey of Salmonella in raw tree nuts at retail in the United States
Journal of Food Science
2021
Rapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting
Frontiers in Microbiology
2021
Whole Genome Sequencing Applied to Pathogen Source Tracking in Food Industry: Key Considerations for Robust Bioinformatics Data Analysis and Reliable Results Interpretation
Genes
2021
Salmonella Genomics and Population Analyses Reveal High Inter- and Intraserovar Diversity in Freshwater
Applied and Environmental Microbiology
2021
Feedborne Salmonella enterica Serovar Jerusalem Outbreak in Different Organic Poultry Flocks in Switzerland and Italy Linked to Soya Expeller
Microorganisms
2021
Occurrence of Listeria monocytogenes in Counter-Sliced Turkey Meat Samples from Independent Delis in New York City
Journal of Food Protection
2021
Genetic changes are introduced by repeated exposure of Salmonella spiked in low water activity and high fat matrix to heat
Scientific Reports
2020
Carbapenemase-producing Pseudomonas aeruginosa in Spain: interregional dissemination of the high-risk clones ST175 and ST244 carrying blaVIM-2, blaVIM-1, blaIMP-8, blaVIM-20 and blaKPC-2
International Journal of Antimicrobial Agents
2020
Microevolution and Gain or Loss of Mobile Genetic Elements of Outbreak-Related Listeria monocytogenes in Food Processing Environments Identified by Whole Genome Sequencing Analysis
Frontiers in Microbiology
2020
Genomic characterization and phylogenetic analysis ofSalmonella entericaserovar Javiana
PeerJ
2020
Genomic diversity of Salmonella enterica isolated from papaya samples collected during multiple outbreaks in 2017
Microbiology
2020
Food Safety Genomics and Connections to One Health and the Clinical Microbiology Laboratory
Clinics in Laboratory Medicine
2020
Microbial Forensics
2020
A quasimetagenomics method for concerted detection and subtyping of Salmonella enterica and E. coli O157:H7 from romaine lettuce
Food Microbiology
2020
Temporal Dynamics of Salmonella enterica subsp. enterica Serovar Agona Isolates From a Recurrent Multistate Outbreak
Frontiers in Microbiology
2020
Evolution of Listeria monocytogenes in a Food Processing Plant Involves Limited Single-Nucleotide Substitutions but Considerable Diversification by Gain and Loss of Prophages
Applied and Environmental Microbiology
2020
Genome sequence analysis of 91 Salmonella Enteritidis isolates from mice caught on poultry farms in the mid 1990s
Genomics
2020
Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream
BMC Infectious Diseases
2020
High Prevalence of Genetically Related Clostridium Difficile Strains at a Single Hemato-Oncology Ward Over 10 Years
Frontiers in Microbiology
2020
Whole-Genome Sequences of Salmonella Isolates from an Ecological Wastewater Treatment System
Microbiology Resource Announcements
2020
Characterization of Mobile Genetic Elements Using Long-Read Sequencing for Tracking Listeria monocytogenes from Food Processing Environments
Pathogens
2020
Typing methods based on whole genome sequencing data
One Health Outlook
2020
Sequence analysis of Salmonella enterica isolates obtained from shelter dogs throughout Texas
Veterinary Medicine and Science
2020
Concordance of SNP- and allele-based typing workflows in the context of a large-scale international Salmonella Enteritidis outbreak investigation
Microbial Genomics
2020
Large scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform
Communications Biology
2020
Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico
Microbial Genomics
2020
Salmonella enterica and Escherichia coli in Wheat Flour: Detection and Serotyping by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple-Displacement Amplification, and Real-Time Sequencing
Applied and Environmental Microbiology
2020
Genomic comparison of Clostridium chauvoei isolates from classical and visceral clinical manifestation
Brazilian Journal of Microbiology
2020
Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication
Epigenetics
2020
Genotypic and Phenotypic Characterization of Incompatibility Group FIB Positive Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources
Genes
2020
Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life
Scientific Reports
2020
Genomic Surveillance of Ceftriaxone-Resistant Escherichia coli in Western New York Suggests the Extended-Spectrum β-Lactamase blaCTX-M-27 Is Emerging on Distinct Plasmids in ST38
Frontiers in Microbiology
2019
Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance
Journal of Clinical Microbiology
2019
Whole-Genome Sequencing Analysis of Nontyphoidal Salmonella enterica of Chicken Meat and Human Origin Under Surveillance in Sri Lanka
Foodborne Pathogens and Disease
2019
Short communication: Persistent contamination by Listeria monocytogenes of bovine raw milk investigated by whole-genome sequencing
Journal of Dairy Science
2019
Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination
Genome Biology
2019
Implications of Mobile Genetic Elements for Salmonella enterica Single-Nucleotide Polymorphism Subtyping and Source Tracking Investigations
Applied and Environmental Microbiology
2019
Whole-Genome Sequencing-Based Characterization of 100 Listeria monocytogenes Isolates Collected from Food Processing Environments over a Four-Year Period
mSphere
2019
Whole genome sequencing used in an industrial context reveals a Salmonella laboratory cross-contamination
International Journal of Food Microbiology
2019
Methods in Molecular Biology
2019
ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data
PeerJ
2019
Assembly and Characterization of a Pathogen Strain Collection for Produce Safety Applications: Pre-growth Conditions Have a Larger Effect on Peroxyacetic Acid Tolerance Than Strain Diversity
Frontiers in Microbiology
2019
Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks
Frontiers in Microbiology
2019
Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella
Frontiers in Microbiology
2019
Defense Against Biological Attacks
2019
Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges
Frontiers in Microbiology
2019
The use of next generation sequencing for improving food safety: Translation into practice
Food Microbiology
2019
Phenotypic Prediction: Linking in vitro Virulence to the Genomics of 59 Salmonella enterica Strains
Frontiers in Microbiology
2019
Comparative Analysis of Tools and Approaches for Source Tracking Listeria monocytogenes in a Food Facility Using Whole-Genome Sequence Data
Frontiers in Microbiology
2019
PLANET-SNP pipeline: PLants based ANnotation and Establishment of True SNP pipeline
Genomics
2019
DNA sequences and predicted protein structures of prot6E and sefA genes for Salmonella ser. Enteritidis detection
Food Control
2019
Food Microbiology
2019
Outbreak of Tattoo-associated Nontuberculous Mycobacterial Skin Infections
Clinical Infectious Diseases
2019
Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP
Microbial Genomics
2018
A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica
Frontiers in Microbiology
2018
A primer on microbial bioinformatics for nonbioinformaticians
Clinical Microbiology and Infection
2018
Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the trace
Frontiers of Medicine
2018
GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from 2015
Microbial Genomics
2018
Sequence Analysis of IncA/C and IncI1 Plasmids Isolated from Multidrug-Resistant Salmonella Newport Using Single-Molecule Real-Time Sequencing
Foodborne Pathogens and Disease
2018
Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:-
PLOS ONE
2018
Whole-Genome Sequencing and Bioinformatic Analysis of Isolates from Foodborne Illness Outbreaks of Campylobacter jejuni and Salmonella enterica
Journal of Clinical Microbiology
2018
Interpreting Whole-Genome Sequence Analyses of Foodborne Bacteria for Regulatory Applications and Outbreak Investigations
Frontiers in Microbiology
2018
Genetic Diversity of Salmonella and Listeria Isolates from Food Facilities
Journal of Food Protection
2018
Prevalence, antimicrobial resistance and phylogenetic characterization of Yersinia enterocolitica in retail poultry meat and swine feces in parts of China
Food Control
2018
Insight into the Significance of Aspergillus fumigatus cyp51A Polymorphisms
Antimicrobial Agents and Chemotherapy
2018
Quasimetagenomics-Based and Real-Time-Sequencing-Aided Detection and Subtyping of Salmonella enterica from Food Samples
Applied and Environmental Microbiology
2018
Serotype to genotype: The changing landscape of listeriosis outbreak investigations
Food Microbiology
2018
Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms
Genome Biology and Evolution
2018
Optimization of subculture and DNA extraction steps within the whole genome sequencing workflow for source tracking of Salmonella enterica and Listeria monocytogenes
Journal of Microbiological Methods
2018
Changing of the Genomic Pattern of Salmonella Enteritidis Strains Isolated in Brazil Over a 48 year-period revealed by Whole Genome SNP Analyses
Scientific Reports
2017
SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology
Microbial Genomics
2017
Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States
PLOS ONE
2017
Draft Genome Sequences of Listeria monocytogenes Strains from Listeriosis Outbreaks Linked to Soft Cheese in Washington State
Genome Announcements
2017
Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations
Nucleic Acids Research
2017
Applied Genomics of Foodborne Pathogens
2017
Whole genome sequencing analyses of Listeria monocytogenes that persisted in a milkshake machine for a year and caused illnesses in Washington State
BMC Microbiology
2017
A Comprehensive Evaluation of the Genetic Relatedness of Listeria monocytogenes Serotype 4b Variant Strains
Frontiers in Public Health
2017
A brief primer on genomic epidemiology: lessons learned fromMycobacterium tuberculosis
Annals of the New York Academy of Sciences
2017
Precision food safety: A systems approach to food safety facilitated by genomics tools
TrAC Trends in Analytical Chemistry
2017
Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
PeerJ
2017
High Throughput Sequencing for Detection of Foodborne Pathogens
Frontiers in Microbiology
2017
Foodborne Pathogens
2017
Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access
Frontiers in Microbiology
2017
Singleton Sequence Type 382, an Emerging Clonal Group of Listeria monocytogenes Associated with Three Multistate Outbreaks Linked to Contaminated Stone Fruit, Caramel Apples, and Leafy Green Salad
Journal of Clinical Microbiology
2017
TreeToReads - a pipeline for simulating raw reads from phylogenies
BMC Bioinformatics
2017
A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens
Frontiers in Microbiology
2017
Whole Genome and Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analyses of Listeria monocytogenes Isolates Associated with an Outbreak Linked to Cheese, United States, 2013
Applied and Environmental Microbiology
2017
PathoBacTyper: A Web Server for Pathogenic Bacteria Identification and Molecular Genotyping
Frontiers in Microbiology
2016
Listeria monocytogenes in Stone Fruits Linked to a Multistate Outbreak: Enumeration of Cells and Whole-Genome Sequencing
Applied and Environmental Microbiology
2016
Whole Genome DNA Sequence Analysis of Salmonella subspecies enterica serotype Tennessee obtained from related peanut butter foodborne outbreaks.
PLOS ONE
2016
Prevalence and Level of Listeria monocytogenes in Ice Cream Linked to a Listeriosis Outbreak in the United States
Journal of Food Protection
2016
Recovery and Growth Potential of Listeria monocytogenes in Temperature Abused Milkshakes Prepared from Naturally Contaminated Ice Cream Linked to a Listeriosis Outbreak
Frontiers in Microbiology
2016
A Primer on Infectious Disease Bacterial Genomics
Clinical Microbiology Reviews
2016
Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation
Clinical Infectious Diseases
2016
Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples
PLOS ONE
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