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2022
Transient and resident pathogens: Intra-facility genetic diversity of Listeria monocytogenes and Salmonella from food production environments
PLOS ONE
2022
In Silico Assessment of Probe-Capturing Strategies and Effectiveness in the Spider Sub-Lineage Araneoidea (Order: Araneae)
Diversity
2021
Transmission patterns of a Mycobacterium avium subsp. paratuberculosis clone within a single heard investigated by Whole Genome Sequencing
Veterinary Microbiology
2021
Performance and Agreement Between WGS Variant Calling Pipelines Used for Bovine Tuberculosis Control: Toward International Standardization
Frontiers in Veterinary Science
2021
Development and Validation of a Quantitative PCR Method for Species Verification and Serogroup Determination of Listeria monocytogenes Isolates
Journal of Food Protection
2020
Single nucleotide polymorphisms (SNPs) provide unprecedented resolution of species boundaries, phylogenetic relationships, and genetic diversity in the mastiff bats (Molossus)
Molecular Phylogenetics and Evolution
2020
Isolation and Characterization of a Novel myovirus Infecting Shigella dysenteriae from the Aeration Tank Water
Applied Biochemistry and Biotechnology
2020
Optimization of Genotype by Sequencing data for phylogenetic purposes
MethodsX
2020
Population Structure of Listeria monocytogenes in Emilia-Romagna (Italy) and Implications on Whole Genome Sequencing Surveillance of Listeriosis
Frontiers in Public Health
2020
Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream
BMC Infectious Diseases
2019
Use of Whole-Genome Sequencing for Food Safety and Public Health in the United States
Foodborne Pathogens and Disease
2018
Serotype to genotype: The changing landscape of listeriosis outbreak investigations
Food Microbiology
2018
Evaluating the use of whole-genome sequencing for outbreak investigations in the lack of closely related reference genome
Infection, Genetics and Evolution
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
Rise and fall of outbreak-specific clone inside endemic pulsotype of Salmonella 4,[5],12:i:-; insights from high-resolution molecular surveillance in Emilia-Romagna, Italy, 2012 to 2015
Eurosurveillance
2018
Microbial sequence typing in the genomic era
Infection, Genetics and Evolution
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
A clade of Listeria monocytogenes serotype 4b variant strains linked to recent listeriosis outbreaks associated with produce from a defined geographic region in the US
PLOS ONE
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
Foodborne Pathogens
2017
A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens
Frontiers in Microbiology
2017
The Importance of Bacterial Culture to Food Microbiology in the Age of Genomics
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
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
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
Listeria monocytogenes in Stone Fruits Linked to a Multistate Outbreak: Enumeration of Cells and Whole-Genome Sequencing
Applied and Environmental Microbiology
2016
A Primer on Infectious Disease Bacterial Genomics
Clinical Microbiology Reviews
2016
NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats
Microbial Genomics
2016
Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks
Frontiers in Microbiology
2016
Genomic Epidemiology: Whole-Genome-Sequencing–Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens
Annual Review of Food Science and Technology
2016
Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks
PLOS ONE
2016
FDA Escherichia coli Identification (FDA-ECID) Microarray: a Pangenome Molecular Toolbox for Serotyping, Virulence Profiling, Molecular Epidemiology, and Phylogeny
Applied and Environmental Microbiology
2016
Prevalence and Level of Listeria monocytogenes in Ice Cream Linked to a Listeriosis Outbreak in the United States
Journal of Food Protection
2016
Outbreak of unusual Salmonella enterica serovar Typhimurium monophasic variant 1,4 [5],12:i:-, Italy, June 2013 to September 2014
Eurosurveillance
2015
CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data
PeerJ Computer Science
2015
Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data
BMC Bioinformatics
2015
The Listeria monocytogenes Core-Genome Sequence Typer (LmCGST): a bioinformatic pipeline for molecular characterization with next-generation sequence data
BMC Microbiology
2015
Concordance and discordance of sequence survey methods for molecular epidemiology
PeerJ
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