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AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

Scientific reports, 2021-06, Vol.11 (1), p.12728-12728, Article 12728

2021

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Interpreting Whole-Genome Sequence Analyses of Foodborne Bacteria for Regulatory Applications and Outbreak Investigations

Frontiers in microbiology, 2018-07, Vol.9, p.1482

2018

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Transient and resident pathogens: Intra-facility genetic diversity of Listeria monocytogenes and Salmonella from food production environments

PloS one, 2022-09, Vol.17 (9), p.e0268470-e0268470

2022

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Prospective modeling and estimating the epidemiologically informative match rate within large foodborne pathogen genomic databases

BMC research notes, 2024-07, Vol.17 (1), p.1-6, Article 191

2024

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Interpretative Labor and the Bane of Nonstandardized Metadata in Public Health Surveillance and Food Safety

Clinical infectious diseases, 2021-10, Vol.73 (8), p.1537-1539

2021

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Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation

Frontiers in microbiology, 2016-01, Vol.6, p.1573-1573

2016

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Genomic evidence of environmental and resident Salmonella Senftenberg and Montevideo contamination in the pistachio supply-chain

PloS one, 2021-11, Vol.16 (11), p.e0259471

2021

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Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)

BMC microbiology, 2013-05, Vol.13 (1), p.114-114

2013

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The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence

PloS one, 2015-08, Vol.10 (8), p.e0128407-e0128407

2015

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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, 2022-07, Vol.23 (1), p.1-488, Article 488

2022

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CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data

PeerJ. Computer science, 2015-08, Vol.1, p.e20

2015

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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, 2016-11, Vol.11 (11), p.e0166162-e0166162

2016

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Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

Genome Biology, 2019-12, Vol.20 (1), p.286-286, Article 286

2019

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Characterization and evolution of Salmonella CRISPR-Cas systems

Microbiology (Society for General Microbiology), 2015-02, Vol.161 (Pt 2), p.374

2015

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Co-enriching microflora associated with culture based methods to detect Salmonella from tomato phyllosphere

PloS one, 2013-09, Vol.8 (9), p.e73079

2013

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Genetic Diversity of Salmonella and Listeria Isolates from Food Facilities

Journal of food protection, 2018-12, Vol.81 (12), p.2082-2089

2018

Volltextzugriff (PDF)

Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation

BMC genomics, 2023-04, Vol.24 (1), p.165-165, Article 165

2023

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TEMPO AND MODE OF MATING SYSTEM EVOLUTION BETWEEN INCIPIENT CLARKIA SPECIES

Evolution, 2012-04, Vol.66 (4), p.1210-1225

2012

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Evaluation of Virulence Determinants Using Whole-Genome Sequencing and Phenotypic Biofilm Analysis of Outbreak-Linked Staphylococcus aureus Isolates

Frontiers in microbiology, 2021-06, Vol.12, p.687625-687625

2021

Volltextzugriff (PDF)

Multinational Outbreak of Listeria monocytogenes Infections Linked to Enoki Mushrooms Imported from the Republic of Korea 2016–2020

Journal of food protection, 2023-07, Vol.86 (7), p.100101-100101, Article 100101

2023

Volltextzugriff (PDF)

Using Evolutionary Analyses to Refine Whole-Genome Sequence Match Criteria

Frontiers in microbiology, 2022-06, Vol.13, p.797997-797997

2022

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Evaluation of Avocados as a Possible Source of Listeria monocytogenes Infections, United States, 2016 to 2019

Journal of food protection, 2021-07, Vol.84 (7), p.1122-1126

2021

Volltextzugriff (PDF)

RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens

Frontiers in bioinformatics, 2024-08, Vol.4

2024

Volltextzugriff (PDF)

Temporal Dynamics of Salmonella enterica subsp. enterica Serovar Agona Isolates From a Recurrent Multistate Outbreak

Frontiers in microbiology, 2020-03, Vol.11, p.478-478

2020

Volltextzugriff (PDF)

Phylogeography of speciation: allopatric divergence and secondary contact between outcrossing and selfing Clarkia

Molecular ecology, 2012-09, Vol.21 (18), p.4578-4592

2012

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AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

Interpreting Whole-Genome Sequence Analyses of Foodborne Bacteria for Regulatory Applications and Outbreak Investigations

Transient and resident pathogens: Intra-facility genetic diversity of Listeria monocytogenes and Salmonella from food production environments

Prospective modeling and estimating the epidemiologically informative match rate within large foodborne pathogen genomic databases

Interpretative Labor and the Bane of Nonstandardized Metadata in Public Health Surveillance and Food Safety

Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation

Genomic evidence of environmental and resident Salmonella Senftenberg and Montevideo contamination in the pistachio supply-chain

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)

The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence

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

CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data

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

Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

Characterization and evolution of Salmonella CRISPR-Cas systems

Co-enriching microflora associated with culture based methods to detect Salmonella from tomato phyllosphere

Genetic Diversity of Salmonella and Listeria Isolates from Food Facilities

Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation

TEMPO AND MODE OF MATING SYSTEM EVOLUTION BETWEEN INCIPIENT CLARKIA SPECIES

Evaluation of Virulence Determinants Using Whole-Genome Sequencing and Phenotypic Biofilm Analysis of Outbreak-Linked Staphylococcus aureus Isolates

Multinational Outbreak of Listeria monocytogenes Infections Linked to Enoki Mushrooms Imported from the Republic of Korea 2016–2020

Using Evolutionary Analyses to Refine Whole-Genome Sequence Match Criteria

Evaluation of Avocados as a Possible Source of Listeria monocytogenes Infections, United States, 2016 to 2019

RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens

Temporal Dynamics of Salmonella enterica subsp. enterica Serovar Agona Isolates From a Recurrent Multistate Outbreak

Phylogeography of speciation: allopatric divergence and secondary contact between outcrossing and selfing Clarkia

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