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

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

2024

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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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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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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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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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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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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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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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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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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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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

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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

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Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples

PeerJ (San Francisco, CA), 2023-01, Vol.11, p.e14596, Article e14596

2023

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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

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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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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

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A longitudinal study to examine the influence of farming practices and environmental factors on pathogen prevalence using structural equation modeling

Frontiers in microbiology, 2023-04, Vol.14, p.1141043-1141043

2023

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Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters

Genome biology and evolution, 2013-01, Vol.5 (11), p.2109-2123

2013

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Corrigendum: 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, 2018-01, Vol.8, p.2598-2598

2018

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Comparative Sequence Analysis of Multidrug-Resistant IncA/C Plasmids from Salmonella enterica

Frontiers in microbiology, 2017-08, Vol.8, p.1459-1459

2017

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Segal's Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project

PeerJ (San Francisco, CA), 2017-06, Vol.5, p.e3480-e3480, Article e3480

2017

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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

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

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

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

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

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

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

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

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

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

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

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

Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples

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

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

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

A longitudinal study to examine the influence of farming practices and environmental factors on pathogen prevalence using structural equation modeling

Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters

Corrigendum: 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

Comparative Sequence Analysis of Multidrug-Resistant IncA/C Plasmids from Salmonella enterica

Segal's Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project

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