H. D. den Bakker

发表

Genomic Epidemiology of Salmonella enterica Serotype Enteritidis based on Population Structure of Prevalent Lineages

Rene S. Hendriksen, Martin Wiedmann, Prerak T. Desai, 2014, Emerging infectious diseases.

Dissemination of the mcr-1 colistin resistance gene.

Hattie E. Webb, H. D. den Bakker, K. Nightingale, 2016, The Lancet. Infectious diseases.

Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens.

Henk C den Bakker, Xiangyu Deng, Xiangyu Deng, 2016, Annual review of food science and technology.

Listeria marthii sp. nov., isolated from the natural environment, Finger Lakes National Forest.

Henk C den Bakker, Martin Wiedmann, B. Swaminathan, 2010, International journal of systematic and evolutionary microbiology.

Characterization of Antimicrobial Resistant (AMR) Salmonella Enterica Isolates Associated With Cattle at Harvest in Mexico

H. D. den Bakker, K. Nightingale, Peter W. Cook, 2019, Meat and Muscle Biology.

Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

M. Wiedmann, C. Cummings, M. Furtado, 2010, BMC Genomics.

Genome sequencing identifies Listeria fleischmannii subsp. coloradonensis subsp. nov., isolated from a ranch.

Henk C den Bakker, Martin Wiedmann, M. Wiedmann, 2013, International journal of systematic and evolutionary microbiology.

FSL J1-208, a Virulent Uncommon Phylogenetic Lineage IV Listeria monocytogenes Strain with a Small Chromosome Size and a Putative Virulence Plasmid Carrying Internalin-Like Genes

M. Wiedmann, H. D. den Bakker, Barbara M Bowen, 2012, Applied and Environmental Microbiology.

Evolutionary Dynamics of the Accessory Genome of Listeria monocytogenes

Allison D. Griggs, J. E. Peters, B. Haas, 2013, PloS one.

Molecular Source Tracking and Molecular Subtyping

Xiangyu Deng, Heather Carleton, Peter Gerner-Smidt, 2019, Food Microbiology.

RIBOSOMAL RNA GENE DIVERSITY, EFFECTIVE POPULATION SIZE, AND EVOLUTIONARY LONGEVITY IN ASEXUAL GLOMEROMYCOTA

Nicholas W. VanKuren, H. D. den Bakker, T. Pawlowska, 2013, Evolution; international journal of organic evolution.

Heat Inactivation of Listeria monocytogenes on Pecans, Macadamia Nuts, and Sunflower Seeds

H. D. den Bakker, F. Diez-Gonzalez, Meghan den Bakker, 2021, Microbiology spectrum.

Genomic characterization provides new insight into Salmonella phage diversity

M. Wiedmann, H. D. den Bakker, A. M. Moreno Switt, 2013, BMC Genomics.

Two Draft Genome Sequences of a New Serovar of Salmonella enterica, Serovar Lubbock

H. D. den Bakker, K. Nightingale, M. Bugarel, 2015, Genome Announcements.

Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States

M. Wiedmann, C. Cummings, R. Fang, 2014, BMC Genomics.

Characterization of the cytolethal distending toxin (typhoid toxin) in non-typhoidal Salmonella serovars

M. Wiedmann, H. D. den Bakker, G. Duhamel, 2015, Gut Pathogens.

Prevalence and antimicrobial resistance of Salmonella in conventional and no antibiotics ever broiler farms in the United States

Cortney M. Leone, H. D. den Bakker, H. Thippareddi, 2021, Food Control.

Molecular ecology of Listeria spp., Salmonella, Escherichia coli O157:H7 and non‐O157 Shiga toxin‐producing E. coli in pristine natural environments in Northern Colorado

M. Wiedmann, H. D. den Bakker, K. Nightingale, 2018, Journal of applied microbiology.

Interrogation of single nucleotide polymorphisms in gnd provides a novel method for molecular serogrouping of clinically important Shiga toxin producing Escherichia coli (STEC) targeted by regulation in the United States, including the "big six" non-O157 STEC and STEC O157.

H. D. den Bakker, K. Nightingale, M. Bugarel, 2016, Journal of microbiological methods.

Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species “L. swaminathanii”

H. D. den Bakker, Lauren K. Hudson, Thomas G. Denes, 2022, Scientific Reports.

High-Resolution Genomic Comparisons within Salmonella enterica Serotypes Derived from Beef Feedlot Cattle: Parsing the Roles of Cattle Source, Pen, Animal, Sample Type, and Production Period

H. D. den Bakker, Robin C. Anderson, H. M. Scott, 2020, bioRxiv.

Integrative Assessment of Reduced Listeria monocytogenes Susceptibility to Benzalkonium Chloride in Produce Processing Environments

Xiangyu Deng, H. D. den Bakker, H. Oliver, 2022, Applied and environmental microbiology.

Genomic characterization provides new insight into Salmonella phage diversity

M. Wiedmann, H. D. den Bakker, A. M. Moreno Switt, 2013, BMC Genomics.

Draft Genome Sequence of Enterococcus faecium Strain J19, Isolated from Cabbage

H. D. den Bakker, K. Nightingale, Peter W. Cook, 2018, Genome Announcements.

Draft Genome Sequence of Lactobacillus salivarius L28 Isolated from Ground Beef

H. D. den Bakker, K. Nightingale, Peter W. Cook, 2017, Genome Announcements.

Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics.

M. Wiedmann, H. D. den Bakker, R. Orsi, 2011, International journal of medical microbiology : IJMM.

A phylogenetic study of Boletus section Boletus in Europe

H. D. den Bakker, M. Noordeloos, G. Zuccarello, 2008, Persoonia.

Identiﬁcation and Characterization of Psychrotolerant Sporeformers Associated with Fluid Milk Production and Processing

M. Wiedmann, H. D. den Bakker, K. Boor, 2022 .

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

Hattie E. Webb, Guy H. Loneragan, H. D. den Bakker, 2016, PloS one.

Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov. and Listeria grandensis sp. nov., from agricultural and natural environments.

Henk C den Bakker, Martin Wiedmann, Angela Burrell, 2014, International journal of systematic and evolutionary microbiology.

A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type

M. Wiedmann, C. Cummings, R. Fang, 2011, Applied and Environmental Microbiology.

Equine Stomachs Harbor an Abundant and Diverse Mucosal Microbiota

M. Wiedmann, H. Erb, S. Dowd, 2012, Applied and Environmental Microbiology.

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

Xiangyu Deng, H. D. den Bakker, F. Diez-Gonzalez, 2020, Applied and Environmental Microbiology.

Selection and Characterization of Phage-Resistant Mutant Strains of Listeria monocytogenes Reveal Host Genes Linked to Phage Adsorption

M. Wiedmann, H. D. den Bakker, C. Guldimann, 2015, Applied and Environmental Microbiology.

Pre-harvest internalization and surface survival of Salmonella and Escherichia coli O157:H7 sprayed onto different lettuce cultivars under field and growth chamber conditions.

H. D. den Bakker, M. Erickson, Peter W. Cook, 2019, International journal of food microbiology.

Transcriptomic Analysis of the Adaptation of Listeria monocytogenes to Growth on Vacuum-Packed Cold Smoked Salmon

Teresa M. Bergholz, T. Bergholz, M. Wiedmann, 2015, Applied and Environmental Microbiology.

SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data

Jessica C. Chen, P. Fields, Xiangyu Deng, 2019, Applied and Environmental Microbiology.

Zoonotic Source Attribution of Salmonella enterica Serotype Typhimurium Using Genomic Surveillance Data, United States

B. Bruce, P. McDermott, Shaohua Zhao, 2019, Emerging infectious diseases.

Genomic Diversity of Listeria monocytogenes Isolated from Clinical and Non-Clinical Samples in Chile

M. Toro, H. D. den Bakker, H. Bello-Toledo, 2018, Genes.

Evolution and host specificity in the ectomycorrhizal genus Leccinum.

T. Kuyper, H. D. den Bakker, M. Noordeloos, 2004, The New phytologist.

An ITS phylogeny of Leccinum and an analysis of the evolution of minisatellite-like sequences within ITS1

T. Kuyper, B. Gravendeel, H. D. den Bakker, 2004, Mycologia.

Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica

M. Wiedmann, C. Cummings, M. Furtado, 2011, BMC Genomics.

Genomic comparison of sporeforming bacilli isolated from milk

M. Wiedmann, H. D. den Bakker, A. M. Moreno Switt, 2014, BMC Genomics.

Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations

Lorin D. Warnick, Martin Wiedmann, Laura M. Carroll, 2017, Applied and Environmental Microbiology.

Whole-Genome Sequencing Allows for Improved Identification of Persistent Listeria monocytogenes in Food-Associated Environments

M. Wiedmann, H. D. den Bakker, H. Oliver, 2015, Applied and Environmental Microbiology.

Phylogeny of the Bacillus altitudinis Complex and Characterization of a Newly Isolated Strain with Antilisterial Activity.

H. D. den Bakker, Lauren K. Hudson, Thomas G. Denes, 2021, Journal of food protection.

Ultra-fast search of all deposited bacterial and viral genomic data

Phelim Bradley, Henk C den Bakker, Eduardo P C Rocha, 2019, Nature Biotechnology.

High-Resolution Genomic Comparisons within Salmonella enterica Serotypes Derived from Beef Feedlot Cattle: Parsing the Roles of Cattle Source, Pen, Animal, Sample Type, and Production Period

H. D. den Bakker, Robin C. Anderson, H. M. Scott, 2021, Applied and environmental microbiology.

Ultrafast search of all deposited bacterial and viral genomic data

G. McVean, E. Rocha, Z. Iqbal, 2019, Nature Biotechnology.

Identification and Characterization of Novel Salmonella Mobile Elements Involved in the Dissemination of Genes Linked to Virulence and Transmission

J. E. Peters, M. Wiedmann, C. Cummings, 2012, PloS one.

Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes

Tyson A. Clark, J. Korlach, Khai Luong, 2016, Applied and Environmental Microbiology.

Clonality and recombination in the life history of an asexual arbuscular mycorrhizal fungus.

Nicholas W. VanKuren, H. D. den Bakker, T. Pawlowska, 2010, Molecular biology and evolution.

Salmonella bacteriophage diversity reflects host diversity on dairy farms.

M. Wiedmann, H. D. den Bakker, K. Hoelzer, 2013, Food microbiology.

Silage Collected from Dairy Farms Harbors an Abundance of Listeriaphages with Considerable Host Range and Genome Size Diversity

M. Wiedmann, E. Fortes, H. D. den Bakker, 2012, Applied and Environmental Microbiology.

Comparative Genomic and Morphological Analyses of Listeria Phages Isolated from Farm Environments

M. Wiedmann, H. Ackermann, H. D. den Bakker, 2014, Applied and Environmental Microbiology.

Lineage specific recombination rates and microevolution in Listeria monocytogenes

M. Wiedmann, E. Fortes, X. Didelot, 2008, BMC Evolutionary Biology.

Complete Genome Sequence of a Serotype 7 Listeria monocytogenes Strain, FSL R9-0915

H. D. den Bakker, Z. Kučerová, Lauren K. Hudson, 2021, Microbiology Resource Announcements.

Complete Genome Sequence of the Porcine Strain Brachyspira pilosicoli P43/6/78T

L. Ponnala, M. Wiedmann, M. Stanhope, 2013, Genome Announcements.

Complete Genome Sequences of Three Listeria monocytogenes Bacteriophage Propagation Strains

H. D. den Bakker, Lauren K. Hudson, Thomas G. Denes, 2021, Microbiology Resource Announcements.

Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique

T. Nagaraja, D. Renter, H. D. den Bakker, 2015, Applied and Environmental Microbiology.

A Population Genetics-Based and Phylogenetic Approach to Understanding the Evolution of Virulence in the Genus Listeria

Renato H. Orsi, Martin Wiedmann, M. Wiedmann, 2010, Applied and Environmental Microbiology.

Comparison of Typing Methods with a New Procedure Based on Sequence Characterization for Salmonella Serovar Prediction

Martin Wiedmann, M. Wiedmann, H. D. den Bakker, 2013, Journal of Clinical Microbiology.

Molecular detection and quantification of viable probiotic strains in animal feedstuffs using the commercial direct fed microbial Lactobacillus animalis NP51 as a model.

H. D. den Bakker, K. Nightingale, K. R. Kottapalli, 2018, Journal of microbiological methods.

Sanitation and customer service strategies implemented during COVID-19 correlated with lower Listeria monocytogenes prevalence in retail delicatessens

H. D. den Bakker, H. Oliver, Sophie Tongyu Wu, 2021, Food Control.

Determination of Evolutionary Relationships of Outbreak-Associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b by Whole-Genome Sequencing

Teresa M. Bergholz, T. Bergholz, L. Katz, 2015, Applied and Environmental Microbiology.

Multilocus sequence typing of outbreak-associated Listeria monocytogenes isolates to identify epidemic clones.

M. Wiedmann, E. Fortes, H. D. den Bakker, 2010, Foodborne pathogens and disease.

Listeria booriae sp. nov. and Listeria newyorkensis sp. nov., from food processing environments in the USA.

Henk C den Bakker, Martin Wiedmann, M. Wiedmann, 2015, International journal of systematic and evolutionary microbiology.

Salt stress phenotypes in Listeria monocytogenes vary by genetic lineage and temperature.

Teresa M. Bergholz, T. Bergholz, M. Wiedmann, 2010, Foodborne pathogens and disease.

Quantitative dynamics of Salmonella and E. coli in feces of feedlot cattle treated with ceftiofur and chlortetracycline

B. Norby, H. D. den Bakker, H. M. Scott, 2019, PloS one.

Rapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis

Z. Iqbal, M. Wiedmann, M. Allard, 2014, Emerging infectious diseases.

Listeriosis Outbreak in Dairy Cattle Caused by an Unusual Listeria Monocytogenes Serotype 4b Strain

M. Wiedmann, E. Fortes, H. D. den Bakker, 2011, Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc.

Prevention of surface colonization and anti-biofilm effect of selected phytochemicals against Listeria innocua strain.

H. D. den Bakker, F. Diez-Gonzalez, M. Simões, 2023, Colloids and surfaces. B, Biointerfaces.

Characterizing the gut microbiome of broilers raised under conventional and no antibiotics ever practices

H. D. den Bakker, H. Thippareddi, M. Bailey, 2023, Poultry science.

Environmental sponge sampling: We are only scraping the surface

H. D. den Bakker, H. Oliver, John L. Burnett, 2023, Food and Humanity.

Real-time search of all bacterial and viral genomic data

Phelim Bradley, Gil McVean, Zamin Iqbal, 2017, bioRxiv.