Henk C. den Bakker
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View article: Kalamari: a representative set of genomes of public health concern
Kalamari: a representative set of genomes of public health concern Open
Kalamari is a resource that supports genomic epidemiology and pathogen surveillance. It consists of representative genomes and common contaminants. Kalamari also contains a custom taxonomy and software for downloading and formatting the da…
View article: Survival of Listeria Monocytogenes on D’Anjou Pears Co-Inoculated with Bacillus Thuringiensis, Aureobasidium Pullulans, and Penicillium Expansum During Nine Months of Cold Storage
Survival of Listeria Monocytogenes on D’Anjou Pears Co-Inoculated with Bacillus Thuringiensis, Aureobasidium Pullulans, and Penicillium Expansum During Nine Months of Cold Storage Open
View article: Mashpit: sketching out genomic epidemiology
Mashpit: sketching out genomic epidemiology Open
View article: Analysis of Microbial Composition of Edible Insect Products Available for Human Consumption within the United States Using Traditional Microbiological Methods and Whole Genome Sequencing
Analysis of Microbial Composition of Edible Insect Products Available for Human Consumption within the United States Using Traditional Microbiological Methods and Whole Genome Sequencing Open
Edible insects offer a promising protein source for humans, but their food safety risks have not been previously investigated within the United States. Therefore, the aim of this study was to investigate the microbial content of processed …
View article: Fasten: a toolkit for streaming operations on fastqfiles
Fasten: a toolkit for streaming operations on fastqfiles Open
There are still many gaps in basic command line tools for the handling of standard file formats in the field of bioinformatics.Bioinformaticians have been able to use many tools to manipulate sequence data files in the fastq format, such a…
View article: Fasten with Pipes
Fasten with Pipes Open
Fasten is a versatile bioinformatics tool suite developed to address gaps in the manipulation of sequence data files in the fastq format. Existing tools often lack support for interleaved fastq files and Unix-style pipe file control. Faste…
View article: 16S microbiome analysis of microbial communities in distribution centers handling fresh produce
16S microbiome analysis of microbial communities in distribution centers handling fresh produce Open
Little is known about the microbial communities found in distribution centers (DCs), especially in those storing and handling food. As many foodborne bacteria are known to establish residence in food facilities, it is reasonable to assume …
View article: Characterizing the gut microbiome of broilers raised under conventional and no antibiotics ever practices
Characterizing the gut microbiome of broilers raised under conventional and no antibiotics ever practices Open
Meat from broilers raised without the use of antibiotics is becoming increasingly popular among consumers. Consequently, interest in the microbial profiling of chickens produced under nonconventional practices is growing, however, research…
View article: Environmental sponge sampling: We are only scraping the surface
Environmental sponge sampling: We are only scraping the surface Open
Drains located in retail deli departments are known harborage points for pathogenic and spoilage microorganisms. Previous studies have used sequencing approaches to study the microbial consortia found in drains and biofilms in various food…
View article: Integrative Assessment of Reduced Listeria monocytogenes Susceptibility to Benzalkonium Chloride in Produce Processing Environments
Integrative Assessment of Reduced Listeria monocytogenes Susceptibility to Benzalkonium Chloride in Produce Processing Environments Open
Our study demonstrates an integrative approach to improve food safety assessment and control strategies in food processing environments through the collective leveraging of genomic surveys, laboratory assays, and processing facility sampli…
View article: Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species “L. swaminathanii”
Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species “L. swaminathanii” Open
View article: Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species “L. swaminathanii”
Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species “L. swaminathanii” Open
Recently, a new Listeria species, “Listeria swaminathanii”, was proposed. Here, we phenotypically and genotypically characterize two additional strains that were previously obtained from soil samples and compare the results to the type str…
View article: Draft Genome Sequences of Two Lactobacillus johnsonii and Three Ligilactobacillus salivarius Strains Isolated from Intestinal Microbiomes of Chickens
Draft Genome Sequences of Two Lactobacillus johnsonii and Three Ligilactobacillus salivarius Strains Isolated from Intestinal Microbiomes of Chickens Open
This report describes the genome sequences of two Lactobacillus johnsonii strains (AER105 and AER25) and three Ligilactobacillus salivarius strains (AER35, AER36, and AER04) recovered from broiler chicken gastrointestinal tracts in the sou…
View article: Sepia, a taxonomy oriented read classifier in Rust
Sepia, a taxonomy oriented read classifier in Rust Open
Here we present Sepia, a fast and accurate read classifier. It is implemented in Rust, has the ability to switch between different taxonomies, can detect inconsistencies in taxonomies, and can estimate similarities between organisms in a q…
View article: Heat Inactivation of Listeria monocytogenes on Pecans, Macadamia Nuts, and Sunflower Seeds
Heat Inactivation of Listeria monocytogenes on Pecans, Macadamia Nuts, and Sunflower Seeds Open
Listeria monocytogenes is a major concern for the food industry in ready-to-eat (RTE) foods. In recent years, large-scale recalls have occurred with contaminated sunflower seeds and macadamia nuts that triggered product withdrawals.
View article: SneakerNet: A modular quality assurance and quality check workflow for primary genomic and metagenomic read data
SneakerNet: A modular quality assurance and quality check workflow for primary genomic and metagenomic read data Open
Laboratories that run Whole Genome Sequencing (WGS) produce a tremendous amount of data, up to 10 gigabytes for some common instruments. There is a need to standardize the quality assurance and quality control process (QA/QC). Therefore we…
View article: High-Resolution Genomic Comparisons within <i>Salmonella enterica</i> Serotypes Derived from Beef Feedlot Cattle: Parsing the Roles of Cattle Source, Pen, Animal, Sample Type, and Production Period
High-Resolution Genomic Comparisons within <i>Salmonella enterica</i> Serotypes Derived from Beef Feedlot Cattle: Parsing the Roles of Cattle Source, Pen, Animal, Sample Type, and Production Period Open
Salmonella serotypes isolated from outbreaks in humans can also be found in beef cattle and feedlots. Virulence factors and antibiotic resistance are among the primary defense mechanisms of Salmonella , and are often associated with clonal…
View article: Complete Genome Sequences of Three Listeria monocytogenes Bacteriophage Propagation Strains
Complete Genome Sequences of Three Listeria monocytogenes Bacteriophage Propagation Strains Open
Bacteriophages can be used as a biocontrol for the foodborne pathogen Listeria monocytogenes . Propagation of phages is a necessary step for their use in experimental studies and biocontrol applications. Here, we present the complete genom…
View article: Complete Genome Sequence of a Serotype 7 Listeria monocytogenes Strain, FSL R9-0915
Complete Genome Sequence of a Serotype 7 Listeria monocytogenes Strain, FSL R9-0915 Open
Listeria monocytogenes serotype 7 lacks glycosidic constituents in wall teichoic acids. Here, we present the complete genome sequence of L. monocytogenes serotype 7 strain FSL R9-0915 and an analysis of genes known to affect L. monocytogen…
View article: Additional file of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss
Additional file of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss Open
Additional file of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss
View article: Additional file of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss
Additional file of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss Open
Additional file of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss
View article: Additional file of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss
Additional file of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss Open
Additional file of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss
View article: Additional file 3 of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss
Additional file 3 of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss Open
Additional file 3:Excel file containing presence/absence data of genes in the Listeria pan-genome. (XLS 1 MB)
View article: Additional file 2 of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss
Additional file 2 of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss Open
Additional file 2:Excel file SNP differences between L. monocytogenes F2365 and its duplicate FSL R2-574 and results of Sanger sequencing SNP confirmation. (XLS 18 KB)
View article: Additional file 7 of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss
Additional file 7 of Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss Open
Additional file 7:Table in MS Excel with presence or absence of 78 virulence associated genes in the genomes of the genus Listeria. (XLS 43 KB)
View article: High-resolution genomic comparisons within <i>Salmonella enterica</i> serotypes derived from beef feedlot cattle: parsing the roles of cattle source, pen, animal, sample type and production period
High-resolution genomic comparisons within <i>Salmonella enterica</i> serotypes derived from beef feedlot cattle: parsing the roles of cattle source, pen, animal, sample type and production period Open
Salmonella enterica is a major foodborne pathogen, and contaminated beef products have been identified as the primary source of Salmonella -related outbreaks. Pathogenicity and antibiotic resistance of Salmonella are highly serotype- and s…
View article: 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
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 Open
Enterohemorrhagic Escherichia coli (EHEC) and Salmonella are of serious concern in low-moisture foods, including wheat flour and its related products, causing illnesses, outbreaks, and recalls. The development of advanced detection methods…
View article: Listeria monocytogenes is prevalent in retail produce environments but Salmonella enterica is rare
Listeria monocytogenes is prevalent in retail produce environments but Salmonella enterica is rare Open
View article: Mashtree: a rapid comparison of whole genome sequence files
Mashtree: a rapid comparison of whole genome sequence files Open
In the past decade, the number of publicly available bacterial genomes has increased dramatically.These genomes have been generated for impactful initiatives, especially in the field of genomic epidemiology (Brown, Dessai, McGarry, & Gerne…
View article: Quantitative dynamics of Salmonella and E. coli in feces of feedlot cattle treated with ceftiofur and chlortetracycline
Quantitative dynamics of Salmonella and E. coli in feces of feedlot cattle treated with ceftiofur and chlortetracycline Open
Antibiotic use in beef cattle is a risk factor for the expansion of antimicrobial-resistant Salmonella populations. However, actual changes in the quantity of Salmonella in cattle feces following antibiotic use have not been investigated. …