• Organization: Department of Agriculture
• Updated: 2025-11-21

This entry contains all data and code required to reproduce the analysis of immune response data presented in the manuscript: Yeh, H.-Y., J. G. Frye, C. R. Jackson, Q. D. Read, J. E. Line, and A....

• rmd
• html
• xlsx
• xlsx

• Organization: Department of Agriculture
• Updated: 2024-02-15

IncA/C plasmids are a class of plasmids from Enterobacteraciae that are relatively large (49 to >180 kbp), are readily transferred by conjugation, and carry multiple antimicrobial resistance...

• html

• Organization: Department of Agriculture
• Updated: 2024-02-14

Treating Shiga toxin-producing Escherichia coli (STEC) gastrointestinal infections is difficult. The utility of antibiotics for STEC treatment is controversial, since antibiotic resistance among...

• html

• Organization: Department of Agriculture
• Updated: 2025-05-06

Draft genome sequences of five Enterococcus faecium, two Enterococcus hirae, and one Enterococcus gallinarum from enviromental sources and chicken carcass rinsates. Isolates were selected for...

• html

• Organization: Department of Agriculture
• Updated: 2025-11-21

ComBase includes a systematically formatted database of quantified microbial responses to the food environment with more than 65,000 records, and is used for: Informing the design of food safety...

• html

• Organization: Department of Agriculture
• Updated: 2025-11-21

This repository contains the code and data to reproduce the figures and analyses in the paper "Microbiota of maize kernels as influenced by Aspergillus flavus infection in susceptible and...

• gz

• Organization: Department of Agriculture
• Updated: 2023-12-18

Salmonella enterica subsp. enterica bacteria are important foodborne pathogens with major economic impact. Some isolates exhibit increased heat tolerance, a concern for food safety. Analysis of a...

• html

• Organization: Department of Agriculture
• Updated: 2024-02-13

Campylobacter jejuni subsp. jejuni infections are a leading cause of foodborne gastroenteritis and the most prevalent antecedent to Guillain-Barré syndrome (GBS). Penner serotype HS:19 is among...

• html

• Organization: Department of Agriculture
• Updated: 2025-11-21

This repository contains all data and code required to reproduce the growth curve-fitting analysis from the manuscript: McMillan, E. A., Berrang, M. E., Read, Q. D., Rasamsetti, S., Richards, A....

• csv
• rmd

• Organization: Department of Agriculture
• Updated: 2024-02-21

DNA sequences of each allele for 165 loci found in a population of 147 fully sequenced IncI2 plasmids with allelic identifiers.Data is based on whole-genome sequences in the National Center for...

• fas

• Organization: Department of Agriculture
• Updated: 2025-11-21

Data for the article: "Modeling the Formulation pH of Elderberry Syrup with multiple weak acids", https://doi.org/10.1111/1750-3841.16664. To develop methods to assess the influence of the...

• xlsx

• Organization: Department of Agriculture
• Updated: 2025-11-21

Single cell suspensions enriched for epithelial cells were obtained from duodenum, jejunum, and ileum of a 7.5-week-old pig and subjected to single-cell RNA sequencing (scRNA-seq). scRNA-seq was...

• tar

• Organization: Department of Agriculture
• Updated: 2025-11-21

Shiga toxin-producing Escherichia coli (STEC) and Listeria monocytogenes are responsible for severe foodborne illnesses in the United States. Current identification methods require at least four...

• fasta
• fasta
• fasta
• fasta
• fasta
• fasta
• +51 more

• Organization: Department of Agriculture
• Updated: 2025-11-21

Note: This dataset is superseded by: https://doi.org/10.15482/USDA.ADC/30210112Note: Data files will be made available upon manuscript publicationThis dataset contains all code and data needed to...

• Organization: Department of Agriculture
• Updated: 2025-04-30

Datasheet for the abundance of total bacteria, gram positive indicator bacteria, horizontal gene transfer indicator genes and antibiotic resistance genes in the soil measured over 3 years. ...

• xlsx
• xlsx
• csv
• csv
• csv

• Organization: Department of Agriculture
• Updated: 2025-11-21

Escherichia coli survival in soils containing either composted poultry litter (CPL), heat-treated poultry pellets (HTPP), poultry litter (PL) or unamended (chemical fertilizer). Test plots were...

• pdf
• csv
• xlsx
• csv
• xlsx

• Organization: Department of Agriculture
• Updated: 2025-11-21

The data presents the antimicrobial susceptibility testing results in three separate files: 1) third generation cephalosporin resistant E. coli isolates obtained on cefotaxime supplemented media;...

• xlsx
• xlsx
• xlsx

• Organization: Department of Agriculture
• Updated: 2025-11-21

Identifying and developing effective and sensitive detection methods for antimicrobial resistant Salmonella enterica from surface water is a goal of the U.S. National Antimicrobial Resistance...

• xlsx
• xlsx
• xlsx
• xlsx
• xlsx
• xlsx

• Organization: Department of Agriculture
• Updated: 2025-11-21

Files pertaining to data analyses performed and presented in the preprint, 'Porcine intestinal innate lymphoid cells and lymphocyte spatial context revealed through single-cell RNA sequencing' by...

• tar
• tar
• tar
• tar
• tar
• tar
• +4 more

• Organization: Department of Agriculture
• Updated: 2025-11-21

This dataset contains files reconstructing single-cell data presented in 'Reference transcriptomics of porcine peripheral immune cells created through bulk and single-cell RNA sequencing' by...

• zip
• tar
• csv
• csv
• csv
• csv
• +5 more