Laboratory Sampling Data
The U.S. Department of Agriculture's (USDA) Food Safety and Inspection Service (FSIS) inspects meat, poultry, and egg products to verify whether the food produced is safe, wholesome, and properly labeled. Verification activities serve to protect the public from foodborne hazards. A key FSIS inspection verification activity is the sampling of product for microbiological contaminants or chemical residues. This page contains data and data documentation for sampling programs that assess the presence of microbiological contaminants in various commodities. The data documentation should be reviewed before any analysis is conducted as it describes the fields present in the datasets, identifies when changes in laboratory testing methods occurred, and explains how certain results are possible (e.g., why a poultry sample might have a result for Salmonella but not Campylobacter).
Data postings are part of the Agency's efforts to prevent pathogens from entering the food supply throughout the farm-to-fork continuum. Posting these datasets may help industry identify repetitive subtypes and implement control measures. It may allow researchers to identify trends to address basic research questions or to develop new diagnostics or therapies such as vaccines.
These datasets are posted for informational purposes only and are not sufficient to determine if there is an association between multiple samples. Therefore, this data should not be used to identify foodborne illness outbreaks, associate samples with foodborne illness outbreaks or determine whether two or more samples are causally related.
The FSIS number is a unique identifier for retrieving whole genome sequence data from the National Center for Biotechnology and Information (NCBI) Pathogen Detection Isolates Browser. The allele codes included in this dataset provide a convenient naming method for reporting WGS data. Because allele codes can change over time as more WGS data becomes available, a date stamp allows the data to be used in reports.
FSIS, the Centers for Disease Control and Prevention (CDC) and other public health partners monitor WGS information gathered from samples in real time and use sophisticated epidemiological tools to identify whether the cumulative findings might signal a foodborne illness outbreak. Outbreaks identified through this process are announced to the public through CDC's website and FSIS' Outbreak Response Page. The FSIS investigative process is described in FSIS Directive 8080.3.
FSIS publicly releases datasets on laboratory sampling results and updates these datasets quarterly and annually. For each laboratory sampling results topic two datasets are provided: archived and current. The archived dataset provides data starting from October 1, 2013, up to the final day of the previous fiscal year (FY) of the report execution date (e.g., the data posted in April 2022 was through the end of FY21). The archived dataset is updated annually. The current dataset provides data starting from the first day of the FY following the final date available in the archived dataset through the end of the previous fiscal quarter of the report execution date (e.g., data posted in April 2022 was through the end of FY22 Quarter 1). The current dataset is updated quarterly.
The data posted reflect a snapshot in time that has already passed. Datasets include the date on which the data is pulled to enhance transparency.
Each row in the datasets represents one sample collected and sent to an FSIS laboratory for analysis. Isolate characterization data will not be publicly posted in the datasets until the full characterization profile is completed.
Data contained in this dataset on tested product from establishments are not sufficient to determine an association with human illnesses. Further epidemiologic information is needed to determine if there is an association among the non-clinical isolates and human illnesses.
Information about FSIS laboratory sampling and procedures can be found on the FSIS website on the following web pages: Laboratories & Procedures and Microbiology Laboratory Guidebook.
Question: What is the FSIS number and how may it be used?
The FSIS number is a unique identifier, generated by FSIS, used to retrieve whole genome sequencing (WGS) data for an FSIS isolate from the National Center for Biotechnology and Information (NCBI) Pathogen Detection Isolates Browser.
The FSIS number allows users to associate a particular FSIS sampling result to a particular WGS profile found on NCBI's publicly available database.
Question: What are allele codes and how does FSIS use them?
An allele code is a code assigned by the Centers for Disease Control and Prevention's PulseNet (a national laboratory network that connects foodborne, waterborne, and One Health-related illness cases to detect outbreaks) based on differences in predefined genes in the WGS data. With allele codes, complex WGS data is converted to a naming system that simplifies how to describe relatedness with WGS data. FSIS uses allele codes to track the occurrence of bacteria in food products, food contact surfaces, and the establishment environment.
In FSIS reports and datasets, allele codes include the date when FSIS retrieved the allele code from PulseNet. Allele codes can change over time as more WGS data becomes available, therefore, this date-stamp allows the data to be used in reports.
Question: Why is FSIS releasing the FSIS number and date stamped allele codes?
FSIS is releasing the FSIS number and date stamped allele codes to enhance data transparency and access to Agency generated information. Data postings are part of the Agency's effort to prevent pathogens from entering the food supply throughout the farm-to-fork continuum.
Question: What limits are there on the use of this WGS data?
The FSIS number and allele codes are posted for informational purposes only and are not sufficient, on their own, to determine if there is an association between multiple samples or to determine a causal association with human illness.
Question: Where to direct questions about FSIS WGS results?
For answers to questions about specific FSIS WGS data, submit questions to AskFSIS.
Please see the FSIS Resources for Public Health Partners webpage for more information on FSIS foodborne illness investigations.
Instructions for Opening Comma Separated Values (CSV) Files from the FSIS Website in Common Spreadsheet Software
Download the data file from the FSIS Website to any directory on the device.
In Microsoft Excel [1]:
As of Microsoft Excel Version 2304 on Microsoft Windows
- Create a new Blank workbook (This can be done by going to the File > New and selecting Blank Workbook).
- On the Data tab, in the Get & Transform Data group, select From Text/CSV.
- Navigate to the file that was downloaded from the FSIS Website and select Open.
- In the preview dialog box, ensure the file Delimitator is set to Comma.
- Select Load to open the dataset.
In LibreOffice Calc [2]:
As of Version 7.5.4
- Go to File>Open
- Ensure that you are looking at All Files and navigate to the file that was downloaded from the FSIS Website. Select Open.
- In the Text Import dialog box, select Comma under Separator Options and unselect the other separators. Select OK to close the dialog box and load the data.
- To filter the data, go to the Data menu, and select AutoFilter.
In Google Sheets [3]:
As of July 5, 2023
- Upload the dataset that was was downloaded from the FSIS Website onto Google Drive
- Go to File > Import.
- Select the Import Location as Create new spreadsheet and Separator type as Comma.
- Select Import Data
- To filter data, go to the Data > Create a filter.
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