USDA and HHS Publish Article on ExPEC in Foods Journal

Agencies of USDA – FSIS, the USDA Animal and Plant Health Inspection Service (APHIS) – as well as agencies of the Department of Health and Human Services – the U.S. Food and Drug Administration (FDA), and the Centers for Disease Control and Prevention (CDC) – have published a research article titled “Use of Large-Scale Genomics to Identify the Role of Animals and Foods as Potential Sources of Extraintestinal Pathogenic Escherichia coli That Cause Human Illness” in Foods, an international, scientific, peer-reviewed, open access journal of food science.

This interagency research focused on a group of E. coli called the Extraintestinal Pathogenic Escherichia coli (ExPEC), which can cause urinary tract infections and other potentially life-threatening invasive infections in people. While the origins of ExPEC are not always clear, food producing animals are considered a potential source of ExPEC.

The interagency team used large sets of genomic data from five U.S. government organizations to evaluate the sources of ExPEC and their potential to cause illnesses. The publication summarizes the different sources of ExPEC based on newly established relative risk groups – low, medium, and high – taking into account a broad range of virulence and antimicrobial resistance genes. Based on the relative risk groups defined in this study, over 90% of food source isolates belonged to low relative risk groups. Only a small fraction of ExPEC from food animals and retail meats were categorized in the high and medium relative risk categories. Antimicrobial resistance genes were more likely to be associated with ExPEC in the high relative risk categories.

Additional research is needed to further understand and confirm the role of ExPEC in food producing animals and their potential risk to humans.

FSIS Posts Next Set of Establishment-Specific Datasets

Today, FSIS published the expanded Laboratory Sampling Establishment-Specific Datasets with the FSIS Number — a unique identifier assigned to pathogen isolates that have been characterized using whole genome sequencing, or WGS — and allele codes with date stamps. The FSIS number update will apply to sampling results for Listeria monocytogenes, Salmonella, Campylobacter, and Shiga toxin-producing E. coli (STEC). The allele codes with date stamps will only be applied for Listeria monocytogenes, Salmonella, and STEC.

In the July 1, 2022, Constituent Update, FSIS announced that it was reviewing public comments on the expansion of these datasets and would announce the revised date for their publication in the future. After reviewing the public comments received, FSIS added additional language on the appropriate use of the data and the ability to draw associations with human illness to three locations to minimize the potential for misuse, namely: (1) the laboratory sampling data webpage, (2) newly added cover pages within the datasets themselves, and (3) in the data documentation.

The information posted provides data from October 2013 through March 2022. Establishment-specific datasets are currently updated and posted on a quarterly basis, with a quarter lag. Subsequent postings will follow the regular posting schedule for establishment-specific datasets in which new datasets are typically released the first Friday of the next quarter with a quarter lag, meaning data for FY2022 Q3 (April, May and June) are planned to be released around October 7, 2022, data for FY2022 Q4 (July, August, and September) are planned to be released around January 6, 2023, and so forth.

FSIS Posts Updated Quarterly Humane Handling Report

Today, FSIS posted the quarterly humane handling inspection report on the agency’s website. The report includes: (1) the number of administrative enforcement actions taken, (2) the number of humane handling verification tasks performed, (3) the number of humane handling verification tasks that resulted in a noncompliance record (NR), and (4) the number of hours spent observing and verifying the humane treatment of livestock. This posting will contain the most recent four quarters of data by district, HACCP size, and quarter.

Policy Update

FSIS notices and directives on public health and regulatory issues are available on the FSIS Policy webpage. The following policy update was recently issued:

FSIS Notice 41-22 - Instructions for Training on the 2021 Cooking Guideline (Revised Appendix A) and Stabilization Guideline (Revised Appendix B)

Export Requirements Update

The Library of Export Requirements has been updated for products for the following:

• Mexico
• United Kingdom
• European Union
• Myanmar
• Kiribati
• China
• Dominican Republic
• Taiwan
• Japan
• Vietnam
• United Arab Emirates
• Jordan
• Canada
• Solomon Islands
• New Caledonia
• French Polynesia (Tahiti)
• Hong Kong
• India
• New Zealand

Complete information can be found at the FSIS Import & Export Library.