• Whole genome sequencing (WGS) determines the order of all of the DNA building blocks (nucleotides) in an organism’s entire genome in a single laboratory process.  A comparison of the DNA sequence of an isolated bacterial pathogen to the sequences from other samples in a DNA database can pinpoint the source of a foodborne disease outbreak.  The analytical tools for WGS have become increasingly accurate, easy, and affordable such that health agencies have moved to WGS as the preferred tool for investigating foodborne illnesses from Listeria, Salmonella, and pathogenic strains of Escherichia coli, including E. coli O157:H7.

 

  • As reported here, the United States Department of Agriculture’s (USDA) Food Safety and Inspection Service (FSIS) held a meeting to discuss the state of the art and FSIS’s plans for collecting and analyzing WGS data for bacteria isolated from official samples.  For fiscal year 2017, all bacterial pathogens isolated under FSIS testing programs have been analyzed in parallel using both pulsed-field gel electrophoresis (PFGE) analysis and WGS.  A FSIS Constituent Update (December 14, 2018) announces that FSIS will suspend routine PFGE analysis and transition to using only WGS for Shiga toxin-producing E. coli (STEC), effecting January 15, 2019, and for Salmonella isolates, effective March 15, 2019.

 

  • FSIS inspects almost 6,500 establishments daily and collects a very large volume of microbial samples on a routine basis.  Under the FSIS Microbial Testing Program for Ready-To-Eat (RTE) Meat and Poultry in 2017, for example, FSIS collected and analyzed 6,892 RTE food samples for Salmonella and Listeria monocytogenes (Lm) and analyzed 4,614 samples from food-contact surfaces for Lm.  As the technology expands, WSG will become an increasingly valuable tool for quickly tracing diseases to their source and perhaps someday identifying pathogens in the environment early enough to prevent contamination of food altogether.

 

  • Whole genome sequencing (WGS) provides insight into the genetic fingerprint of a pathogen by sequencing the chemical building blocks that make up its DNA and is increasingly being employed in food safety efforts. Since 2012, the U.S. Food and Drug Administration (FDA) has regularly turned to WGS to better understand foodborne pathogens, including identifying the nature and source of microbes that contaminate food and cause outbreaks of foodborne illness.
  • This week, the Centers for Disease Control and Prevention (CDC) announced that the use of whole genome sequencing to monitor for outbreaks of Listeria, Salmonella, Campylobacter and coli that are commonly transmitted through food and animal contact has expanded to 38 states and two cities. This data is reported in the CDC’s Antibiotic Resistance (AR) Investment Map, which shows early progress by states to combat antibiotic resistance. This year’s Antibiotic Resistance Investment Map features more than 170 state-reported successes, including rapidly identifying and containing rare and concerning resistant germs to protect communities. Each state reported multiple successes.
  • You can learn more about CDC’s AR Solutions Initiative and ongoing work to combat antibiotic resistance at cdc.gov/DrugResistance.
  • Whole genome sequencing (WGS) provides insight into the genetic fingerprint of a pathogen by sequencing the chemical building blocks that make up its DNA and is increasingly being employed in food safety efforts.  Since 2012, the U.S. Food and Drug Administration (FDA) has regularly turned to WGS to better understand foodborne pathogens, including identifying the nature and source of microbes that contaminate food and cause outbreaks of foodborne illness. In 2012, FDA launched GenomeTrakr.  GenomeTrakr is an international network of laboratories that sequences microbial foodborne pathogens and uploads the data to a common public database in real time.
  • At a recent Codex Alimentarius Commission meeting in Geneva, FDA scientists explained that WGS has fundamentally changed the way microbiological food hazards in the U.S. are detected and noted that the most effective use of WGS in foodborne disease surveillance requires coordination and collaboration.
  • The FDA hopes that other countries currently using WGS will share their data with GenomeTrakr. FDA is aiming to include developing countries as they are able to join. As it stands, GenomeTrakr consists of 13 federal labs, 25 state health and university labs, one U.S. hospital lab, two other labs located in the U.S., 20 labs located outside of the U.S., and collaborations with independent academic researchers.
  • To date, GenomeTrakr has collected more than 142,000 sequenced strains.  Proponents of WGS proffer that greater availability and coordination of WGS data could go a long way towards helping to identify the source and extent of outbreaks more quickly so fewer people get sick from preventable foodborne illnesses.
  • Whole genome sequencing (WGS) provides insight into the genetic fingerprint of a pathogen by sequencing the chemical building blocks that make up its DNA and is increasingly being employed in food safety efforts.  Since 2012, the U.S. Food and Drug Administration (FDA) has regularly turned to WGS to better understand foodborne pathogens, including identifying the nature and source of microbes that contaminate food and cause outbreaks of foodborne illness. For example, FDA reports that WGS was recently used to help match samples of soft cheese to the genetic fingerprint of Listeria monocytogenes involved in a deadly foodborne illness outbreak in early March 2017.
  • On September 22, 2017, the Food Safety and Inspection Service (FSIS) announced that it will host a public meeting on October 26 and 27, 2017, to discuss overall federal food safety agency practices and, more specifically, plans for collecting and analyzing whole genome sequence (WGS) data of bacteria isolated from official samples, including the state of the science and other issues surrounding use of this technology. During the meeting, FSIS also intends to discuss the Agency’s recent experience in using WGS as well as its intention to expand its use in the future.
  • It remains to be seen the extent to which WGS may potentially revolutionize the way in which food regulatory bodies – in the U.S. and abroad – achieve their enumerated food safety and public health goals.
  • For further information concerning the upcoming October 26–27, 2017, please visit the FSIS Meetings and Events page.
  • As background, whole genome sequencing (WGS) essentially provides insight into the genetic fingerprint of a pathogen by sequencing the chemical building blocks that make up its DNA.  Since 2012, FDA has regularly turned to WGS to better understand foodborne pathogens, including identifying the nature and source of microbes that contaminate food and cause outbreaks of foodborne illness. For example, FDA reports that WGS was recently used to help match samples of soft cheese to the genetic fingerprint of Listeria monocytogenes involved in a deadly foodborne illness outbreak in early March 2017.
  • Two FDA officials leading the Agency’s WGS efforts in the food safety realm recently explained in a podcast that FDA laboratories are currently testing new genome sequencers that are said to be faster, cheaper and more mobile – with the potential to fit into a briefcase that could go out to the consumer safety officer and actually do field testing.  FDA is also working with global partners to advance this technology.
  • It remains to be seen the extent to which WGS may potentially revolutionize the way in which food regulatory bodies, including the FDA, achieve their enumerated food safety and public health goals.
  • As our readership is well aware, foods from genetically engineered (GE) plants must meet the same food safety requirements as foods derived from traditionally bred plants under the Federal Food, Drug, and Cosmetic Act.  As a routine premarket step, developers of new plant varieties, including those produced using genome editing, typically consult with FDA regarding the safety and regulatory status of foods derived from such plants.  These consultations serve to help ensure that applicable safety and legal questions are resolved prior to marketing.
  • To complement the existing framework in place for assuring the safety of products of biotechnology, including new plant varieties produced using genome editing, on September 16, 2016, the Obama administration’s Emerging Technologies Interagency Policy Coordination Committee released a National Strategy for Modernizing the Regulatory System for Biotechnology Products.  This strategy document sets forth a vision for ensuring that the federal regulatory system is equipped to assess efficiently the risks, if any, associated with future products of biotechnology.
  • On January 18, 2017, FDA issued a request for comments related to the regulation of human and animals foods derived from plants produced using genome editing technologies to help inform its regulatory approach.  The Agency’s questions, include, but are not limited to:
    • In what ways are the food safety risks associated with human and animal foods from genome edited plants the same as or different from those associated with other plant development methods (g., hybridization, chemical or radiation-induced mutagenesis and non-targeted genetic modifications using in vitro recombinant DNA technologies)?
    • Are there categories of genome edited plant varieties for which there are scientific bases to conclude that foods from such categories are unlikely to present food safety risks different from or greater than those for traditional plant breeding?
    • Are there categories of genome edited plant varieties for which there are scientific bases to conclude that foods from these categories are more likely than traditionally-bred plants to present food safety risks?; and
    • What steps can FDA take to help small firms, including those who may be considering using genome editing to produce new plant varieties for use in human or animal food, to engage with FDA about any questions related to food safety or the regulatory status of foods from their new plant varieties?
  • FDA will be accepting comments until April 19, 2017.  It remains to be seen how the information received will impact the new administration’s approach to regulating foods derived from genome edited plants.
  • The United States Department of Agriculture’s (USDA) Food Safety and Inspection Service (FSIS) routinely monitors clusters of illnesses to determine if FSIS-regulated products may be the source of food-borne illnesses.  FSIS posts information on active outbreak investigations to a table on its website when there is compelling evidence that an FSIS-regulated product is the source.  The primary pathogens involved in FSIS outbreak investigations are Salmonella, Shiga toxin–producing Escherichia coli (STEC), Listeria monocytogenes (Lm), and Campylobacter.
  • In a November 19, 2021 Constituent Update, FSIS announced that it has posted on its website an after-action review report for the investigation of a 2018 multi-state outbreak of Lm illnesses associated with ready-to-eat (RTE), Asian-style pork patty products that resulted in 4 hospitalizations.  Whole genome sequencing (WGS) analysis of bacterial isolates from routine FSIS product and environmental samples indicated the historical presence of the outbreak strain at a single FSIS-regulated establishment.  The Investigation further revealed that the pork patty products were cooked using a process that was not validated to ensure all pieces were thoroughly cooked, and there was a history of Lm harborage and opportunities for contamination after cooking that were not considered by the establishment.
  • The Lm outbreak linked to pork patties was only the second reported multistate outbreak of listeriosis linked to a FSIS-regulated product since 2005.  Nevertheless, as noted in the investigation report, FSIS may consider an update of Directive 10240.4 (Verification Activities for the Lm Regulation and the RTE Sampling Program) to include additional instructions for inspection personnel when verifying if a product is exposed to the environment after undergoing a cooking step.
  •  Certain food establishments, referred to as dual jurisdiction establishments (DJEs), are under the jurisdiction of both the Food and Drug Administration (FDA) and the U.S. Department of Agriculture’s Food Safety Inspection Service (FSIS).  In January 2018, the FDA and FSIS announced a formal agreement, i.e., memorandum of understanding (MOU) 225-99-2001, to make the oversight of food more efficient and effective by bolstering coordination between the two Agencies.
  • In an August 6, 2021 Constituent Update, FSIS announced an updated agreement, MOU 225-20-2019, signed July 28, 2021, to further facilitate the exchange of information about DJEs.  DJEs under this MOU are limited to human food operations and exclude animal food operations, which are regulated by FDA.  The new MOU improves upon previous information exchange by:
    • Adding headquarters-level contacts for each agency to improve awareness of findings or emerging issues that may warrant more than local or regional coordination.
    • Updating the types of findings to be shared to reflect advances in understanding microbiological food hazards, including microbiological or other sampling findings in DJEs or products, which may provide information about sanitary conditions in those establishments or indicate serious adverse health consequence of products under either agency’s jurisdiction.  These results will include microbe characteristics (e.g., serotype, whole genome sequence, antimicrobial resistance profile, etc.) where applicable, and other information related to categorizing and tracking pathogens.
  • The new MOU 226-20-2019 supersedes the earlier MOU 225-99-2001 as well as MOU 225-14-0009, a formal agreement on the examination and inspection of Siluriformes fish and fish products, which was entered on April 30, 2014 following the handover of jurisdiction of Siluriformes species from FDA to USDA.
  • FDA published a report on June 11 that expresses concerns with farm animal operations located nearby fields growing produce. The report focuses on a 2020 Salmonella enteritidis outbreak in peaches that affected 101 people across 17 states and explains FDA’s testing and traceback processes from the outbreak.
  • The report explains that FDA connected pathogen samples from peaches and peach tree leaves to a strain of Salmonella on an adjacent chicken operation using whole-genome sequencing on chicken isolates from the same period as the outbreak. The results prompted additional testing around the company’s orchards where other strains of Salmonella were connected to genetically identical pathogens found in beef and cattle isolates from an adjacent cattle feedlot. The findings helped FDA quickly identify and prioritize investigations at certain peach packing and holding operations and other peach orchards.
  • The report states these findings underscore FDA’s concern about the potential impact adjacent land uses have on produce safety, including the potential impact of dust exposure. Past outbreaks have been linked at least in part to animal feeding operations, including a 2018 E. coli outbreak in romaine lettuce. FDA encourages collaboration between neighboring farms to identify areas of concern and tailor their land management to the specific practices and conditions on individual farms.
  • The U.S. Food and Drug Administration (FDA) and industry are continually seeking innovative ways to curb foodborne illness outbreaks. As covered previously on this blog, FDA has undertaken a robust surveillance sampling program intended to promote food safety. In 2014, the Agency launched a proactive sampling program for a variety of commodities to learn more about the prevalence of disease-causing bacteria, including identification of patterns that may help predict and prevent future contamination events. The Agency’s sampling approach involves the collection of a statistically determined number of samples of targeted foods over a 12- to 18-month period, and the testing of samples for microbial contaminants.
  • On January 22, 2020, FDA released interim data from its sampling program of frozen berries. As of September 30, 2019, the Agency indicates it has tested 339 domestic samples and 473 import samples of frozen berries. Of the frozen berries sampled, FDA found genetic material from hepatitis A virus in five samples and genetic material from norovirus in eight samples, using multiple-laboratory validated RT-qPCR methods for the detection of those viral sequences in soft fruit. These 13 samples were then further tested by the “Sanger sequencing” method to see if the viral material could be further characterized by examining a separate, distinct section of the viral genomes. Nine of the 13 samples could be further characterized using this technique. Upon detection of genetic material from hepatitis A virus or norovirus in a sample, the Agency notified the firm of the findings and worked with them to take appropriate action to protect the public health.
  • The information released is interim data, and FDA indicates that testing remains ongoing and no conclusions can be drawn at this time.