• 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 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.
  • On November 20, the Centers for Disease Control and Prevention (CDC), in conjunction with the Food and Drug Administration (FDA) and several state agencies, announced that it is currently investigating an outbreak of Shiga toxin-producing E. coli (STEC) O157:H7 infections that has so far impacted at least 17 people across 8 states. The first reported illnesses date back to September 24, 2019. Investigators are looking into a branded chicken Caesar salad as a potential source, after the Maryland Department of Health (MDH) identified E. coli O157 in an unopened package. However, MDH is still conducting a whole genome sequencing (WGS) analysis to determine if it is closely related genetically to the E. coli identified in this outbreak.
  • As previously reported on this blog, in January 2019, FDA’s Food Safety and Inspection Service (FSIS) transitioned to using only WGS for Shiga toxin-producing E. coli (STEC) in an effort to update its analytical methods to the state of the art. The method of WGS determines the order of all of the DNA building blocks (nucleotides) in an organism’s entire genome in a single laboratory process, and 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 recent outbreak follows a similar outbreak of E. coli 0157:H7 from 2018 that was ultimately traced to romaine lettuce. The 2018 outbreak included 62 cases from 16 states and the District of Columbia, and prompted FDA to issue recommendations for leafy greens growing operations as well as a partnership between FDA and leafy greens stakeholders in Arizona to enhance food safety. Subsequent research from the U.S. Department of Agriculture’s Agricultural Marketing Service found that pest flies were a potential vector in the spread of the E. coli O157:H7 and contamination of leafy greens.
  • Drs. Susan Mayne, head of the Food and Drug Administration’s (FDA’s) Center for Food Safety and Applied Nutrition (CFSAN), and Dennis Keefe (head of CFSAN’s Office of Food Additive Safety) published a post on the FDA Voices blog on March 21 discussing FDA’s  Voluntary Plant Biotechnology Consultation Program (the Consultation Program) and the Plant and Animal Biotechnology Action Plan.
  • Under the Consultation Program, which has been in existence since 1995 and has conducted 184 consultations, companies are encouraged to provide FDA with information on the biotechnology so that FDA can provide individualized guidance on the data needed to address potential issues arising out of the biotechnology.  The company then presents the data to FDA and they work together to address any residual issues.  At the conclusion of the review, FDA provides the company a letter and posts relevant information about the review on its website.  More details on the Consultation Program can be found in FDA’s Statement of Policy.
  • On October 30, 2018, FDA announced its new Plant and Animal Biotechnology Innovation Action Plan.  As outlined in the Daily Intake Blog at the time, “the priorities are intended to ensure the safety of plant and animal biotechnology products, foster continued public confidence in FDA’s regulation of these products, and avoid unnecessary barriers to future innovation consistent with FDA’s mission to protect and promote the public health”.   See our blog post or FDA’s landing page for more.
  • On March 21, FDA’s Center for Veterinary Medicine (CVM) announced a webinar on the topic of “Genome Editing in Animals” scheduled for April 25. This webinar, originally scheduled for December 3, and long linked to the Plant and Animal Biotechnology Innovation Action Plan, “will be focused on information for those using genome editing to develop animals with genomic alterations. In the future, CVM intends to provide opportunities for other stakeholders, such as animal producers and farmers, who may be interested in raising genome-edited animals”.  The webinar is open to the public, but advance registration is required.
  • As previously reported on this blog, in November 2018 FDA, in conjunction with the CDC, state officials, and Canadian food and public health officials, investigated an outbreak of E. coli O157:H7 infections in multiple US states and Canadian provinces. The investigation determined the cause of the outbreak was the consumption of contaminated romaine lettuce. Indeed, thirty (83%) of 36 ill consumers interviewed reported eating romaine lettuce the week before illness onset. All E. coli O157:H7 isolates from ill consumers had a rare genetic fingerprint, as determined by whole genome sequencing (WGS), that was closely related to one previously seen in ill consumers in the fall of 2016 and the fall of 2017. The November 2018 outbreak was declared over in the US on January 9, 2019.
  • On February 13, 2019, FDA released the findings from the Agency’s investigation of the November 2018 outbreak. With the help of WGS, investigators were able to narrow down the growing location of the romaine lettuce to specific California counties. The traceback investigation further identified multiple farms that may have been the cause of the outbreak.
  • In their report, FDA identified factors that most likely contributed to the contamination of romaine lettuce, specifically from one farm in Santa Maria in Santa Barbara County, California. Those factors include the following:
    • The outbreak strain of E. coli O157:H7 was found in the sediment of an on-farm water reservoir in Santa Maria.
    • The outbreak strain was not found anywhere else in sampling done during the investigation in various California leafy greens growing areas and counties.
    • The water from the on-farm water reservoir most likely led to contamination of some of the romaine lettuce. The water was likely not effectively sanitized. The water may have come in contact with the romaine through multiple avenues, including direct harvest/postharvest application and/or use of water on harvest equipment.
    • FDA is not sure how the water became contaminated.
    • Other ranches owned by the same farm, as well as other farms, may have sold contaminated lettuce.
    • Due to the fact that the same specific strain of E. coli O157:H7 occurred in 2016 and 2017, it may be likely that the strain remained in the environment or repeatedly introduced from an unknown source.
  • Based on these findings, FDA provided recommendations for the prevention of future outbreaks. Such recommendations include adhering to the recommendations of the Environmental Assessment associated with the spring 2018 STEC outbreak, FSMAs Produce Safety Rule, and FSMAs Preventive Controls for Human Foods Rule. And specifically for growers of leafy greens, FDA recommends assessing the growing operations, assuring all agricultural water is safe and of adequate sanitary quality, and performing a root cause analysis when a foodborne pathogen is identified.
  • The findings provide hope that growers and public health officials will be able to prevent or mitigate potential future outbreaks.

The full FDA report can be accessed here.