Role of whole genome sequencing in food safety
Food safety is becoming a public health priority and governments are making efforts to develop policies and regulatory frameworks, establish and implement effective food safety systems to ensure that food producers and suppliers along the entire food chai
Ways to establish and implement food safety systems for food suppliers to operate responsibly and supply safe food to consumers.
Food safety is becoming a public health priority and governments are making efforts to develop policies and regulatory frameworks, establish and implement effective food safety systems to ensure that food producers and suppliers along the entire food chain operate responsibly and supply safe food to consumers.
The epidemiological investigation of a food-borne outbreak, which includes identification of pathogen, source attribution, removal of contaminated food items from the supply chain and development of other intervention strategies, depends on the ability to subtype the etiological agent at a high enough resolution to differentiate related from non-related cases. The traditional phenotypic subtyping methods used include serotyping, phage typing and biotyping. Since 1990, the field of subtyping has been revolutionized with the advent of molecular and Dna-based subtyping methods, which allow more sensitive discrimination than the traditional methods. Commonly used molecular subtyping/genotyping methods include banding pattern-based Pulse Field Gel Electrophoresis (PFGE), and DNA sequencingbased Multi Locus Sequence Typing (MLST), and Multiple Locus Variable Number Tandem Repeat Analysis (MLVA). The establishment of Pulsenet in USA in 1996 and its expansion as “Pulsenet International” was instrumental in advancing the adoption of molecular subtyping for bacterial food-borne disease surveillance. Pulsenet selected PFGE as the primary genotyping methodology, which substantially advanced food-borne disease surveillance and outbreak investigation.
Whole genome sequencing (WGS)
Whole genome sequencing (WGS) is a laboratory procedure that determines the complete DNA sequence in the genome of an organism in one process. Recent advances in sequencing technologies and bioinformatics tools have made WGS a viable and advanced solution for epidemiologic investigation and surveillance of food-borne bacterial pathogens. Due to its advantages over PFGE, WGS is now becoming the preferred method for organism identification and comparison among isolates.
Advantages/benefits of WGS
• WGS provides significantly improved subtype discrimination as well as interpretation of evolutionary relatedness of isolates • WGS can provide location specificity for disease outbreak investigations, help in understanding how pathogens spread within and between geographic areas
• WGS is becoming inexpensive and is easier to use since it has identical sample preparation for all pathogens • The data generated by WGS yields additional information on virulence factors, antibiotic resistance, mobile genetic elements and geographic location
Applications of WGS in food safety (a) Regulators and public health agencies
Whole Genome Sequencing (WGS) has already been used in a few countries to subtype common foodborne pathogens wherein the high-resolution WGS subtyping data has enhanced the outbreak detection and facilitated epidemiological investigations. The high specificity and sensitivity of WGS provides greater confidence in regulatory decisions made by authorities on food safety, public health etc.
US FDA is utilizing WGS since 2008 and is coordinating efforts by federal, state, and international public health agencies to sequence pathogens collected from food-borne outbreaks, contaminated food products, and environmental sources and make their genomic sequences publicly available in a database called Genometrakr. Genometrakr, established by the FDA in late 2012, is the first distributed network of labs to utilize WGS for pathogen identification and can be used to help pinpoint the contamination sources of current and future outbreaks. As on September 2016, this network has sequenced more than 71,000 isolates, and closed more than 175 genomes.
Since 2012, FDA is using WGS of food-borne pathogens for regulatory purposes in various ways (http://www.fda.gov): • Differentiating sources of contamination, even
within the same outbreak • Determining which ingredient in a multiingredient food harbored the pathogen associated with an illness outbreak • Narrowing the search for the source of a contaminated ingredient, even when the source is far off place • As a clue to the possible source of illnesses - even before a food has been associated with illnesses by traditional epidemiological methods WGS and potential role in FSMA compliance: Under US FDA’S new Food Safety Modernization Act (FSMA), food industry is expected to have environmental monitoring programs (EMPS), especially when ready-to-eat food is exposed to environment prior to packaging, to verify the effectiveness of their processing and sanitation controls in their processing plants. With several recent cases, wherein FDA has linked environmental positives in facilities from previous years with illnesses occurring today, food industry is expected to embrace WGS technology to check if they have resident strain of a pathogen in their ready-toeat product facilities. Recently, California based Clear Labs Inc. released WGS test based on their proprietary next generation sequencing (NGS) platform. The test will allow food companies in identifying pathogen strains in samples, determine how different pathogen strains are evolutionarily related, what regions they come from, and from which food groups they originate.
Whole Genome Sequencing (WGS) has already been used in a few countries to subtype common food-borne pathogens wherein the highresolution WGS subtyping data has enhanced the outbreak detection and facilitated epidemiological investigations.
In Canada, WGS is being routinely applied in parallel to other methods like PFGE during cluster investigation or outbreak response; to monitor trends in emerging pathogens, anti-microbial resistance and to identify novel virulence factors. Canadian Food Inspection Agency is in the process of incorporating information from WGS into health risk assessments and epidemiological surveillance and the expansion of the Pulsenet Canada laboratory network refers to the transition to include WGS as a primary subtyping method.
Public Health England (PHE) has been using WGS routinely as part of specialist microbiology and epidemiology services and has benefitted from the application of WGS through improvements in surveillance and outbreak investigation. In June 2014, a Wgs-based investigation by PHE identified the root cause of a Salmonella outbreak through eggs and prevented further outbreaks. By 2014, over 28,000 bacteria and virus genomes were sequenced including over 3,500 salmonella genomes (www.gov. uk). PHE is also using whole genome sequencing (WGS) to detect antibiotic resistance genes. In Denmark, food and environment monitoring for Listeria monocytogenes together with health surveillance using WGS was implemented in 2013.
Industry players like Mars, Nestle, Conagra & Dupont are implementing WGS in their own food safety programs. Industry can use WGS to monitor ingredient supplies, to determine the effectiveness of preventive and sanitary controls and determine the persistence of pathogens in the environment. WGS can provide a much faster response time for outbreaks and recalls in the food industry.
International efforts on WGS for food safety
When compared to developed countries, the application of WGS for food safety management in developing countries has been very limited. In the developed countries, a well-established reporting system used by public health agencies is resulting in the proper documentation of incidence of food-borne illness in populations. This reporting system is absent or almost negligible in the developing countries and there is a need to establish this reporting/ surveillance system in the developing countries before WGS can be effectively used in food safety management. The Food and Agricultural Organization (FAO) is leading global efforts to build capacity to detect, control, and prevent food-borne diseases. As part of these efforts, FAO convened a technical meeting on the impact of WGS on food safety management within a “One Health Framework” in May 2016, which was attended by participants from 50 countries. “One Health Framework” advocates the idea of fully connecting the clinical, food and farm environment as an integrated whole rather than being disconnected parts.
Global outreach for WGS in food safety will require concerted efforts and coordination among various organizations like WHO, FAO, International Standards Organization, (ISO) etc. There is a great need for training in WGS technology, its validation, harmonization, effective data-sharing and integration across the global community.
Industry players like Mars, Nestle, Conagra & Dupont are implementing WGS in their own food safety programs. Industry can use WGS to monitor ingredient supplies, to determine the effectiveness of preventive and sanitary controls and determine the persistence of pathogens in the environment.
How can India use WGS for food safety
Indian food industry has been adopting various Food Safety Management Systems (mostly private standards like FSSC 22000, BRC, SQF, etc) largely to meet the customer/ export country requirements. US FDA is already using WGS in narrowing its search for the source of a contaminated ingredient. As part of the 2012 Salmonella outbreak investigation, FDA found that the Salmonella Bareilly DNA for the samples tied to the 2012 outbreak was very similar to the Salmonella Bareilly DNA isolated from shrimp that came from a processing plant in southwest India several years earlier. With FSMA in force, US FDA is expected to increase its use of WGS to link environmental positives in ready-to-eat product facilities from previous years with illnesses occurring today. In the next few years, there is possibility of WGS becoming mandatory for exports, specifically to few countries having WGS supported food surveillance systems in place. This could affect the economy of several countries
including India, which do not have this technology for food safety.
There is an imperative need for assessing India’s readiness in deploying WGS for food safety. For implementing WGS, India already has good infrastructure and pre-requisites in terms of sequencing capacity, high capacity storage & data analysis, good internet connectivity and bio-informatics support. There are several research institutes in India with WGS facilities and research programs. There are also a few private service providers for WGS, supporting research in agriculture and health care areas.
The major challenge for India in adopting WGS for food safety would be the database construction and the validation since food-borne disease surveillance in India is lacking. Food-borne disease surveillance is essential for monitoring of food-borne diseases and their trends, evaluating strategies for the control and prevention of food-borne diseases, detection, etc. India lacks systematic studies in understanding the types of foods involved and the agent causing the disease. Most of the food-borne disease outbreaks in India go unreported or are not investigated and some of them are only noticed after a major health issue or economic loss has occurred.
The Food Safety and Standards (FSS) Act 2006, stipulates the duties and functions of Food Safety and Standards Authority of India (FSSAI), which include regulating and monitoring the manufacture, processing, distribution, sale and import of food so as to ensure safe and wholesome food. As per the Act, the Food Authority shall also search, collect, collate, analyze and summarize relevant scientific and technical data, particularly relating to (i) food consumption and the exposure of individuals to risks related to the consumption of food; (ii) incidence and prevalence of biological risk; (iii) contaminants in food. The Food Authority shall also promote, co-ordinate and issue guidelines for the development of risk assessment methodologies and monitor and conduct and forward messages on the health and nutritional risks of food to the government.
Epidemiological, environmental, and clinical components should integrate closely for carrying out food-borne disease investigation. Routine collection and analysis of clinical, food, and environmental samples is a pre-requisite for implementing WGS. Hopefully, FSSAI will coordinate with the agencies concerned and take initiatives in building basic epidemiology, surveillance, food monitoring and testing infrastructure for implementing effective food safety systems in the country.
Whole Genome Sequencing is a powerful tool that can be used for a wide range of public health and food safety applications. WGS is now being used to monitor emerging food pathogens and understand how pathogens spread within and between geographic areas. It can help the food industry to monitor ingredient supplies, determine the effectiveness of preventive and sanitary controls and determine the persistence of pathogens in the environment. The high specificity and sensitivity of WGS provides greater confidence in regulatory decisions made by authorities on food safety, public health as well as decisions made by food industry. However, basic food-borne disease surveillance systems need to be established in developing countries including India, before WGS can be used for food safety.
There is an imperative need for assessing India’s readiness in deploying WGS for food safety. For implementing WGS, India already has good infrastructure and prerequisites in terms of sequencing capacity, high capacity storage & data analysis, good internet connectivity and bio-informatics support.
The writer is a Senior Manager at Sathguru Management Consultants and leads the Food Processing and Retail practice. He can be reached at firstname.lastname@example.org.