The Indian food industry has been adopting various Food Safety Management Systems to meet the customer and industry requirements, for which Genome Sequencing has proved to be a powerful tool in the US, England, Thailand, Switzerland, Bangladesh and India. The food industry in India has started to become more aware of this area and wish to have a constructive dialogue with government agencies; however, there can be lack of knowledge regarding the technology and the potential uses of it in an industrial setting. As there is an imperative need for assessing India’s readiness in deploying WGS for food safety, we take a closer look.
Increasingly used by food regulatory agencies to facilitate, investigation, and control of foodborne bacterial outbreaks, Whole Genome Sequencing (WGS) is a cutting-edge technology that the United States Food and Drug Administration (FDA) has put to a novel and health-promoting use. Globally, WGS has helped the food industry to monitor ingredient supplies, determine the effectiveness of preventive and sanitary controls and determine the persistence of pathogens in the environment. Apart from this, genomic sequencing has already shown benefit in refining diagnoses and guiding therapeutic approaches like development of food as therapeutics.
For implementing WGS, India already has good infrastructure and pre-requisites in terms of sequencing capacity, high-capacity storage and data analysis. The major challenge for India to adopt WGS for food safety would be database construction and validation since foodborne disease surveillance in India is lacking. Keeping in view the challenges and benefits of WGS, several research institutes in India like Indian Institutes of Science Education and Research (IISER) Bhopal, have sequenced the genome of turmeric and giloy for the first time in the world.
Industry players like Mars, Nestle, ConAgra & DuPont are implementing WGS in their own food safety programmes. To monitor ingredient supplies, determine the effectiveness of preventive and sanitary controls, WGS can provide a much faster response time for outbreaks and recalls in the food industry.
Dr Ajaikumar B Kunnumakkara, Professor, Department of Biosciences and Bioengineering, IIT Guwahati said, “The availability of diagnostic services for detecting infections is particularly critical in India, because, without it, we are forced to depend only on syndromic monitoring, which lacks the sensitivity and specificity required. Prior to the implementation of WGS, the Indian government at central and state levels must have a system in place to collect isolates and relevant metadata from both clinical and food/environment samples. Unless these issues are solved, WGS will remain a technique that is exclusively employed in research projects. The proper application of international rules and regulations may be able to assist India in dealing with this issue. For data manipulation and comparative studies, the development and processing of WGS data necessitates the transportation of huge packets of data between laboratory locations involved in the exploitation of this information, distant computer sites, and internet databases.”
He added, “A centralised dedicated laboratory is needed for storing, analysing and interpretation of the WGS isolates across the country. Even for relatively small laboratories with minimal operational budgets, the high-tech requirements of the WGS can be handled in a variety of ways. There are several opportunities for food inspection, public health, and academic laboratories to combine their resources and work together to protect populations from preventing food-borne disease.”
Monitoring ingredients for Implementing WGS
As defined by the FDA, genomic data from foodborne pathogens is a robust resource that can be used: to determine which illnesses are part of an outbreak and which are not; to determine which ingredient in a multi-ingredient food is responsible for an outbreak; to identify geographic regions from which a contaminated ingredient may have originated; to differentiate sources of contamination, even within the same outbreak; to link illnesses to a processing facility even before the food product vector has been identified; to link small numbers of illnesses that otherwise might not have been identified as common outbreak; and to identify unlikely routes of contamination.
The Indian food industry has been continuously working to develop food crop varieties that are resistant to diseases and offer better nutritional values, and are publicly releasing the genome to continue to broadly advance crop research.
Turmeric
A team of researchers from the Indian Institute of Science Education and Research (IISER) Bhopal led by Dr Vineet K Sharma, Associate Professor, Department of Biological Sciences, have sequenced the genome of the turmeric plant for the first time in the world.
The researchers have used two techniques – the short-read sequencing of 10x Genomics (Chromium) and long-read Oxford Nanopore sequencing – to unravel the genetic makeup of turmeric. The genome sequencing of this medicinal plant provides new insights on the origin of the medicinal properties of this plant and will also aid further studies on this species, genus, and family.
Highlighting the uniqueness of his research Dr Sharma, said, “We have, for the first time in the world, sequenced the genome of Turmeric, the golden spice of India.” This work is significant because turmeric has been focused in more than 3,000 publications, but the whole genome sequence was not known until the IISER team’s work on it.
Tulsi
The Central Institute of Medicinal & Aromatic Plants (CIMAP), Lucknow, has published the whole genome sequence of Ocimum Sanctum, the wonder plant ‘Holy Basil’ or ‘Tulsi’. This is the first report of a complete genome sequence of a traditional and most respected medicinal plant of India, using a composite next generation sequencing technology.
Considering the metabolic and therapeutic potential of this revered plant, the availability of whole genome sequence is the first step to understand and unravel the secrets of this herb and provide scientific validity to the traditional claims of its utility in diverse medicinal usage.
Apart from the therapeutic potential, the plant is used in the preparations to cure various diseases like bronchitis, bronchial asthma, malaria, diarrhoea, dysentery, skin diseases, arthritis, painful eye diseases, chronic fever, insect bite etc. It has also been described to possess anti-fertility, anti-cancer, anti-diabetic, anti-fungal, anti-microbial, hepatoprotective, cardioprotective, antiemetic, antispasmodic, analgesic and diaphoretic actions. Many of the basil oil constituents have found applications as medicinal ingredients, flavours, fragrance, etc.
Giloy
The IISER Bhopal scientists have sequenced the genome of Giloy (Tinospora cordifolia), a plant with medicinal properties, for the first time in the world.
The genome and transcriptome sequencing of Giloy is important due to its tremendous use in pharmaceuticals and ayurvedic formulations to treat various health conditions including COVID-19 and can provide deep insights into the genomic basis of its medicinal properties.
Elaborating the highlights of this research, Dr Sharma, said, “Giloy also has anti-microbial activity and is used in skin diseases, urinary tract infection, and dental plaque, among others. It is also found to reduce the clinical symptoms in HIV-positive patients and its antioxidant activity has anti-cancer and chemo-protective properties. Giloy extracts are found to be potential candidates in treating various cancers like brain tumour, breast cancer, and oral cancer, as well.”
Commenting on the other developments by IISER, he said, “We have completed the genomic sequencing of the important plants like Aloe vera, turmeric, giloy, and ginger. Recently we have published the preprints of the genomes of banyan tree and peepal tree and many more herbs and other plants are in the pipeline but cannot be revealed at this stage. In fact, from our lab, we have sequenced the National bird- Peacock, National tree- Banyan, National animal- Tiger, and several varieties of Indian cows.”
Wheat
A team of international researchers, including 18 from India decoded the wheat genome, considered insurmountable so far. In the research article– authored by more than 200 scientists from 73 research institutions in 20 countries. A team of 18 Indian scientists co-authoring this paper, led by Dr Kuldeep Singh at Punjab Agricultural University (PAU) Ludhiana, Prof. J P Khurana at the University of Delhi South Campus, and Prof. Nagendra Singh at ICAR-National Research Centre on Plant Biotechnology, New Delhi, contributed to the decoding of Chromosome 2A of the wheat genome. This project was financially supported by the Department of Biotechnology, Government of India.
The availability of high-quality reference genome would accelerate the breeding of climate-resilient wheat varieties to feed the ever-increasing world population and help address global food security in the decades to come.
Benefits of WGS
To understand and characterise the pathogenicity of viruses, genome sequencing is already established in the areas of plant/animal breeding, and in animal health. The technique has proved to be a great success in the area of outbreak investigation of foodborne illness.
The DNA sequences are like fingerprints, that are unique to each organism and its strain. Whole genome sequencing allows food safety experts to identify the DNA sequence of an organism quickly and efficiently.
One of the greatest benefits of scientific technology like WGS is that it helps food safety experts react retroactively to a foodborne illness outbreak. Outbreak investigations like the Salmonella Typhimurium outbreak, that caused 31 reported illnesses and four hospitalisations in the US between June and August 2021.
The US FDA worked with the US Centres for Disease Control and Prevention (CDC) and state partners to investigate the outbreak, which was linked through epidemiology and traceback to packaged salad greens during the summer of 2021. This outbreak is believed to be the FDA’s first domestic investigation of a foodborne illness outbreak associated with leafy greens grown in a Controlled Environment Agriculture (CEA) operation.
Outbreak investigations are the most common application for WGS. Beyond that, one of the greatest benefits of WGS when it comes to outbreak investigation is the ability to match the genome sequence of a foodborne pathogen with its geographic origin.
With its benefits, WGS is surely helping to track down pathogens:
- WGS adds a level of precision to the surveillance leading to faster and more efficient decision making in the preparedness and response to foodborne infections.
- WGS makes it easier to tell what the pathogen is and the type of illness it can cause.
- WGS can determine source of contamination
According to Sathguru Management Consultants, the WGS technology has now become fast and cheap enough to efficiently replace nearly all the other methods of bacterial identification and pathogenicity assessment. The older methods used for genotyping, DNA and genetic fingerprinting or identification of single nucleotide polymorphism (SNP) using Pulsed Field Gel Electrophoresis (PFGE) and the Restriction Enzymes (REs) are not only slow, inefficient and uncertain but now more costly than WGS.
Giving insights on the benefits of genomic sequencing of food, Rachit K Saxena, Professor (Plant Biotechnology), Gujarat Biotechnology University (GBU) stated, “With the advancement of sequencing methodologies and analysis tools, the field of plant genome sequencing has grown rapidly in the past two decades. It has resulted in the better understanding of plant genomic architecture and subsequently enriched the quantity and quality of available genomic resources. India has diverse climatic zones, with crops facing multiple challenges including disease, drought, water logging, salinity, etc. Therefore, it is important to make our crops more resilient and ready for climate change. This will drive modernisation of crop improvement efforts through genomics assisted breeding (GAB).”
A game changer
In a country like India, food safety is jeopardised due to the presence of an unorganised sector that does not adhere to appropriate hygiene norms. Thereafter, food regulatory agencies are using genome sequencing to examine and detect the presence of harmful microorganisms in food. Genome sequencing can not only aid in the research of foodborne outbreaks, but helps to improve our understanding of virulence, pathogenicity, survival, adaptability, antibiotic and biocide/antiseptic resistance of microorganisms.
As pointed out by Prof. Rachit, “The genome revolution has already proved to be a game changing technology across the world. The growing wealth of genomic data from an increasingly diverse set of crop species is unprecedented and is allowing for a better understanding of genome architecture and evolution of crops. This information has been revolutionising crop improvement programmes in recent years in both the public and private sector.”
Dr Kunnumakkara stated, “The discovery of genomics and its integrations to the food industry has brought a paradigm shift in the food surveillance, safety and security programmes. Agricultural genomics is a vast area that has aided in crop development breakthroughs for decades. Advances in genome revolutions have led to development from reference genome sequencing to genotyping for genome-wide association studies. These have resulted in production of top cultivars with traits like high yield, stress tolerance, and insect resistance that are beneficial in agriculture. In addition, the potential to detect genetic markers linked to virulence, antibiotic resistance, and other features essential in the identification, risk profiling, and typing of foodborne bacterial isolates is crucial in influencing regulatory decisions and identifying food contamination sources.”
Speaking on the challenges before India to adopt WGS for food safety, Prof. Saxena, said “Enhanced awareness among policy makers and a centralised policy to support WGS efforts in crops species should be priority. Further, a clear long term road map needs to be established on how WGS will help develop a better understanding of crops and new varieties. At present there is a disconnect between the native range of crops species and the regional affiliation of the researchers studying them. Therefore, a consortium approach is required to reap the benefits of WGS or GAB. Fortunately, falling WGS costs and enhanced availability of analytical tools provide key opportunities to improve our status in WGS and further its deployment in achieving food safety.”
Perhaps, it is the right time for India to sequence the prominent crops and plants which are the key constituents of the Indian diet. As pointed out by Dr Sharma, “The advancement in new sequencing technologies and in fact, the availability of multiple methods, high performance computing machines and a trained expertise available in the sequencing labs like at IISER Bhopal, provides the much-needed platform to India to mark their presence at the global level and also to make a genetic catalogue of the biodiversity of the unique plants, animals and microbiome endemic to this region.”
Pooja Yadav