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The Revolutionizing Prospects of Next Generation DNA Sequencing Of Schlundt J and Tay MYF, J Food Sci Nutr 2020, 6: 072 DOI: 10.24966/FSN-1076/100072 HSOA Journal of Food Science and Nutrition Review Article this has been a major problem in the past, novel DNA sequenc- The Revolutionizing Prospects ing methodologies are now providing promising new potential. The case is made for the potential to develop a global, equitable sys- of Next Generation DNA tem of whole microbial genome databases to aggregate, share, mine and use microbiological genomic data, to address global food Sequencing of Microorganisms safety and public health challenges and most importantly to reduce for Microbiological and foodborne and infectious disease burden. Keywords: Antimicrobial resistance; Food safety; Genomic data AMR Identification and sharing; Global microbial identifier; Microbiology; Next generation Characterization-the GMI sequencing; One health; Surveillance; Zoonotic diseases Singapore Sequencing Statement Abbreviations AGP: Antimicrobial Growth Promoters; Joergen Schlundt1,2* and Moon Yue Feng Tay1,2 AMR: Antimicrobial Resistance; 1School of Chemical and Biomedical Engineering, Nanyang Technological BSE: Bovine Spongiform Encephalopathy; University (NTU), 62 Nanyang Drive, Singapore EHEC: Enterohaemorrhagic Escherichia Coli; EFSA: European Food Safety Authority; 2Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore FAO: Food and Agriculture Organization of the United Nations; GFN: Global Foodborne Infections Network; GMI: Global Microbial Identifier; INFOSAN: International Food Safety Authorities Network; Abstract MERS: Middle East Respiratory Syndrome; A cascade of technological DNA sequencing advancements has MDR: Multidrug Resistant; decreased the cost of Whole Genome Sequencing (WGS) very fast. NGS: Next Generation Sequencing; At the same time, the enormous potential of WGS in the surveil- SARS: Severe Acute Respiratory Syndrome; lance of microorganisms and Antimicrobial Resistance (AMR) is in- WGS: Whole Genome Sequencing; creasingly realized. One Health Solutions-based on cross-sectoral WHO: World Health Organization; typing and source attribution are increasingly spreading in relation to OIE: World Organisation for Animal Health; foodborne disease and AMR prevention. Collaboration for disease prevention between human, veterinary and food sectors is already Introduction instituted in some countries and has in some cases resulted in sig- nificant reduction in foodborne disease risk, as well as AMR risk. The The disease burden of zoonotic diseases has been generally recog- success of One Health risk mitigation is to a large part based on the nized, but not very well characterized until recently. While significant potential to link relevant microbiological data from different sectors zoonotic diseases (e.g. Rabies, Lyme’s disease) relate to the direct (animal, food and human) as the basis for science-based decision contacts with animals (bites), most important zoonoses relate in some support to reduce the risk of foodborne diseases and AMR. Such way to animals in the food production chain. For many decades, food linkage is only possible if the methodologies used, or at least the safety events in most countries have been significantly affected by a outcome microbiological characterizations, are comparable. While lack of collaboration between the animal health, the food control and the human health sectors. Nevertheless, it was primarily the outbreaks *Corresponding author: Joergen Schlundt, School of Chemical and Biomedical of SARS (Severe Acute Respiratory Syndrome), zoonotic influenza Engineering, Nanyang Technological University (NTU), 62 Nanyang Drive, Sin- (avian flu-H5N1 and swine flu-H1N1) and BSE (Bovine Spongiform gapore; Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Tel: +65 98351808; E-mail: Encephalopathy) which alerted the world to the need for a One Health [email protected] approach. This is a bit disappointing since we have known for some time that endemic cases of traditional foodborne zoonoses (salmo- Citation: Schlundt J, Tay MYF (2020) The Revolutionizing Prospects of Next nellosis, campylobacteriosis, listeriosis, norovirus) causes a much Generation DNA Sequencing of Microorganisms for Microbiological and AMR Identification and Characterization-the GMI Singapore Sequencing Statement. larger-and continuous-disease burden than these dramatic global out- J Food Sci Nutr 6: 072. breaks [1]. Received: June 09, 2020; Accepted: June 12, 2020; Published: June 24, 2020 In the beginning of this millennium, zoonotic influenza outbreaks Copyright: © 2020 Schlundt J, et al. This is an open-access article distributed spread very quickly, either in the Animal Population (e.g. H5N1) or under the terms of the Creative Commons Attribution License, which permits un- directly in the Human Population (e.g. H1N1) and formed a glob- restricted use, distribution, and reproduction in any medium, provided the original al threat for human health. H1N1 was therefore characterized by author and source are credited. Citation: Schlundt J, Tay MYF (2020) The Revolutionizing Prospects of Next Generation DNA Sequencing of Microorganisms for Microbiological and AMR Identification and Characterization-the GMI Singapore Sequencing Statement. J Food Sci Nutr 6: 072. • Page 2 of 7 • the World Health Organization (WHO) as a pandemic. Although, as [10], but it is-again-important to note that although outbreaks are of- mentioned, the human disease burden related to the endemic bacterial ten picked up by the press, the real AMR problem is actually an en- zoonoses is many fold higher than these influenza outbreaks, it is ba- demic problem, not an epidemic problem [11]. In fact, it is estimated sically these relatively few but fast spreading outbreaks that have put that in the absence of significant risk mitigation, the number of annual One Health on the global agenda. The failure to predict, monitor and deaths globally from AMR will reach 10 million, significantly sur- control the spread of these diseases in animals presented regulators passing the present 7-8 million deaths from cancer [12]. and especially politicians with a wake-up call and made them demand (better) cross-sectoral collaboration between the animal and human The use of antimicrobials in humans and animals has resulted in a health sectors. selective pressure for AMR microorganisms, contributing significant- ly to the human health problem of AMR bacteria. A WHO publication Therefore, the one health concept was formulated to character- ize the benefit of cross-sectoral collaboration. Taking the cue from [13], covers the broader scope of AMR in relation to both animals and high-level intergovernmental meetings, the relevant intergovernmen- humans. Thus, a One Health approach has explicitly been proposed tal organizations suggested the set-up of systems and solutions based by international organizations to mitigate the risk of AMR. In partic- on one health solutions. The first such intergovernmental description ular, the use in animals as Antimicrobial Growth Promoters (AGP) is of the one health concept is from the publication “Contributing to questionable, as the concentrations used are sub-therapeutic, thus re- One World, One Health” [2], but the concept was later more clearly sulting in selection for resistance but not efficient kill of relevant mi- enunciated as “One Health” in the seminal paper by WHO, croorganisms. One Health systems, including cross-sectoral typing, may provide scientific basis for risk mitigation relative to microbio- World Organisation for Animal Health (OIE) and Food and Agri- logical and AMR problems in both human and animal reservoirs (Fig- culture Organization of the United Nations (FAO), “The FAO-OIE- WHO Collaboration: Tripartite Concept Note-Sharing responsibili- ures 1 and 2). However, there seems to be a problem in assessing the ties and coordinating global activities to address health risks at the relative importance of human and animal use and the veterinary and animal-human-ecosystems interfaces” [3]. It can only be character- medical professions are still hotly debating this [14-17]. It is therefore ized as astounding that these three intergovernmental organizations important to be able to compare data on AMR from both the animal had not at an earlier stage clearly described this need for coordination, and the human side enabling integrated source attributions. Again, although it must be recognized that in the food safety standards area novel DNA sequencing methodologies are now providing promising the FAO/WHO Codex Alimentarius Commission as well as the FAO/ new potential (see Section New characterization and typing method- WHO Expert Committees have actually been a beacon for intersec- ology). toral coordination since at least 1963! Collaboration between sectors is generally a benefit in many re- spects, especially the potential linkage of relevant microbiological data is important. Since there is an obvious need for science-based decision support to reduce the risk of zoonotic diseases, the specific comparison of microbiological isolates from animal, food and human is now recognized as crucial. Such comparison is only possible if the methodologies used, or at least the outcome microbiological charac- terizations, are comparable. While this has been a major problem in the past, novel DNA sequencing methodologies are now providing promising new potential (see Section New characterization
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