Scientists are urging government officials to consider helping to develop an international database to share and analyze DNA sequences.
Such a system is a platform for storing whole genome sequencing (WGS) data on the full genomes of investigated microorganisms such as bacteria, viruses and parasites, providing quick characterization and treatment options of such organisms when they are detected in sick patients or food.
In the United States the federal Centers for Disease Control and Prevention works with states to collect sequences of pathogens in the PulseNet database. It has been credited with helping to detect outbreaks and assisting investigations.
More than 250 scientists and experts from 40 countries met at Nanyang Technological University in June to discuss strategies to combat foodborne disease and food poisoning outbreaks. The 12th meeting of the Global Microbial Identifier (GMI) conference was organized by the NTU Food Technology Centre.
Seize the opportunity
Joergen Schlundt, professor Food Science at Nanyang Technological University Food Technology Centre (NAFTEC), said the GMI suggested such a database be created but it needs political agreement among all countries.
“I think the main takeaway is that a lot of scientists and technical people see a giant opportunity for scientists and countries to work together to build science in this microbiological area with the new technology because this is one of the first times where if we connect all our data together in one or several big databases, researchers all over the world will gain from that,” he told Food Safety News.
“If the system was functioning, public, animal and plant health would benefit because you would end up having a system that could always answer what your microorganism is, what is the name, where it comes from, how you can treat it and maybe also if it is causing foodborne outbreaks.
“It is a huge resource that we could build if we wanted to, technically it is not a big deal, but we need countries to discuss whether it makes sense, whether they want to share their data and whether they want to fund it collectively. Optimal use is dependent on policies and the willingness and ability of countries to share genomic sequences across borders and in real-time.”
Databases on DNA sequences already exist such as those run by the National Center for Biotechnology Information (NCBI) and European Nucleotide Archive (ENA) but Schlundt said these are passive.
“It would be an active system that would give you an answer as soon as you send your sequence. So you have your microorganism, you put it through the sequencer, you get a sequence so four million letters in an excel or another file, you send that off to the machine and five minutes later it will give you the answer, so it is like searching on Google. The answer is the species, subtype and resistance of the microorganism and there could be other information.”
Improve outbreak response
Sharing of sequencing results would allow early detection of emerging threats and rapid identification, investigation, and prevention of national, regional and global disease outbreaks. Equal access and implementation of such sequencing technology between countries could reduce the global burden of disease by enabling real-time surveillance of animal and human diseases and food safety risks.
Schlundt said if most countries take up the idea then there would be an almost perfect standardized real-time surveillance system for diseases.
“It could be there is a foodborne outbreak in a number of different European countries and it is the same Salmonella typhimurium subtype, the system would see the one that is in Berlin is the same strain that is in Marseille and Rome so it can link it together like that. They are starting to do something like this in the U.S. with their system so they find many more national outbreaks than before because they used this type of methodology.”
Data privacy and anonymity could be protected as there are already ways to separate metadata from the four million letters that is the sequence.
“In that system where you can go in and look you cannot see this strain number, or any details about the patient, or the animal or food this comes from. That would be hidden. You would only be able to get that metadata through a special route, for instance if there was an outbreak. So there would be safeguards against privacy concerns in relation to the single patient and so on,” said Schlundt.
Letters sent to agencies worldwide
One of the reasons GMI was founded was to include developing countries in discussions on new techniques and technology.
Schlundt said the organization sent letters in 2018 to 186 countries to push for such a database and got answers back from 15 of them.
“We sent a second round of letters at the beginning of 2019 to 30 countries, the 15 countries that answered us and some other countries we know are interested in this area. From that second round, we have received six or seven replies. They don’t go into any detail but most of them say they agree it is an important issue and there needs to be international discussions about it,” he said.
“We’re hopeful France, Germany or the U.S. might bring it up in connection with G20 Health. If you want to have big movement in things like this you need to get nation states involved. The whole thing is predicated upon an agreement that you want to share this data and that has to be an inter-governmental discussion, it cannot be only between scientists.”
GMI will keep pushing on the issue through the “friendly” countries and international organizations, said Schlundt but while he would like it to happen in the next few years it may take decades.
“In my opinion, international organizations should take their own initiative on this. The World Health Organization (WHO) especially but also the Food and Agriculture Organization (FAO). They are agreeing with us but they are not actively pursuing this. We have to rely on member states that might be interested in this as a major potential for public health and all microbiology.”
GMI 13 will take place June 8 to 11, 2020 in Vancouver, Canada.
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