The European Food Safety Authority (EFSA) and EU Commission’s Inter-European Union Reference Laboratories (EURL) Working Group on Next Genome Sequencing (NGS) organized the second Science Meets Policy conference this week. More than 100 people from 20 countries attended in-person while online viewers peaked at 257.

Stefano Morabito, from the Italian National Institute of Health (ISS); George Haringhuizen, at the Dutch National Institute for Public Health and the Environment (RIVM); João André Carriço, of bioMérieux; Katja Alt, from the German Federal Ministry of Food and Agriculture and Coen van der Weijden, from the Netherlands Food and Consumer Product Safety Authority (NVWA) were featured on a panel discussion.

Panelists highlighted the need for flexibility, especially as there are 27 countries in Europe at different stages in use of Whole Genome Sequencing and as outbreaks can involve nations outside the EU. They discussed the types of data needed, data quality and comparability, resource issues, how to build trust and the role of different parties including regulators and industry.

EFSA and ECDC’s One Health WGS system has been operating since July 2022 and while things are going well, not all member states are contributing equally.

Data sharing dilemmas

Bernhard Url, EFSA’s executive director, said genomic data sharing is now at a turning point.

“We believe that from a technological and methodological point of view we are ready to use WGS data more widely and with more impact. Many of the problems have been solved and the technical infrastructure has been built. There is no doubt, at least within the community, that data sharing adds value, because it leads to faster outbreak detection and better tracing. It increases the likelihood of connecting sporadic cases to clusters and to detect outbreaks and there is measurable economic impact,” he said.

However, despite the knowledge that sharing data helps, there are still some obstacles that prevent wider use, said Url.

“There are technological gaps as not all member states or organizations use WGS on a routine basis. There is also a worry that people and countries say we don’t have a robust legal basis to share data. There is a fear that people lose control of data, they produce the data, share it but don’t know what happens afterwards. There is a concern that if this technology would be used widely, many more clusters would be detected, which is good from a public health point of view, but it also would increase the workload of national authorities to follow-up and deal with these clusters.”

Url said it would be “unwise” to wait for legislators to define the rules of the game.

“The WGS community must do our part to create the conditions for success. We think there is a lot we can do to move data sharing forward in the current legislative framework. We still have to work on creating a mutual understanding about benefits and limitations of this technology. We have to agree on common guidelines, processes and procedures, otherwise we wouldn’t know how to compare different outcomes,” he said.  

“We want to act as openly as possible but as confidential as needed, there is a fine line that we have to find. EFSA has invested resources in creating a technological infrastructure for enabling WGS data sharing, mainly to tackle foodborne threats. We will continue to do our part to move genomic data sharing forward.”

United States perspective

Eric Stevens, from the U.S. Food and Drug Administration, said the GenomeTrakr network is the result of 12 years of work. At the end of 2021, there were 600,000 genomes in the public database, today it is more than 1,000,000 sequences.

“After more than a decade of experience, it is not the sequencing that is the challenge when transitioning to this data, it is how you are going to analyze it, train staff, gain the skills and enable the entire system to utilize it effectively,” he said.  

“Metadata helps to tell a complete picture, without it you have a DNA sequence, which can only tell you some stuff. Contextual data gives that data life, it tells you where those bacteria came from, how they were living and when we are starting to think about the interventions we can make, we need that information to understand the complete picture.

“For us, the best use is making it open data available to anyone because somebody maybe interested in Salmonella, somebody else in E. coli and sometimes they overlap with interventions you can make for preventive controls and reducing contamination.”

Stevens said once data is in the database, a variety of things can be looked at.

“When you start thinking of the global food chain you can think where do we need more data from and start doing some projects to tackle those problems to better understand how food becomes contaminated in the first place. You wouldn’t know any of this unless you had the data that can help point the way,” he said.

“GenomeTrakr is responsible for almost 100,000 food and environmental isolates to tell a more complete picture of linking clinical isolates back to their sources, so we can not only respond to foodborne outbreaks but then try to prevent them. When you start looking at where your sources of food and environmental isolates linked to human illnesses come from, you can start doing source attribution and more preventive targeting. If we can get to a point where we can upload data in real time we can start to make those connections as early as possible to get a contaminated product out of the market.”

It can also help in moving from responding to outbreaks to trying to prevent contamination occurring.

“In a facility for example, you are not going to do WGS to identify a pathogen, you can do a quick culture method to see presence or absence. But if you have a facility that is concerned about whether they have a resident pathogen you would 100 percent like this information from WGS. You could expand that further to farms and potential water sources,” said Stevens.  

“When you start doing projects in different parts of the world you start understanding that everybody has issues that maybe aren’t issues for you. We’ve done a lot of work in Latin America and the big problem in getting started in sequencing is availability of reagents. We hear it costs five to seven times more than what we pay. When we talk about this being utilized by the world we have to start focusing on those issues that are going to make the most impact.”

(To sign up for a free subscription to Food Safety News, click here.)

Researchers from the Quadram Institute and the University of East Anglia in England isolated Salmonella from 42 food samples.

Salmonella isolates collected from food using whole genome sequencing (WGS) were compared to isolates from humans in the UK.

Raw foods were collected at retail in Norfolk, including 311 samples each of chicken, leafy greens, and pork, 279 prawns, and 157 salmon between May 2018 and November 2019.

Positive chicken results

Work was funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Food Standards Agency (FSA) and published in the journal Microbial Genomics.

A previous study by some of the same scientists found that imported chicken and salmon were more likely to be contaminated than domestic products.

In the latest work, 17 percent of 88 imported chicken samples contained Salmonella related to human-derived isolates, but in domestic chicken, the figure was only 2.3 percent of 214 samples. However, most imported chicken samples were frozen while domestic chickens were mainly chilled, so that the differences may be due to unsafe cooking practices associated with frozen chicken. Chicken samples that contained Salmonella Enteritidis originated from multiple countries, including Poland.

Salmonella was isolated from 30 chicken, eight prawns, and four pork samples and included 14 serovars, of which Salmonella Infantis and Salmonella Enteritidis were the most common. Salmonella Enteritidis was only isolated from imported chicken.

Salmonella Newport twice and Salmonella Enteritidis (nine times) were only isolated from imported chicken samples. Salmonella Kedougou and Salmonella Mbandaka were found once and Salmonella Ohio twice from domestic samples. Salmonella Infantis was isolated 14 times from both domestic and imported chicken.

Linking food and human samples

Monophasic Salmonella Typhimurium was the only type found in multiple commodities. Isolates were collected from two domestic pork and one domestic chicken sample from three supermarkets.

All Salmonella Weltevreden-positives in the study were four samples of black tiger prawns from Vietnam, one from Indonesia, and one of unknown origin. Other samples were positive for Salmonella Bovismorbificans, Brunei, Derby, Newport, Reading, and Schwarzengrund.

Closely related human isolates were collected up to three years before or a year after those from food samples. According to researchers, further epidemiological data are required to assess the source of human cases.

Only monophasic Salmonella Typhimurium, Salmonella Enteritidis, and Salmonella Infantis found in food were similar to isolates from sick people.

A quarter of contaminated foods harbor diverse Salmonella strains that wouldn’t have been detected if only a single isolate were sampled.

“Whole genome sequencing identified foods associated with clinically important Salmonella and foods with genetically diverse Salmonella, which may hinder outbreak investigations and source attribution,” said Dr. Samuel Bloomfield from the Quadram Institute and lead author of the study.

Researchers looked at each sequence for genes that confer resistance to antibiotic drugs. They found 5.1 percent of chicken and 0.64 percent of pork samples had genes that would make them resistant to multiple antibiotics. This information could be useful for directing treatment.

”Food sources, farming and production practices, and consumer behavior are constantly changing, altering the types of foods associated with foodborne disease. Preventing future salmonellosis outbreaks relies on continued surveillance of Salmonella on retail food with the high resolution of WGS to relate food and human isolates.”

(To sign up for a free subscription to Food Safety News, click here.)

Michael Vasser, from the CDC, gave details about the reoccurring, emerging and persisting (REP) strain during a recent presentation at the International Association for Food Protection.

An REP strain is a reoccurring, emerging and persisting group of bacteria, closely related by whole genome sequencing, that continues to cause illness over time. The CDC recently reported that almost 3,000 infections from a persistent strain of Salmonella Infantis since 2012 are linked to chicken.

“Since the full transition to whole genome sequencing to detect multi-state outbreaks, at CDC we’ve been able to identify strains that continue to see cases over time. We saw an outbreak of Salmonella Newport return in 2018 after it was originally investigated in 2016 and 2017. The outbreak caused more than 400 illnesses that resulted in a very large ground beef recall,” said Vasser.

“That begs the question, had we understood the strain in 2016-17 could we have prevented such a large outbreak from occurring? We decided to collaborate with other state and federal regulatory partners to create this new concept, which is reoccurring, emerging and persisting strains.”

Vasser said approaches to investigating REPs may be different than traditional outbreak methods and about 20 REP strains are currently being monitored.

“We know that most illnesses reported through PulseNet are not linked to a source. The goal is to use REPs to drive down the incidence of illness and to better understand sporadic illness. REP strains offer a means of tracking and investigating problems that are larger in scope than traditional outbreaks but we know we need to keep pushing on translating tracking into action and prevention.”

Listeria example and potato link
Vasser gave an example of long running related Listeria infections. The PulseNet laboratory network identified a cluster of six clinical isolates in February 2017 from four states. People fell ill between May 2016 and February 2017. The same pattern was also seen in two isolates from 2011. Patients reported consumption of ice cream, so multiple production facilities were inspected and samples collected but the outbreak strain was not found.

By March 2018, there were 23 illnesses from 12 states. Open-ended interviews then suggested various frozen foods such as pizzas, meals and snacks. However, in May 2018, isolates from U.S. potatoes were uploaded to the NCBI database by the National Service of Health for Food Safety and Food Quality (SENASICA) in Mexico. Isolates were collected from fresh, raw potatoes grown in the U.S. and tested at export by Mexico.

The REP code was officially assigned in June 2021 with 66 illnesses from 21 states. Potatoes were not on the original Listeria questionnaire but now a potato specific version is being used and all 13 patients interviewed reported consuming potatoes in some form. For nine people, it was frozen potato products.

Currently, 82 cases have been reported from 23 states, with Texas the most affected. Sick people range from less than 1 to 104 years old. The latest case was in April 2023. A total of 66 have been hospitalized, 18 are pregnancy-associated and 12 have died.

“This REP is challenging given the related raw potato isolates and the enormity of items made with fresh potatoes. It is still unclear if potatoes are actually the source of infections or if contaminated potatoes seeded the strain in facilities or environments where other foods are grown or processed. It could be that both potatoes and others foods are contaminated. Sampling of products will likely be our best bet to determining the source of foods causing illness,” added Vasser. 

(To sign up for a free subscription to Food Safety News, click here)

The World Health Organization (WHO) will launch a guide in July that outlines the capacities that need to be in place before WGS can be useful for foodborne disease surveillance and outbreak response; options for implementing it; and how to integrate WGS within existing systems.

Dr. Eric Brown, from the Center for Food Safety and Applied Nutrition (CFSAN) at the U.S. Food and Drug Administration, said WGS has been one of the greatest recent impacts in science.

“For us, WGS has been tantamount, to an advancement in food safety, as the Hubble telescope has been for astronomy, to put it in perspective and that is not an understatement. There is no question that WGS has revolutionized the way we can monitor and survey for contamination in the food supply,” he told attendees of a WHO Health Talks webinar.

Development of WGS use
Two incidents highlighting the power of WGS in the early days of its use were shared by Brown.

“One involved nut butter, because we saw illnesses across multiple parts of the country, just 2 or 3 illnesses, we were able to put those together with high-resolution WGS, figure out a nut butter contamination event was beginning to emerge, and stop it before it became an outbreak. The second was a Latin-style cheese event where we were able to link multiple states on the East Coast back to a common cheese provider. It meant we could now sort through a large area of geography quickly and link related illnesses and contaminated products as quickly as possible.”

Brown said the paradigm shift was using WGS for traceability with data openly available in real-time.

“This gave rise to the field of genomic epidemiology, where instead of epidemiology always leading the way, sometimes a genomics signal could be produced early that might show a linkage, and then epidemiology can trace that back and forward,” he said.

“A few characteristics of WGS that make it so powerful are fewer clinical cases are needed, much higher unambiguous scope and definition of an outbreak, we can determine what is related or not more quickly, we can also do source tracking now. Raw ingredients can be traced and this gives rise to enhanced root cause analysis because it can tell you what raw ingredient from what part of the world contamination might be coming from. Complex food vehicles like a salad can have ingredients that start anywhere around the world.”

Brown cited two recent examples of data sharing in the GenomeTrackr database.

“In a series of events related to tahini that was exported internationally, multiple countries were able to identify a common source of tahini contamination. Another example is the Listeria outbreaks associated with enoki mushrooms. This involved four countries in particular: Australia, South Korea, Canada, and the U.S. who shared their data and you could see a linkage from a root cause that came out across multiple countries,” he said.

“Right now we continue to improve the process and the database with greater data integrity, capacity building to get the technology in more people’s hands around the world and make sure we can share as much as we can in real-time. As my FDA colleague Marc Allard likes to say, for every thousand genomes we can get into the database, we can prevent six more illnesses each year. We now know increased use of WGS leads to more outbreaks and contamination events that we can identify and that equates to fewer sick people.”

Key components of the WHO guide
Dr. Kirsty Hope, manager of the Foodborne and Waterborne Diseases and One Health Branch in New South Wales, Australia, said early detection helps to reduce the burden of disease in the community.

“WGS has greater sensitivity and specificity in foodborne pathogen sub-typing. It gives a lot of information on virulence factors and antimicrobial resistance. It allows us to compare strains nationally or internationally. The module enhances our routine surveillance in place already for foodborne pathogens, allows for outbreak detection, helps in outbreak response, and incorporates the One Health response, with animal health and food safety people, laboratories, and databases of sequences and isolates that allow early detection,” she said.

The WHO guidance document covers principles to consider when deciding if it is appropriate to use WGS. Countries need an established surveillance and response system that can be built on. There is a need for political and financial buy-in and a resource burden when using WGS. Three modules include the introduction, surveillance and outbreak investigations.

“We tried to recognize that countries are all at different places in their development and use of WGS, the modules are set up so you can pull out a component and use it solely or you can use the whole document. The first module defines the minimum capabilities that are needed before a country can embark on this journey of WGS to enhance outbreak investigations and routine surveillance. It also gives them options of different ways to implement WGS,” said Hope.

“The second module is about outbreak investigations and how to use WGS. It is meant for countries at the initial stages of lab-based surveillance for food pathogens so you can start building on that. It talks about how you can use it to detect outbreaks and the response process. The third module is around surveillance. It is for countries that have a lab-based surveillance system and it has been in use for quite some time. There is some overlap between the outbreak and surveillance modules. The modules are used as a process to help you step through, think about, and plan within your countries and different agencies on how to move forward with WGS.”

Case studies by the CDC, UKHSA, and PHAC and mock outbreaks are included in the guidance.

“For surveillance and response, we are trying to stop illnesses from occurring and taking public health action. To do that we use information from epidemiologists and our food safety and animal health colleagues. WGS is one part and is helping to do our work with more precision but traditional epidemiology and collaboration is still required. It’s also important to be clear on the questions you are asking to get the answers you want or you may get more questions,” said Hope.

(To sign up for a free subscription to Food Safety News, click here)

The large listeriosis outbreak with 55 cases affected Germany, Austria, Denmark, and Switzerland during 2020 and 2021. Three people died.

Investigations of food samples identified Listeria monocytogenes from smoked rainbow trout filets from Agustson, a Danish producer, grouping with isolates from cases. Patient interviews confirmed the consumption of rainbow trout as the likely infection source. 

The outbreak was identified by molecular surveillance in Germany. Routine whole genome sequencing (WGS) of clinical Listeria monocytogenes isolates was implemented in the country in 2018. 

Details of people sick
In November 2020, a sudden increase in related isolates was detected. Information on the cluster was shared via the Epidemic Intelligence Information System (EPIS) platform of the European Centre for Disease Prevention and Control (ECDC) in the same month.

This returned two recent closely related isolates in both Austria and Denmark and one in Switzerland, indicating the possible cross-border distribution of a contaminated food item.

In total, 68 isolates were recorded between September 2020 and January 2022 in the four affected countries with 63 in Germany. The last isolate was collected on Jan. 31, 2022, according to the study published in the journal Microbiology Spectrum.

Overall, 55 notified cases could be allocated to the outbreak isolates. They were reported from October 2020 to January 2022 with the majority from mid-October to mid-November 2020. Seven cases were reported later in 2021, and one was reported in January 2022.

Of these cases, 50 were from Germany, two each from Austria and Denmark, and one from Switzerland.

Of German patients, 22 were female, and their median age was 80 with a range from less than 1 to 94 years old. Three people died but for one case, another cause of death was notified, and for two people, the cause was not reported. Two cases were pregnancy-associated.

The outbreak had a sudden and marked increase in case numbers and was of a comparably short duration. Other listeriosis outbreaks in Germany are normally active for years before they are detected and stopped.

Researchers interviewed 19 of the 55 cases about food consumption prior to disease onset, and 16 recalled having eaten smoked trout. It was the most frequently reported food item from the standardized questionnaire in Germany, followed by Gouda cheese.

Search for source
A matching food isolate was detected inside an emptied and reclosed package of smoked rainbow trout filets from the waste bin of a patient in Germany. The product was manufactured by Agustson in Denmark.

In December 2020, the Rapid Alert System for Food and Feed (RASFF) warned of Listeria monocytogenes in another batch of smoked rainbow trout filets of this brand in an official sample taken in October, which exceeded the limit for Listeria ready-to-eat products. At the time of the notification, the affected batch had already expired. This isolate was also similar to samples from patients.

The same brand of smoked trout was sold in supermarkets in the four countries where listeriosis cases were identified. Altogether, this strongly indicates the outbreak was caused by rainbow trout filets from the Danish producer, said scientists.

A recall was issued in December 2020 and investigations at the processing facility in Denmark identified Listeria monocytogenes, but the isolate did not belong to the outbreak cluster. Hygiene and disinfection measures at the plant were intensified.

“Our report demonstrates that international food trade can cause multi-country outbreaks that necessitate cross-border outbreak collaboration. It also corroborates the relevance of ready-to-eat smoked fish products as causes for listeriosis,” said scientists.

(To sign up for a free subscription to Food Safety News, click here.)

People have until Feb. 17 to apply for a place and FAO will select participants from 10 to 12 low- and middle-income countries.

The event is for government-sector professionals from low- and middle-income countries to discuss the application and integration of WGS into national food safety work.

In many developing countries, the understanding of the benefits and implications concerning the use of genome sequencing in food safety has been low, said FAO.

The UN agency said the COVID-19 pandemic changed the context around the use of genomic sequencing and its usefulness to detect, quantify and analyze microorganisms. Many people, including the general public and policymakers, have become familiar with terms such as the genome, PCR, variants, and sequencing.

A workshop at FAO headquarters in Rome, Italy from April 18 to 20 will discuss the needs and practical applications of the technology to improve food safety. The event is in-person and no real-time streaming or online participation is planned.

Practical guidance will support understanding the use of WGS in food safety management, benefits, drawbacks, and challenges for countries with limited capacities and resources.

Experts named on the scientific panel
Meanwhile, the Joint FAO/WHO Expert Meetings on Microbiological Risk Assessment (JEMRA) has announced its line-up for 2023 to 2027. A total of 93 scientific experts from 33 countries were selected in response to a call for applications in 2022.

The list features 20 people based in the United States including Arie Havelaar, William Burkhardt, Kathleen Gensheimer, Donald Schaffner, John Mark Carter, Clare Narrod, and Todd Callaway.

Members will be considered for JEMRA activities such as meetings, preparation of review papers, and peer reviews, according to the expertise required. They participate as individuals and not as representatives of their countries, governments, employers, or organizations. Experts are required to declare any potential interests associated with the subjects under consideration.

JEMRA provides scientific advice on microbiological hazards including risk management options aimed at improving food safety. 

(To sign up for a free subscription to Food Safety News, click here.)

The Statens Serum Institut, Danish Veterinary and Food Administration (Fødevarestyrelsen) and DTU Food Institute are trying to find the sources of these outbreaks.

One had already been reported but the Statens Serum Institut has updated the number of people sick. This incident has affected nine people, all of them have been hospitalized and four have died. Five cases are men and four are women.

Patients range from 33 to 93 years old and all had an underlying disease or other immune system issue prior to infection that made them particularly vulnerable, such as meningitis or sepsis. Eight are from the Hovedstaden region of the country. Sample dates range from May 13 to June 6, 2022.

Whole genome sequencing found the strains were closely related and of the sequence type (ST) 37.

Speaking earlier in June, Nikolas Hove from Fødevarestyrelsen said it was rare to see so many Listeria infections in such a short period of time and officials were working to find out which foods were the cause of illness, so the outbreak could be stopped.

Fødevarestyrelsen has written to a number of large industry organizations calling for their members to sharpen in-house monitoring of Listeria. If they find the bacterium in the environment or products, they can have it typed for free at Fødevarestyrelsen’s laboratory.

Two other outbreaks
In the second outbreak, 12 people have been infected with the same type of Listeria since October 2020. Two cases were reported in 2020, nine in 2021 and one in 2022.

Patients are seven men and five women over the age of 70 and they live across the country. Three people in the outbreak have died and all were hospitalized.

Whole genome sequencing of bacteria isolated from sick people found they were closely related and of the sequence type 11.

The Statens Serum Institut is responsible for sequencing isolates from patients and interviewing them or their relatives to identify the possible sources of infection.

Denmark usually sees an average of four listeriosis cases per month.

In the third outbreak, seven people have been infected with the same type of Listeria since October 2021. One case was recorded in 2021 and there have been two in April, one in May and three in June 2022.

Those sick are four men and three women over the age of 50 and they live throughout the country. One person has died and all sick people were hospitalized.

Whole genome sequencing has been used in the outbreak involving isolates from patients with sequence type 8.

The Statens Serum Institut has asked if other countries have matching Listeria cases through the European Centre for Disease Prevention and Control (ECDC) network but as yet no countries have replied saying they have infections with the same outbreak strains. 

(To sign up for a free subscription to Food Safety News, click here.)

Only 8 percent reported using WGS in a routine, real-time way, highlighting minimal uptake of the technology for foodborne disease surveillance outside the United States, Canada, and Europe.

The main barriers for implementation were lack of funding, gaps in expertise, and training, especially for data analysis and interpretation, according to the study published in the journal Foodborne Pathogens and Disease.

PulseNet International (PNI) did the study to identify challenges countries were facing concerning WGS. The group consists of national, regional, and sub-regional labs and laboratory networks in 88 countries that track foodborne disease globally.

Sequencing stats
Forty-one institutions from 33 of 54 countries in Africa, Asia-Pacific, Latin America, the Caribbean and the Middle East completed the survey in early 2020. Two-thirds of respondents were national reference laboratories, including those from national public health, agriculture, and food safety authorities.

One in five use WGS for outbreak investigations after they are identified by other means and 28 percent use it for research and pilot studies only.

Of the labs that do not have WGS implemented, 40 percent outsource sequencing to another institution, but they have plans to take up WGS in-house during or after 2022.

Twenty percent of labs do not use WGS for foodborne disease surveillance, although sequencing is performed onsite for other purposes. The majority of labs that use WGS for investigations after an outbreak or for pilot studies do sequencing at their own institution.

In 2019, only 5 percent of labs sequenced more than 1,000 isolates. Although 66 percent sequenced 0 to 100 isolates that year, the remaining labs sequenced between 100 and 1,000 isolates. The majority of testing was performed on key foodborne pathogens such as Salmonella, E. coli, Shigella, Vibrio, Campylobacter and Listeria.

Data analysis issues
The capacity for generating sequences is generally higher than that for analyzing or interpreting the data. Capacity for computation and bioinformatics was found to be generally low.

Forty-four percent of respondents said their laboratories’ capacity and expertise to utilize, develop, optimize, and troubleshoot bioinformatics analysis protocols for WGS data was little or none.

The majority of labs do not have established guidelines for interpreting WGS data such as the number of allele or SNP differences for outbreak detection.

End-user knowledge for effective use of WGS data is low. Only a third of labs said the level of knowledge and ability to use WGS data for public health decision-making was good or excellent.

Dissemination of WGS results is largely through traditional methods, and data sharing is limited. Traditional ways, including excel spreadsheets, hard copies including fax, and in-person or by telephone dominated over modern methods such as laboratory information management systems and internal websites.

More than half of labs do not exchange sequence data with external partners within their country and only half of respondents make their sequencing data publicly available sometimes.

Half of labs believe that PNI should focus on training, especially in WGS data analysis, and that having access to globally standardized and validated analysis tools and pipelines are key to progress toward worldwide foodborne disease surveillance using WGS.

(To sign up for a free subscription to Food Safety News, click here.)

Whole genome sequencing enables the FDA and other public health laboratories to identify, characterize, and track foodborne pathogens based on their genetic sequence.

According to the FDA, this seminar will focus on bacterial genome sequencing using the MinION from Oxford Nanopore Technologies, an inexpensive and portable sequencer that can be used to complement current sequencing strategies.

Neal-McKinney is a research microbiologist in the Applied Technology Branch at the Pacific Northwest Food and Feed Laboratory. Neal-McKinney’s current research is focused on evaluating new sequencing technologies and developing assays to detect bacteria and parasites in FDA-regulated foods. Neal-McKinney’s previous work experience includes research and development for the IEH Laboratories and Consulting Group. He obtained his Ph.D. in microbiology from Washington State University.

Those interested in attending the webcast can register here.

About FDA Grand Rounds
The FDA Grand Rounds is an educational presentation that is webcast monthly to highlight cutting-edge research underway across the Agency and its impact on protecting and advancing public health. Each session features an FDA scientist presenting on a key public health challenge and how FDA is applying science to its regulatory activities. The 45-minute educational presentation is followed by questions from the audience. You can view past Grand Rounds presentations here.

(To sign up for a free subscription to Food Safety News, click here)

The UK Health Security Agency, Food Standards Agency and Food Standards Scotland are investigating the Listeria monocytogenes outbreak.

Whole genome sequencing has identified 12 linked cases of listeriosis since 2020, with six since January 2022. Sick people live in England and Scotland. The majority reported eating smoked fish. One pregnant woman was also affected.

Smoked fish is a chilled, ready-to-eat food product that can be already cooked so often does not require further cooking.

Change in public advice
Professor Saheer Gharbia, interim deputy director gastrointestinal infections and food safety (One Health) at UKHSA, said: “Listeria infection in most people is usually either unnoticed or may cause very mild gastrointestinal illness. However, it can have more serious consequences for some people, particularly those with pre-existing health conditions that cause weakened immunity, and people who are pregnant.”

Information for pregnant women has been updated to advise that they thoroughly cook smoked fish before eating it, even if it’s packaging says it has been cooked. Advice for avoiding listeriosis infection is being changed to include smoked fish as a high-risk product which should be thoroughly cooked before being eaten by anyone in a high risk group.

Tina Potter, FSA head of incidents, said members of the public do not need to avoid smoked fish products, but should ensure risks are reduced as far as possible.

“You can do this by keeping chilled ready-to-eat smoked fish cold at 5 degrees C (41 degrees F) or below, always using products by their use-by date, following the storage and usage instructions on the label, and cooking or reheating smoked fish until it is piping hot right through,” she said.

About Listeria infections
Food contaminated with Listeria monocytogenes may not look or smell spoiled but can still cause serious and sometimes life-threatening infections. Anyone who has developed symptoms of Listeria infection should seek medical treatment and tell their doctors about the possible Listeria exposure.

Also, anyone who has eaten any of the recalled products should monitor themselves for the food poisoning symptoms during the coming weeks because it can take up to 70 days after exposure to Listeria for symptoms of listeriosis to develop.

Symptoms of Listeria infection can include vomiting, nausea, persistent fever, muscle aches, severe headache, and neck stiffness. Specific laboratory tests are required to diagnose Listeria infections, which can mimic other illnesses.

Pregnant women, the elderly, young children, and people such as cancer patients who have weakened immune systems are particularly at risk of serious illnesses, life-threatening infections, and other complications. Although infected pregnant women may experience only mild, flu-like symptoms, their infections can lead to premature delivery, infection of the newborn, or even stillbirth.

(To sign up for a free subscription to Food Safety News, click here.)

An opinion by the Scientific Committee of the Federal Agency for the Safety of the Food Chain (FASFC) made several recommendations about implementing the technology in Belgium.

Different foodborne pathogens including Salmonella, Listeria monocytogenes and Shiga Toxin-producing E. coli (STEC) are covered in the report. These are the initial focus of a WGS database developed by the European Food Safety Authority (EFSA) and European Centre for Disease Prevention and Control (ECDC).

The committee advised FASFC, also known as AFSCA or FAVV, to start making the transition to WGS for the analysis of food isolates in the near future. This would allow labs time to get experience and ensure they have the necessary infrastructure.

Current situation and future potential
In Belgium, the use of WGS for food safety monitoring and control purposes is not yet harmonized but some labs are using the technique. Whole genome sequencing is mainly done to confirm an outbreak and only in specific cases to proactively detect a potential incident. For the food industry, available WGS data is limited and there is not yet a centralized database.

In the future, WGS will be the preferred method for bacterial food safety investigation, because of its high discriminatory power and the phasing out of older typing methods internationally. It will become the technology of choice for outbreak investigation, pathogen strain typing, national surveillance, and source attribution, said the experts.

Despite the fact that WGS methods and pipelines for data analysis are still evolving and improving, WGS is ready to be used in outbreak investigation and surveillance activities. However, there are limitations for routine and uniform implementation. Efforts should be made to validate the WGS methodology and to facilitate data sharing and comparison.

When using WGS for subtyping strains, as part of an outbreak investigation, validated or internationally recognized methods and bioinformatics tools should be used, and interpreted according to the pathogen involved and taking into account the epidemiological evidence and metadata on the strains. This data should include things such as location, isolation source, collection date, the organization performing collection and sample and strain names.

Role of epidemiological investigation
The technology could also be used to investigate presence of pathogens in food processing environments and to follow up cleaning and disinfection processes.

By June 2022, the joint European database will be operational between EFSA’s WGS database with isolates from food products and ECDC’s TESSy with clinical isolates from humans.

The committee warned about correctly interpreting results and communicating about the source of contamination during an outbreak. They recommended that WGS-based results on the relatedness of strains in outbreak investigations are interpreted by a multi-disciplinary team including microbiologists, bio-informaticians and epidemiologists with sufficient expertise.

It is not possible to define a clear threshold for the number of genetic differences between strains from a common source. WGS data should be combined with metadata informing the epidemiological part of outbreaks, according to the scientists.

It is also difficult to estimate to what extent food businesses will adopt WGS in their self-monitoring and how willing they will be to share data.

(To sign up for a free subscription to Food Safety News, click here.)

A total of 99 responses were submitted, mainly from government or ministries officers, followed by the private sector, NGOs and academic institutions, United Nations agencies and other IGOs and individuals.

The draft strategy for 2022 to 2030 is as a blueprint for member states to strengthen national food safety systems, promote regional and global cooperation and reduce the burden of foodborne diseases.

Preparing draft strategy
After being asked to update the 2002 strategy this past year, the World Health Organization established a Technical Advisory Group on food safety. In total, 24 experts representing WHO’s six regions were selected to provide technical advice on the refresh.

The update is needed to integrate food safety into national and regional policies on health, agriculture, trade, environment and development.

Two virtual meetings of the group were held in February and April to discuss the structure and content of the plan and offer guidance. From May to July, WHO launched a public web-based consultation on the draft updated strategy to get feedback.

It was recognized that the food safety systems of many countries need significant improvement in areas such as regulatory infrastructure, enforcement, surveillance, inspection and laboratory capacity and capability, emergency response and education and training.

Responding nations were the United States, Canada, Columbia, Chile, Nigeria, Zimbabwe, United Kingdom, France, Germany, Spain, Malaysia, Singapore, Australia, Indonesia, Mexico, Oman, United Arab Emirates as well as comments from the European Commission.

Main themes from feedback
Some respondents expressed concerns that the strategy is not focused enough on food safety and tries to cover nutrition and antimicrobial resistance. Some topics such as food allergens and chemical hazards and risks like aflatoxin were not or rarely mentioned. They said while it highlights the short-term health issues of unsafe food, there is a lack of links to the long-term health effects on child growth and development.

All comments welcomed the setting of global indicators and targets but concerns were also expressed. Some said the targets were too ambitious and should consider the impact of COVID-19 while others wanted a tiered approach given the different regional and national starting points.

Submissions praised the mention of a One Health approach in the draft. However, it should highlight foodborne pathogens and how they move between the environment, animals, and humans.

The section on emerging technologies was not balanced enough with promotion of Whole Genome Sequencing (WGS) questioned by respondents. They said more consideration should be given to the feasibility of adopting new technologies in low resource settings.

People said it was important to show how it will interact with the FAO’s food safety strategy, also due for publication in 2022, and other international organizations.

The WHO global strategy for food safety will be submitted to the executive board meeting in 2022.

(To sign up for a free subscription to Food Safety News, click here.)

Surveillance of salmonellosis in Belgium depends on voluntary referral of human Salmonella isolates to the National Reference Center (NRC). Isolates are accompanied by a form with epidemiological information that includes the age, gender, and postal code of the patient, associated clinical picture and recent travel history.

The work, funded by Sciensano (the Belgian Institute for Health) contributed to a more accurate estimate of the burden of salmonellosis in Belgium and shows the systems help with interpreting surveillance data and trends over time.

Researchers assessed coverage of the NRC surveillance system based on a survey among licensed Belgian medical laboratories in 2019 and a study from 2016 to 2020 using the sentinel network of laboratories surveillance system. The number of labs in this network ranged between 38 and 47 in these five years. Results were published in the journal PLOS One.

WGS potential
Coverage of the NRC surveillance system was estimated to be 83 percent and 85 percent, based on results of the survey and the study. These figures are higher than reported in other European countries such as France and Netherlands.

Molecular subtyping by multiple-locus variable number tandem repeat analysis (MLVA) is routine for the two most important serotypes which are Enteritidis and Typhimurium. Whole genome sequencing is used in cases involving multidrug-resistant, invasive or outbreak-related strains.

High coverage of the NRC surveillance system advocates for the implementation of WGS at this central level to help earlier detection of outbreaks, said researchers.

Changes in laboratory practice such as use of culture-independent diagnostic tests (CIDTs) may impact the current surveillance system that relies upon culture confirmation and referral of isolates. However, the survey found use of CIDTs to identify Salmonella was limited in January 2020 in Belgium. Only five of 113 laboratories used a CIDT such as multiplex PCR to diagnose Salmonella cases.

Survey and study findings
The survey was linked to the mandatory external quality assessment (EQA) in January 2020 for medical labs to assess the quality of laboratory analyses.

It revealed labs do not make a selection based on serotype when sending isolates to the NRC. No regional differences in lab practice were seen that explain the higher incidence of Salmonella Typhimurium in Flanders.

Scientists said they are confident that the observed difference in incidence in serotypes between the different regions reflects the reality and is not because of selective sending of isolates. Possible explanations for the higher incidence of Salmonella Typhimurium in Flanders could be differences in food consumption patterns and/or a higher environmental spread due to abundant pig farms.

The main factors for sending isolates to the NRC were epidemiological reasons, for confirmation and/or antibiotic resistance, and for further serotyping.

The capture-recapture study showed coverage of the NRC surveillance network remained stable in the past five years. Even in 2020, when there was a decrease in Salmonella cases, likely related to the impact of COVID-19, coverage of the NRC surveillance remained high. The NRC database showed 1,631 Salmonella infections in 2020 compared to 2,619 in 2019.

(To sign up for a free subscription to Food Safety News, click here.)

Pathogen Surveillance in Agriculture, Food and the Environment (PATH-SAFE) involves the Food Standards Agency (FSA); Food Standards Scotland (FSS); Department of Environment, Food and Rural Affairs (Defra); Department of Health and Social Care (DHSC); Public Health England (PHE); and the Environment Agency.

The aim is to establish the infrastructure and sampling frameworks needed to monitor the source and spread of foodborne pathogens and antimicrobial resistance (AMR) genes between the environment, animals, food and people.

Three-year project
Professor Robin May, chief scientific adviser for the FSA, said: “This project is designed to help safeguard UK food, agriculture and consumers by using cutting edge technology to understand how pathogens and AMR spread. Tracking the source of these issues will ultimately help us to develop better control strategies to reduce illness and deaths.”

May mentioned the project while presenting an annual update to the FSA Board earlier this year.

Professor Gideon Henderson, chief scientific adviser for Defra, said: “UK sales of antibiotics for food-producing animals have halved in the last six years. This vital new project will build on that progress, and ensure antibiotics continue to remain effective for both people and animals.”

Professor David Gally, FSS chief scientific adviser, said: “The funding will allow the UK to build on its expertise in whole genome sequencing of infectious diseases to improve our knowledge of the origins and threats posed by pathogens and AMR in our environments and the food chain, and help us to target control strategies for protecting public health.”

Government funding of almost £20 million ($26.7 million) will support the three-year project to develop a pilot national surveillance network, using DNA-sequencing technology and environmental sampling to improve the detection and tracking of foodborne and antimicrobial resistant pathogens through the agricultural food system from farm to fork.

It will include a new database to allow the analysis, storage and sharing of pathogen sequence and source data collected from locations across the UK by government and public organizations.

Neil Woodford, deputy director, National Infection Service, Public Health England, said: “Our ongoing and established surveillance work of antibiotic resistance in samples from patients with gastrointestinal infections will form an important part of this joint initiative and help ensure that information is shared across the system.”

Consumer survey results
Meanwhile, the FSA has published findings from a survey measuring self-reported knowledge, attitudes and behaviors on issues including food safety amongst adults in England, Wales, and Northern Ireland. It was conducted between November 2020 and January 2021 with 5,900 adults.

Most respondents had no concerns about the food they eat. Of those that had concerns, the most common concerns related to food production methods and food safety and hygiene.

From a list of 10 options, people were most concerned about the amount of sugar in food and food waste but food poisoning and food fraud or crime were also mentioned by about half of respondents.

People were more likely to report confidence in farmers, shops and supermarkets than in takeaways and food delivery services.

Of respondents who reported having a food allergy, 35 percent had an allergy to fruit.

When asked about changes in eating habits in the past 12 months, 16 percent had bought food close to its use-by date more, 9 percent kept leftovers for longer before eating and 8 percent had eaten food past its use-by date more. Of those who had changed eating habits for financial reasons, 21 percent had kept leftovers for longer before eating and 17 percent had eaten food past its use-by date more.

Almost half of respondents had eaten bagged salad or cheese past their use-by dates in the past four weeks. One quarter of people reported they had eaten eggs past the best before date in the past month. A third of respondents wash raw chicken at least occasionally, which goes against the advice of food safety experts.

(To sign up for a free subscription to Food Safety News, click here.)

Weidmann’s presentation was part of the Center for Produce Safety’s Session IV of its Research Symposium webinar series. Moderated by Senior Vice President of United Fresh Produce Association Jennifer McEntire, the session included research reports, research posters and a Q and A period. 

The featured presentation by Wiedmann, Ph.D., Gellert Family Professor of Food Safety at Cornell University, was titled, “Outbreaks: Past, Current, and Future with WGS Data.”

Wiedmann’s session focused on how WGS is being used by the FDA, CDC, FSIS and others to detect foodborne outbreaks. He stressed that identification and announcement of outbreaks without clear sources can lead to something he calls ‘WGS innuendo,’ which is coming to conclusions and making assumptions without the complete picture.

The ease and accessibility of data sharing of WGS have led to these innuendos. “Again this is something everyone can do, you don’t need a password, you don’t need permission,” Wiedmann said. 

Clear and accurate communication of WGS data is important because it can easily be misinterpreted and lead to the so-called innuendos.

Wiemann provided some action steps that industry can take:

• Have someone in your company or affiliated with your company that knows how to utilize and search NCBI Pathogen Detection;
• Set up alerts for WGS clusters of concern;
• Have a plan for what to do when you get “the call” from FDA or CDC; and
• Plan when, where and how you can utilize WGS data.

Research Reports

• “Analysis of the presence of Cyclospora in waters of the Mid-Atlantic States and evaluation of removal and inactivation by filtration.”

Kalmia Kniel, Ph.D, Professor of Microbial Food Safety, University of Delaware.

Kniel’s research project has two main objectives, to provide an understanding of the impact of C. cayetanensis on waters in the Mid-Atlantic region of the United States, and elucidate the efficacy of ZVI filtration in the removal and inactivation of parasitic pathogens to improve pre-harvest food safety.

The full abstract can be viewed here.

• “Illuminating the role of whole genome sequencing in produce safety.”

Kerry Cooper, Ph.D, Assistant Professor of Animal and Comparative Biomedical Sciences, University of Arizona.

The goal of Cooper’s research is to determine the mutation rates of Salmonella, Listeria, and Escherichia coli O157:H7 during long-term persistence in agricultural soil and irrigation water maintained under different geographical conditions.

The full abstract can be viewed here.

• “Investigation of potential pre-harvest and post-harvest treatments targeting Salmonella spp. risk reduction on peaches in Australia.” 

Kim-Yen Phan-Thien, Ph.D., Lecturer in Food Science, University of Sydney. 

Phan-Thien’s research was a rapid response to last year’s Salmonella outbreak linked to peaches in North America.

The full abstract can be viewed here.

• “Environmental microbial risks associated with vented produce in distribution centers.” 

Laurel Dunn, Ph.D, Assistant Professor of Food Science & Technology, University of Georgia.

Food Safety News reported on this research in Dec. 2020.

This full abstract can be viewed here.

(To sign up for a free subscription to Food Safety News, click here.)

The European Centre for Disease Prevention and Control (ECDC) hosts the Epidemic Intelligence Information System for food- and waterborne diseases (EPIS-FWD) platform, which includes Urgent Inquiries.

Urgent inquiries (UI) are launched by countries or ECDC to assess the potential multi-country aspect of national events.

Salmonella main issue
In 2020, 72 urgent inquiries were initiated compared to 88 in 2019, the highest number since the platform was launched. This past year, alerts came from 16 of 52 countries in the network and one on vibriosis was started by ECDC. Almost half were due to Salmonella.

Overall, they related to salmonellosis, listeriosis, Shiga toxin-producing E. coli (STEC) infection, hepatitis A, shigellosis, campylobacteriosis, yersiniosis, botulism, norovirus, psittacosis, tick-borne encephalitis virus and vibriosis. On average, 10 countries replied to each alert.

There was a reduction in detection and response to food and waterborne outbreaks in the first weeks of COVID-19 but the number of incidents being monitored increased during summer and autumn. In 2020, supporting the European COVID-19 response became the main activity of the agency, consuming most of its time and resources.

A six-month inquiry into the performance of ECDC during the pandemic by the European Ombudsman found gaps in transparency practices and a need to improve data received from national authorities.

EPIS is to be replaced by an Event and Threat Management Solution (ETMS), a new tool for detecting and managing events and threats.

WGS developments
By the end of 2020, nine countries were submitting whole genome sequencing listeriosis surveillance data routinely, and eight nations as part of outbreak investigations. In total, 28 possible multi-country clusters of Listeria monocytogenes were detected in Europe. Of these, 16 were found by member states through an UI and 12 by ECDC.

National contact points for food- and waterborne diseases met virtually in March 2020 and discussed the potential cross-border spread of Campylobacter. Later in the year, Sweden launched an UI and the first, WGS-verified cross-border spread of Campylobacter infections was confirmed involving Sweden, Denmark, Norway and Luxembourg.

In 2020, ECDC published two outbreak assessments with the European Food Safety Authority (EFSA): a third update on a multi-country Salmonella Enteritidis outbreak linked to eggs and one on Salmonella Typhimurium and Salmonella Anatum infections linked to Brazil nuts.

ECDC developed a system for the collection, management, analysis and storage of whole genome sequencing data that will allow for real-time analysis and visual comparison of sequences to identify common strains and detect outbreaks. It will first be applied to pathogens including Listeria, Salmonella and STEC. Publication was put back because of the pandemic but is set for this year.

Preparatory work on collecting and analyzing WGS data from human and food isolates continued in 2020. In the future, ECDC and EFSA databases will remain separate, but exchange data in real time to search and detect sequences among human and non-human isolates.

(To sign up for a free subscription to Food Safety News, click here.)

The study showed that roughly half of human infections belong to genetic clusters, almost one third of clinical isolates match a chicken source, and most large clusters can be linked to poultry by WGS.

Researchers hope the knowledge and awareness raised will lead to a decrease in the Danish chicken-associated cases of campylobacteriosis in coming years.

Denmark had 5,389 cases in 2019 and 33 percent of conventional chicken meat samples were positive for Campylobacter at slaughter. One third of infections are estimated to be travel-related.

Typing-based surveillance of Campylobacter infections in 2019 enabled detection of large clusters and matched them to retail chicken isolates to react to outbreaks. Surveillance was also able to detect prolonged or reappearing outbreaks to help earlier interventions, according to the study published in the journal Eurosurveillance.

Sample findings
Scientists used WGS on 701 isolates from infected people and 164 from chicken meat. The primary focus was on one area, northern Jutland, but isolates from Funen and Zealand were also included.

Campylobacter isolates from Danish Veterinary and Food Administration control programs were sequenced and compared with clinical isolates. Fresh chicken and beef were sampled at stores in northern Jutland and at distribution centers covering retail chains while organic and free range broilers were sampled at slaughterhouses.

For the WGS-based surveillance, 626 clinical Campylobacter jejuni and Campylobacter coli isolates were collected. Also, 75 isolates from October 2018 through February 2019 were included as a follow-up on an outbreak. The study represented 12.4 percent of all reported cases in 2019.

Campylobacter was detected in 22 percent of 909 retail chicken meat samples. In total, 163 of 852 Danish-produced samples were positive as were 33 of 57 non-Danish samples.
Campylobacter was found in 84 of 123 skin samples from organic and free range broilers. A total of 128 isolates from food samples and 36 isolates from control samples at the slaughterhouse as part of the outbreak investigation were sequenced.

Some strains were only present in chicken meat or people for a few weeks or months, whereas occurrence of other strains fluctuated over time in a way that could be related to the production cycles in each farm.

Outbreak detection
Seventy-two clusters were detected with most being small at between two to four people but 14 large ones involved five to 91 patients.

The largest cluster included 91 people. It was detected at the beginning of surveillance in March 2019, and continued during the whole year, peaking from May to August. A retrospective analysis showed this strain was found in patients in October 2018.

The cluster matched four chicken isolates from retail meat sampled in May and August 2019. These isolates were traced back to a single slaughterhouse belonging to HKScan in Vinderup. An additional 30 isolates were found: 20 from meat samples at the slaughterhouse between late February and August 2019 and 10 from the slaughterhouse environment in late October.

Results supported a link between the outbreak strain and one farm. From August 2019, the slaughterhouse decided that meat from this farm should be frozen to reduce the level of Campylobacter. It also outlined an action plan for optimizing procedures and equipment.

A few cases with the outbreak strain were seen in the beginning of 2020 and it is possible it had spread to multiple farms or other slaughterhouses.

Certain issues identified by researchers included follow-up on each genetic cluster of Campylobacter is not feasible because of the large number, which would require a lot of resources and the time factor, as most cluster types have already disappeared before it is possible to take action.

Also, WGS-based surveillance of human infections without the comparison to food isolates is of limited public health value.

(To sign up for a free subscription to Food Safety News, click here.)

The virtual event was organized by the Food and Agriculture Organization of the United Nations (FAO) and World Health Organization (WHO) to mark the third annual World Food Safety Day.

FAO Director General QU Dongyu and WHO Director General Tedros Adhanom Ghebreyesus gave video messages at the session that more than 600 people attended.

“Nobody should die from eating food. These are preventable deaths. When food safety is improved we reduce hunger, malnutrition and infant mortality. Children miss fewer days at school, adults increase their productivity, and the strain on health systems is reduced,” said Ghebreyesus.

Understanding risk and hazards
Soumya Swaminathan, chief scientist at WHO, said science is central to food safety.

“It is important to understand the nature and level of hazards in the food chain because your interventions to ensure food safety depend on understanding, which will have the most impact in reducing the risk,” she said.

“For example, microbiological hazards can multiply or diminish and the risks to consumers depends on how much exposure there is by the time the food reaches the point of consumption. In contrast, levels of chemical hazards generally remain constant once introduced into the food.

“One of the priorities for WHO is to help member states make evidence-informed decisions on risk management. Scientific advice provided by the WHO and FAO to Codex is critical for the development of food safety international standards.”

Swaminathan said when addressing any issue it is important to understand what it is, where it is and the burden of the problem.

“Not all countries have good data systems to capture this so one of our focuses has been on strengthening health information and data systems so countries can start capturing data on what is happening to their populations. We then need to understand the nature of the risks and where contamination may be happening,” she said.

Role of technology emphasized
Whole genome sequencing should be used more widely in food safety, according to Swaminathan.

“We know by sequencing the contaminant and uploading the sequences into public databases, scientists around the world will be in a better position to be able to track and estimate which pathogens are causing problems where and track the origins of some of these contaminants. WGS has become more widely available but it’s still limited in many countries. One of the lessons from the pandemic is we need to invest in laboratory science, training bioinformatics experts and molecular biology,” she said.

“We need explicit targets and indicators to measure progress because we all know what cannot be measured cannot be managed and measuring performance, results and impact is important for any program. These indicators help countries when they do self-assessment to identify strengths and weaknesses as well as measure improvements.”

Ismahane Elouafi, chief scientist at FAO, mentioned the agency’s food safety strategy which is in development and the recently published Microbiological Risk Assessment Guidance for Food, which provides a framework to assess the risk of microbiological hazards using different techniques.

“There is an increasing role of new and emerging technologies in food production, post-harvest treatment, processing, packaging and sanitary treatment. One of the major technologies we need to use properly is whole genome sequencing and also gene editing. WGS allows us to understand better in epidemiological surveillance, food testing, monitoring and outbreak investigation but we need to do more. We need policies and regulation to provide a better environment to use those technologies to protect us and increase the safety of our food systems,” Elouafi said.

“We need to use more artificial intelligence, blockchain and intelligent packaging that can ensure food is authentic, safe and of good quality from the farm level to the consumer.

“We are in an era where we have the ability to gather and analyze big data and connect the different things. We didn’t have that power 10 years ago. The last technology I want to mention is nanotechnology. We are able to see and change things that are very small. Cell-based meat and lab-grown dairy are new technologies we need to invest more in and put them in perspective and provide with the safety net, the right policies and the right connections.”

(To sign up for a free subscription to Food Safety News, click here.)

Researchers evaluated costs and benefits of routine WGS through case studies at eight laboratories in Europe and the Americas, including five which work with foodborne pathogens. All labs reported benefits from using WGS for pathogen identification and surveillance.

Work focused on the investment case for implementing WGS compared with conventional methods, based on costs and benefits in different periods between April 2016 and April 2019. For the five labs that do surveillance of foodborne pathogens, the reference period was typically a year.

These institutions — Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna (IZSLER, Italy), Administración Nacional de Laboratorios e Institutos de Salud (INEI-ANLIS, Argentina), Maryland Department of Health (MDH), Public Health Agency of Canada (PHAC), and Public Health England (PHE) — use WGS for characterization of bacterial isolates in pathogen surveillance, mostly Salmonella, Listeria, E. coli and Shigella.

In the 12-month period, IZSLER did 175 routine surveillance samples, INEI-ANLIS did 320, MDH did 1,767, PHAC did 8,630 and PHE did 15,791, according to the study published in the journal Eurosurveillance.

Higher costs vs. more info
Costs considered included equipment, consumables, staff and other expenses directly accrued by the institutions. Cost of equipment for the WGS workflow in the year of purchase ranged from €75,000 ($91,400) to €3.2 million ($3.9 million) for several sequencers and custom bioinformatics infrastructure.

The economic evaluation compared costs of using WGS to processing the same number of samples with the next-best conventional methods for pathogen identification and characterization.

Overall per-sample costs of WGS exceeded the price of conventional methods in all labs analyzed. Use of WGS was between 1.2 and 4.3 times more expensive. The average cost for the five reference labs that used WGS for routine surveillance of foodborne pathogens was €209 ($255) per sample.

Foodborne labs often relied on less costly equipment for conventional methods than the other sites and had a greater difference between the equipment costs for WGS and for conventional methods.

IZLER reported that the introduction of WGS had changed how food safety officials conduct sampling, by moving from looking at products to environmental sampling.

For foodborne pathogens, WGS analysis provided insights into how bacterial strains diversify over time, allowing strains to be identified as linked when they would have been considered unrelated under previous methods, according to PHE.

Outbreak detection impact
Labs that used WGS in routine surveillance of foodborne pathogens said there was a simplification of workflows and a reduced number of hands-on steps for analysis. The usual turnaround time was 5 to 10 days for WGS analysis. The time for full analysis of a foodborne pathogen using conventional methods was typically 4 to 15 days, depending on the pathogen and analysis required.

WGS affected the number and size of clusters detected and can reduce cases of illness, if public health systems are equipped and adequately funded to take effective measures. Clusters identified with conventional methods were confirmed or split with the help of sequence data, and a larger number of smaller outbreaks was found.

PHAC reported the number of Listeria outbreaks detected had decreased in the first year of WGS implementation, as PFGE had been detecting ones that did not exist and had led to an inefficient use of resources investigating non-existent outbreaks.

WGS allowed PHAC to identify 17 separate outbreaks of Salmonella Enteritidis infections associated with raw frozen breaded chicken products, which had not been picked up with conventional methods.

For the five labs that conduct Salmonella surveillance, researchers calculated the number and proportion of reported cases of salmonellosis that would need to be avoided to make use of WGS cost-neutral. The annual number to break even on costs ranged from one within INEI-ANLIS’ area of jurisdiction in Argentina to 82 within PHAC’s area of Canada.

The break-even analysis indicates that for Salmonella surveillance, only a modest percentage of reported salmonellosis cases would need to be avoided each year through the use of WGS to make adoption of the technology cost-neutral from a public health perspective, according to researchers.

The research took place through the COMPARE EU project funded by Horizon2020 that began in 2014 and ended in 2019.

(To sign up for a free subscription to Food Safety News, click here.)

An international outbreak investigation is ongoing and the European Centre for Disease Prevention and Control (ECDC) is helping with cross-border coordination.

Between March 26 and April 26, 24 cases of Salmonella Braenderup have been reported to the Statens Serum Institut in Denmark. Those affected live all over the country with 17 women and seven men aged 1 to 90 years old sick. The median age is 67 years of age.

Work is underway to clarify the cause of the outbreak and identify the source of infection, which is suspected to be a widely distributed food.

Whole genome sequencing found the strains were sequence type 22 and closely related to each other. That means a single source is likely.

Earlier this month, the Public Health Agency of Sweden (Folkhälsomyndigheten) reported that a Salmonella Braenderup outbreak had affected 14 people in less than two weeks in 10 different regions of the country.

Sweden now has 22 confirmed cases, 17 females and five males, between less than 1 to 91 years old. The median age is 40. Onset of disease ranges from April 13 to May 1.

The Swedish Food Agency (Livsmedelsverket) and the Public Health Agency of Sweden are involved in the outbreak investigation.

About Salmonella
Food contaminated with Salmonella bacteria does not usually look, smell, or taste spoiled. Anyone can become sick with a Salmonella infection. Infants, children, seniors, and people with weakened immune systems are at higher risk of serious illness because their immune systems are fragile, according to the CDC.

Anyone who has developed symptoms of Salmonella infection should seek medical attention. Sick people should tell their doctors about the possible exposure to Salmonella bacteria because special tests are necessary to diagnose salmonellosis. Salmonella infection symptoms can mimic other illnesses, frequently leading to misdiagnosis.

Symptoms of Salmonella infection can include diarrhea, abdominal cramps, and fever within 12 to 72 hours after eating contaminated food. Otherwise, healthy adults are usually sick for four to seven days. In some cases, however, diarrhea may be so severe that patients require hospitalization.

Older adults, children, pregnant women, and people with weakened immune systems, such as cancer patients, are more likely to develop a severe illness and serious, sometimes life-threatening conditions. Some people get infected without getting sick or showing any symptoms. However, they may still spread the infections to others.

(To sign up for a free subscription to Food Safety News, click here.) 

Two closely related types of Salmonella Typhimurium, called U288 and sequence type (ST) 34, are particularly dominant in pigs and differed in colonization of the intestine and surrounding tissues and severity of disease they produced. The ST34 variant accounts for more than half of all UK human Salmonella Typhimurium infections, while U288 is rarely associated with human infection.

Professor Rob Kingsley from the Quadram Institute and professor Mark Stevens from the Roslin Institute worked with scientists at the Earlham Institute to look at common variants of Salmonella in pigs in the UK.

Using whole genome sequencing the research team found that the two types of Salmonella Typhimurium have been circulating in UK pigs since 2003. Researchers previously examined the emergence and spread of Salmonella in pigs.

Predicting risk and control strategies
In the pork industry, it can impact the health and welfare of pigs and have potential effects on productivity. Salmonella Typhimurium is relatively common in pig herds and processes at slaughterhouses try to prevent contamination of meat destined for the food chain.

Findings from the study, published in the journal Communications Biology, could help to predict the risk of Salmonella variants to animals and people, and help strategies to prevent or control infections.

“Understanding how variants of Salmonella emerge and pinpointing the genetic signatures responsible for adaptation to different hosts and the ability to produce disease will provide opportunities to improve diagnostics and surveillance. In turn this will help to predict the risk that Salmonella variants pose to animal health and food safety,” said Stevens.

The study analysed the genetic makeup of Salmonella strains isolated from pigs and people, to identify variants and understand how they evolved and behave. Samples were collected from human clinical infections during routine diagnosis and from animals during routine surveillance.

This included 1,826 Salmonella Typhimurium isolates from human infections in England and Wales between April 2014 and December 2015 and 79 Salmonella Typhimurium U288 strains isolated from animals in the UK in 2014 and 2015 as part of APHA surveillance and 77 others from 2005 to 2016.

Strain differences
Work involved Public Health England and the Animal and Plant Health Agency (APHA) and was funded by the Biotechnology and Biological Sciences Research Council.

Considerably more viable ST34 bacteria were recovered following desiccation for 24 hours, compared to U288. Monophasic Salmonella Typhimurium ST34 also replicated at a higher rate than U288 in culture, a trait that experts said may result in a higher level of contamination in food.

The U288 variant evolved to acquire genes associated with antimicrobial resistance and variations in molecules linked to virulence as well as growing slower in the lab.

“We have seen these types of changes before in variants of Salmonella that have become adapted to specific host species and cause a more invasive disease, including the type of Salmonella that causes typhoid fever in people but does not affect other species,” said Kingsley.

“One of the interesting findings is just how rapidly pathogens can adapt, and how even a few genomic changes can lead to very different disease outcomes,” said Dr. Matt Bawn, a researcher on the study based at the Earlham Institute and Quadram Institute.

(To sign up for a free subscription to Food Safety News, click here.)

Consumers, industry and governments typically desire foods that are free of any risk but scientists said zero risk is unattainable in food production regardless of the severity of inactivation treatments or stringency of sampling programs.

Risk-based approaches such as Microbial Risk Assessment (MRA) are increasingly used to manage food safety hazards, evaluate risks and identify control strategies that reduce risks to an acceptable level.

Researchers Marcel Zwietering, Alberto Garre, Martin Wiedmann and Robert Buchanan presented the study, published in Current Opinion in Food Science, at IAFP Europe.

They defined residual risk as what remains even after a fully compliant food safety system has been implemented. Every product has a residual risk but severity varies because it depends on a variety of factors such as the perspective or consequences.

Traditional sampling limitations
Researchers said if decisions were based only on testing, it could falsely be concluded that if a hazard has not been detected, the associated risk must be zero.

“As an example, the fact that a given pathogen has never been detected in a product does not ensure that the implemented safety controls assure a hazard-free or zero risk product,” according to the researchers.

“Because sampling is limited, it is feasible that the microorganism entered the system at some point, but it was not yet detected or identified. Alternatively, it is also possible that the hazard has not yet entered the system, but that does not ensure it will never in the future. The absence of a positive is no proof of the absence of risk in the current, past or future.”

Researchers gave the example of the risk of Salmonella in chocolate bars assuming contamination of one Salmonella enterica cell per 10,000 of 25,000 bars of 25-grams, and that the company produces 100,000 bars a day. Testing is limited to five samples per day, each sampling unit is a whole bar, and probability of a false negative or false positive is zero.

“The probability of detecting Salmonella in each sampling unit equals 0.01 percent, and the probability of detecting it in the product in a given day is 0.05 percent. In other words, we expect a single positive every 5.5 years. On the basis of this result, it could seem reasonable to conclude that the risk of salmonellosis is insignificant.

“However, a single cell of Salmonella enterica has a probability of causing illness that has been estimated to be 1 case per 400. Therefore, if we consider that 10 bars of the 100,000 daily production contain a single Salmonella enterica cell, the expected number of yearly cases of salmonellosis is 9.125, a value that is certainly not insignificant. Although sampling will rarely show a positive, there is clearly a residual risk.”

Better tech and more production
Researchers said between large scale production lots with low levels of a pathogen and modern molecular epidemiology systems, there could be detection of an outbreak at levels below that which a manufacturer can verify by traditional testing. This was illustrated using the Salmonella and chocolate example.

Increases in the scale of manufacturing for dry products means production may take place over multiple days, weeks, or months without a break for complete hygienic cleaning of a facility. Globalization and the development of worldwide distribution increases the likelihood that a single, multi-day production lot could be sent to multiple countries, according to the study authors.

Improved surveillance systems such as those using whole genome sequencing can detect small outbreaks and potentially link cases to a product, even when they are consequences of residual risk rather than a non-compliant food safety system.

“This leads to the potential policy gaps when regulatory agencies or food distributors/retailers provide realistic and practical testing guidelines and specifications for foods that are substantially less stringent than the ability to detect a low-level outbreak after literally millions of servings have been consumed by the public. This hypothetical example shows how residual risks of microbial hazards is to be topic of substantial debate and legal challenges in the coming decades,” according to the study.

(To sign up for a free subscription to Food Safety News, click here.) 

Marta Hugas, from the European Food Safety Authority (EFSA), said regulatory agencies face challenges ranging from current priorities, such as tackling AMR and food waste, to identifying emerging risks, where methodologies or data may be lacking, such as microplastics in the food chain.

Hugas told attendees at IAFP’s European Symposium there are difficulties when providing scientific advice to policy makers and the public.

“First of all is the complexity, every time the volume of evidence keeps increasing so assessing thousands of papers takes a lot of time. We are experimenting with using Artificial Intelligence for pre-selection of papers and adding some inclusion and exclusion criteria. The methodologies are also evolving and we need to be able to capture and apply this methodology,” she said.

“Societal expectations are also very demanding. They want us to have a holistic approach, so not to look at pesticide by pesticide but the whole exposure of chemicals to public health. Also, they want us to be transparent so they can scrutinize what we do and at the same time, the desire to participate, which is valid but poses some challenges on how to organize that.”

Emerging risks and novel food
Policy developments such as the EU’s Green Deal and product innovation like novel foods require risk assessors to identify potential issues and then advise risk managers to protect European consumers from food-related risks.

One of EFSA’s tasks is emerging risks identification and the Emerging Risks Exchange Network (EREN) met this past month to discuss topics including the health risks of coconut oil, prohibited pesticide residues in food and Shiga toxin producing E. albertii.

“We identify an emerging risk when there is a new hazard that may pose a risk to health with adverse effects or it is a known hazard that has changed with increased exposure, the population has increased susceptibility, the hazard has increased pathogenicity or toxicity or product composition or intake has changed,” said Hugas.

“Initially we call them issues as we don’t know if they are risks or not. We use a process with expert knowledge and literature to help us identify if it may become an emerging risk. However, there is a lot of uncertainty so it is important not to create concerns.”

Hugas said it can be difficult to assess innovation in the food sector.

“Industry is ahead and experimenting with innovation in their products. When an innovative product comes to us we need to be ready with a methodology to assess that product. One of these is alternative proteins, today there is a market and consumer drive for diversification of available proteins also to be less dependent on animal proteins. When we assess applications for novel foods, the focus is on the safety of the product taking into account its intended use,” she said.

AMR and the circular economy
A recent report found resistance levels still were high in bacteria causing foodborne infections.

Hugas said antimicrobial resistance contributes significantly to the burden of disease and is a threat to public health.

“In EFSA we keep working on AMR. We see that it doesn’t really improve a lot so we need to keep investing efforts in reducing consumption. In a report from several years ago it was clear that to combat AMR, we need to reduce the use of antimicrobials and replace them by other substances and rethink the way husbandry systems are implemented in the EU.”

When asked what upcoming hazards in the food chain might be, Hugas said AMR could be the next pandemic if controlling resistance and the usage of antimicrobials is not taken seriously.

In 2020 to 2021, EFSA launched three projects to identify emerging risks related to the circular economy, food fraud, and new food and feed sources and production techniques.

The EU Green Deal calls for a circular economy and while this brings positives there may be some vulnerabilities, said Hugas.

“We have commissioned a project which aims to identify vulnerabilities of the circular economy for food and feed safety, plants and animal health and the environment. We know we have to be vigilant as in the past a threat to public health came from the BSE crisis. We need to be aware of possible disadvantages to prevent them as far as possible.”

Sector’s WGS approach
Another session at the event discussed Whole Genome Sequencing (WGS) from an industry perspective. The Forum for Food Microbiology is a network including 45 members from 28 companies that has quarterly meetings and will soon publish a guidance document.

Adrianne Klijn, of Nestlé, presented findings from a workshop and survey in 2019 involving 33 people from 18 companies although a further 12 firms declined the opportunity.

The included businesses were Arla Foods, Bonduelle, Cargill, Church Brothers Farms, Conagra Brands, Danone, Darling Ingredients, DSM, Fonterra, Greenyard, Hochdorf, Kerry, Kraft Heinz, Mars, Mondelëz International, Nestlé, Unilever, and Vion Food Group.

In total, 83 percent said they used WGS either frequently or infrequently. However, 12 said they were still using serotyping routinely meaning it was unlikely WGS will replace all other typing tools in the near future. Klijn said there are good subtyping tools for Salmonella but there is room for improvement when it comes to Listeria and Cronobacter.

Lab cross contamination is a good example of where the discriminatory power of WGS is needed, according to Klijn.

From 16 companies, 15 said they were only using WGS for pathogen source tracking while just a few were doing it for strain characterization.

The survey and workshop found the laboratory part is mostly outsourced with only two having in-house sequencing. Most used Illumina sequencing platforms. Bioinformatics was split three ways between in-house, outsourcing and doing both.

“The authorities deal with positive samples with isolates all the time, in the food industry we have a lot less positive samples, so we have fewer isolates and this low sample throughput means the cost per analysis is high with a low return on investment in the equipment. The reason [bioinformatics] is less outsourced is there is a lack of method standardization and analyzing the data in house will ensure a consistent approach,” said Klijn.

Barriers that remain include the regulatory pressure to share WGS data, absence of a legal framework, a lack of clarity on data ownership, time to result and total cost including equipment, IT infrastructure and expertise in sequencing, bioinformatics and microbial genomics.

(To sign up for a free subscription to Food Safety News, click here.) 

The national food poisoning outbreak highlights the potential for a multi-drug resistant strain of Shigella sonnei to be transmitted via a food vehicle that is distributed across a wide geographic area, according to the accepted manuscript in the journal Epidemiology and Infection.

It was linked to food at multiple restaurants in different areas that were not part of a franchise. Whole genome sequencing helped the identification of potential links between the restaurants.

Poor hygiene practices during cultivation, distribution or preparation of fresh produce were likely contributing factors to the contamination, said researchers.

Found to be related incidents
In March 2018, Public Health England was told of Shigella sonnei infections in people who had eaten at three different catering outlets in England. The outbreaks were initially investigated as separate events but whole genome sequencing showed they were caused by the same strain.

A total of 33 patients, linked to seven different venues specializing in Indian or Middle Eastern cuisine were identified. Five outlets were linked to two or more patients. All outlets used fresh coriander, although a shared supplier was not found.

Two-thirds of confirmed cases were male. The age of patients ranged from 12 to 59 years old. Symptom onset dates for the bulk of them ranged from March 26 to April 3, 2018. Four people were hospitalized for between two and five nights.

Patients were exposed at the implicated venues between March 24 and 31, 2018. The earliest exposure was at a site in Bedford, followed by venues in the West Midlands and two sites in Bradford.

Environmental health officers noted poor temperature control and cleaning standards plus a lack of hand hygiene facilities at one of the West Midlands outlets. It had a food hygiene rating of 1. Following the outbreak, the restaurant was refurbished, and given advice on kitchen routing improvements.

Food traceback investigations revealed fresh coriander leaves were the only common ingredient supplied to all venues attended by patients. In total, 86 percent of cases in the cohort study reported eating dishes containing coriander.

Three venues purchased fresh coriander from local markets and the other bought it from a national supermarket chain. It was not possible to identify where the coriander was grown.

Likely point of contamination
The outbreak control team said the most plausible explanations for the outbreak were either coriander was contaminated at the point of production or during wholesale distribution.

Bulk supplies of coriander entering the wholesale market are broken down into smaller batches or bunches at multiple locations. This is done by hand, providing an opportunity for contamination by an infected food handler. There was no evidence infected food handlers contaminated the coriander in restaurants as none were known to be sick.

Because of the time-lag between local identification of outbreaks and confirmation by WGS, coriander leaves were not sampled as part of initial outbreak investigations.

Food samples were collected six and nine days after patient exposures, making it unlikely that they were the same batch as people had consumed prior to onset of illness.

Analysis of WGS data also demonstrated a close association between the outbreak strain and isolates from UK cases with recent travel to Pakistan.

(To sign up for a free subscription to Food Safety News, click here.)

A total of 142 cases of listeriosis were reported in England and Wales compared to 157 the year before. This represents an 11.5 percent decline versus the average number in the preceding six years.

There were four outbreaks of listeriosis investigated in England in 2019. For two of them, with three and two clinical cases, the source of infection was unknown. One international outbreak involving five people from 2018 to 2019 was linked to pork products of Romanian origin.

Listeria sandwich outbreak
The other involved prepacked sandwiches served in National Health Service (NHS) hospitals. This outbreak was detected in North West England after two patients were infected with Listeria monocytogenes in the same hospital and subsequently died. Other cases were later identified across seven NHS Trusts using whole genome sequencing (WGS).

Between May 16 and June 14, 2019, nine confirmed cases associated with the outbreak were identified and seven people died. All nine received care at hospitals supplied by The Good Food Chain, the implicated sandwich manufacturer. Consumption of prepacked sandwiches from this company was confirmed for eight people.

Listeria monocytogenes isolates from chicken sandwiches and cooked chicken samples supplied by the sandwich manufacturer and a meat producer called North Country Cooked Meats were confirmed as the outbreak strain by WGS analysis.

May was the peak month for listeriosis reporting in 2019, with the outbreak influencing this result. In 2017 and 2018 numbers peaked in July, with no outbreaks in those months.

Overall, age-specific incidence rates were highest in people 80 years and over. Of 26 cases in the 10 to 19, 20 to 29 and 30 to 39 age groups, 24 were female, of which 19 were associated with pregnancy.

Severe outcome
The outcome of listeriosis during pregnancy remains severe with a third of infections resulting in miscarriages or stillbirths. In 2019, 25, which is less than a fifth of cases, were associated with pregnancy which was comparable to previous years. Amongst pregnancy-associated cases, 64 percent of pregnancies resulted in live births and 36 percent in stillbirth or miscarriage.

There were 23 deaths among 117 non-pregnancy cases, compared to an average of 43 deaths among reported cases from 2013 to 2018.

Of the 23 fatalities, 15 were known to have listeriosis recorded as a cause on the death certificate. This represented a fatality rate of 12.8 percent, compared to 8.5 percent in the previous year.

London had the highest incidence rate with 35 infections whilst the East of England had the lowest with seven patients. Wales recorded three cases.

Incidence of listeriosis was lower in men than women, but reports among men aged 60 to 69 were seven times higher than women in this age range.

Five incidents were investigated involving sporadic cases in 2019 that were microbiologically linked to food or a food environment by detection of the same strain of Listeria monocytogenes by whole genome sequencing.

“As a predominantly foodborne infection, this severe disease is largely preventable. It remains imperative that sporadic cases of illness and clusters of disease continue to be monitored and investigated to inform the continued risk assessment of the food chain,” according to the report.

About Listeria infections
Food contaminated with Listeria monocytogenes may not look or smell spoiled but can still cause serious and sometimes life-threatening infections. People with symptoms of Listeria infection should seek medical treatment and tell their doctors about any possible Listeria exposure.

It can take up to 70 days after exposure to Listeria for symptoms of listeriosis to develop.

Symptoms of Listeria infection can include vomiting, nausea, persistent fever, muscle aches, severe headache, and neck stiffness. Specific laboratory tests are required to diagnose Listeria infections, which can mimic other illnesses.

Pregnant women, the elderly, young children, and people such as cancer patients who have weakened immune systems are particularly at risk of serious illnesses, life-threatening infections, and other complications.

(To sign up for a free subscription to Food Safety News, click here.)

The three-year strategy is part of a series of steps taken by authorities, including funding a project and organizing an event, to prevent another outbreak.

Phases 1 and 2 of the control plan for Listeria Monocytogenes in Andalusia were developed by the Ministry of Health and Families.

The outbreak caused by La Mecha brand chilled roasted pork produced by Magrudis affected more than 200 people. During the alert between August and October 2019 three people died and there were five abortions.

A first phase covered the last quarter of 2019. In that period, almost 1,500 official controls were carried out with the number of food samples for Listeria doubling to more than 700 and surface samples almost tripled to nearly 400.

The aim was to raise awareness and improve the preparedness of meat companies against Listeria. Authorities said firms now have a more agile response in the event of an incident, through implementation of preventive measures and surveillance of production environments and surfaces.

Second phase
The Ministry of Health and Families developed guidelines for the control of Listeria in meat products for Andalusian companies in the sector and those involved in official controls.

The second phase, during 2020, involved characterizing all companies and their products with respect to the risk of Listeria and including this information in the official control database. Work included evaluating the effectiveness of controls adopted by the companies; verifying compliance with Listeria limits; and increasing effectiveness of official controls.

Phase 2 was extended to all those that put food at risk of Listeria contamination on the market, including the fish, dairy and vegetable sectors. The number of tests is above what was planned in 2019 with more than 1,100 Listeria samples in Andalusia for 2020. Analytical results showed 11 positives from 704 samples in 2019 and 15 positives out of 1,135 samples in 2020.

Tracking and monitoring systems have been modernized with whole genomic sequencing of Listeria strains, training and use of the FoodChain-Lab software. Work on a third phase, covering 2021 and onward, is ongoing.

Andalusian authorities previously set aside €100,000 (U.S. $113,000) for research to learn from the region’s outbreak. The project is looking at the epidemiological, microbiological and clinical aspects of the incident.

In early 2019, nearly 700 experts met in Seville to discuss Spain’s largest ever Listeria incident at the International Symposium on the Andalusian Listeriosis outbreak.

(To sign up for a free subscription to Food Safety News, click here.)

Scientists hope that understanding how and why new strains of Salmonella emerge in livestock will help develop improved strategies to reduce the incidence and make the food supply safer.

Work was led by the Quadram Institute and the University of East Anglia with Public Health England, the Animal and Plant Health Agency, the Earlham Institute, and the Teagasc Food Research Centre. It was funded by the Biotechnology and Biological Sciences Research Council and published in the journal Microbial Genomics.

Viruses are very small packages of genetic material that require cells to replicate this material and cause disease. There are also viruses, called bacteriophages, that use bacteria to replicate and in doing so kill the bacterium. However, some are able to hide inside the bacterial cell by merging with the bacteria’s genetic material.

Helping Salmonella spread
Researchers said this is what happened perhaps hundreds of times during the emergence of one strain which has helped the bacteria spread globally.

This gene is sporadically distributed within Salmonella and rare in Salmonella Typhimurium, but was acquired multiple times during clonal expansion of the currently dominant monophasic Salmonella Typhimurium sequence type (ST) 34 clone.

Monophasic Salmonella Typhimurium ST34 emerged in Europe around 2005, initially in pig populations. Half of all Salmonella infections in the European Union are linked to pigs.

In the UK, more than half of all Salmonella Typhimurium infections are caused by ST34. Salmonella Typhimurium has made up a growing proportion of all Salmonella infections for the past decade, largely due to the emergence of this new strain, according to the study.

Unlike Salmonella Enteritidis that has been largely controlled in layer hen flocks in the UK, little progress has been made on Salmonella Typhimurium. Occasional replacement of the dominant strain of Salmonella Typhimurium causing disease makes it a moving target. So, understanding why new strains emerge and what makes them distinct from previous ones is important to find ways of tackling this pathogen.

Growing dominance
Researchers found the common ancestor of the strain in UK pigs existed around 30 years ago but went unnoticed until 2005 when surveillance by the Animal and Plant Health Agency found ST34 in low numbers. Analysis of the genome sequence from human infections using data from Public Health England indicated that a bacterial virus called mTmV infected ST34 multiple times starting around 2002.

By analyzing the population structure of ST34 it was found that Salmonella harboring this virus in their genetic material became more numerous over time and gained a competitive advantage over those lacking the virus. The virus carries the sopE gene encoding a toxin known to help Salmonella infect their animal host species, cause diarrhea, and be passed on to new hosts in food and feed.

Researchers investigated the distribution of sopE in 1,697 Salmonella Typhimurium and monophasic variant Salmonella Typhimurium from human infections in England and Wales between 2012 and 2016 and found it was rare. They also looked at variation in the whole-genome sequences of Salmonella Typhimurium isolated from UK pigs between 2006 and 2015.

Of 442 monophasic Salmonella Typhimurium ST34 isolates from sources including humans, food, environment, livestock, companion and wild animals in 29 countries, 25 percent encoded the sopE gene.

The mTmV transfer to other Salmonella serovars in vitro was limited but included the common pig-associated Salmonella Derby. This may explain mTmV in Salmonella Derby co-circulating on farms with monophasic Salmonella Typhimurium ST34, highlighting the potential for further transfer of the sopE virulence gene in nature.

(To sign up for a free subscription to Food Safety News, click here.)

Peter Ben Embarek gave the John H. Silliker Lecture on this final day of the International Association for Food Protection’s (IAFP) annual conference and meeting.

When asked what was keeping him up at night, Ben Embarek said for the past few months it has been COVID-19 while on a previous occasion it was the Middle East respiratory syndrome (MERS).

“Even though it is a public health issue, it is an infectious disease, it also has a food-related element. They are both linked to how we are producing food. They both started in these environments where animals and humans are closely interacting in the process of producing food animals.”

Evolving COVID-19 situation
Ben Embarek said when Switzerland was locked down earlier this year the only shops open were pharmacies and supermarkets.

“This shows how critically important it was and still is to maintain our food supply, to make sure people still have access to food even though everything else is shut down. At that time it was clear that we needed to have guidance, recommendations, and tools to help industry and national food safety authorities to keep our food supply running and make sure we kept workers throughout the food production chain healthy. This guidance, after a few months, is already in need of updating showing how fast our understanding and knowledge around COVID is evolving.”

Another important element was the need to understand to what extent the virus can survive on food surfaces and food.

“We know it survives on frozen and refrigerated food and when these products are moving in international trade they start to create a problem as we have seen in recent months, in particular in China. There are regular findings of frozen imported products contaminated with the virus and they are taking trade measures against these products,” said Ben Embarek.

“It is true in many instances it is probably only the RNA we are detecting but apparently in some instances, viable viruses are also found and we know from experimental studies that the virus doesn’t lose viability during the freezing period of several weeks corresponding to normal trading patterns in international commerce.

“Another concerning element is in August, the Chinese CDC announced the conclusions of investigations into one of their largest outbreaks in Beijing in June where they had some 800 cases linked to a wholesale market. They concluded the virus was introduced through the frozen goods brought into the market. We haven’t seen any details from this investigation and to what extent transmission could have happened. We have to be a bit cautious and even if there it is not a huge risk or problem, we need to better understand what is happening under these conditions where we are handling frozen and refrigerated products in wet and humid environments.”

Same pathogens, different products
Ben Embarek also runs the International Food Safety Authorities Network (INFOSAN).

“The trends we have seen in recent years is an increase in events involving traditional pathogens in new commodities such as outbreaks linked to fruits, vegetables, salads and increasingly they involve frozen berries being traded internationally,” he said.

“These are quite interesting because with new technologies and agricultural know-how berries are being produced cheaply all over the planet in places where hygiene and attention to water quality and irrigation are perhaps not what it should be. It illustrates the changes we are seeing in world production and the spread of production technologies without having the associated spread of tight control and high hygiene standards and that is unfortunately what is characterizing the food safety picture today. This disconnect between capacities to produce almost anything everywhere without having the associated high level of food control.”

The use of whole-genome sequencing helped in understanding the large South African Listeria outbreak in 2017 and 2018, said Ben Embarek.

“Without the use of this technology we would have had a much larger outbreak and it would have been much more difficult, and perhaps impossible, to find the source. At the same time as this large outbreak was unfolding, the country was also having a number of smaller outbreaks in the background with different strains of Listeria linked to different products. Without the use of WGS it would have been difficult to disentangle these different outbreaks from the large one and identify the source,” he said.

“It is not going to be the technology that will solve everything in the future but it will help detect and solve outbreaks much faster. Finding the source of an outbreak helps us understand what went wrong and each time we have that information we can correct and learn from these errors and problems we were not aware of in raw materials and processes. It will help us slowly build a safer food safety environment. It is true we will still need food microbiologists and people able to culture bacteria to understand the biology of bacteria and viruses in food and the environment.”

Food safety is not like selling T-shirts
Certain food safety regulators, producers, and researchers are learning from these events but there is a large group that doesn’t seem to be learning anything, said Ben Embarek.

“Clearly there are too many cowboys out there producing and distributing food that should not be allowed to do that because managing food hygiene and safety is something that requires a certain level of understanding of the problems and seriousness of dealing with these things,” he said.

“It is not like producing a T-shirt where if you cut corners and the consumer is not happy with your T-shirt it will last three months and next time he or she will not buy the same T-shirt but you will still be producing T-shirts and no harm will have been done.

“If you cut corners when producing the food you might end up killing somebody or someone’s baby and that is far more serious. Unfortunately, we seem to have the same laissez-faire attitude towards allowing who can produce and who cannot and that is something that will and must change, we cannot continue to have that type of dual level of seriousness in the way we produce food. We are in a globalized environment where any food product can end up on any table around the globe.”

There also needs to be a way of engaging different stakeholders, according to Ben Embarek.

“Food producers are sitting on an enormous goldmine of information through all the data they are generating compared to national authorities, inspection services, and research institutions. The bulk of the data is with industry and unfortunately, that goldmine is not being tapped, we are just throwing away all this data after it is used for the purpose for which they are generated and we forget that if we combine with data generated elsewhere and by others we could have a better understanding of our food environment.

“We are still, in 2020, in the dark when we look at our food supply and environments, we have small windows of light here and there where we have a semi ok understanding of what is in our food and how it is evolving in terms of hazards and risks but the vast majority of information is not visible.”

Ben Embarek also spoke about the challenges involved in feeding a growing world population, food waste, food production by robots, and changing diets with a move away from meat.

(To sign up for a free subscription to Food Safety News, click here.)

The “Next Generation Sequencing to Tackle Foodborne Diseases in the EU” event was originally planned for March at the Istituto Superiore di Sanità in Italy but was moved online and to late September because of the coronavirus pandemic.

A survey with 100 responses during the conference revealed absence of a legal framework, issues with data confidentiality and ownership, an absence of bioinformatics expertise, and lack of funds to be some of the stumbling blocks.

Speakers included Martial Plantady of the European Commission, Saara Kotila from the European Centre for Disease Prevention and Control (ECDC) and Valentina Rizzi of the European Food Safety Authority (EFSA).

Almost all of those surveyed agreed that WGS-based surveillance and monitoring at the EU level would be beneficial. The most useful features included deepness of the analyses, it can replace most, if not all, other methodologies, it is automated and the sensitivity.

Plantady said it was too soon for rules on making WGS compulsory as part of official controls.

“I am convinced in the coming years more member states will perform WGS and share data. At that point we will reflect internally with them on imposing use of the tool under certain circumstances but now is too early. We encourage, and put in place the European Union Reference Laboratory (EURL) network, to build capacity in National Reference Laboratories (NRL) and private labs doing official controls. WGS is not standardized enough to be part of official controls so it is a vicious circle,” he said.

WGS findings need epi data
Saara Kotila from ECDC said WGS-based methods have quickly become standard in foodborne and waterborne outbreak investigations.

“The high discriminatory power of the method allows you to confirm a link between cases and isolates, which was not possible with older methods, however to clarify the nature of the link other data is needed, such as epidemiological and sequence data from non-human isolates of various origins such as food, animals and the environment to track possible foodborne sources and vehicles,” she said.

“There are various different ways of analyzing WGS data available and used in different countries and laboratories. It is important that these can draw the same conclusions from the same raw data and that the full dataset is analyzed – this is why sequence data sharing between institutes is needed.”

Epidemiological data could include age, gender, region of country, travel information and consumption and exposure data of patients.

ECDC has been coordinating WGS-enhanced listeriosis surveillance since March 2019.

“Eighteen of 30 clusters containing microbiologically closely related patient isolates detected since beginning the surveillance had less than five isolates, which at EU level is small. We have a draft criteria as to at what point a cluster should be escalated,” said Kotila.

Escalation can mean more countries becoming involved but all clusters are communicated to affected nations. The level of escalation depends on the number of cases and countries involved.

“We want to have six or more isolates from the past 12 months from two or more countries. Every time an urgent inquiry is launched (usually done by national health institutes but can also be by ECDC), it is voluntary for countries to answer. This means work for them, and it is even more resource-intensive to start further investigations in collaboration with food safety authorities,” said Kotila.

“If too many urgent inquiries and investigations would be launched, national authorities would struggle with resources and possibly stop contributing. There is always a need for finding a balance of resources and public health value to prioritize investigations.”

EFSA to collect WGS data from non-human isolates
Valentina Rizzi, from EFSA, said centralized WGS data collection is needed to support prompt investigation of multi-country foodborne outbreaks.

“When there is the need to collect sequences from countries in the context of a multi-country outbreak investigation, EFSA is supported by the European Union Reference Laboratories for foodborne pathogens and their network of National Reference Laboratories,” she said.

“Starting from the end of next year EFSA will be able to collect from countries WGS data from non-human isolates of Listeria monocytogenes, Salmonella and E. coli submitted on a voluntary basis through the One Health WGS system. Foreseen data users of the new system will be competent authorities and laboratories of EU member states and other reporting countries that will sign a bilateral agreement with EFSA.”

The One Health WGS system will be two interoperating systems, one in EFSA and one in ECDC, collecting and storing data. The aim is to collect baseline typing information to detect clusters of foodborne diseases and to generate hypotheses on the possible food vehicles involved.

Data dilemma
Survey respondents said the main drawbacks of posting data in the public domain include disclosure of sensitive information that might affect the privacy of people, use by other scientists, and a lack of harmonization and standardization of methodological processes.

Kotila said firms might be worried about cases being linked to their products, harming reputation, and having an economic impact on sales.

“But they could benefit from these investigations, as outbreaks could be detected earlier and controlled before possible escalation, e.g. ending up under intense press attention and/or court cases. On the other hand, sequencing data can also show that a company is not linked to a specific outbreak,” she said.

“Some worries have been that someone takes out the available data and makes scientific publications without acknowledging the data source/owner, which may want to do their own publications with the same data. Hopefully, when more and more institutes/people share sequence data, others will follow as they will see that there is nothing to worry about.”

Rizzi said data submission will contribute to food safety and protection of consumers within the EU.

“Submitting data to our system should provide an added value for the providers. It is essential to stress that the ownership belongs to the producers of the data. In the EFSA system the data owner will be the provider organization who bears the responsibility to obtain the consent for data sharing from the original data producer,” she said.

“Data from industry should be collected at country level and their sharing at EU level is under the responsibility of the data provider officially nominated in the country. Confidentiality is ensured through the data sharing in a secure network and data management regulated by agreements.”

An example of EFSA services is giving back to data providers the results related to their data and how they relate with other isolates in the database.

George Haringhuizen and Eelco Franz both from the Dutch Institute for Public Health and the Environment, Annemarie Kaesbohrer, of the German Federal Institute for Risk Assessment, and Patrick McDermott, director of the National Antimicrobial Resistance Monitoring System  also presented at the event organized by the EURL working group on NGS and Med-Vet-Net Association.

(To sign up for a free subscription to Food Safety News, click here.)

The European Centre for Disease Prevention and Control (ECDC) hosts the Epidemic Intelligence Information System for food- and waterborne diseases (EPIS-FWD) platform. The network is a restricted web-based platform for experts to help with early detection and coordination of response to multi-country outbreaks through sharing information.

It consists of Urgent Inquiries and associated forums, which are the outbreak alert and investigation tools. The forums allow information to be shared about the outbreak investigation among a restricted number of experts. Nominated people outside the EPIS-FWD network, such as food safety and environmental experts or veterinarians from network countries or any expert or organization outside the network can also be invited to join.

In 2019, 88 Urgent Inquiries were initiated by 23 of the 52 network countries and one by ECDC. On average, 11 countries replied to each alert and 31 replied to at least one.

A record high
The number of Urgent Inquiries in 2019 was the highest since the platform was launched and 54 percent higher than the annual average in the past five years. In previous years, an annual mean of 57 Urgent Inquiries was published.

An ECDC spokesman told Food Safety News that the record number was good news.

“This reflects probably two aspects; one is the introduction of Whole Genome Sequencing as a tool to enhance surveillance to detect and investigate outbreaks leading to a much higher probability to detect the source and implement control measures. WGS enables also efficient follow up of effectiveness of control measures as new cases can be detected through WGS relatively rapidly, and two; increased sequencing capacity in member states and subsequent network participation,” he said.

Urgent Inquiries were related to salmonellosis (44 percent), followed by listeriosis (23 percent), Shiga toxin-producing E. coli (STEC) (12 percent) infection, and hepatitis A (9 percent).

“The number of listeriosis clusters has increased substantially after the introduction of WGS-enhanced surveillance in March 2019 but molecular epidemiology of Salmonella is more complex and challenging, even with the support of WGS. However, Salmonella is a much more common infection in humans than severe Listeria infection, which means usually more risk assessments related to Salmonella than to Listeria,” said the ECDC spokesman.

Monitoring threats and outbreak assessments
In 2019, ECDC opened and monitored 58 new threats in the threat tracking tool in addition to the 12 carried over from previous years. This is less than the 71 issues monitored in 2018. Of threats opened and monitored in 2019, 38 affected European countries.

Nine involved food and waterborne diseases compared to eight in 2018. One example is related to the difficulty to control Salmonella Enteritidis in poultry products, particularly eggs.

In 2019, ECDC and the European Food Safety Authority (EFSA) produced three joint rapid outbreak assessments. One due to Salmonella Poona in infant formula, another because of Listeria in cold-smoked fish and the last one a Listeria outbreak in ready to eat meat products.

So far this year, one has been published updating the multi-country outbreak of Salmonella linked to eggs from Poland and another is planned with EFSA on a multi-country outbreak of Salmonella linked to Brazil nuts involving the United Kingdom, France, Luxembourg, the Netherlands, and Canada.

(To sign up for a free subscription to Food Safety News, click here.)