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Improved Food Safety and Public Health by Using Whole Genome Sequence Analysis


The Meeting

A public meeting is being hosted by the Food Safety and Inspection Service (FSIS), the Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), and the National Center for Biotechnology Information (NCBI) on Thursday and Friday, October 26 and 27, 2017. The purpose of the meeting is to protect consumers from foodborne illnesses in the USA and countries all over the world by laying the foundation for the use of whole-genome sequencing (WGS).

Why Whole-Genome Sequencing (WGS)

WGS analyses can determine the relationship between different bacterial isolates with higher resolution than other analytical methods, and can characterize genes and other features of bacterial genomes.
The FSIS intends to analyze and generate WGS data and use it as part of the decision-making in investigations of foodborne outbreaks, and share this data with Federal food safety partners.
The FSIS is currently considering WGS analysis as an important tool in the characterization of food pathogens. The method uses 1-10 million base units for each bacterium, almost the entire genomic sequence. WGS provides a sturdy estimate of the relationship between sequences, allowing for further classification of individual genes. WGS can reveal the bacterial genetic fingerprints and can show clues about antimicrobial resistance, genetic relationships, and key markers that help scientists respond more effectively to food contamination.
Another use of the WGS is to identify antimicrobial resistance genes to identify genes related to emerging resistance to beta-lactamase, colistin, linezolid and other critically essential antibiotics.
According to the FSIS, WGS is rapid, precise, cost-effective, and easy-to-use and can be applied universally to all foodborne pathogens.

The Database

The database GenomeTrakr was started by the FDA in 2012, as an international network of laboratories sequencing microbial foodborne pathogens and uploading the data to a common public database in real time. The data is stored at the National Center for Biotechnology Information (NCBI), can be accessed by researchers and public health officials.
 GenomeTrakr started with a pilot study of WGS-based surveillance for Listeria monocytogenes (Lm). Since its establishment GenomeTrakr and the use of WGS, more illness clusters were detected, and they were detected sooner, and in more cases the illness was linked to Lm food source.  The data from a study by Jackson et al., 2016 shows specific improvements that can be gained using WGS, as compared to the use of PFGE analyses. The most successful use of WGS is in foodborne disease surveillance. However, it requires coordination and collaboration to provide a global health benefit for every country that shares its data.
GenomeTrakr has already collected more than 142,000 sequenced strains. It made them available to anyone in the world. This undertaking demonstrates that this kind of large databases can be used to improve food safety in the USA and around the world.

The future

The FSIS claims that it intends to continue to upload all WGS data to the database and make it readily accessible to all food safety and public health partners and stakeholders.  The utilization of WGS will enhance resource allocation and decision-making by the FSIS. It expects to obtain greater efficiencies from what was learned from the pilot study of Lm, by improving laboratory workflows for bacterial characterization.
The FSIS and its partners are planning to use WGS in combination with traceback data and epidemiologic evidence to identify the sources of outbreaks more expeditiously. Preventive action based upon WGS has the potential of preventing foodborne diseases and may identify genes associated with virulence.
A meeting between the FDA and the Codex Alimentarius Commission took place recently in Geneva, discussing how to share WGS data internationally.  The FSIS and the FDA plan to expand the program in 2018, to identify such pathogens as salmonellacampylobacter and E. coli.


The transcript of the proceedings from the public meeting will be available after the meeting on the FSIS Web site.

Cyclospora Infections are up this Summer Sickening Nearly a 1,000 Persons in 36 States


The CDC Report

The CDC reported that since the beginning of 2017 to mid-September there have been 988 Laboratory confirmed cases of Cyclospora infected people in 36 states of the USA. The number of cases this year is significantly higher than in 2016.
The states with the most cases are Texas 28.8%, Florida 12.0%, and New York (including NYC) 10.6%.

Historical View

While the number of cases is higher this year, the director of CDC’s Division of Parasitic Disease, Dr. Monica Parise, said: “The numbers from this year were probably not outside the range that we’ve seen for the last five years,” According to Parise the numbers last year were low.
The CDC claims that it is not unusual to see an increase in Cyclospora infection in the US between May and September. However, as the table shows the increase this year seems to be outside the norm.   In the last decade, only in 2005, the number of cases came close to this year, with 582 people sick in Florida. The outbreak source was identified as basil from Peru.

Reason for the Outbreak

Currently, no specific product has been connected to the infections, and it is unclear if the various cases in the different states are related to each other. The specific vehicles of the infections have not been identified and the sources are being investigated. The CDC report claims that “It is too early to say whether cases of Cyclospora infection in different states are related to each other or to the same food item(s).”

The EPI Curve

The EPI curve shows the progression of illnesses in an outbreak over time. It shows when people become ill by day. There is an inherent delay between the date that an illness starts and the date when the case is reported to public health authorities.  For the Cyclospora outbreaks in 2017, the following curve was generated by the CDC
*N=553. Data are current as of 9/13/17.  These cases occurred in persons with no history of travel outside of the United States or Canada in the 14 days before onset of illness. Illnesses that began after Aug. 2 may not yet have been reported to CDC because of the lag time between a victim’s first doctor visit, lab tests, paperwork and finally reports being filed with public health agencies. 


Cyclosporiasis is an intestinal illness caused by the unicellular parasite Cyclospora cayetanensis. According to the CDC, People can become infected with Cyclospora by consuming food or water contaminated with the parasite.
The oocysts shed in the feces of infected persons must sporulate outside the host, to become infective for another person. Therefore, it is not transmitted usually from person to person, but through food or water. The sporulation process requires days to complete.
Cyclospora is by and large found in tropical and subtropical countries. It is normally not killed by most chemical disinfectants.
Products that historically caused outbreaks include fresh produce: basil, cilantro, lettuce, raspberries and snow peas.


Why do we see a higher number of infections despite FDA preventative measures?
Due to a number of outbreaks traced to fresh cilantro from the region of Pueblo, Mexico, the FDA increased inspection and enforcement there. According to the FDA “Beginning in 2015, from April 1 through August 31, cilantro from this region has been and continues to be detained without physical examination at the U.S.-Mexican border and refused admission into the United States.”
The FDA suggested in September 2016 that the lower number of infections that year correlated with the first full season that the FDA’s Import Alert for fresh cilantro from Puebla was in effect. Therefore, the question should be asked why we see such an increase this year.

FDA Commissioner Announced a Four Year Delay in Implementing Some Produce FSMA Rules

In a speech in front of National Association of State Departments of Agriculture (NASDA), Dr. Scott Gottlieb, the FDA commissioner outlined some immediate steps to facilitate the implementation of the Produce Safety Rule established by the FDA Food Safety Modernization Act (FSMA).
Dr. Gottlieb claims that since being in his post, he gained a deeper appreciation for the challenges and complexity that the globalized farming community is facing.

Agricultural Water Compliance Dates

He announced that the FDA issued a proposed rule that, if finalized, would extend the compliance dates for the agricultural water requirements by an additional two to four years (for produce other than sprouts).  The new agricultural water compliance date the FDA is proposing for the largest farms is January 26, 2022. Small farms would have until January 26, 2023, and very small farms January 26, 2024.
Sprouts, because of their unique vulnerability to contamination, remain subject to applicable agricultural water requirements in the final rule and their original compliance dates. 
He agreed that “microbial quality standards for agricultural water are too complicated, and in some cases too costly, to be effectively implemented.” Dr. Gottlieb also announced that “our intention to explore ways to simplify our approach to make compliance less burdensome and less costly, while still being protective of public health.”
To give the agency and the farmers more time, he is issuing an extension in the compliance dates” for the agricultural water requirements of the produce rule for non-sprout produce by an additional two to four years. This way the earliest non-sprout compliance date for the water standards won’t be until January 2022.”
The proposed extension will give the agency time to take another look at the water standards to ensure that they are feasible for farmers in all regions of the country while protecting public health. The agency has also increased the number of methods that can be used for water testing in agricultural water.

Educational Efforts

Dr. Gottlieb declared that the agency has recognized a need for additional efforts to educate the produce industry and state regulatory agencies on the new produce safety requirements, and will continue its focus on training, guidance development, and outreach over the next year. This is particularly important since the nation’s farming community has not previously been subject to this kind of oversight.
The FDA plans to learn more from farmers, state regulatory partners and other stakeholders about the diverse ways water is used and ensure that the standards will be as practical and effective as possible for all farming operations, during the time extension afforded by the extension.

Produce Inspection

The State Produce Implementation Cooperative Agreement Program that supports 43 states in their development of produce safety programs was awarded $30 million. This funding is in addition to on the nearly $22 million that FDA awarded last year to 42 states to develop produce programs and provide training and technical assistance.
Dr. Gottlieb assured the audiences that routine inspections would not begin until 2019. The additional time should be used to focus on issuing guidance that will be helpful to regulators and farmers.

On Farm Readiness Reviews

The farm readiness review is a voluntary program, where the farms are visited by a team of state officials, cooperative extension agents, and FDA produce experts.  The purpose of the visit is to give the farmers information about their readiness to meet the program requirements. The program will also help the FDA to identify training gaps that will be needed to be filled.


Dr. Gottlieb claimed that through Produce Safety Alliance (PSA) 176 farmer training courses had been conducted in 36 states as of June of 2017. More than 1,000 trainers were trained in these courses. NASDA-FDA working group was formed to work on plans for training state and federal inspectors and is finalizing the training modules.
FDA is also working with NASDA to determine the best training platforms for ensuring that cooperative extension agents can have the training they need to be effective. Training of state regulators will be a top priority for the FDA in 2018.

Updates: Botulism in Nacho Cheese, Salmonella in Maradol Papaya, Listeria in the Environment, and Our New Trending Page


California Department of Public Health confirms that botulism outbreak was Linked to Retail Practices

In May we reported on a Botulism outbreak resulting from the consumption of nacho cheese sauce served at the Valley Oak Food and fuel gas station in Walnut Grove, California.
The outbreak included 10 cases of laboratory confirmed C. botulinum toxin type A. All patients were hospitalized and one death was reported. Customers spread the nacho cheese sauce on chips from a counter-top self-service warming dispenser.
According to a memo from the California Department of Public Health, the operators at the gas station were mainly responsible for the outbreak because the reasons for the outbreak were:
  • The bag of nacho cheese (5 lb) collected at the retail location on May 5, 2017, was consumed past the “Best By” date.
  • The gas station did not maintain records of the time in which the bag nacho cheese was added to the warming unit. Therefore, the cheese might have been left too long in the warmer.
  • The designated tool to open the nacho cheese bag was not used to open the bag of cheese.
The CDPH Food and Drug Branch (FDB) and Sacramento County Environmental Management Department (SCEMD) guided management in such retail store regarding the use of nacho cheese warming and dispensing machines in retail locations, in order to prevent future incidents like this one in the future. 

Multistate Outbreak of Salmonella Anatum Infections Linked to Imported Maradol Papayas

The CDC reports on the newest outbreak relating to papayas from Mexico.  This is the fourth investigation involving to papayas from Mexico this year.
On September 4, 2017, the CDC reported that 14 people in 3 states were infected with the outbreak strain of S. anatum. Five hospitalizations and one death resulted from this outbreak.  Epidemiological and laboratory data indicated that papaya from Mexico imported by Bravo Produce Inc. of San Ysidro, California is the probable source of the outbreak.
On September 10, the FDA and the distributor withdrew the product from the market. The CDC pulseNet data base identified 6 more individuals with the same DNA fingerprint that recently became ill.

Environmental sampling of a plant in Germany linked to Listeria Outbreak

With the increase in environmental sampling mandated by the FSMA, and the numerous recalls resulting from the program, I find it interesting that environmental sampling was inked to a Listeriosis outbreak in Germany.
A conveyor belt in a meat processing plant, moving product before packaging, was most likely the source of the contamination.
In 2015, an outbreak of Listeriosis was reported in Germany, caused by L. monocytogenes ½ a.  In Emerging Infectious Diseases Volume 23, Number 10—October 2017, Molecular Tracing to Find Source of Protracted Invasive Listeriosis Outbreak, Southern Germany, 2012–2016 Kleta et al. using forensic microbiology, had identified several products from one manufacturer contaminated with the outbreak genotype Listeria.
Their conclusion was based on the facts that:
  • L. monocytogenes outbreak strain was isolated from several products of the same manufacturer
  • The outbreak strain was absent in other products collected during the same period
  • Epidemiological findings suggested that the source of the outbreak was from this single factory
  • The meat processing plant predominantly supplied grocery stores of a single company
  • Patience food consumption histories were compatible with the molecular typing results
However, the authors could not prove the producer was the source of the infections. They concluded that public health could benefit from continuous molecular surveillance of isolates from humans and food, which could allow for infectious disease outbreaks to be stopped before emergence.

New Trending Page in BioExpert

We are planning to add a new exciting page in our ask-bioexpert site. The purpose of this additional page is to introduce and discuss current trends in food safety, intriguing articles, and bring to the attention of the food safety community any new topic that might be of interest.  Any registered user will be able to quickly describe any relevant trend or comment on any previously published trend descriptions.
I am hoping that all registered users will contribute to this page thereby creating a compelling new relevant body of information and pointing readers to valuable food safety information. By your active participation, you will be able to help your colleagues to understand the most pressing trends in food safety and determine where to focus their attention.
Please look for an announcement soon.

How Listeria monocytogenes can survive in extreme environmental conditions

It is difficult to eliminate L. monocytogenes from post processing contamination of food production lines since this pathogen is common in various environments outside processing plants, and can endure in food processing environments.  It is one of the main concerns in environmental monitoring due to its ability to survive strict cleaning conditions and remain in the plant environment for months or even years.
Listeria monocytogenes has better survival ability than most other food pathogens, resulting in the colonization of Listeria in food processing environment. L. monocytogenes is capable of adapting to a variety of stress conditions, including pH variations, cold temperature, low water activity, high salt concentration, and different sanitizers such as quaternary ammonium compounds, sodium hypochlorite, and peracetic acid.
In the recent past, researchers have identified several hypervariable (easily changeable regions) regions of the bacterial genome called Genetic Insert Stress Survival Islet 1 (SSI-1). This genetic region exists in some other bacteria. Different genetic sequence inserts are utilized by the bacteria to help tolerate acidic conditions, bile salts, pH fluctuations, salt concentration, low water activity, temperature variations, etc. The SSI-1 is a five-gene islet that contributes to the growth of L. monocytogenes in sub-optimal conditions. However, SSI-1 does not explain the survival of L. monocytogenes during food sanitation conditions that are alkaline and highly oxidative.
In a recent publication by Harter et al., Sep 2017, it was reported that by looking at neighboring gene sequences to SSI-1, they identified a new stress survival islet 2 (SSI-2). SSI-2 is predominantly present in L. monocytogenes ST121 strains and is responsible for survival in alkaline conditions and oxidative conditions present in food processing environment.
Their study showed that SSI-2 is involved in a different stress response than SSI-1. The prevalence of SSI-1 is similar between clinical isolates and strains isolated from food and food processing environments.  SSI-2 strains are mostly present in L. monocytogenes strains isolated from food and food processing environments (84%), and not from clinical isolates.
SSI-2 is mainly contained in strains of ST121, while SSI-1 is present in diverse ST strains. The CC121 are prevalent in isolates from food and processing environment and are very rare among clinical isolates. ST121 strains persist for months in food processing environment, due to their ability to survive the oxidative and alkaline conditions, potentially resulting in contamination of the environment. The authors speculate that SSI-2 seems to have developed in response to the cleaning regime of food processing, because of their much higher prevalence in this environment.
SSI-2 contains two genes (lin0464 and lin0465) that support survival under alkaline and oxidative conditions. One gene is a transcriptional regulator directing the entrance of the second gene which is responsible for protease activity (breaking down proteins during oxidative stress). The broken proteins can be eliminated from the cell relieving the stress.
The SSI-2 are called “stress survival islet,” since both genes help the survival under stress conditions. Under stress conditions, mRNA production increases, as is the increase in transcription of the putative protease gene.
Harter et al. hypnotize that elemental horizontal gene transfer from L. innocua is most plausibly integrated into the L. monocytogenes genome to create the SSI-2.  This is because the two strains are more closely related than other strains of Listeria, and coexist in the same ecological niches.
L. monocytogenes ST121strains containing the SSI-2 genes survive the alkaline and oxidative stresses during cleaning and sanitation procedures. The oxidizing agents (e.g., chlorine dioxide, sodium hypochlorite, hydrogen peroxide) are frequently applied to kill bacteria on surfaces but can be survived by these strains of L. monocytogenes.
Progress has been made to better understand the genetic reasons for the survival of L. monocytogenes in food processing plants. To better understand the survival mechanisms of Listeria, and for the development of new strategies for prevention, these studies are essential.