1. FDA Tree Nut Risk Assessment and Human Salmonellosis
National Pecan Shellers Association
Mid-Winter Meeting, Nashville, TN
March 25, 2014

2. Presentation Outline:
Why is FDA doing a risk assessment and what does this mean?
What does FDA need to know from nut processors?
What is Salmonella and why should I be concerned about it?
What should I be doing about Salmonella?

3. The Federal Register notice: Request for data & comments
Scientific data
Information
Published: 07/18/2013
Comment period:
90-days
Extended 60 days to 12/16/13
On July 18, 2013, the FDA announced that we were beginning a risk assessment of salmonellosis associated with consuming tree nuts. The announcement included a call for data, information on processing and comments. The comment period was extended and closed on December 16, You should know that the agency will still consider comments that come after the closing date and up until such time as the risk assessment is near completion.
Available at:

4. Why is FDA Doing a Risk Assessment?
Model outputs:
Number of cases / serving; number of cases / year
Impact of interventions through “what-if scenarios”
Model will build upon peer-reviewed risk assessment models:
e.g. Lambertini et al., 2012 (developed for U.S. almonds)
Model will evaluate product pathway: harvest to consumption
Expected extensions beyond currently published models:
Adaptation to consider other tree nuts in addition to almonds
Quantification of uncertainty
Sensitivity analysis
FDA does a risk assessment when we want to thoroughly understand the nature of a possible public health problem, in this case the link between tree nut consumption and human salmonellosis. A risk assessment uses all of the available data and information to construct a computer model. The more complete the data and information that goes into the model, the better the model. When data is insufficient, it is necessary to make assumptions and to examine the impact of those assumptions on the model.
Any risk assessment done by FDA is done in as transparent a manner as possible. The risk assessment is peer-reviewed and published in draft form for comment.
The model will help FDA understand the significance of human salmonellosis attributed to tree nuts. The model will permit a comparison of different intervention strategies for reducing the risk of illness. For example, we can test the effect of “what if” scenarios such as: 1) what if we reduce contamination of raw nuts by 50%?; 2) what if nut processing plants are able to better control Salmonella contamination of the plant environment so that we have only half as many contaminated plants?; 3) how effective does a roasting or pasteurization process need to be to reduce the risk of salmonellosis to an acceptable level? Note that these are just examples and the final risk assessment may include other “what if” scenarios. Also, if the data permits, we can compare one tree nut process to another and can use the model to identify the most-cost effective interventions.
What will FDA do with the results of the risk assessment? At the very least, we will publish the risk assessment. The risk assessment will help inform FDA about the efficacy of processes that might be used to reduce Salmonella numbers to an extent that the term “pasteurized” could be used on the product label. If there are gaps in the data, the risk. Regardless of what actions FDA may or may not take, the process will be transparent and there will be ample opportunity to comment on any actions that may be taken.

5. Data gaps: Data needs for the risk assessment
Data needs identified in the FR notice:
Salmonella prevalence & concentration on tree nuts
Salmonella survival, growth or inactivation dynamics
Relevant food consumption practices in the U.S.
Storage, handling and processing conditions
Other comments (e.g., types of tree nuts to include)
Additional information for each data need can be found in the FR notice.
These are the data gaps we have identified for the risk assessment. To date, we have had a very good response to our call for data.
We are pleased with the response to the Federal Register Notice published 07/2013
1. (n=11 submissions)
Data submissions (n=3)
Dr. Buchard ( several published articles on pecans), RF Biocides (inactivation data)
Cosmed Group (inactivation data),
Extension requests (n=7)
Public comments (n=1)
From concerned citizens (n=1)
2. Federal Register Notice published 10/2013 (n=655 submissions):
Data submissions (n=12)
Dr. Farkos (FDA scientist, submitted published article on Salmonella inactivation), Golden Macadamia, Napasol (2 submissions), California Walnut Board, Almond Board of California, Peanut and Tree Nut Processors Association, National Pecan Sheller’s Association, Administrative Committee for Pistachios, Paramount farms
Anonymous (submitted data on consumption, prevalence, inactivation, best practices etc.), Oregon Hazelnuts
Public comments (n=640) from concerned citizens and other interest groups
Other submissions (n=3;one extension request and 2 comments in form of submitted letters)
Data types submitted to the docket:
Consumption / market share data
Salmonella prevalence & concentration data
Salmonella survival & inactivation data
Data on industry practices
By far the largest amount of data available for almonds, pistachios, pecans and walnuts (and hazelnuts except limited prevalence data), fewer data available for brazil nuts, cashews, pine nuts, macadamia nuts

6. Salmonella Basics
Common bacterium found in soil, water, birds, reptiles and mammals
An organism living in the environment from which it infects/colonizes animals and plants
A major cause of occasionally fatal foodborne illness
Becoming more resistant to drugs
A highly evolved organism that persists in the environment for decades
Salmonella is found almost everywhere in the environment. Only a few years ago we thought it was primarily found in the intestinal tract of mammals, birds, amphibians and reptiles. We now know that although Salmonella can colonize animals, its natural reservoir is the environment. It seems to be most common in the sediment of ponds, streams and rivers. It is probably also living in soil. You can expect it to be present on any agricultural commodity grown in or near the soil.
Salmonella is much more than a cause of diarrhea. It typically kills about 1 in 2,000 persons infected. Some serotypes are more virulent for humans and cause higher rates of mortality than others, but all types are thought to be harmful. It can cause long-term health effects. It infects persons of all ages, even healthy young adults. It is more likely to kill persons with other health problems, the very young or the very elderly, but it also kills healthy young adults.
In recent years, Salmonella has become more resistant to antibiotics. Some strains are now very difficult to treat and these drug-resistant strains have been found in foods on occasion.

7. Is Salmonella a Major Problem?
Despite significant efforts by FDA, CDC, and FSIS and the food industry, Salmonella continues to more than hold its own.
The success of Salmonella as a pathogen could be due to:
Its global distribution in the environment
The many routes of contamination of raw foods
Sources of human infection outside the food supply
Inadequate controls for processed food
The Centers for Disease Control and Prevention monitor the number of reported cases of salmonellosis. Each year, we find that the number of salmonellosis cases remains steady or even increases slightly. We have made progress on reducing infections from some sources, such as eggs. However, we continue to see cases from other foods. Because Salmonella is so common, it is difficult to identify and assess the significance of all food sources and routes of contamination. For the vast majority of human salmonellosis cases, we are not able to determine the source food, but we think that nearly all cases come from food. Thanks to new DNA sequencing methods, we are getting better at linking cases of illness to the causative food.
Because cases of salmonellosis are not declining, CDC, FDA and USDA are focusing on potential food sources of Salmonella and asking the food industry to take measures to control the organism in processed foods and meats.
From CDC, Incidence of Human Infection,

8. Salmonella Ecology
This slide shows how Salmonella can be passed from the environment to people and animals. Generally, it moves from the environment to agricultural food commodities, including fresh produce, nuts, grains, spices and other foods grown in or near the ground. It then infects humans and animals when they consume contaminated agricultural commodities. Food processing should destroy Salmonella. However, Salmonella also enters food processing facilities on the feet of workers, on pallets, on raw materials, through roof leaks and from pests like rats and mice. We do not have a quantitative understanding of these routes of movement. For example, how does it contaminate tree nuts? Birds could be a factor, as could irrigation water and even the wind. For nuts that fall onto the ground, we can imagine that soil and water play a role. There are unique and specific interactions between Salmonella and agricultural products. It has recently been proven that Salmonella can infect tomatoes by getting onto the blossom. It can also get into tomato plants from the roots.

9. Salmonella in Peanuts and Tree Nuts
Commonly found in all species of raw tree nuts
Found in 2.3% of raw shelled peanuts when testing 375 grams of nuts1
Similar prevalence found in raw almonds, pistachios, and pecan
Based on the published literature and my own experience, you can expect to find Salmonella at some frequency on every type of tree nut. I think that anyone who says they are not finding it is simply not sampling enough or is not testing with the good methods. If you test enough 375 gram samples, you will likely find Salmonella in approximately 1.0 – 2.5% of raw tree nuts. This number can vary seasonally and geographically, but it seems to be a consistent finding in well-designed studies. The number of Salmonella in a given positive sample is largely unknown. All of the methods for enumerating Salmonella have significant technical shortcomings. However, based on numerous outbreak studies, it does not take very many cells of Salmonella to cause illness, probably as few as 10 cells, maybe even less.
1 Journal of Food Protection, Vol. 76, No. 4, 2013, Pages 575–579

10. The Impact of New Technology
Identifying specific strains of Salmonella
Serotyping
PFGE typing
Genome sequencing
Courtesy New Hampshire
Public Health Lab
Early in the history of public health, it was recognized that we needed to be able to more specifically identify the bacteria that cause disease. It was not enough to simply know that you were dealing with Salmonella – we needed to be able to tell one kind of Salmonella from another. In the early 1900’s, the answer to this problem was serotyping. With serotyping, you can identify at least 2,400 different kinds of Salmonella. We have unique names for each different serotype of Salmonella – by international agreement, Salmonella are named according to where they are first isolated – e.g., Salmonella Minnesota, Salmonella Heidelberg, and Salmonella Panama.
Serotyping worked well until we realized that we needed to further identify strains within a serotype. Thus, in the early 1990’s a method of examining the DNA of Salmonella was devised that allowed us to identify different strains within each serotype. This method is called PFGE typing and it is now widely used in the US and in many other countries. But PFGE was not enough. The answer to this problem was to simply sequence the entire chromosome. In a matter of just one or two days, we can analyze all 4.6 million base pairs in the DNA of Salmonella and uniquely identify it and compare it to other isolates.
Sequencing allows us to determine where the strain might have come from. We can, for example, identify a Salmonella Montevideo from the almond groves of California and distinguish it from S. Montevideo from Asia, or even from the US East Coast.

11. The Good and the Bad The Bad: Salmonella sickens and kills people
An ever greater number of cases are now being linked to the source
Processors involved in an outbreak are often bankrupted or suffer major business reversals
It is possible to entirely prevent Salmonella contamination in processed foods like roasted nuts and nut butters
To briefly review, I’ve told you what a big problem Salmonella is and about recent developments that allow public health agencies to better link cases of illness with the source food and what FDA is doing to better understand the problem.
You can imagine what a disaster it is to have your product linked to an outbreak. All but the largest companies are brought to the brink of bankruptcy by such a connection. Your business liability insurance is almost never enough to cover your monetary loses. Typically, a plant is closed for a period of at least several weeks and often longer. Customers file claims for losses and plaintiff’s attorney’s contact you almost immediately. Just when your business has little or no revenue, you find that you need to spend money to correct deficiencies in the design and construction of your plant and retain consultants who can help you eliminate the Salmonella problem, not to mention significant costs for legal counsel. Even if you are involved in a relatively small outbreak, say fewer than a dozen cases, you can easily incur $30 - $100 million in extraordinary costs. It can take years to get your sales back to pre-outbreak volumes after being caught up in an outbreak. Finally, you may find yourself the target of a criminal investigation.
The good news is that we know how to prevent Salmonella from ever being a problem in roasted or pasteurized nuts. The current state of the science is good enough that you can reduce your risk of causing an outbreak to something close to zero. All it takes is commitment, knowledge, skills and some money. If you spend your money well, it can make your business more competitive and enduring.
The Good:

12. Salmonella Control in Nut Processing
Leadership engagement, understanding and commitment is most important
Implementation of process controls, cGMPs, preventive controls, HACCP, and environmental and finished product testing
Ensuring that the facility is designed and maintained to prevent contamination of the environment
Promote control of Salmonella with others in the industry
Refer to the GMA guidance on Salmonella control:
FDA trains its investigators to look for plants where the management team does not understand Salmonella and has not implemented proper process controls or established an environmental and finished product testing program. Such plants are the kinds of plants where we want to focus our resources.
The CEO, president, or owner must take full responsibility for food safety. This means that the CEO has to master new knowledge and skills. You cannot bet your business and your assets on a QA Manager who may have only a few years of experience? In most of the outbreaks we investigate, we find company leaders who don’t understand food safety.
Consider hiring a Salmonella control expert, if not as an employee, then as a consultant. Please note that not everyone who thinks they are an expert is actually up to the task.
Check up on your pathogen control program often, just as you would audit your financial controls, you need to audit your food safety systems. Also, you need to incentivize employees to implement food safety controls – finding a positive sample is not as bad as missing one.
Spend money on good equipment that can be controlled. There is nut pasteurizing and roasting equipment that easily delivers a 5-log kill of Salmonella. Some of this equipment can even do this on raw nuts in a way that retains most of the sensory qualities of a raw nut.
If must ensure that suppliers of critical ingredients have controls equal to your own. We often see situations where a poor supplier caused the product contamination. If you think about it, you really don’t want to run a food processing business without having all of the processes and procedures that are needed to profitably and consistently producing safe food.