In 2004 an outbreak of Salmonella enterica serotype Enteritidis was identified. The source of the outbreak was traced to raw almonds. Cooperatively, state and federal public health and regulatory agencies, industry trade organizations and the almond industry worked to halt the outbreak and to prevent further illnesses.

What began as an epidemiological investigation of a few cases of illness eventually led to a widespread international recall of almonds, as well as granola-type bars, muesli-type cereals and other products containing almonds. It resulted in changes in processing methods, research into methods for decontamination, and potential changes in U.S. Department of Agriculture (USDA) regulations. This article will explore the details of the outbreak, the epidemiological and analytical methods used to link cases of illness, subsequent product investigations and actions by industry to prevent future outbreaks.

Federal, state and local officials, and industry collaborate in response to foodborne illness outbreaks. State officials conduct investigations for outbreaks occurring within their boundaries. If the outbreak involves a product that is only in intrastate commerce, state officials have authority but may ask for federal assistance. If the outbreak involves a product in interstate commerce, the U.S. Food and Drug Administration (FDA) regulates that product, and if there are illnesses occurring in multiple states, FDA has authority and coordinates the response with the states. In addition, FDA collaborates with the Centers for Disease Control and Prevention (CDC) and other federal agencies, as applicable. FDA provides guidance to the industry on manufacturing and handling practices to reduce microbial contamination and thereby improve food safety.

FDA’s response to suspected foodborne illness outbreaks begins before the epidemiological link to the source has been established. FDA works with the states and CDC to: 1) ascertain whether the outbreak is foodborne; 2) epidemiologically and analytically link the outbreak to a particular food vehicle, and; 3) carry out surveillance for additional cases. Once an FDA regulated product that is in interstate commerce is implicated, FDA works with the state(s) to perform field investigations including traceback and trace forward investigations to determine which specific product lots are involved. FDA and the states also inspect production, processing and storage facilities to determine the history of the food product. In order to prevent additional cases, FDA works with manufacturers to remove the violative product from the food supply and takes enforcement and other follow-up actions to correct the problem or improve safety. Follow-up actions by FDA may entail research, technical assistance, education, or development of new guidance or regulations.

Identifying the Outbreak
The State of Oregon’s public health officials routinely use pulsed-field gel electrophoresis (PFGE) analysis to differentiate all of their Salmonella Enteritidis isolates. On May 12, 2004, using two different DNA restriction enzymes, Xba1 and Bln1, the Oregon Department of Health (ODH) found that the isolates of Salmonella Enteritidis from a cluster of five patients, with illness onsets from February 1 to April 17, 2004, had indistinguishable PFGE patterns. Oregon shared these PFGE patterns through PulseNet. The Xba1 pattern had not been seen in the PulseNet database before October 2003.

Eggs often have been linked to Salmonella Enteritidis outbreaks and were a logical suspect. However, using a questionnaire the ODH had developed to help determine which food vehicle is transmitting foodborne pathogens, the state health department’s epidemiologists interviewed the patients and discovered that they all consumed Store A Brand A raw whole almonds within five days before their illness. The ODH compared the consumption patterns of the five cases with those of 30 controls and linked the outbreak to consumption of raw almonds. On May 13, 2004, the ODH sent FDA and CDC information regarding a possible Salmonella Enteritidis outbreak related to the consumption of almonds. ODH also sent notices to other state public health agencies to gather information on other Salmonella Enteritidis cases.

Soon after, CDC found 13 indistinguishable isolates in eight other states (Alaska, Arizona, Idaho, Massachusetts, Mississippi, South Carolina, Utah and Washington) through a PulseNet database comparison of PFGE analyses. CDC considered all cases potentially associated. CDC requested that all states test their Salmonella Enteritidis isolates from as early as February 2004 and submit PFGE matches to CDC for phage-typing. CDC also worked with ODH to standardize the food history questionnaire for use in other states.

Through additional PFGE comparisons and phage typing, CDC and the states eventually were able to identify other cases of illness. CDC determined that there were 32 clinical cases of Salmonella Enteritidis in the nine states with illness onsets ranging from March 2003 to April 2004. Of these known clinical cases, 18 were traced back to almonds as a possible source. The onset dates for the 18 almond-linked illnesses ranged from September 2003 to April 2004. The case isolates had indistinguishable PFGE patterns that were similar to but distinguishable from PFGE patterns of isolates from a Salmonella Enteritidis outbreak from almonds in 2000-2001, involving over 134 cases in Canada and 71 cases the U.S.[1] The 2000-2001 outbreak was the first time Salmonella infection was reported to be associated with almond consumption.

Traceback and Inspection
Product tracebacks for foodborne illness outbreaks are done to determine the source of the violative food so the remaining product can be removed from the market. Tracebacks involve reviews of records, including shipping and receiving dates, quantities and lot identification, and reviews of batch records and processing logs to determine which lots are or could be involved. FDA inspects firms to gather traceback information and to determine the cause of contamination in order to change or improve storage, processing or production practices. In the case of the raw almonds associated with this outbreak, the traceback was complicated and also identified other suppliers and vendors of the almonds.

On May 14, 2004, Store A pulled all raw almonds from its Oregon stores and put a voluntary hold on the product once ODH and FDA provided epidemiological information. Using store discount cards, with permission from the case patients, Store A was able to determine the dates these customers purchased raw almonds. FDA compared the consumer purchase records and with store records to determine the brands, quantities, and lot numbers involved. FDA determined that Brand A raw almonds were supplied to the northwest region by Processor A, a nationwide almond distributor located in California that grows, hulls, shells and packs almonds from its almond orchards and packs almonds from other almond suppliers.

The traceback then became more complicated. FDA and California Department of Health Services’ (CDHS), Food and Drug Branch, jointly conducted inspections and found that the almonds associated with illness were from lots that contained almond meats from Processor A’s orchards commingled with almond meats from two other huller/shellers, Processors B and C. The raw almonds had been packed in December 2004 or earlier. Processors B and C in turn, had received almonds from various suppliers, including Processor D. FDA’s challenge was determining whether the Salmonella contamination occurred while the almonds were being packed at Processor A; during hulling/shelling at Processor A, B, C, or D; or before or during harvest on the farm. The contaminated almonds were traced back through stores, distributors, processors and huller/shellers and may have originated from one or more of possibly 20 different farms. Further complicating this was the fact that farms supplied almonds to more than one of the huller/shellers. Although both the FDA and the CDHS gathered much information during separate intensive traceback attempts, they could not narrow the source of the almonds to a specific farm or field. The CDHS plans to release their report on the outbreak traceback sometime during the summer of 2005.

Sample Analysis
During the investigation, FDA collected and analyzed unopened packages of Brand A whole raw almonds from a patient’s home and from Processor A, but did not detect Salmonella species in either one. Hulling/shelling of the 2003-2004 crop of almonds had already been completed, so almonds were not being processed on the two dates in May when the CDHS and FDA inspected Processor A and collected environmental and final product samples. However, the inspection did find several objectionable conditions such as bird droppings on food contact surfaces and bird nesting in a production area that was not in use at the time. Salmonella spp. were isolated from the second set of samples collected from the huller/sheller equipment but not from any of the pre-processing equipment, the final product packaging equipment, or the final product samples. FDA also inspected Processors B, C and D and collected environmental samples. Salmonella spp. was isolated in samples from all three processors.

Although raw almonds have been consumed safely, contamination of almonds can occur in orchards and during harvesting. Field contamination would be reduced during the hulling and shelling process. However, pathogens from contaminated almonds could colonize the plant environment and the processing equipment. The equipment in turn could contaminate other almonds during processing. Salmonella spp. have been shown to survive on dry almonds, as well as in processing plant environments, and to multiply on wet shell dust.[2] Several serotypes and strains of Salmonella were isolated from environmental samples collected from Processor A and some of its suppliers, indicating that these environments were contaminated with Salmonella spp.

Recalling the Product
A recall is a firm’s voluntary removal of its product from the distribution chain. Store A had already withdrawn raw almonds from its Oregon stores’ shelves and placed them on hold on May 14, 2004. Because the widespread salmonellosis illness was epidemiologically linked to the raw almonds from Store A and Processor A, FDA was preparing to issue a press release to alert consumers to the contaminated raw almonds. On May 18, 2004, Processor A announced a voluntary recall of approximately five million pounds of whole natural raw almonds sold at retail as Brands A, B and C.[3] Store A sent letters about the recall to customers who purchased the product and to foreign accounts in Mexico and the United Kingdom. On May 21, FDA issued an alert to distributors, wholesalers and consumers about the recall, stating that the almonds had the potential to be contaminated with Salmonella Enteritidis.[3]

Processor A had shipped an additional eight million pounds to other companies, as well as overseas. On May 22, after an additional case of salmonellosis that had occurred three months earlier was found in Michigan, Processor A expanded their recall to include additional “best by” dates, raw diced almonds; and all of its industrial distributors and retailers.[4] Company A noted that the recall did not apply to almonds that undergo processing that eliminates Salmonella spp. (roasted, blanched, sliced or slivered almonds).

In addition to the recall by Processor A, 40 other distributors and wholesalers voluntarily recalled raw almonds and foods containing raw almonds between May 18 and July 9, 2004. These firms received almonds from the same pre-processing or processing lots that Processor A did. In total, approximately 18 million pounds of raw almonds were recalled.

FDA assigns a numerical classification to each recall to indicate the degree of health hazard the product being recalled presented. FDA classified the recalls as Class I recalls. A Class I recall indicates there is a reasonable probability that the use of or exposure to the product will cause serious adverse health consequences or death.[5] The product was recalled at all levels of distribution, including wholesale, retail and consumer. Recalls were international in scope and included raw almonds from Processor A that had been distributed to Mexico, Japan, Korea, Taiwan, Malaysia, France, England and Italy.

Almond Industry Background and Actions
California produces over 75% of the world’s supply of almonds.6 The almond industry in California shipped over one billion pounds of almonds in 2004. Five percent were in-shell almonds, 70% were raw almonds and 25% were in manufactured products. Of the approximately 300 million pounds shipped for the U.S. market in 2004 (including roasted, flavored, processed and raw almonds), 53% of almond shipments were used in manufactured foods, 21% were used in foodservice and 26% were used for snack and baking.[6] The Almond Board of California estimated that less than 5% of this latter category is raw almonds.

The Almond Board of California is an industry-run quasi-governmental organization that manages a Federal Marketing Order for almonds under supervision of the USDA’s Agricultural Marketing Service (AMS) to ensure almond quality. The board worked with food safety and microbiology consultants to develop a plan to improve almond safety following the 2000-2001 outbreak of Salmonella Enteritidis illness from raw almonds. In June 2004, the Almond Board’s Food Quality and Safety Committee approved an action plan to ensure that raw almonds entering commerce are treated to reduce microbial contamination.[7] The plan includes handler-validated 5-log lethal treatment for all raw product shipments before entering commerce. The voluntary program was implemented in August 2004, with plans for 100% voluntary industry compliance once the processes are validated to achieve a 5-log pathogen reduction and are available to the processors.

Some of the processes that could be used to improve raw almond safety include chemical treatment such as with propylene oxide (PPO), chlorine dioxide or various heat treatments.[2] The Almond Board of California submitted studies of protocols for lethal processes, including treatment with PPO, hot water treatment (blanching) and hot oil treatment, to FDA for review. FDA completed its review of the PPO treatment submission and concluded that the process was capable of achieving a 5-log reduction of Salmonella Enteritidis using the parameters described in the study. Each PPO treatment system must be tested and properly calibrated to achieve these processing parameters. FDA also agreed that the term “pasteurized” could be used on the labels of almonds treated with PPO using the study parameters submitted.

The voluntary program specifies that domestic almond shipments are to be treated with PPO or another lethal process that will achieve a 5-log reduction of bacteria. This requirement does not apply to product sold to commercial processors that can subject the almonds to a process achieving a 5-log reduction (Direct Verifiable Customer Processing Program).[7] The Almond Board also recommended that raw product shipped internationally be subjected to a 5-log reduction. An exception would be the Direct Verifiable Customer Processing Program. The Almond Board is working to seek regulatory approval in foreign markets for PPO treated almonds and is also working with USDA to include a mandatory industry-wide pasteurization step in the almond marketing order.

In 2004, molecular analysis of Salmonella Enteritidis isolates from five patients were linked in a case control study to consumption of raw almonds. Through PulseNet database comparison of PFGE analysis, and phage-typing, CDC and the states were able to determine that the outbreak of Salmonella Enteritidis included clinical cases in none states. The raw almonds associated with the illnesses were traced back to stores, distributors, processors and hullers/shellers and may have originated from one or more of possibly 20 different farms. The tracebacks resulted in voluntary recalls of approximately 18 million pounds of raw almonds by 41 firms in May, June and July of 2004.

What is so remarkable is that the outbreak was undetected for months until Oregon used PFGE analysis of case isolates and identified them as an outbreak, rather than sporadic background cases. Some jurisdictions do not have the resources to use PFGE on all their Salmonella Enteritidis isolates, nor to do so in a timely manner. The small number of clinical cases originally identified represented a potentially much larger number of subclinical and unreported cases of salmonellosis, and resulted in a massive and complicated international recall of raw almonds and foods containing raw almonds.

In July 2004, the Almond Board of California announced an action plan to ensure that shipped raw almonds are not contaminated with pathogenic bacteria. The voluntary action plan identified several pasteurization processes such as PPO and heat treatments that may be used, once validated, to treat raw almonds to reduce any possible contamination with Salmonella spp. by 5 logs (100,000-fold reduction). Untreated raw almonds would be available to firms that would further process almonds, such as blanching, roasting, cooking in baked goods, etc., to achieve the reduction. Research and validation of processes are ongoing and some protocols have already been submitted to FDA for review. The Almond Board is working with USDA to move to a mandatory program, which would require new regulations.

Elisa L. Elliot, Ph.D., is a microbiologist for the Emergency Coordination and Response Staff of the Office of Compliance at FDA’s Center for Food Safety and Applied Nutrition. She began her 16-year career with FDA as a researcher developing methods for Vibrio species.

Series editor Sebastian Cianci is a policy analyst and a member of the CFSAN’s Office of Food Safety, Defense, and Outreach. He has worked for FDA for 15 years and serves as the Center’s trade press liaison.

The authors acknowledge the following organizations for their efforts: Almond Board of California, California Department of Health Services, Centers for Disease Control and Prevention, U.S. Food and Drug Administration, Oregon State Department of Health, and Linda J. Harris, University of California, Davis.

1. Chan E. S., J. Aramini, B. Ciebein, D. Middleton, R. Ahmed, M. Howes, I. Brophy, I. Mentis, F. Jamieson, F. Rodgers, M. Nazarowec-White, S.C. Pichette, J. Farrar, M. Gutierrez, W.J. Weis, L. Lior, A. Ellis, and S. Isaacs. Natural or raw almonds and an outbreak of a rare phage type of Salmonella Enteritidis infection. Can. Commun. Dis. Rep. (28), pp. 97-99. 2002.
2. Harris, L.J. Salmonella in Almonds – Research Relevant to Huller/Shellers. Presentation to Huller/Sheller Association, July 27, 2004. (Department of Food Science and Technology, University of California, Davis).
3. Food and Drug Administration. Raw Almond Recalls. 2004. Available at the following link:
4. Centers for Disease Control and Prevention. Outbreak of Salmonella Serotype Enteritidis Infections Associated with Raw Almonds—United States and Canada, 2003—2004 MMWR 53(22), pp. 484-487.
5. Food and Drug Administration. Investigations Operations Manual 2005, Chapter 8 – Recall Activities, p. 358. 2005.
6. Almond Board of California. Almond Fact Sheets. Available at the following link:
7. Almond Board of California. Action Plan Details. 2004. Available at the following link:
8. Centers for Disease Control and Prevention. MMWR Surveillance Summaries. Appendix B, Guidelines for Confirmation of Foodborne-Disease Outbreaks. 49(SS01); 54-62. March 17, 2000.
9. Medus, C., S. Abbott, R. Marcus, M. Park, T. McGivern, D. Swerdlow, and the EIP FoodNet Working Group. Exploration of the Utility of Pulse-Field Gel Electrophoresis Subtyping in Surveillance for Salmonella Enteritidis Infections in FoodNet Sites. 2nd International Conference on Emerging Infectious Diseases, Atlanta, GA, July 2000.
10. Food and Drug Administration, Food Safety and Inspection Service, and Centers for Disease Control and Prevention. Healthy People 2010 Focus Area 10 Data Progress Review: Food Safety: Challenges, Barriers, Strategies and Opportunities, May 11, 2004.