Cyclospora Prevention, Response and Research Action Plan

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Cyclospora Prevention, Response and Research Action Plan


A. Prevention

A1. Continue to develop and deliver C. cayetanensis education and outreach on prevention measures for growers in collaboration with industry, academia, regulators and other partners.

The FDA intends to continue to build on available educational resources and seeks additional engagement opportunities for farmers working with academia, domestic and international regulatory partners, and industry to provide additional background on C. cayetanensis including its unique characteristics, sources and routes of contamination, and misconceptions. These education and outreach opportunities are intended to help growers understand preventive measures for C. cayetanensis that can be implemented on farms to help prevent contamination of produce.

In July 2022, the FDA updated a fact sheet on C. cayetanensis for farmers.

In June 2021, FDA sent a letter to the FFVA to share concerns about the public health risks associated with C. cayetanensis and to call on produce growers in St. Lucie, FL to consider produce safety requirements and best practices for controlling potential routes and sources of C. cayetanensis within their operations.

From April 2021 to May 16, 2022, FDA delivered a total of 9 webinars in collaboration with regional stakeholders. These webinars were designed to educate farmers and stakeholders on C. cayetanensis, including background, basic information, risk assessment and preventive measures. These webinars will continue to be updated and conducted, including with US and international partners as well as industry groups.

A. Prevention

A2. Engage with industry, academia, and test kit companies to encourage the modification of available rapid tests kits to specifically detect C. cayetanensis, and to develop industry best practices that can be used to test for C. cayetanensis.

The FDA has provided technical assistance to test companies that are exploring the feasibility of development or modification of Cyclospora detection kits.

In February 2023 the FDA entered into a research collaboration agreement with Rheonix to develop a fully automated screening assay for the detection of C. cayetanensis in fresh produce, soil and surface agricultural water. The development was completed and announced in June 2023.  The new detection method will allow for low levels of the parasite to be detected in a shorter amount of time. 

A. Prevention

A3. Work with industry to research and identify practical ways of controlling C. cayetanensis in the environment and on produce.

Typical chemical treatments used on farms are not effective against C. cayetanensis, and therefore, farmers have limited options to control, reduce or eliminate Cyclospora once introduced to the environment. Certain control measures that have been shown to be effective against other parasites can be evaluated for C. cayetanensis. The FDA has been engaging with industry representatives on how best to pursue this research.

The FDA has provided technical input into various projects funded by the Center for Produce Safety.

A. Prevention

A4. Advance Root Cause Analysis procedures following outbreaks linked to cyclosporiasis.

Root cause analyses can help both FDA and industry identify and implement necessary prevention measures to mitigate or reduce future outbreaks.

FDA is providing training opportunities to members of the FDA Cyclospora Task Force in root cause analysis (RCA). FDA plans to implement RCA processes for cyclosporiasis outbreaks starting in 2023.

B. Response

B1. Expand the capacity of FDA, states, foreign governments, and academia to sample and test for C. cayetanensis.

Specifically, the FDA seeks to update and deliver laboratory training to state and foreign governments on FDA C. cayetanensis BAM methods 19b and 19c and on collecting dead-end ultrafiltration (DEUF) samples of agricultural water; utilize the Laboratory Flexible Funding Model (LFFM) to include as an option testing for C. cayetanensis; expand collaboration with universities to conduct surveillance sampling and testing under the Produce Safety Research Consortium (PSRC) managed by the FDA’s Center for Food Safety and Applied Nutrition’s Office of Applied Research and Safety Assessment.

The FDA is currently updating methods for sampling and testing for C. cayetanensis. Stakeholders can find our standard operating procedures for methods at this time here: Other Analytical Methods of Interest to the Foods Program.

FDA developed training videos on DEUF sample collection procedures for water.

FDA has established a collaboration with The Northeast Center to Advance Food Safety as part of the PSRC where we are planning to collect water samples to test for the presence of the parasite in agricultural water sources. 

Through the Food Safety Partnership with Mexico we worked with SENASICA and COFEPRIS to conduct training June 26-28, 2023 which allowed for the expansion of Mexico’s laboratory capacity to test for C. cayetanensis.

B. Response

B2. Develop and provide training and updates for FDA, state and foreign regulators on Cyclospora.

The intent of this training is to help regulators assess farms for risk of contamination from C. cayetanensis, including potential sources and routes of contamination. This information will be particularly useful during outbreak investigations.

The FDA provided technical assistance on the Association of Food and Drug Officials (AFDO) tool for regulators on Cyclospora

FDA presented at the AFDO webinar to state regulators on June 30, 2021.

FDA Office of Regulatory Affairs (ORA) Produce Safety Network (PSN) investigators received training on DEUF sampling throughout 2020.

The FDA conducted training for FDA investigators on Cyclospora in May 2021:

AFDO Cyclospora: Part one – Association of Food and Drug Officials

AFDO Cyclospora: Part two — regulatory approach – Association of Food and Drug Officials

The FDA provided a presentation at APHL Conference on May 18, 2022 on the detection of the pathogen on produce and in water in the session Parasites: A Cause for Concern as an Emerging Food Safety Threat.

Through the Food Safety Partnership, FDA developed and delivered a virtual and in-person laboratory training series on the Cyclospora detection methodology for SENASICA and COFEPRIS, competent authorities in Mexico.

The FDA is in the process of developing additional training materials and will continue conducting training for investigators to meet the needs of state and foreign regulators

B. Response

B3. Develop a farm investigation questionnaire (FIQ) specific to Cyclospora. 

The intent of the FIQ is for use in the investigation of a produce farm implicated in a cyclosporiasis outbreak. The FIQ will be used to document conditions and practices through in-person observations and help guide the produce investigator through the assessment of the environment to determine potential sources and routes of contamination.

The FDA developed a C. cayetanensis Farm Investigation Questionnaire (cFIQ) to be used by investigators during outbreak investigations and sampling assignments. The cFIQ (Cyclospora-specific FIQ) includes unique questions specific to Cyclospora and Cyclospora-related conditions. The cFIQ guides the investigator through an environmental assessment to determine potential sources and routes of Cyclospora contamination and supports consistency of Cyclospora-related investigations. The FDA will continue to improve and adapt this living document based on evolving data and trends following each outbreak investigation.   

B. Response

B4. Engage with the states to evaluate C. cayetanensis in the environment or on produce.

Continued surveillance of domestic and imported produce, as well as, environmental factors is important to understand trends related to C. cayetanensis contamination, such as seasonality or geography. It can also assist FDA in identifying potential produce vehicles associated with outbreaks.

In 2021 the FDA completed microbiological surveillance sampling of domestic and imported fresh herbs, which includes testing for C. cayetanensis. An analysis of the sampling work will be published on FDA.gov following completion.

The FDA has and will continue to collaborate with state partners to conduct follow up and provide regulatory support whenever C. cayetanensis is detected on fresh produce samples collected for surveillance purposes.

C. Filling Knowledge Gaps

C1. Evaluate for trends and distribution of cyclosporiasis cases in the US.

There is a need to gather and evaluate data to better understand the prevalence (including distribution of cases) of cyclosporiasis in the United States.; identify? the different species possibly causing illnesses and use this information to target research on potential sources and routes of transmission.

FDA continues to collaborate with CDC to better understand  cyclosporiasis prevalence (including case distribution) in the US outside of the outbreak cases. Two new Cyclospora species associated with human illness, have been described based on analysis of Cyclospora isolates from outbreak cases.  The new discovery emphasizes the significant knowledge gaps, since these new species can have different epidemiological profile.   

C. Filling Knowledge Gaps

C2. Advance the development of genotyping methods for C. cayetanensis in clinical, food and environmental samples.

The FDA is working with CDC to advance genotyping methods (developed by CDC); the MLST/TADS approach will allow us to 1) genetically link cases of illness as one cluster (CDC), 2) genetically link cases to product and/or environmental samples, and 3) genetically link product samples to environmental samples.

The FDA began using genotyping tools on food and environmental samples for the first time during outbreak investigations in 2022.

The FDA developed a new targeted amplicon sequencing genotyping assay for C. cayetanensis that expands the number of genetic targets for distinguishing among samples and also allows genotyping of food samples with low contamination levels. The FDA and CDC are working to harmonize the method for clinical, food, and environmental samples.

C. Filling Knowledge Gaps

C3. Work with the National Advisory Committee on Microbiological Criteria for Foods (NACMCF) to address knowledge gaps related to Cyclospora.

Specifically, the FDA will develop and submit a charge document to NACMCF with the goal of having the multidisciplinary committee lead the development of a report that will improve our understanding of sources and routes of contamination, prevalence, and control measures based on available science.

The FDA developed a charge document related to knowledge gaps of C. cayetanensis which was accepted by NACMCF in early 2021. The FDA has met with NACMCF to discuss the charge document related to knowledge gaps of C. cayetanensis. The charge document includes specific questions that can be invaluable for the FDA to move forward with actions and research plans to advance in the control of cyclosporiasis.

NACMCF expects to conclude work on this charge in 2023 and will develop a report on their findings.

C. Filling Knowledge Gaps

C4. Identify opportunities to foster conversations with Cyclospora cayetanensis experts outside the FDA, including to explore future collaborations, share data and define research priorities.

The Joint Institute for Food Safety and Nutrition (JIFSAN) held a meeting in 2019 to bring together industry, academia and government, both domestic and international, to discuss the current state of science related to C. cayetanensis, identify knowledge gaps and research priorities and opportunities for collaboration.  JIFSAN planned to hold additional meetings bi-annually however due to COVID-19, additional meetings were not scheduled.

Beginning in November 2022, the FDA began holding monthly meetings with domestic and international Cyclospora experts focused on food safety research. Between November 2022 and June 2023 experts from US and Canada have presented novel data on Cyclospora research through webinars organized by the FDA Cyclospora Task Force This activity is providing essential information to refine the FDA plans to advance in Cyclospora food safety research. In addition, the FDA continues to engage with produce industry stakeholders, by participating in outreach activities, such as the one hosted by the International Fresh Produce Association (IFPA).

C. Filling Knowledge Gaps

C5. Collaborate with industry, academia, states, local and foreign partners to promote research to better understand the prevalence of C. cayetanensis in agricultural water.

The FDA participated in a discussion on C. cayetanensis with other produce safety researchers at the Center for Produce Safety Symposium on June 15, 2021.

The FDA plans to continue sampling of surface water for C. cayetanensis at various locations in the United States.

C. Filling Knowledge Gaps

C6. Explore the role of wastewater in contributing to C. cayetanensis contamination in produce.

The FDA intends to begin discussions with federal partners to seek collaboration and assistance on FDA’s research priorities to help better understand the role that wastewater and biosolids may have in C. cayetanensis contamination and to explore possible mitigation measures such as treatments.

For example, FDA and CDC are developing a method to detect C. cayetanensis in wastewater. 

FDA and CDC are working to develop a method to detect C. cayetanensis in wastewater.  In addition, the FDA is currently exploring collaborations with federal partners to obtain samples of wastewater, biosolids, and other environmental samples from locations that are close to agricultural regions in the United States.

C. Filling Knowledge Gaps

C7. Encourage sharing of Cyclospora environmental and/ or product sampling data that can help identify trends associated with produce, as well as spur research.

The FDA and CDC published an article in Food Safety Magazine summarizing data on all cyclosporiasis outbreaks from 2013 to 2020. This article provides specific details about the related outbreak investigations, describes the results from FDA sampling efforts, and explains challenges that both FDA and CDC will face when establishing actions to reduce the public health burden caused by cyclosporiasis. 

C. Filling Knowledge Gaps

C8. Development of a repository of C. cayetanensis oocysts to use in Agency research efforts.

Purified viable oocysts from human samples are essential to advance Cyclospora research. These oocysts can be used for different biological studies, e.g., viability and in vitro propagation studies ; and to enhance detection and genomic characterization methods for regulatory applications.

FDA has made significant progress in working with international partners to develop a repository of Cyclospora oocysts from biological samples which will support food safety research and operational scientific and laboratory functions

C. Filling Knowledge Gaps

C9. Advance studies towards in vitro propagation, viability and infectivity of C. cayetanensis.

The FDA has provided technical assistance for a project funded by the Center for Produce Safety.


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