produce safety research at the office of applied research
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Slide 1-1www.fda.gov
Produce Safety Research at the Office of Applied Research and
Safety AssessmentMarianne Miliotis-Solomotis, Ph.D.
Office of Applied Research and Safety Assessment (OARSA) CFSAN/FDA
North Central Region Center for FSMA Training, Extension, and TechnicalAssistance
Annual Conference and Meeting April 2, 2020
Acknowledgements
• Mary Torrence, DVM, Ph.D., DACVPM
• Socrates Trujillo, Ph.D.
• Bacteria/metagenomics/Soil chemistry• Laurel Burall, Ph.D.• C-K Hsu, Ph.D. (ORISE)• Chris Grim, Ph.D.• Karen Jarvis, MS• Susan Leonard, Ph.D.• Baoguang Li, Ph.D.• Alice Hayford, Ph.D.• Uma Babu, Ph.D.• Kannan Balan, Ph.D.• Lisa Plemons, Ph.D.
• Viruses• Christine Yu, Ph.D.• Zhihui (Hui) Yang, M.D., M.S., M.S.• Efi Papafragkou, Ph.D.• Haifeng Chen, Ph.D.• Qianru Yang, Ph.D. (ORISE)
• Cyclospora: • Alex DaSilva, Ph.D.• Mauricio Durigan, Ph.D.• Sonia Almeria, Ph.D.
• Josie Freeman• Elizabeth Dennard
Slide 1-2
Slide 1-3www.fda.gov
FDA is responsible for ensuring the safety of all domestic and imported fruits and vegetables.
Develop control and preventive measures. The Produce Safety Rule was published in November 2015 A risk assessment that was conducted by FDA led to the
conclusion that use of poor agricultural practices could lead to contamination and illness. both pre-harvest and post-harvest:
agricultural water, biological soil amendments of animal origin worker health and hygiene equipment, tools buildings and sanitation domesticated and wild animals growing, harvesting, packing and holding activities.
Introduction
OARSA Produce
Safety Research
Consortium
A research network with collaborative partners from academia and government agencies (UGA, USDA-ARS, NCSU, OSU, and FDA/CFSAN/OARSA) to
– Leverage on-going projects– Facilitate collaborations – Provide produce-related and on-farm
environmental collections for prioritized and identified research areas
– Support PS Rule and FSMA– Facilitate and fill data gaps through
observational and experimental studies
– Expand OARSA’s contributions to complement other ongoing PS research programs and to GenomeTrakr
www.fda.gov
Specific Objectives
• Compare prevalence of different bacterial pathogens (Salmonella, Listeria monocytogenes, Campylobacter, STEC), viruses (HAV, NoV), Cyclospora cayetanensis
• Compare regional and farming practice differences for soil microbiome and presence of pathogens.
• Focus on raw manure, treated manure and untreated manure
• Investigate presence of pathogens and survival in different water sources (and drip tape where applicable)
• Compare regional and seasonal differences
• Compare different irrigation practices
• Investigate the physical and chemical properties and moisture content of soil from farm soils in produce production facilities from different regions in North America
• Investigate the relationships between foodborne pathogen survival and persistence, and the different soil compositions (untreated vs BSAAO vs BSA) and soil microbiome diversity
www.fda.gov
Specific Objectives
cont.
• Microbiome (community members; indicators)• Soil (amended and non amended) • Water• Produce• Presence of antimicrobial resistance genes
• Determine potential transfer from water, soil to plant to produce for bacteria and viruses
• Collect metadata• Amendments
• Is the soil amended?• What is the amendment?• When is it applied?• How much and how often is the
amendment applied?
• Animal husbandry• Animals on the farm• Distance of animal feeding to planting fields
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Contributions of the PSRC
to This Work
Provides water source, soil and produce samples from the natural environment.
Provides isolates; DNA
Provides a conduit to gain information about field management and topology that could explain observed patterns. Can we discern impact of watershed or
farmer practices on resident pathogens and microflora?
Metadata
Adding More Pieces To Solve The Puzzle?
BSAAO application
Microbiome
Soil Properties
Air
Soil amendment applied on Ohio and Georgia fields
Type of Field Amendment
dairy manure (DM)
composted dairy manure (CDM)
poultry manure (PM)
composted poultry manure (CPM)
no biological soil amendment (N)
fallow fields (F)
green compost (GC)
Soil Microbiome Sample Diversity
Processing lettuce for storage
harvest
cut and wash
Inoculation with E. coli O157:H7 (stx -, rif +)
Modified Atmosphere Packaging Salinas, CA
Albany, CA
Slide 1-12www.fda.gov
Microbiomes of lettuce: field through storage USDA ARS field, spring 2018
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
DA1F DA2F DA3F TT1F TT2F TT3F DA1Z DA2Z DA3Z TT1Z TT2Z TT3Z DA1E DA2E DA3E TT1E TT2E TT3E
other taxaWolbachia spp.Serratia spp.Leuconostoc mesenteroidesRahnella aquatilisStenotrophomonas spp.Exiguobacterium spp.Duganella zoogloeoidesCronobacter turicensisEnterobacter cloacaeBuchnera aphidicolaErwinia spp. (other)Erwinia persicinaErwinia gerundensisPantoea spp. (other)Pantoea agglomeransPseudomonas spp. (other)Pseudomonas viridiflavaPseudomonas syringaePseudomonas seleniipraecipitansPseudomonas putidaPseudomonas moraviensisPseudomonas luteaPseudomonas koreensisPseudomonas granadensisPseudomonas fluorescensPseudomonas abietaniphilaEscherichia coli phylogroup EErysiphe spp.DA TT
Inoculated processed lettuce before storage
MAP lettuce after storage at 6°C (14 days)
Rela
tive
abun
danc
e
(Inoculated E. coli O157:H7)
Unprocessed lettuce from field
DA TTDA TT
DA: good SLTT: poor SL
Pseudomonadaceae/(Erwiniaceae+Enterobacteriacea) ratio different in the two romaine lettuce varieties after cold storage
Slide 1-13www.fda.gov
Summary
Third year Preliminary data
Data not all analyzed yet; still in the process of testing Soil between GA and OH very different in texture, moisture Developing new/modified methods for detection, esp. soil/water
Viruses Cyclospora Bacterial pathogens
Role of metagenomics
Future Directions
• Analyze 3 year data to determine where to focus
• Expand the PSRC• Growth Chambers
– Simulating real life environmental conditions
• Humidity• Temperature• Irrigation type• Air flow
– Soil type and pathogen survival/persistence
– Transfer efficiency – Oocyst sporulation
THANKS FOR YOUR ATTENTION!
Slide 1-15
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