The Global Symposium on Soil Pollution #GSOP18 | 2 - 4 May 2018 | FAO Hq Mr. David Ingram, FDA/CFSAN, US

2. Global Symposium on Soil Pollution (GSOP18)
May 2, 2018
Food Safety and Soil Health: An FDA
Perspective
Eric L. Stevens, Ph.D. David T. Ingram, Ph.D.

3. 3
Food Safety Modernization Act (FSMA)
• Standards for Growing, Harvesting, Packing and Holding of
Produce for Human Consumption
• cGMP and HA and Risk Based Preventive Controls for Human Foods
• cGMP and HA and Risk Based Preventive Controls for Animal Foods
• Foreign Supplier Verification Programs (FSVP)
• Mitigation Strategies to Protect Food Against Intentional Adulteration
• Sanitary Transport of Human and Animal Food
• Voluntary Qualified Importer Program (VQIP)

4. 4
Produce Safety Rule
• FDA issued proposed rule on Jan. 16, 2013.
• FDA issued supplemental notice of proposed rulemaking on Sept. 29, 2014
• FDA issued Final Produce Rule on Nov. 11, 2015
• Four public meetings; various outreach efforts
• About 36,000 submissions, including over 15,000 unique comments, in response to both
2013 and 2014 documents
• Input from various sectors of stakeholder community
• Implementation Dates staggered by net sales of Fruits and Vegetables
• x ≥ $500,000 – Jan. 26, 2018
• $250,000 ≤ x ≤ $500,000 – Jan. 28, 2019
• $25,000 ≤ x ≤ $250,000 – Jan. 27, 2020

5. 5
Conditions and practices identified as potential
contributing factors for microbial contamination
•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
•Sprouts requirements

6. 6
Biological Soil Amendments of Animal Origin
6

7. 7
Part 112 – Subpart F – Biological Soil Amendments of
Animal Origin and Human Waste
§ 112.51 – Determining status of a BSAAO (treated / untreated)
§ 112.52 – How to handle, convey, and store BSAAO
§ 112.53 – Prohibitions regarding use of human waste ?
§ 112.54 – Treatment processes for a BSAAO
§ 112.55 – What microbial standards apply to the treatment
processes in §112.54 ?
§ 112.56 – Application requirements and minimum application
intervals apply to BSAAO ?
§ 112.60 – What requirements apply regarding records?

8. 8
Regulatory Context
§112.56 – Application Requirements
• Untreated BSAAO – MUST Apply in a manner that does not contact covered produce during
application
(a)(1)(i) – and minimizes potential for contact with covered produce after application – [Reserved]
harvest interval
(a)(1)(ii) – and No contact after application – 0 day harvest interval
Application Harvest

9. 9www.fda.gov
Pathogen levels on
crops may be impacted
by harvesting practices,
processing practices,
storage conditions, etc.
Pathogens may be
transferred from
amended soil to
produce through
different pathways
(e.g., water splash,
wind, animal
encroachment)
Pathogens may persist
in amended soil for a
long time period
considering
environmental factors
(e.g., soil moisture,
temperature)
0 50 100 150
0
1
2
3
4
Time (Days)
Level(Log10CFU/g)
Contaminated water
Non-contaminated water
Pathogens may be
present in BSAAO prior
to application
2 3 41
BSAAO Risk Assessment – FDA in Consultation with USDA

10. 10www.fda.gov
Likelihood and level of pathogens
in manure, amended soil, water,
and on crops
Fate (survival) of pathogens in
manure, amended soil, and on
crops
Likelihood and rate of transfer of
pathogens from amended soil to
crops
Data Elements Potential Impacting Factors
Soil type (sandy, loam, clay, conventional vs/ organic)
Geographic region (East, West, South, North)
Agricultural practices (BSAAO application method
(surface vs/ tillage) , irrigation technique, etc.)
Climatic factors (temperature, rainfall, wind, soil
moisture, UV, etc.)
Crop type (root, low growing, stem)
Manure type (cattle, chicken, horse)
Pathogen strains and inoculation level (high vs. low)
BSAAO Risk Assessment

11. 11
Next steps
www.fda.gov
• Research collaborators submit manuscripts describing studies, data, and
results to peer-reviewed scientific journals
• FDA analyze full data set to enhance and expand meta-analysis and build
quantitative models.
• The risk assessment (RA) model, currently under development, will combine
different data sets to provide new insights into food safety issues related to
use of BSAAO
• The risk assessment will evaluate the impact of interventions, such as use of
time interval(s) between application of soil amendment and crop harvest, on
the risk to consumers, to inform policy decisions within Subpart F (Biological
Soil Amendments of Animal Origin and Human Waste) of the Final Produce
Rule

12. 12
For More Information
• Web site: www.fda.gov/fsma
• Subscription feature available
• To submit a question about FSMA, visit www.fda.gov/fsma and go to
Contact Us
12

13. 13
What is Whole-Genome Sequencing?
• Purpose of Sequencing:
- Determining the number and order of nucleotides that make up a
given molecule of DNA.
• Current WGS Methodology for Outbreak Detection:
- Isolate bacterial genome and break it up into many small fragments
(200 – 300 nucleotides in length)
- Sequence those fragments many times (these are called your
sequencing reads and there will be millions of them)
- Take your sequencing reads and assemble them back into the entire
genomic sequence of the isolate
- Find nucleotide differences between isolates (SNPs)
- Use SNPs to create a phylogenetic tree to inform investigation
www.fda.gov

14. 14www.fda.gov

15. 15www.fda.gov
Why WGS data needs to be shared with the world
Microbial
Sequencing
Improve microbial
disease diagnosis
Safer food
Better
agricultural
practices
Risk assessment
Better AMR
stewardship
microbial genetic
variation
Improved
human health

16. 16www.fda.gov
Using WGS to inform better agricultural practices

17. 17
Tomato Agriculture
• Fumigation and Plastic
mulch
• Drip irrigation
• Seedlings planted by
hand
• Filtered irrigation water
• Stringing, staking by
hand
• Routine application of
pesticides, fungicides

18. 18
Key Conclusions from VA surveys
• Sampled Areas:
– Virginia Tech Agricultural Research and Extension Center (AREC): 2009-2011
– 6 environmental waters and sediments: 2011, 2012, 2014-2015
– Roadside stand tomatoes: 2010-2011
• Salmonella Pattern 61 and other clinically relevant isolates found consistently
in waters and sediments at AREC and the 6 other locations
• Environmental waters and sediments are potential reservoirs for Salmonella
• Agricultural practices related to the use of contaminated surface waters may
introduce Salmonella onto crop plants

19. 19
Pathogen Colonization and
Internalization Studies
Newport, Javiana, Montevideo, and Saintpaul were all recovered from within developing tomatoes
70% of inoculated blossoms resulted in Salmonella isolated from within or on the developing fruit
COCKTAIL:
Newport
Javiana
Montevideo
Saintpaul
Typhimurium
Newport
Javiana
Montevideo
Saintpaul
Newport
Javiana
Montevideo
Saintpaul
Newport
Javiana
Montevideo
Saintpaul
Salmonella Newport internalization through root system was internalized to stem (20%) and fruit (5%)
Newport
Javiana
Montevideo
Saintpaul
Typhimurium
X
Appl Environ Microbiol. 2013 Apr;79(8):2494-502.
Colonization and internalization of Salmonella
enterica in tomato plants.
Zheng J et al

20. Any Questions ?