Food Protection Trends - November/December 2019 - 485

In the end, the strongest tracebacks led to approximately
23 farms, spread out across 50 miles, separated by many
apparently unaffected farms. This suggested a widespread
though patchy contamination event occurred. It ended after
repeated warnings and the end of harvest. WGS brought
together 22 different PFGE patterns among the cases into two
clades, both of which we found in the water freely flowing in the
irrigation canal that supplied the area. The largest clade had
caused two outbreaks the preceding year, one among persons
swimming in a small lake in California 500 miles away, and
another in a group who became ill after exposure to a
salad bar in the Midwest. This recurrent clade needs heightened surveillance, new prevention measures and research
into where and how it persists in the environment. We are
following this clade of concern throughout 2019, ready to rapidly
investigate any clusters that may occur. In April of this year, the
Leafy Green Marketing Agreement of California introduced a
new requirement for farmers to sanitize surface water before
it is sprayed on leafy greens for irrigation or aerial application
in the three weeks before harvest, an important step forward
in prevention.
A second example is an emerging clade of Salmonella
Infantis, whose multiple PFGE types are unified by WGS.
This clade is resistant to or has decreased susceptibility to
10 antimicrobials, including ceftriaxone and ciprofloxacin, the
two first line agents for treating severe salmonellosis. The
first strains appeared in 2012 among travelers returning from
Peru. The first non-travel associated case was seen in 2014,
and the numbers increased rapidly in 2017-2018. The first
isolate found by FSIS in chickens was in 2013, and those also
increased rapidly in 2017. After one single PFGE type within
this clade surged in 2018, we focused investigation on that
one type. Eighty-nine percent of those interviewed had eaten
or prepared raw chicken products, of many different types,
brands, and purchased from many different stores. The same
PFGE pattern was found in strains from chickens at slaughter
and chicken meat from many different processors. This multidrug resistant strain has appeared in chickens from many
farms, upstream from the processing sites. Although the PFGE
type that increased in 2018 has declined, the broader emerging
clade still persists in humans and chickens. The emergence of
this clade was discussed with the chicken industry, along with
the need for industry-wide approaches to prevention. Again,
more detailed preharvest investigations and interventions are
needed to improve prevention.
In broad terms, these "clades of concern" revealed by
WGS are groups of closely-related strains that cause repeated
outbreaks, persist in specific reservoirs or geographic areas,
and emerge in people consuming specific commodities. They
may be multi-drug resistant and difficult to treat, which adds to
the concern. To prevent these infections, we collectively need
sustained surveillance, better understanding of their persistence,
and investigation of the root causes leading to contamination
and spread. Commodity-specific prevention strategies are going
to be critical, whether it be treating the water that is sprayed
onto leaves, vaccinating food animals, or other measures. I
am confident that prevention can be improved if attention is
focused on the problem at hand.
To help target the more general interventions by developing
general estimates of the fraction of foodborne infections that
can be attributed to individual food commodities, an interagency work group called the Interagency Food Safety Analytics
Consortium (IFSAC) has been analyzing the surveillance information available. IFSAC members have constructed a model
based on foodborne outbreaks reported over the last 18 years,
giving more weight to the most recent five years, and parsing
the number of illnesses across 17 major food categories, for
four major pathogens. The most recent summary is based on
outbreaks from 1988-2016, and the plan is to update this annually. Thus, the 2016 IFSAC estimates for Salmonella attribute
19% of foodborne salmonellosis to seeded vegetables, like
tomatoes, cucumbers and peppers; 13% to chicken; 11% to

pork; 10% to fruits; and 7-9% to other produce, eggs, and
beef. The 2016 estimates for foodborne E. coli O157 infections
differ, attributing 43% to vegetable row crops like leafy greens,
30% to beef, and 8% to dairy products. These estimates are
helping guide the priorities to prevention efforts for these and
other pathogens.
Now, whole genome sequencing offers new tools to help
improve the targeting of foodborne disease prevention efforts
more generally. As I have shown you, we can define broad
clades of concern among human pathogens that are emerging,
persisting or recurring. We can examine the frequency of those
same clades in isolates from meats, poultry and food animals,
and in the more limited libraries of isolates from other foods
and environmental sources. IFSAC is now taking up the effort
of refining the attribution estimates by clade within the main
pathogens. With international collaboration, we can be alert
for the emergence of clades in other countries and find them
quickly when they appear here.
Because microbiology never stays still, new tools for
clinical laboratories are changing diagnostic practices in human
medicine. Since 2015, the use of rapid multi-pathogen diagnostic
panels has been increasing, providing proprietary PCR-based
detection of many pathogens within a few hours. The result is
that more people are being tested for more pathogens, including
some that could not be routinely detected before, and fewer are
culture-confirmed. This means that we now need to account
in our surveillance for the changes in diagnostic testing taking
place in clinical laboratories. These tests do not yield a living
bacterial isolate, unless the specimen that was positive in the
test is then cultured for that organism. Access to the isolate
is necessary for PulseNet subtyping, so if a clinical laboratory
decides not to perform these "reflex" cultures, they may send
the positive specimen to the public health laboratories to be
cultured there. This challenge of the culture-independent diagnostic test is part of the changing landscape of food safety.
So how do we in public health stay on the cutting edge as
microbiological and diagnostic methods march forward? As big
an advance as it is, whole genome sequencing still requires an
isolate, and still can take upwards of two weeks to turn results
around. In the future, public health is going to need more
advanced molecular methods for direct use on clinical specimens to get the same sequence information in hours. Clinical
researchers are exploring metagenomic methods now that
would provide identification and sequences for all organisms
represented in the sample, and work has begun at CDC as
well. The rapidly expanding WGS databases of pathogens are
a bridge to this post-isolate future. Five to ten years from now,
we may see diagnosis and pathogen sequencing using metagenomic methods, providing results in close to real time and
moving from the laboratory to the patient's bedside.
As we contemplate how to make food safer in the 21st
century, I hope you will agree that whole genome sequencebased surveillance is an important evolutionary step forward.
This approach offers more precise subtyping, which, combined
with better capacity for patient interviews and faster tracebacks, will mean that more food safety gaps can be found and
corrected. The methods allow us to track antibiotic resistance,
serotype and virulence profiles in close to real time, as well.
These methods can be applied to many other infections as
well as to enteric bacteria. They are also helping us to define
broader clades of concern that emerge, recur and persist,
offering new targets for more prevention earlier in the food
supply chain. These methods can help us refine our estimates
of attribution to better target broad prevention strategies, and
they provide a bridge to the future when public health will have
culture-independent tools providing sequence information
rapidly. We anticipate that in the longer term, the effect will be
to help industry, regulators, researchers and consumers drive
down the number of outbreaks and the incidence of foodborne
infections. Thanks to all of you for the roles that you play in
food safety and for staying to the end of the conference.
November/December Food Protection Trends

485

25



Food Protection Trends - November/December 2019

Table of Contents for the Digital Edition of Food Protection Trends - November/December 2019

Food Grade Dye for Assessment of Biofilm Removal from Stainless Steel by Cleaning and Sanitizing Agents
Coming Events
Industry Products
General Interest Paper The Need for Prevention-based Food Safety Programs for Fresh Produce
PDG Highlight Developing Food Safety Professionals PDG
Beyond the Bio Steve Murphy
Validating Responses to a Food Safety Survey with Observations of Food Preparation Behaviors Among Limited Resource Populations
IAFP 2019 IN REVIEW
Food Protection Trends - November/December 2019 - Cover1
Food Protection Trends - November/December 2019 - Cover2
Food Protection Trends - November/December 2019 - 435
Food Protection Trends - November/December 2019 - 436
Food Protection Trends - November/December 2019 - 437
Food Protection Trends - November/December 2019 - 438
Food Protection Trends - November/December 2019 - 439
Food Protection Trends - November/December 2019 - 440
Food Protection Trends - November/December 2019 - 441
Food Protection Trends - November/December 2019 - Food Grade Dye for Assessment of Biofilm Removal from Stainless Steel by Cleaning and Sanitizing Agents
Food Protection Trends - November/December 2019 - 443
Food Protection Trends - November/December 2019 - 444
Food Protection Trends - November/December 2019 - 445
Food Protection Trends - November/December 2019 - 446
Food Protection Trends - November/December 2019 - 447
Food Protection Trends - November/December 2019 - 448
Food Protection Trends - November/December 2019 - Validating Responses to a Food Safety Survey with Observations of Food Preparation Behaviors Among Limited Resource Populations
Food Protection Trends - November/December 2019 - 450
Food Protection Trends - November/December 2019 - 451
Food Protection Trends - November/December 2019 - 452
Food Protection Trends - November/December 2019 - 453
Food Protection Trends - November/December 2019 - 454
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Food Protection Trends - November/December 2019 - 461
Food Protection Trends - November/December 2019 - 462
Food Protection Trends - November/December 2019 - 463
Food Protection Trends - November/December 2019 - 464
Food Protection Trends - November/December 2019 - IAFP 2019 IN REVIEW
Food Protection Trends - November/December 2019 - 466
Food Protection Trends - November/December 2019 - 467
Food Protection Trends - November/December 2019 - 468
Food Protection Trends - November/December 2019 - 469
Food Protection Trends - November/December 2019 - 470
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Food Protection Trends - November/December 2019 - 485
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Food Protection Trends - November/December 2019 - 539
Food Protection Trends - November/December 2019 - 540
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Food Protection Trends - November/December 2019 - 563
Food Protection Trends - November/December 2019 - 564
Food Protection Trends - November/December 2019 - 565
Food Protection Trends - November/December 2019 - 566
Food Protection Trends - November/December 2019 - 567
Food Protection Trends - November/December 2019 - Beyond the Bio Steve Murphy
Food Protection Trends - November/December 2019 - 569
Food Protection Trends - November/December 2019 - 570
Food Protection Trends - November/December 2019 - PDG Highlight Developing Food Safety Professionals PDG
Food Protection Trends - November/December 2019 - General Interest Paper The Need for Prevention-based Food Safety Programs for Fresh Produce
Food Protection Trends - November/December 2019 - 573
Food Protection Trends - November/December 2019 - 574
Food Protection Trends - November/December 2019 - 575
Food Protection Trends - November/December 2019 - 576
Food Protection Trends - November/December 2019 - 577
Food Protection Trends - November/December 2019 - 578
Food Protection Trends - November/December 2019 - 579
Food Protection Trends - November/December 2019 - Industry Products
Food Protection Trends - November/December 2019 - 581
Food Protection Trends - November/December 2019 - 582
Food Protection Trends - November/December 2019 - 583
Food Protection Trends - November/December 2019 - 584
Food Protection Trends - November/December 2019 - 585
Food Protection Trends - November/December 2019 - Coming Events
Food Protection Trends - November/December 2019 - Cover3
Food Protection Trends - November/December 2019 - Cover4
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