Food Protection Trends - November/December 2019 - 484
The experience was not limited to Listeria. In 2015, the
Minnesota state public health laboratory began WGS typing of
Salmonella serotype Enteritidis (SE), a serotype that has been
difficult to resolve with PFGE, which provides only a few main
subtypes. That summer, within months of starting to type SE,
they identified two separate outbreaks related to two similar
products that were frozen stuffed breaded raw chicken products. Each was caused by two different PFGE types, but WGS
showed that the strains in each outbreak had closely related
sequences, and matching strains were found in the two brands
of product. Again, relying on PFGE probably would have
meant that these outbreaks would not have been detected at
all. Though the number of cases identified in Minnesota was
small, five in one outbreak and seven in the other, the actual
outbreaks were probably much larger; both implicated products
were distributed to many states, and both were recalled nationwide. We don't really know how long these outbreaks had
been going on. Problems like this have been identified before,
but these two outbreaks in one summer underlined the ongoing
risk of this particular product type. Efforts had been made to
improve the consumer instructions on the packaging, so it was
interesting that many people who became ill told the investigators that they read and followed the directions for cooking, and
some used a meat thermometer to be sure it was cooked thoroughly. The event raised concern that the tactile clues provided
by a dry, breaded and browned product may override instructions about desired food safety behaviors always needed after
handling raw chicken products.
The following year, a second state health department
began evaluating WGS for Salmonella Enteritidis. In 2016
Tennessee found a small cluster of six closely-related infections; who all ate at a restaurant where steak with raw egg
bearnaise sauce was the exposure they had in common. The
eggs came from a small local farm, with fewer than 3,000 hens;
sampling on the farm did not yield SE. A month later, a second
outbreak occurred due to a strain of SE that was three single
nucleotide polymorphisms different from the first outbreak
cluster (the technical term I use is "DNI or darned near identical"). These ill persons had eaten at a second restaurant,
making raw egg mayo using eggs from the same small farm.
This time, reinvestigation of the farm identified SE in the
chicken litter, and more specific advice and control measures
were instituted. Again, WGS helped to find and link these small
outbreaks and point to a gap in our food safety system, as the
2010 egg regulation applies only to flocks that have at least
3,000 hens.
This showed us that subtyping based on genetic relationships can give us better separation of truly related infections
from those that are not improving our definitions of case vs.
non-case. While PFGE could only say "same" vs. "different",
WGS provides a scale of genetic difference. Some very common PFGE types can be divided into meaningful subtypes, as
may often be the case with Salmonella Enteritidis. Some WGS
clusters of closely-related strains may bring together a variety
of PFGE patterns, that appear different because variable plasmid content masks a fundamental genetic similarity. Applied
across human, food, animal and environmental isolates, it can
suggest and confirm relationships with more confidence than
PFGE did.
Starting in 2017, we began preparing the transition to
WGS in PulseNet. With support from several funding sources,
including the Initiative to Combat Antibiotic Resistant Bacteria
to support better surveillance for antibiotic resistance, and the
Advanced Molecular Detection program, we began to expand
our information backbone, and to equip, train and certify state
health department laboratories in this new method. We partnered closely with the USDA/FSIS and with the FDA's Genome TrakR program that was equipping food laboratories in
many states with WGS. In 2018, many states began sequencing their Listeria strains, and on July 15, 2019, we made the
transition to WGS as the standard PulseNet method for E. coli
O157 and Salmonella. As we saw in the Listeria pilot program,
we now expect to find more clusters of all these pathogens
that are truly genetically related, leading to more successful
epidemiological investigations, and defining more targets for
improved prevention. Anticipating the need for more epidemiological investigators in state health departments, we have also
been supporting more capacity for investigation in many state
health departments around the country, so there are staff to
handle the growing number of clusters of illness identified.
It is important to understand that just showing that clinical
strains have very similar sequences to a strain from a food, or
that two strains separated by several years are closely related
genetically does not by itself prove that they are from the same
source. We still need to investigate what foods the patients ate,
looking for unexpected similarities in exposures, and tracing
suspect foods back to their sources. There are many dotted
lines that need to be filled in, and investigations are not always
successful. The genetic similarity certainly provides a strong
clue, or hypothesis, to the investigators, but those investigations are critical to solving the outbreak.
It is important to be alert for multiclonal outbreaks. Not every
outbreak is caused by a single strain or subtype. A product may
be heavily contaminated with many different pathogens. For
example, last year we investigated an outbreak of at least 199
infections linked to consuming kratom, the leaves of a South
East Asian shrub in the coffee family, used for its opioid-like
effects. People buy it at smoke or vape shops in many states,
or online. The samples tested by FDA yielded Salmonella with
85 different WGS profiles, and strains in six serotypes matched
strains from ill persons who had been using kratom. There
seem to be major flaws in kratom processing that somehow are
leading to extraordinarily high contamination with many strains
in this imported product.
It is also important to remember that it is not always food.
We have every year many infections with enteric pathogens
that are related to backyard chickens, pet reptiles, and other
animal exposures. When we approach a cluster of genetically
related infections, we must consider a range of hypotheses
beyond the things that they may have eaten.
This greater confidence in taxonomic genetic relationships provided by WGS means that the definition of what an
outbreak is seems to be broadening. We can see beyond
the classic cluster of focused tightly in place and time, to find
broader events caused by taxonomically-related groups, that
last for years rather than just weeks or months, that may signal
a long-lasting harborage site somewhere in the production
system. We can discern the spread of a group of related strains
that emerges in a food animal species or a produce growing
area, that can manifest as repeated or sustained events affecting many herds, flocks or fields at once. To describe these
broader groups, I borrow a taxonomic term, "clade," derived
from the Greek word klados for "branch," that geneticists
already use to describe broad groups of related organisms
with more precision.
Here are two examples of recurring or emerging "clades"
of concern. In the spring of 2018, a large outbreak of E. coli
O157 infections was traced to Romaine lettuce. This outbreak
was the largest O157 outbreak in a decade, with 210 confirmed
cases in 36 states, leading to 96 hospitalizations and five
deaths. It started in one state as a local cluster of infections related to several outlets of a restaurant chain, and then was quickly recognized across the country. Thanks to rapid investigation
by public health epidemiologists in many states, and great
efforts to trace suspect lettuce back, it was linked to Romaine
lettuce from the Yuma growing area. One noteworthy investigation occurred in Nome, Alaska, where an outbreak in the local
jail was linked to whole head Romaine that could be traced to
a single farm, while products implicated in other clusters were
mixed, chopped and bagged Romaine from multiple farms.
(Continued on next page)
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Food Protection Trends November/December
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
Food Protection Trends - November/December 2019 - 455
Food Protection Trends - November/December 2019 - 456
Food Protection Trends - November/December 2019 - 457
Food Protection Trends - November/December 2019 - 458
Food Protection Trends - November/December 2019 - 459
Food Protection Trends - November/December 2019 - 460
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
Food Protection Trends - November/December 2019 - 471
Food Protection Trends - November/December 2019 - 472
Food Protection Trends - November/December 2019 - 473
Food Protection Trends - November/December 2019 - 474
Food Protection Trends - November/December 2019 - 475
Food Protection Trends - November/December 2019 - 476
Food Protection Trends - November/December 2019 - 477
Food Protection Trends - November/December 2019 - 478
Food Protection Trends - November/December 2019 - 479
Food Protection Trends - November/December 2019 - 480
Food Protection Trends - November/December 2019 - 481
Food Protection Trends - November/December 2019 - 482
Food Protection Trends - November/December 2019 - 483
Food Protection Trends - November/December 2019 - 484
Food Protection Trends - November/December 2019 - 485
Food Protection Trends - November/December 2019 - 486
Food Protection Trends - November/December 2019 - 487
Food Protection Trends - November/December 2019 - 488
Food Protection Trends - November/December 2019 - 489
Food Protection Trends - November/December 2019 - 490
Food Protection Trends - November/December 2019 - 491
Food Protection Trends - November/December 2019 - 492
Food Protection Trends - November/December 2019 - 493
Food Protection Trends - November/December 2019 - 494
Food Protection Trends - November/December 2019 - 495
Food Protection Trends - November/December 2019 - 496
Food Protection Trends - November/December 2019 - 497
Food Protection Trends - November/December 2019 - 498
Food Protection Trends - November/December 2019 - 499
Food Protection Trends - November/December 2019 - 500
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Food Protection Trends - November/December 2019 - 504
Food Protection Trends - November/December 2019 - 505
Food Protection Trends - November/December 2019 - 506
Food Protection Trends - November/December 2019 - 507
Food Protection Trends - November/December 2019 - 508
Food Protection Trends - November/December 2019 - 509
Food Protection Trends - November/December 2019 - 510
Food Protection Trends - November/December 2019 - 511
Food Protection Trends - November/December 2019 - 512
Food Protection Trends - November/December 2019 - 513
Food Protection Trends - November/December 2019 - 514
Food Protection Trends - November/December 2019 - 515
Food Protection Trends - November/December 2019 - 516
Food Protection Trends - November/December 2019 - 517
Food Protection Trends - November/December 2019 - 518
Food Protection Trends - November/December 2019 - 519
Food Protection Trends - November/December 2019 - 520
Food Protection Trends - November/December 2019 - 521
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Food Protection Trends - November/December 2019 - 523
Food Protection Trends - November/December 2019 - 524
Food Protection Trends - November/December 2019 - 525
Food Protection Trends - November/December 2019 - 526
Food Protection Trends - November/December 2019 - 527
Food Protection Trends - November/December 2019 - 528
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Food Protection Trends - November/December 2019 - 530
Food Protection Trends - November/December 2019 - 531
Food Protection Trends - November/December 2019 - 532
Food Protection Trends - November/December 2019 - 533
Food Protection Trends - November/December 2019 - 534
Food Protection Trends - November/December 2019 - 535
Food Protection Trends - November/December 2019 - 536
Food Protection Trends - November/December 2019 - 537
Food Protection Trends - November/December 2019 - 538
Food Protection Trends - November/December 2019 - 539
Food Protection Trends - November/December 2019 - 540
Food Protection Trends - November/December 2019 - 541
Food Protection Trends - November/December 2019 - 542
Food Protection Trends - November/December 2019 - 543
Food Protection Trends - November/December 2019 - 544
Food Protection Trends - November/December 2019 - 545
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Food Protection Trends - November/December 2019 - 548
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Food Protection Trends - November/December 2019 - 553
Food Protection Trends - November/December 2019 - 554
Food Protection Trends - November/December 2019 - 555
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Food Protection Trends - November/December 2019 - 557
Food Protection Trends - November/December 2019 - 558
Food Protection Trends - November/December 2019 - 559
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Food Protection Trends - November/December 2019 - 561
Food Protection Trends - November/December 2019 - 562
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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