The murder of George Floyd last week is an image that I keep seeing in my mind although I haven’t written or said anything about it outside of my family.
George Floyd represents so many others whose names are known, and many others who aren’t as prominent.
I didn’t know what to say. I didn’t want to say something incorrect. So I said nothing.
I got busy and focused on other things. And that’s the problem, and why what is happening all across the U.S. and the world right now is so important: It’s easy to focus on other things and make this someone else’s problem to fight.
A close friend and colleague called me on my silence today saying that not addressing the events, by not acknowledging what was happening was hurtful.
Not doing anything is essentially condoning the history of systemic racism that is so rampant in this country. My friend is absolutely right.
I feel terrible, I have let them, and so many other people who I know and love, down.
We have to change. I have to change. Black lives matter. We have to fight for the safety of our loved ones. We have to ensure that we change the system for them.
One of the paralyzing aspects of this terrible situation is how complex the problem has become. I want to be part of the solution.
Outbreaks of E. coli illness sickened 188 people last year who ate romaine lettuce in three separate outbreaks.
There have been so many outbreaks going back to spinach in 2006, and beyond that, my favorite salad now is a Greek salad – without the lettuce.
If the Leafy Greens Marketing Association was as rigorous as its press releases maintain this would be minimized.
Instead, between 2009 and 2018, federal authorities identified 40 food-borne outbreaks of E. coli in the U.S. “with a confirmed or suspected link to leafy greens,” the FDA said.
Investigators concluded the most recent outbreaks were centered on ranches and fields owned by the same grower and that were located downslope from public land where cattle grazed.
So if LGMA is doing internal audits, why didn’t they notice this dude?
Because it’s PR not gumshoes, people out in the field.
We figured out 20 years ago that gumshoes are required.
The U.S. Food and Drug Administration published the findings of an investigation into the contamination of romaine lettuce implicated in three outbreaks of E. coli O157:H7 during the Fall of 2019.
The investigation was conducted at several farms identified in the outbreak tracebacks, as well as at other businesses and public access areas and resulted in several key findings:
Each of these three outbreaks, identified in the report as Outbreaks A, B and C was caused by distinctly different strains of E. coli O157:H7 as determined by whole genome sequencing (WGS) analysis;
Traceback investigations of multiple illness sub-clusters and supply chain information identified a common grower with multiple ranches/fields which supplied romaine lettuce during the timeframe of interest to multiple business entities associated with all three outbreaks.
The same strain of E. coli O157:H7 that caused Outbreak A was found in two different brands of fresh-cut salads containing romaine lettuce in 2019;
This same outbreak strain of E. coli O157:H7 in Outbreak A was detected in a fecal–soil composite sample taken from a cattle grate on public land less than two miles upslope from a produce farm with multiple fields tied to the outbreaks by the traceback investigations;
Other strains of Shiga toxin-producing E.coli (STEC), while not linked to any of the outbreaks, were found in closer proximity to where romaine lettuce crops were grown, including two samples from a border area of a farm immediately next to cattle grazing land in the hills above leafy greens fields and two samples from on-farm water drainage basins.
These findings, together with the findings from earlier leafy greens outbreaks dating back to 2013, suggest that a potential contributing factor has been the proximity of cattle—a persistent source of E. coli O157:H7 and other STEC—to the produce fields identified in traceback investigations.
Because of the reoccurring nature of outbreaks associated with leafy greens, the FDA recently released a 2020 Leafy Greens STEC Action Plan, which outlines a three-pronged approach for tackling this problem. It describes the FDA’s plans for working with industry, federal partners, state and local regulators, academia and others to address the safety of leafy greens by advancing work in three areas: prevention, response, and addressing knowledge gaps.
Outbreak investigation of E. coli: Romaine from Salinas, California (November 2019)
Persons in congregate work and residential locations are at increased risk for transmission and acquisition of respiratory infections.
COVID-19 cases among U.S. workers in 115 meat and poultry processing facilities were reported by 19 states. Among approximately 130,000 workers at these facilities, 4,913 cases and 20 deaths occurred. Factors potentially affecting risk for infection include difficulties with workplace physical distancing and hygiene and crowded living and transportation conditions.
Improving physical distancing, hand hygiene, cleaning and disinfection, and medical leave policies, and providing educational materials in languages spoken by workers might help reduce COVID-19 in these settings and help preserve the function of this critical infrastructure industry.
COVID-19 among workers in meat and poultry processing facilities—19 States, April 2020, 08 May 2020
Morbidity and Mortality Weekly Report pp. 557-561d
Jonathan W. Dyal, MD1,2; Michael P. Grant, ScD1; Kendra Broadwater, MPH1; Adam Bjork, PhD1; Michelle A. Waltenburg, DVM1,2; John D. Gibbins, DVM1; Christa Hale, DVM1; Maggie Silver, MPH1; Marc Fischer, MD1; Jonathan Steinberg, MPH1,2,3; Colin A. Basler, DVM1; Jesica R. Jacobs, PhD1,4; Erin D. Kennedy, DVM1; Suzanne Tomasi, DVM1; Douglas Trout, MD1; Jennifer Hornsby-Myers, MS1; Nadia L. Oussayef, JD1; Lisa J. Delaney, MS1; Ketki Patel, MD, PhD5; Varun Shetty, MD1,2,5; Kelly E. Kline, MPH6; Betsy Schroeder, DVM6; Rachel K. Herlihy, MD7; Jennifer House, DVM7; Rachel Jervis, MPH7; Joshua L. Clayton, PhD3; Dustin Ortbahn, MPH3; Connie Austin, DVM, PhD8; Erica Berl, DVM9; Zack Moore, MD9; Bryan F. Buss, DVM10,11; Derry Stover, MPH10; Ryan Westergaard, MD, PhD12; Ian Pray, PhD2,12; Meghan DeBolt, MPH13; Amy Person, MD14; Julie Gabel, DVM15; Theresa S. Kittle, MPH16; Pamela Hendren17; Charles Rhea, MPH17; Caroline Holsinger, DrPH18; John Dunn19; George Turabelidze20; Farah S. Ahmed, PhD21; Siestke deFijter, MS22; Caitlin S. Pedati, MD23; Karyl Rattay, MD24; Erica E. Smith, PhD24; Carolina Luna-Pinto, MPH1; Laura A. Cooley, MD1; Sharon Saydah, PhD1; Nykiconia D. Preacely, DrPH1; Ryan A. Maddox, PhD1; Elizabeth Lundeen, PhD1; Bradley Goodwin, PhD1; Sandor E. Karpathy, PhD1; Sean Griffing, PhD1; Mary M. Jenkins, PhD1; Garry Lowry, MPH1; Rachel D. Schwarz, MPH1; Jonathan Yoder, MPH1; Georgina Peacock, MD1; Henry T. Walke, MD1; Dale A. Rose, PhD1; Margaret A. Honein, PhD
Tahini is a common food product in the Mediterranean area that is used as a main ingredient in variety of ready-to-eat foods. The objective of the current study was to investigate the inhibitory effect of thyme oil (TO) or cinnamon oil (CO) on E. coli O157:H7 viability in tahini and diluted tahini at different storage temperatures.
Addition of 2.0% CO to tahini reduced E. coli O157:H7 numbers by 1.38, 1.79 or 2.20 log10 CFU/mL at 10, 25 or 37 °C, respectively, by 28d. In diluted tahini at 10 °C, no viable cells of E. coli O157:H7 by 21d were detected when 1.0% CO was used. However, at 25 and 37 °C, no viable cells were detected by 14d when CO was added at 0.5% level. Addition of 2.0% TO to tahini, resulted in 1.82, 2.01 or 1.65 log10 CFU/mL reduction in E. coli O 157:H7 numbers was noted at 37, 25 or 10 °C, respectively, by 28d. In diluted tahini, TO at 0.5% or 1.0% induced complete reduction in the viability of E. coli O157:H7 by 28d storage at 37 or 25 °C. At 10 °C, a 3.02 log10 CFU/mL reduction was observed by 28d compared to the initial inoculation level in samples treated with 2.0% TO.
Inhibitory effect of thyme and cinnamon essential oils against e. coli O157:H7 in tahini, 08 May 2020
Food Science and Technology
Anas Al-Nabulsi, Tareq Osaili, Amin Olaimat, Weam Almarsi, Murad Al-Holy, Ziad Jaradat, Mutamed Ayyash, Saddam Awaisheh, Richard Holley
Jimmy John’s LLC reported that all of its restaurants stopped serving clover sprouts on February 24, 2020.
People usually get sick from Shiga toxin-producing E. coli (STEC) 1 to 10 days (average of 3 to 4 days) after swallowing the germ.
Symptoms vary, but often include severe stomach cramps, diarrhea (often bloody), and vomiting. Some people may have a fever, which usually is not very high (less than 101˚F/38.5˚C).
Some people with a STEC infection may get a type of kidney failure called hemolytic uremic syndrome (HUS).
Antibiotics are not recommended for patients with suspected E. coli infections until diagnostic testing can be performed and E. coli infection is ruled out. Some studies have shown that administering antibiotics to patients with E. coli infections might increase their risk of developing HUS, and a benefit of treatment has not been clearly demonstrated.
CDC, public health and regulatory officials in several states, and the U.S. Food and Drug Administration (FDA) investigated a multistate outbreak of E. coli O103 infections linked to clover sprouts.
Public health investigators used the PulseNet system to identify illnesses that were part of this outbreak. PulseNet is the national subtyping network of public health and food regulatory agency laboratories coordinated by CDC. DNA fingerprinting is performed on E. coli bacteria isolated from ill people by using a standardized laboratory and data analysis method called whole genome sequencing (WGS). CDC PulseNet manages a national database of these sequences that are used to identify possible outbreaks. WGS gives investigators detailed information about the bacteria causing illness. In this investigation, WGS showed that bacteria isolated from ill people were closely related genetically. This means that people in this outbreak were likely to share a common source of infection.
A total of 51 people infected with the outbreak strain of E. coli O103 were reported from 10 states. A list of the states and the number of cases in each can be found on the Map of Reported Cases.
Illnesses started on dates ranging from January 6, 2020, to March 15, 2020. Ill people ranged in age from 1 to 79 years, with a median age of 29 years. Fifty-five percent of ill people were female. Of 41 ill people with information available, 3 were hospitalized and no deaths were reported.
Seventeen (63%) of 27 people interviewed reported eating sprouts at a Jimmy John’s restaurant. Jimmy John’s LLC reported that all of their restaurants stopped serving clover sprouts on February 24, 2020. Clover sprouts are no longer available at Jimmy John’s restaurants.
Additionally, FDA identified the outbreak strain of E. coli O103 in samples of Chicago Indoor Garden products that contain sprouts. On March 16, 2020, Chicago Indoor Garden recalledexternal icon all products containing red clover sprouts.
FDA’s traceback investigationexternal icon showed that a common seed lot was used to grow both the sprouts recalled by Chicago Indoor Garden and sprouts that were served at some Jimmy John’s locations. The same seed lot was also used to grow sprouts linked to an outbreakexternal icon of the same strain of E. coli O103 infections in 2019.
As of April 22, 2020, this outbreak appears to be over.
Enteroinvasive Escherichia coli (EIEC) and Shigella spp. are both Gram-negative bacteria causing diarrheal disease worldwide [1,2]. The clinical presentations of these two pathogens are very similar [3,4] and commonly manifested through diarrhoea, abdominal cramps, nausea and fever both in children and adults [5,6]. In addition to a similar clinical picture, EIEC and Shigella share laboratory features that can make it difficult to distinguish between them in routine clinical laboratory practice. Both pathogens are transmitted via the faecal-oral route and infections are frequently associated with consumption of contaminated food and water [7–10]. While Shigella is associated with large-scale food-borne outbreaks [11,12], outbreaks caused by EIEC are rarely recorded.
High prevalence of EIEC infections have been documented in rural areas and settings with poor sanitation in high-risk countries [5,13] while EIEC infections in Europe are typically sporadic and travel related . Nevertheless, a few EIEC outbreaks have been reported in Europe, with the most recent ones having occurred in Italy in 2012  and in the United Kingdom (UK) in 2014 . These outbreaks affected 109 cases and 157 probable cases, respectively, highlighting the fact that EIEC, like Shigella, has the capacity to cause large gastrointestinal disease outbreaks. The outbreak strain identified in these recent European outbreaks, EIEC O96:H19, is an emergent type of EIEC that has phenotypic characteristics more resembling those of non-invasive Escherichia coli (E. coli) than those described for Shigella . These characteristics are suggested to contribute to improved survival abilities as well as the ability to better adapt to different ecological niches .
Traditionally, culturing of faecal specimens has been the mainstay of laboratory diagnostics for enteric bacteria, and EIEC has been differentiated from Shigella by assessing a combination of several phenotypic characteristics, including biochemical, motility and serological traits [18,19]. This is now changing as PCR-based methods are becoming routine in many diagnostic laboratories . In contrast to non-invasive E. coli, EIEC and Shigella can invade and multiply in intestinal epithelial cells , a process that is partially mediated by the products of the invasion plasmid antigen (ipa) genes . For this reason, PCR targeting the ipaH gene can separate EIEC from other non-invasive E. coli, but cannot differentiate between EIEC and Shigella . The lacY gene has been proposed as an additional molecular marker for which most E. coli are positive and Shigella is negative . Its use as a PCR target in separating Shigella and EIEC is restricted to bacterial isolates since many faecal samples are lacY positive because of the presence of E. coli in the normal flora.
Which is considered too time consuming for most clinical laboratories. For this reason, it is likely that a patient with specimens that are ipaH PCR-positive but culture negative would not be notified as a case if the diagnostic algorithm at the laboratory requires a detected Shigella isolate. In addition, PCR is a more sensitive method than culturing  and Shigella is known for its limited survival ability in faecal samples , which also may lead to samples being ipaH PCR-positive but culture negative.
Shigellosis is notifiable by law in Sweden as in the majority of countries in Europe . In 2017, the incidence was 2.1 per 100,000 inhabitants in Sweden, and the majority of cases had been infected abroad . The mandatory reporting of diseases allows the implementation of a series of public health actions, including public health management and surveillance activities, and helps define risk exposures. In contrast to shigellosis, reporting is not mandatory for EIEC and the occurrence of this pathogen in Sweden is currently unknown.It requires additional laboratory procedures such as screening large numbers of colonies,
Outbreak of gastroenteritis highlighting the diagnostic and epidemiological challenges of enteroinvasive Escherichia coli, county of Halland, Sweden, November 2017, 12 December 2019
Shiga toxin-producing Escherichia coli (STEC) strains are important zoonotic foodborne pathogens, causing diarrhea, hemorrhagic colitis, and life-threatening hemolytic uremic syndrome (HUS) in humans. However, antibiotic treatment of STEC infection is associated with an increased risk of HUS. Therefore, there is an urgent need for early and effective therapeutic strategies.
Here, we isolated lytic T7-like STEC phage PHB19 and identified a novel O91-specific polysaccharide depolymerase (Dep6) in the C terminus of the PHB19 tailspike protein. Dep6 exhibited strong hydrolase activity across wide ranges of pH (pH 4 to 8) and temperature (20 to 60°C) and degraded polysaccharides on the surface of STEC strain HB10. In addition, both Dep6 and PHB19 degraded biofilms formed by STEC strain HB10.
In a mouse STEC infection model, delayed Dep6 treatment (3 h postinfection) resulted in only 33% survival, compared with 83% survival when mice were treated simultaneously with infection. In comparison, pretreatment with Dep6 led to 100% survival compared with that of the control group. Surprisingly, a single PHB19 treatment resulted in 100% survival in all three treatment protocols. Moreover, a significant reduction in the levels of proinflammatory cytokines was observed at 24 h postinfection in Dep6- or PHB19-treated mice. These results demonstrated that Dep6 or PHB19 might be used as a potential therapeutic agent to prevent STEC infection.
IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen worldwide. The Shiga-like toxin causes diarrhea, hemorrhagic colitis, and life-threatening hemolytic uremic syndrome (HUS) in humans. Although antibiotic therapy is still used for STEC infections, this approach may increase the risk of HUS. Phages or phage-derived depolymerases have been used to treat bacterial infections in animals and humans, as in the case of the “San Diego patient” treated with a phage cocktail. Here, we showed that phage PHB19 and its O91-specific polysaccharide depolymerase Dep6 degraded STEC biofilms and stripped the lipopolysaccharide (LPS) from STEC strain HB10, which was subsequently killed by serum complement in vitro. In a mouse model, PHB19 and Dep6 protected against STEC infection and caused a significant reduction in the levels of proinflammatory cytokines. This study reports the use of an O91-specific polysaccharide depolymerase for the treatment of STEC infection in mice.
A novel tail-associated O91-specific polysaccharide depolymerase from a podophage reveals lytic efficacy of shiga toxin-producing Escherichia coli, 28 February 2020
I’ll say it again, as a comic in all seriousness: Lettuce is overrated.
My favorite salad is a Greek one with all those veggies and no lettuce.
The U.S. Food and Drug Administration announced last week that between 2009 and 2018, FDA and the Centers for Disease Control and Prevention (CDC) identified 40 foodborne outbreaks of Shiga toxin-producing E. coli (STEC) infections in the U.S. with a confirmed or suspected link to leafy greens.
This is why The Tragically Hip were so great, and why they never appealed much beyond Canada.
I feel the same about academia.
And why Osterholm called me 15 years ago as a consultant for Fresh Express, and asked me how dare I the lettuce and skull picture, and I said because I can and it was fairly apt given there have been 40 outbreaks.
Holy shit (this is me echoing my John Oliver voice).
Coronavirus is just confirming: Go public, go often, go hard.
It’s the only way people will pay attention.
And as this story in the N.Y. Times points out, there have been spectacular public health failures by people who tell others, just shut the fuck up.
According to the FDA, it has an unwavering commitment to advancing the safety of fresh leafy greens. Leafy greens are among the most widely consumed vegetables and an important part of an overall healthy diet. While millions of servings are consumed safely every day, this produce commodity has been implicated too often in outbreaks of foodborne illness, and we believe that FDA, along with leafy greens sector stakeholders, can do more.
Between 2009 and 2018, FDA and Centers for Disease Control and Prevention (CDC) identified 40 foodborne outbreaks of Shiga toxin-producing E. coli (STEC) infections in the U.S. with a confirmed or suspected link to leafy greens. While most strains of E. coli are harmless, STEC can cause bloody diarrhea, anemia, blood-clotting problems, and kidney failure – conditions that are potentially life-threatening. The most common STEC, E. coli O157:H7, is the type most often associated with outbreaks.
Most leafy greens are grown outdoors, where they are exposed to soil, animals, and water, all of which can be a source of pathogen contamination. In addition, leafy greens are mostly consumed raw, without cooking or other processing steps to eliminate microbial hazards. The Produce Safety Rule under the FDA Food Safety Modernization Act (FSMA) sets science-based standards to help ensure that water, soil amendments (e.g., fertilizer or compost), food contact surfaces and other materials that touch produce during growing, harvesting, packing, and holding do not contribute to produce contamination. The Produce Safety Rule also addresses animal intrusion into fields and worker hygiene.
Due to the recurring nature of outbreaks associated with leafy greens, FDA has developed this commodity-specific action plan. What follows is an overview of the actions FDA plans to take in 2020 to advance work in three areas: (1) prevention, (2) response, and (3) addressing knowledge gaps.
Faculty members from the Kansas State University College of Veterinary Medicine have developed a faster, more efficient method of detecting “Shiga toxin-producing E. coli,” or STEC, in ground beef, which often causes recalls of ground beef and vegetables.
“The traditional gold standard STEC detection, which requires bacterial isolation and characterization, is not amenable to high-throughput settings and often requires a week to obtain a definitive result,” said Jianfa Bai, section head of molecular research and development in the Kansas State Veterinary Diagnostic Laboratory.
The new method developed by Bai and colleagues requires only a day to obtain confirmatory results using a Kansas State University-patented method with the partition-based multichannel digital polymerase chain reaction system.
“We believe the new digital polymerase chain reaction detection method developed in this study will be widely used in food safety and inspection services for the rapid detection and confirmation of STEC and other foodborne pathogens,” said Jamie Henningson, director of the Kansas State Veterinary Diagnostic Laboratory.
When ingested through foods such as ground beef and vegetables, STEC can cause illnesses with symptoms including abdominal pain and diarrhea. Some illnesses caused by STEC may lead to kidney failure and can be life-threatening.
“Some E. coli strains do not produce Shiga toxins and thus do not affect human health as much,” said Xuming Liu, research assistant professor. “Because cattle feces and ground beef can contain harmless or less pathogenic E. coli along with STEC, the most commonly used polymerase chain reaction cannot identify pathogenic E. coli strains in a complex sample matrix.”
The new digital polymerase chain reaction test was developed for research and food safety inspections that require shorter turnaround and high throughput, without sacrificing detection accuracy.
“While the current, commonly used testing method is considered to be the gold standard, it is tedious and requires many days to obtain results that adequately differentiate the bacteria,” said Gary Anderson, director of the International Animal Health and Food Safety Institute at the K-State Olathe campus.
The study, “Single cell-based digital PCR detection and association of Shiga toxin-producing E. coli serogroups and major virulence genes,” which describes the test design and results, was published in the Journal of Clinical Microbiology.