Why whole genome sequencing is important for food safety

In 1999, I gave a talk to hundreds of farm leaders in Ottawa and told them that DNA fingerprinting – via PulseNet – would revolutionize foodborne illness outbreak investigations and that farmers better be prepared (the pic is from a 2003 awards ceremony where I was acknowledged for my outreach and extension efforts, the hair was fabulous).

Twenty years later and whole genome sequencing is even further piecing together disparate outbreaks.

Joanie Stiers of Farm Flavor writes that Michigan’s laboratory toolbox now includes whole-genome sequencing, allowing public health officials to stop the spread of foodborne illness faster than ever.

Since January of 2017, the Michigan Department of Agriculture and Rural Development (MDARD) has actively used whole-genome sequencing to precisely identify illness-causing pathogens and defend against widespread outbreaks of foodborne diseases.

MDARD’s Geagley Laboratory works in tandem with laboratories in the U.S. Food & Drug Administration’s GenomeTrakr network, which allows global collaboration in the fight against foodborne illness.

“With food now being distributed worldwide, illness can be spread from anywhere in the world,” says Ted Gatesy, laboratory manager of the microbiology section at Geagley Lab, which houses the whole-genome sequencing. “Using whole-genome sequencing, an illness can be tracked, for the most part, to the point in the food chain where it originated.

Fun with fermentations: Latic acid can maybe make sprouts safer

Legume seeds and sprouts are a rich source of phytoestrogens in the form of isoflavonoids. For the first time, lactic acid fermentation of four types of legume sprouts was used to increase the content of isoflavonoids and microbiological safety.

After germination, the highest content of isoflavonoids was observed in the clover and chickpea sprouts, which amounted to 1.1 g/100 g dw., whereas the lactic acid fermentation allowed the increase to as much as 5.5 g/100 g dw. The most beneficial properties were shown by fermented chickpea sprouts germinated in blue light.

During fermentation the number of lactic acid bacteria increased by 2 Log10CFU/mL (LU), whereas mold decreased by 1 LU, E.coli and Klebsiella sp. by 2 LU, Salmonella sp. and Shigella sp did not occur after fermentation, similar to Staphylococcus epidermidis, while S. aureus and S. saprophyticus decreased by 3 LU and in some trials were not detected.

Lactic acid fermentation of legume seed sprouts as a method of increasing the content of isoflavones and reducing microbial contamination

6.feb.19

Food Chemistry, https://doi.org/10.1016/j.foodchem.2019.01.178

GrażynaBudryn, ElżbietaKlewicka, JoannaGrzelczyk, IlonaGałązka-Czarnecka, Radosław Mostowski

https://www.sciencedirect.com/science/article/pii/S0308814619302675

Washing does almost nothing, except remove the snot from the 3-year-old who sneezed on it

This is a risk communication embarrassment.

Stop Foodborne Illness published this thing the other day, about Rylee & Rusty (not sue if those names were chosen by focus group).

Anyone who writes in all caps is compensating for something, just like I’ve always told my daughters, anyone who says trust me is immediately untrustworthy.

One day when Rylee and Rusty were walking home after school, Rusty pulled an apple out of his bag and started to take a bite. Rylee, grabbing his arm asked, “Hey! Did you wash that?” “I dunno. My mom probably did,” Rusty replied completely puzzled. “HOW old are you?” Rylee asked. “You know food safety is everybody’s responsibility,” she exclaimed with exasperation. “Oh Rylee!” Rusty replied with a shrug of his shoulders, “Why are you making such a big deal out of this?” With her hands on her hips Rylee scowled at him and raised her voice, “WHY am I making a BIG DEAL?!” “Yeah, why?” he asked, calm as ever. “You have heard of E. coli O157:H7, right?” For a minute there Rylee sounded like Ms. Coffman, but then she said, “I sit next to you in science class every day Rustin Archibald Brown. Have you not been listening?” Rusty replied with an uncertain, “No?” “Well,” Rylee said, “E. coli is a kind of bacteria that can make you really sick. So sick, in fact… that if you had to choose between cleaning your room or being sick from E. coli, you’d pick cleaning your room any day of the week!” “That’s pretty sick,” said Rusty, “I hate cleaning my room.” Rylee continued, “Your stomach feels like an elephant is standing on it, you’re puking your guts out, and… well, let’s just say ya make a big mess in the bathroom.” “What did she just say?” he thought to himself. Clutching his stomach Rusty groaned, “Yuck! RY-LEE, stop!” Rylee paused for just a second to take a breath and then Rusty cut in, No more.

BS: Academics feel the invisible hand of politicians and big agriculture

Another takedown piece on conspiracies rather than science.

I got lots of money from big ag and was never compromised in my evidence-based writings.

70 peer-reviewed papers and book chapters, not a lot, but not bad, since they get cited daily, somewhere (thanks to Amy for keeping me up to date, I admit I’m somewhat humbled but also don’t care; I know what we did).

Kate Cox and Claire Brown of The Guardian write that in a windowless conference room epidemiologist Steve Wing was frantically blacking out chunks of his own research.

Wing had been working on a study looking into the impacts of industrial-scale hog operations on health for the University of North Carolina. But the state’s Pork Council had caught wind of the research, and filed a Freedom of Information Act Request (FOIA) to gain access to his findings. “They went after Steve, asking him to turn over any documentation. They went directly to the university and got the lawyers to try and make him hand it over,” says Naeema Muhammad, one of Wing’s community partners.

I consulted on risk communication activities for the U.S. National Pork Board back in the 1990s or thereabouts. I received no money.

The others on the advisory committee were honest and devoted to their research.

Academia don’t pay much (and when it does, they find a reason to dump ya).

Me, I always spoke my mind and never felt any industry pressure – the only pressure I got was from green groups culminating in death threats taped to my lab door.

We had to involve the university cops, which was somewhat hilarious because a couple of grad students had bailed me out of jail or other situations (should be a grad student requirement).

Yes I took money. Yes we did good research that was published in peer-reviewed journals (and sometimes won awards). Yes, like my four Canadian daughters, those students have gone on to have remarkable and varying lives.

Look how young Steve Cropper and Duck Dunn are in this Stax Records clip.

Trump gets his news here: Fox News host says he has not washed his hands in 10 years ‘Germs are not a real thing’

To the chagrin of his co-hosts, Fox and Friends presenter Pete Hegseth told the show’s audience Sunday morning that he hasn’t washed his hands in a decade.

Katherine Hignett of Newsweek writes the revelation came after co-hosts Ed Henry and Jedediah Bila questioned Hegseth’s off-camera consumption of pizza left out after National Pizza Day Saturday. Hegseth had argued that pizza “lasts for a long time.”

Bila then quipped Hegseth “might take a chomp out of” anything on a table “that’s not nailed down”—including mugs.

“My 2019 resolution is to say things on air that I say off air… I don’t think I’ve washed my hands for 10 years. Really, I don’t really wash my hands ever,” Hegseth continued, prompting laughter from his co-hosts.

“Someone help me,” Bila said. “Oh man.”

“I inoculate myself. Germs are not a real thing. I can’t see them. Therefore the’re not real,” Hegseth said.  

“So you’re becoming immune to all of the bacteria,” Bila replied, rolling her eyes. “My dad has that theory too.”

Hegseth later shared a Tweet in support of his unusual concept of health and hygiene with the hashtag “DontWash.”

But the Centers for Disease Control and Prevention states that handwashing is a vital way to prevent the transmission of disease. By washing your hands—especially after using the bathroom—you prevent the spread of harmful bacteria like Salmonella and E.coli that can persist in tiny, invisible particles of human feces

It’s also important to wash your hands after handling raw meat, as this can harbor germs leftover from animal feces.

“A single gram of human feces—which is about the weight of a paper clip—can contain one trillion germs,” the CDC reports.

Filion, K., KuKanich, K.S., Chapman, B., Hardigree, M.K., and Powell, D.A. 2011. Observation-based evaluation of hand hygiene practices and the effects of an intervention at a public hospital cafeteria. American Journal of Infection Control 39(6): 464-470.

Background

Hand hygiene is important before meals, especially in a hospital cafeteria where patrons may have had recent contact with infectious agents. Few interventions to improve hand hygiene have had measureable success. This study was designed to use a poster intervention to encourage hand hygiene among health care workers (HCWs) and hospital visitors (HVs) upon entry to a hospital cafeteria.

Methods

Over a 5-week period, a poster intervention with an accessible hand sanitizer unit was deployed to improve hand hygiene in a hospital cafeteria. The dependent variable observed was hand hygiene attempts. Study phases included a baseline, intervention, and follow-up phase, with each consisting of 3 randomized days of observation for 3 hours during lunch.

Results

During the 27 hours of observation, 5,551 participants were observed, and overall hand hygiene frequency was 4.79%. Hygiene attempts occurred more frequently by HCWs than HVs (P = .0008) and females than males (P = .0281). Hygiene attempts occurred more frequently after poster introduction than baseline (P = .0050), and this improvement was because of an increase in frequency of HV hand hygiene rather than HCW hand hygiene.

Conclusion

The poster intervention tool with easily accessible hand sanitizer can improve overall hand hygiene performance in a US hospital cafeteria.

Wilson, S.M., Jacob, C.J. and Powell, D.A. 2011. Behavior-change interventions to improve hand hygiene practice: A review. Critical Public Health 21: 119-127.

http://www.informaworld.com/smpp/content~content=a934338802~db=all~jumptype=rss

Despite the role of hand hygiene in preventing infectious disease, compliance remains low. Education and training are often cited as essential to developing and maintaining hand-hygiene compliance, but generally have not produced sustained improvements. Consequently, this literature review was conducted to identify alternative interventions for compelling change in hand-hygiene behavior. Of those, interventions employing social pressures have demonstrated varying influence on an individual’s behavior, while interventions that focus on organizational culture have demonstrated positive results. However, recent research indicates that handwashing is a ritualized behavior mainly performed for self-protection. Therefore, interventions that provoke emotive sensations (e.g., discomfort, disgust) or use social marketing may be the most effective.

Dead lizard found in Irvins salted egg fish snack: Singapore

A packet of salted egg fish skin snack that contained a dead lizard was manufactured at Irvins Salted Egg’s previous premises, which ceased operations in November last year, the Agri-Food and Veterinary Authority (AVA) said.

That facility is understood to be located in Admiralty Street.

In a statement on Monday (Feb 11), the AVA said that it had completed investigations into the Singapore-based food company, after a Bangkok customer found a dead lizard coated with salted egg in a packet of the popular snack in December.

The AVA said that it had since inspected Irvins’ current premises and told the company to improve its quality control checks.

Quality control checks include conducting regular refresher training for quality control operators, sourcing ingredients from reputable suppliers and conducting regular audits.

“Irvins has made improvements in these areas, as well as stepped up inspections on the production line,” the AVA said.

The authority added that it will continue to do periodic audits and enforcement checks on the company.

The AVA urged food manufacturers to be responsible in complying with food safety standards or requirements as well as maintaining robust food safety management systems, even as it continued to carry out periodic checks.

Consumers should also adhere to good food safety practices, the AVA said in its statement.

Some good food safety guidelines for consumers include the following:

– Examine packaged food carefully. Do not buy if the packaging is damaged or open as it may contain harmful micro-organisms that could cause food poisoning.

– Keep foodstuff – such as coffee, tea, powdered milk and biscuits – in clean, air-tight containers, away from heat and moisture.

– Inspect food regularly for insect infestation, mould, and other signs of spoilage. Discard when necessary.

– Check food storage cupboards regularly to ensure that they are free from insect infestation or contamination.

– Keep cupboards meant for food storage uncluttered and clean.

I’m not sure what consumers can do about reptiles in pre-packaged foods.

Everyone has a camera: Vancouver bakery edition

The Canadian Food Inspection Agency (CFIA) has issued a recall for Betty brand and Nancy’s Fancy Yummy in the Tummy brand bakery products.

The agency says the products may be unsafe due to possible contamination from mice infestation at the manufacturing plant.

The affected products were sold in Ontario and Quebec up to and including Feb. 8, and may contain harmful bacteria.

CFIA says there have been no reports of illness linked to the products.

Evidence-based barf: Gwyneth Paltrow and Goop on new Netflix show

My friend, Timothy Caufield, a prof at the University of Alberta and author of, Is Gwyneth Paltrow Wrong about Everything? will get loads of material from this after the Goopster confirmed with ABC News that she had signed a deal with Netflix that would see 30-minute episodes of a docuseries focused on physical and spiritual wellness.

CULVER CITY, CA – JUNE 09: Gwyneth Paltrow speaks onstage at the In goop Health Summit at 3Labs on June 9, 2018 in Culver City, California. (Photo by Neilson Barnard/Getty Images for goop)

Set to air later this year, Paltrow and Goop chief content officer Elise Loehnen will co-host the show and talk to experts, doctors and researchers. The pair already have a popular podcast series.

Paltrow started the company more than 10 years ago and has been criticised for promoting products like jade eggs, that Goop alleged improved vaginal muscle tone, hormonal balance and chi, but which health practitioners warned were dangerous.

Other health practices Paltrow and Goop have promoted include vaginal steaming, bee sting facials, bio frequency stickers (to “rebalance the energy frequency in our bodies”) and earthing.

She was married to that singer from Coldplay, and they suck.

Speaks volumes.

Going public: Norovirus ‘sweet spot’ at Pennsylvania college

“It hit me like a train wreck.” This is how one of the many infected students described his symptoms of what is likely norovirus.

Stool tests performed on those who are ill haven’t confirmed this diagnosis, but Director of Health Services Dr. Goldstein said that norovirus is “likely” the culprit of the students’ symptoms, which include vomiting, diarrhea and stomach pain. Resident Advisors on campus have reported 103 cases of students having contracted the debilitating stomach bug as of Wednesday evening, according to Goldstein, Director of Health Services.

Goldstein first notified the campus community about the virus in a campus-wide email sent Monday, Feb. 4 at 2:40 p.m., but didn’t name the illness as norovirus at that time.

Some students, however, felt this email did not come soon enough. Haley Matthes ‘19 voiced her frustrations and warned students to be aware of its spreading in a post in the Lafayette College Class of 2019 Facebook group on Feb. 2.

“I’m just tired of the school waiting for a campus-wide sickness to escalate to a point where they need to send out a bulletin [or] cancel classes,” Matthes said in a follow-up email.

Matthes was also upset that extended hours weren’t offered at Bailey Health Center.

Several students in the Phi Kappa Psi fraternity have also had the virus. According to Mikey Burke ‘21, approximately 12 to 15 members of the fraternity had contracted the virus as of Tuesday, although he said he expected that number to grow.

“I think it just spread really quickly throughout the house, it originated there and spread to a lot of the brotherhood, I live in McKeen and only hung out at the [Phi Psi] house for a couple hours…and got sick,” Burke said in an email.

Bobby Longo ‘21, another Phi Psi fraternity member to have the virus, said he believed the email warning on Monday was “too late.”

“Norovirus is an extremely contagious stomach virus that spreads like wildfire. After the first or second case on campus we should have been notified… it ramps up as people go from class to class spreading it,” Longo said in an email.

According to Goldstein, his level of concern about the virus was raised when the health center began receiving phone calls and emails from concerned students and parents, as the health center was “not overwhelmed” by the number of students coming to Bailey about the virus. 

Goldstein said he wanted to find a “sweet spot” of not raising a level of hysteria but also communicating with the students. He decided to send the campus-wide email more based on “the feedback from students,” Goldstein said.

“I think what’s happening is students are self-treating and getting through this without needing to see a provider, but the numbers are pretty significant on campus. The students communicating with me was a good thing,” he said.

According to Goldstein, reports from Resident Advisors and Bailey total a little over 150, but Goldstein said there may be overlap among these reports, if for example, a student both went to Bailey and reported their illness to their RA.

While Goldstein said that the discussion of the school closing “hasn’t happened yet,” he believes certain social gatherings will be cancelled if the virus continues spreading rapidly. One event, the Lunar New Year dumpling making party hosted by ISA and ACA, was cancelled on Tuesday as a result of the spreading sickness.

University students’ hand hygiene practice during a gastrointestinal outbreak in residence: What they say they do and what they actually do
01.sep.09
Journal of Environmental Health Sept. issue 72(2): 24-28
Brae V. Surgeoner, MS, Benjamin J. Chapman, PhD, and Douglas A. Powell, PhD

Abstract
Published research on outbreaks of gastrointestinal illness has focused primarily on the results of epidemiological and clinical data collected postoutbreak; little research has been done on actual preventative practices during an outbreak. In this study, the authors observed student compliance with hand hygiene recommendations at the height of a suspected norovirus outbreak in a university residence in Ontario, Canada. Data on observed practices was compared to post-outbreak self-report surveys administered to students to examine their beliefs and perceptions about hand hygiene. Observed compliance with prescribed hand hygiene recommendations occurred 17.4% of the time. Despite knowledge of hand hygiene protocols and low compliance, 83.0% of students indicated that they practiced correct hand hygiene during the outbreak. To proactively prepare for future outbreaks, a current and thorough crisis communications and management strategy, targeted at a university student audience and supplemented with proper hand washing tools, should be enacted by residence administration.

5 sick with Salmonella from Tahini

The U.S. Food and Drug Administration is posting this information to ensure the widest possible dissemination to the public.

FDA, along with the Centers for Disease Control and Prevention (CDC), and state and local partners, is investigating a multistate outbreak of Salmonella Concord illnesses linked to tahini imported from an Israeli manufacturer, Achdut Ltd., located in Ari’el, Israel.

On November 28, 2018, in response to the on-going investigation, Soom Foods voluntarily recalled the following additional products:

12 oz. Chocolate Sweet Tahini Halva Spread 071318CH. Packed from tahini lot 18-123.

And tahini in the following sizes and types:

40 lb. Organic Tahini.

40 lb. Premium Tahini.

16 oz. Premium Tahini.

16 oz. Organic Tahini.

11 oz. Premium Tahini.

The tahini product lot codes range from 18-097 through 18-141.

Some of the above listed products were included in the original voluntary recall by Achdut Ltd. on November 27, 2018. The FDA is advising consumers not to eat recalled Achva, Achdut, Soom, S&F, and Pepperwood brand tahini and Soom brand Chocolate Sweet Tahini Halva Spread (lot code 071318CH) with expiration dates ranging from April 7, 2020 to May 21, 2020 and Baron’s brand tahini with the expiration date of May 5, 2021. The product lot codes range from 18-097 to 18-141. Consumers should discard the product or return the product to the store for a refund.

Some brands of tahini manufactured by Achdut Ltd. may lack specific dates or may have labels that are written in Hebrew. Consumers who have purchased a tahini product and are uncertain of where the product was manufactured or cannot identify the brand by lot codes or expiration dates should discard the product or return the food to the store for a refund. More product information and pictures of the recalled product labels can be found in Achdut ‘s recall announcement. View Soom Foods’ recall announcement.

Retailers and restaurants should not use any of the recalled tahini manufactured by Achdut Ltd. at their establishments. Retailers and restaurants should throw the product out. 

Firms that may have used the recalled tahini (either repacked or used as an ingredient in a food without a kill step) should consider recalling their products.

(One of the only U2 songs I like, because of the guitar and it was inspired by a Tom Robbins novel.)