Rise of the machines: Tools to know if Salmonella will hit your livestock

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Increasingly, routine surveillance and monitoring of foodborne pathogens using whole-genome sequencing is creating opportunities to study foodborne illness epidemiology beyond routine outbreak investigations and case–control studies.

Using a global phylogeny of Salmonella enterica serotype Typhimurium, we found that major livestock sources of the pathogen in the United States can be predicted through whole-genome sequencing data. Relatively steady rates of sequence divergence in livestock lineages enabled the inference of their recent origins.

Elevated accumulation of lineage-specific pseudogenes after divergence from generalist populations and possible metabolic acclimation in a representative swine isolate indicates possible emergence of host adaptation.

We developed and retrospectively applied a machine learning Random Forest classifier for genomic source prediction of Salmonella Typhimurium that correctly attributed 7 of 8 major zoonotic outbreaks in the United States during 1998–2013. We further identified 50 key genetic features that were sufficient for robust livestock source prediction.

Zoonotic source attribution of Salmonella enterica serotype Typhimurium using genomic surveillance data, United States

Emerging Infectious Diseases vol. 25 no. 1

Shaokang Zhang, Shaoting Li, Weidong Gu, Henk den Bakker, Dave Boxrud, Angie Taylor, Chandler Roe, Elizabeth Driebe, David M. Engelthaler, Marc Allard, Eric Brown, Patrick McDermott, Shaohua Zhao, Beau B. Bruce, Eija Trees, Patricia I. Fields, and Xiangyu Deng 

Septin proteins act as cellular police to identify, imprison and kill Shigella

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A team, led by the London School of Hygiene & Tropical Medicine, has uncovered the strongest evidence yet that septins take Shigella prisoner.

It reveals for the first time that these proteins can detect where bacteria will split for division and prevent it from doing so by forming cage-like structures around the bacteria.

The research team say that although septins are a powerful, natural mechanism to restrict Shigella, future work is required to determine how septin biology can be harnessed for therapeutic purposes. It is hoped that these new findings may lead to a novel way to boost the human immune system and treat a wide variety of bacterial infections.

Lead author Professor Serge Mostowy from the London School of Hygiene & Tropical Medicine said: “We are actively working to engineer this discovery for human health application. If we can use drugs to boost septin caging, we have a new way to stop infection.”

In 2010, researchers first observed that septin cages can entrap Shigella, opening up the tantalising prospect of a new way to stop the bacteria spreading in the body. However, how cells recognise Shigella for entrapment, and the fate of entrapped bacteria, was mostly unknown.

The authors acknowledge limitations of the study including the possibility that some bacteria have evolved to avoid septin cage entrapment, and the need for in vivo study prior to application in humans.

Glitter not always so good says FDA

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This holiday season, the Food and Drug Administration has issued an important, somehow not obvious piece of advice to the public: Please don’t eat or use glitter in your baked goods unless it’s clearly labeled as edible.

Ed Cara of Gizmodo writes the FDA’s advice came courtesy of a consumer update sent out Friday morning. The update featured a short video showcasing an admittedly delicious-looking cake covered in non-edible glitter.

“FDA wants you to be aware that some decorative glitters and dusts promoted for use on foods may, in fact, contain materials that should not be eaten,” the agency said. “But consumers need to be aware that these materials may contain materials that should not be eaten.”

Amazingly, it’s not the first time the FDA has felt obligated to step in and tell people to put down the forkful of glitter. In November, the agency sent out a warning about the trend, which itself was an update to a similar warning released in 2016. The origin of the mess seems to be tied to a trend in recent years of celebrity bakers, cooking shows, and restaurants using decorative glitter on their cakes and other treats.

Luckily for those hoping to reenact their preschool days, there are lots of sparkly products that are perfectly safe to eat. According to the agency, these usually spell out on their labels that they are edible, or contain ingredients like sugar, acacia (gum arabic), maltodextrin, cornstarch, and color additives specifically approved for food use. Glitters with no list of ingredients or with labels that only say they’re “non-toxic” or “decorative” probably aren’t the kind for eating. Don’t eat those ones.

It’s explained by shit in irrigation water: Santa Barbara farm first fingered with outbreak strain of E coli O157 in Romaine lettuce that sickened 59 in US, 28 in Canada: Tumble those dice

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Welcome to Washington, D.C., Frank, and government PR.

On Nov. 20, the U.S. Food and Drug Administration and the Centers for Disease Control and Prevention warned the American public of a multi-state outbreak of E. coli O157:H7 linked to romaine lettuce and advised against eating any romaine lettuce on the market at that time.

According to FDA Commissioner Scott Gottlieb, M.D. and FDA Deputy Commissioner Frank Yiannas, we  have new results to report from this investigation tracing the source of the contamination to at least one specific farm. Based on these and other new findings, we’re updating our recommendations for the romaine lettuce industry and consumers.
Today, we’re announcing that we’ve identified a positive sample result for the outbreak strain in the sediment of a local irrigation reservoir used by a single farm owned and operated by Adam Bros. Farms in Santa Barbara County.

The FDA will be sending investigators back to this farm for further sampling. It’s important to note that although this is an important piece of information, the finding on this farm doesn’t explain all illnesses and our traceback investigation will continue as we narrow down what commonalities this farm may have with other farms that are part of our investigation. While the analysis of the strain found in the people who got ill and the sediment in one of this farm’s water sources is a genetic match, our traceback work suggests that additional romaine lettuce shipped from other farms could also likely be implicated in the outbreak. Therefore, the water from the reservoir on this single farm doesn’t fully explain what the common source of the contamination. We are continuing to investigate what commonalities there could be from multiple farms in the region that could explain this finding in the water, and potentially the ultimate source of the outbreak.

As of Dec. 13, our investigation yielded records from five restaurants in four different states that have identified 11 different distributors, nine different growers, and eight different farms as potential sources of contaminated romaine lettuce. Currently, no single establishment is in common across the investigated supply chains. This indicates that although we have identified a positive sample from one farm to date, the outbreak may not be explained by a single farm, grower, harvester, or distributor.

At the same time, the U.S. Centers for Disease Control updated its warning to advise U.S. consumers to not eat and retailers and restaurants not serve or sell any romaine lettuce harvested from certain counties in the Central Coastal growing regions of northern and central California. If you do not know where the romaine is from, do not eat it.

  • Some romaine lettuce products are now labeled with a harvest location by region. Consumers, restaurants, and retailers should check bags or boxes of romaine lettuce for a label indicating where the lettuce was harvested.
      • Do not buy, serve, sell, or eat romaine lettuce from the following California counties: Monterey, San Benito, and Santa Barbara.
      • If the romaine lettuce is not labeled with a harvest growing region and county, do not buy, serve, sell, or eat it.
      • The Public Health Agency of Canada has identified ill people infected with the same DNA fingerprint of E. coliO157:H7 bacteria in Canada.

Raw is still risky: Say no to raw dough

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My mother used to make and lot of cakes and brownies with her groovy 1960s hand mixer and I always got to lick the beaters.

No more.

And it’s not just the raw eggs, it’s the raw flour.

In June, 2009, an outbreak of shiga-toxin producing E. coli (STEC, primarily O157:H7) in Nestle Toll House cookie dough sickened at least 77 people in 30 American states. Thirty-five people were hospitalized – from cookie dough.

The researchers could not conclusively implicate flour as the E. coli source, but it remains the prime suspect. They pointed out that a single purchase of contaminated flour might have been used to manufacture multiple lots and varieties of dough over a period of time as suggested by the use-by dates on the contaminated product.

The study authors concluded that “foods containing raw flour should be considered as possible vehicles of infection of future outbreaks of STEC.”

So it wasn’t much of a surprise when 63 people fell sick from the outbreak strain of E. coli O121 from Dec. 2015 to Sept. 2016 linked to raw General Mills flour.

There have been about a dozen other flour-related outbreaks. STEC means people – and kids – get quite sick.

Flour is a raw commodity, crops the flour is derived from could be exposed to anything, and testing is so much better than it used to be.

There are some brands of pasteurized flour out there, but people seem to have gotten used to flour as a cheap source of play-dough-like stuff for kids and something to throw at people.

The U.S. Centres for Disease Control says, nope.

This is not a Christmas conspiracy (although I prefer Solstice Season): it’s CDC providing information, like they are supposed to.

People can, and will, do what they want.

As Maggie Fox of NBC reports, “Do not taste or eat any raw dough or batter, whether for cookies, tortillas, pizza, biscuits, pancakes, or crafts made with raw flour, such as homemade play dough or holiday ornaments,” the CDC advises.

“Do not let children play with or eat raw dough, including dough for crafts.”

Handling food, including flour, requires care and hygiene.

“Keep raw foods such as flour or eggs separate from ready-to eat-foods. Because flour is a powder, it can spread easily,” the CDC notes. “Follow label directions to refrigerate products containing raw dough or eggs until they are cooked. Clean up thoroughly after handling flour, eggs, or raw dough.”

As a comedian in all seriousness: What happens when B. cereus invades human cells

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Tegan Taylor of ABC asks, what’s happening inside your body when you have food poisoning?

Research published today has given us a slightly clearer idea, at least for one type of bacteria.

A team from the Australian National University looked at the way the body responds to the bacteria Bacillus cereus, which can cause food poisoning and sometimes lead to serious infections elsewhere in the body, including sepsis, pneumonia and meningitis.

They found a toxin secreted by the bacteria binds directly to cells in the human body and punches holes in the cells to kill them, triggering an immune response.

Understanding the way toxins produced by this bacteria provoke inflammation in the body is a key to understanding how to treat it, said lead researcher Anukriti Mathur.

“Our immune system acts as a double-edged sword in these kinds of cases,” Ms Mathur said.

“In certain cases where you’ve got a bacterial infection it would be really essential to boost our immune system so that it is stronger.

“However in cases such as sepsis, where you’ve got unwanted inflammation happening in your body, you want to dampen the inflammatory responses.

“A very unique balance is required in protecting us against different kinds of infections.”

But what is it about this bacteria punching holes in your cells that leaves you hunched over a toilet bowl?

It has to do with the parts of your nervous system being targeted by the toxins produced by the bacteria, according to Vincent Ho, a University of Western Sydney gastroenterologist and researcher who was not involved in the study.

Bacillus cereus produces more than 12 different toxins. One triggers vomiting and another diarrhea, Dr Ho explained.

The vomit-inducing toxin, called cereulide, binds to serotonin receptors in the stomach and small bowel and stimulates the vagus nerve, which controls muscle movement in the gut.

“That signals back up to the vomiting centres of the brain,” he said.

“And in a very similar way that is how the diarrheal form also works too. It’s causing direct stimulation of the small bowel, and that’s triggering a reactive response of reflex mechanism called the gastro-colic reflex.

“The toxins are stimulating against receptors in the gut lining … triggering a lot more movement of the muscle in the gut and the colon.”

Bacillus cereus can be found in vegetables, rice and pasta, as well as meat and fish, and will grow in these foods if they are stored at the wrong temperature.

Raw is risky: 83 now sick with Salmonella from raw milk cheese in France

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The number of people sick from Salmonella in reblochons, a type of raw milk cheese specific to the Savoy region of the Alps in France, has risen from 14 to 83.

Public Health France first withdrew the reblochons on Nov. 24, 2018.

Of the 83 people identified so far, 65 were able to be interviewed by the ARS Auvergne-Rhône-Alpes and Public Health France about their symptoms and their food consumption before the onset of symptoms. Symptoms range from 16/09 to 19/11, with a peak in week 40 (from 1st to 07/10/2018). Fifteen people were hospitalized for their salmonellosis: they are now out and are well; no deaths have been reported. Consumption of reblochon with raw milk before the onset of symptoms is reported by 80% of the cases confirmed by the CNR and interviewed.

Make it mandatory: More evidence that restaurant inspection disclosure matters

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This work describes the relationship between compliance with food hygiene law as reflected in food hygiene scores; measures of microbiological contamination of food samples taken from consumer-facing food businesses in England, Northern Ireland and Wales; and outbreaks of foodborne illness.

This paper demonstrates an association between the results of food hygiene inspections done by trained inspectors, using a rigorous and consistent procedure, with microbiological contamination of actual food samples from those premises. A proposed theoretical model further demonstrates the reduction in foodborne illness that would result if there were increased compliance with food hygiene law.

As clean as they look? Food hygiene inspection scores, microbiological contamination, and foodborne illness

Fleetwood, Janet, Shamim Rahman, Darren Holland, David Millson, Laura, Thomson, Guy Poppy. 2019.

Food Control. 96: 76-86

https://doi.org/10.1016/j.foodcont.2018.08.034

https://www.sciencedirect.com/science/article/pii/S0956713518304432

Shiga-toxin E. coli at UK nursery sparks NHS probe

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PA reveals a Perthshire school was involved in an E.coli scare last week.

NHS Tayside launched an investigation after a suspected case of the bacteria in a child at Errol Primary School’s nursery.

The nursery will undergo three days of deep cleaning as a “precautionary measure”.

Parents at the school were issued with letters from the health board with information on the infection.

The child was being tested for a non-O157 strain.

Speaking on Friday a spokesperson at NHS Tayside confirmed: “NHS Tayside’s health protection team is aware of and currently investigating a single suspected case of E. coli non O157 infection in a child who attends a nursery in Perthshire.

“As a precaution, a letter has been issued to parents of children at the nursery for information and reassurance.

“The risk to the wider public is very low.”

UK father paralysed after food poisoning issues safety warning to others

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ITV news reports a father who became paralysed after contracting a rare illness from food poisoning has issued a warning to others about food safety.

Dai Braham, 40, was left paralysed from the nose down after becoming unwell while watching his six-year-old son play rugby in April.

Within a matter of days, he was in an induced coma.

Father-of-two Dai was a keen bodybuilder and fitness fanatic

It was only later that medical staff discovered the fitness fanatic from Bridgend had been suffering from food poisoning campylobacter – which led to the rare autoimmune disorder Guillian-Barré Syndrome.

At his worst point, he found himself unable to breathe without a ventilator and without a voice.

“It’s the scariest thing in the world. You are basically locked in your own body”, Dai said.

“Your mind is fine and you know what you want your body to do but you just can’t do it.

“It was horrible, I couldn’t communicate with anyone. I could blink to say yes or no or use a letter card. Then I would use words on a board to spell out certain words.”

Dai has spent the last eight months in hospital and has only recently learned to walk again.

What is Guillain-Barré syndrome?

It is thought to be caused by a problem with the immune system, and can be triggered by infections including food poisoning and the flu as well as by vaccinations, surgery or injury.

Symptoms of the condition include numbness, pins and needles, muscle weakness, and problems with balance and co-ordination.