Whole genome sequencing PR in Australia

In a press release story that oozes with promotional fanfare, foodborne illnesses caused by bugs such as salmonella could be cut by a third in NSW within five years, with food and health authorities adding a “revolutionary” tool to their arsenal.

NSW Health and NSW Food Authority have started using whole genome sequencing technology to more quickly identify a foodborne outbreak and connect it with its source, which could reduce illnesses and even deaths.

“[It’s] a significant breakthrough that could help revolutionise how food-borne illnesses are identified, understood, tracked and managed,” said Dr Craig Shadbolt, the Food Authority’s acting chief executive.

“This will be invaluable in terms of achieving the NSW Government’s Food Safety Strategy goal of reducing foodborne illnesses caused by salmonella, campylobacter and listeria by 30 per cent by 2021.”

That sounds nice, but some practical steps, like not using raw eggs in mayo, aoili, or baked Chinese ice cream, would go farther. In Australia, rates of foodborne salmonella poisoning have climbed from 38 per 100,000 people in 2004 to 76 per 100,000 in 2016, with a record-breaking 18,170 cases last year, according to the National Notifiable Diseases Surveillance System.

A table of raw-egg-based outbreaks in Australia is available at: http://barfblog.com/wp-content/uploads/2017/05/raw-egg-related-outbreaks-australia-5-1-17.xlsx-

Cyclospora gets around

As summer grinds on in the Northern Hemisphere, Cyclospora is again spreading: at least 78 in the UK; 57 in Canada (which appear to be locally acquired; and, 712 lab-confirmed cases in the U.S.

The Centers for Disease Control reports Cyclospora cayetanensis is a single-celled parasite that causes an intestinal infection called cyclosporiasis.

As of August 16, 2017 (3pm EDT), CDC has been notified of 712 laboratory-confirmed cases of cyclosporiasis in persons who became ill in 2017. This number includes persons who reported international travel as well as persons who did not report travel. The reports have come from 36 states.

At least 347 (49%) of these persons did not report international travel (i.e., likely were infected in the United States) and became ill on or after May 1, 2017 (a date after which cases tend to increase each year). These 347 persons were from the following 31 states: Arizona (1), California (5), Colorado (6), Connecticut (18), Florida (36), Georgia (4), Illinois (11), Indiana (3), Iowa (8), Kansas (2), Louisiana (3), Maryland (3), Massachusetts (11), Michigan (1), Minnesota (10), Missouri (8), Montana (2), Nebraska (5), New Hampshire (2), New Jersey (10), New Mexico (1), New York (excluding NYC) (12), New York City (27), North Carolina (19), Ohio (6), Pennsylvania (1), Rhode Island (2), South Dakota (4), Texas (116), Utah (1), Virginia (2), and Wisconsin (7).

At this time, no specific vehicle of interest has been identified, and investigations to identify a potential source (or sources) of infection are ongoing. It is too early to say whether cases of Cyclospora infection in different states are related to each other or to the same food item(s).

Previous U.S. outbreaks of cyclosporiasis have been linked to various types of imported fresh produce (e.g., basil, cilantro, mesclun lettuce, raspberries, snow peas). Consumers should continue to enjoy the health benefits of eating fresh fruits and vegetables as part of a well-balanced diet.

Sprouts still suck: FDA sampling shows sprouts a problem

There’s a reason Walmart and Costco and Kroger stopped selling raw sprouts: they suck, meaning that, like raw milk, they cause a disproportionate percentage of illness based on low consumption rates.

The U.S. Food and Drug Administration wrote in a recent report sprouts are especially vulnerable to pathogens given the warm, moist and nutrient-rich conditions needed to grow them. From 1996 to July 2016, there were 46 reported outbreaks of foodborne illness in the U.S. linked to sprouts. The U.S. outbreaks accounted for 2,474 illnesses, 187 hospitalizations, and three deaths (and, tragically, many more in Canada, Australia, Japan and Europe).

A table of sprout-related outbreaks is available at http://barfblog.com/wp-content/uploads/2016/02/Sprout-associated-outbreaks-2-23-16.xlsx.

From the executive summary:

The U.S. Food and Drug Administration (FDA) set out to collect and test sprouts in 2014 as part of a new proactive and preventive approach to deploying its sampling resources with the ultimate goal of keeping contaminated food from reaching consumers.

The new approach, detailed in the Background section of this report (page 4), centers on the testing of a statistically determined number of samples of targeted foods over a relatively short period of time, 12 to18 months, to ensure a statistically valid amount of data is available for decision making. This approach helps the agency determine if there are common factors – such as origin, season, or variety – associated with pathogen findings.

The FDA issued the sprouts assignment in January 2014 under its new sampling model. The assignment targeted sprouts at three points in the production process (seeds, finished product and spent irrigation water), with the aim of collecting and testing 1,600 samples to determine the prevalence of select pathogens in the commodity. As background, the FDA designed its sampling plan such that if contamination of one percent or greater was present in the commodity, the agency would detect it. The FDA monitored the assignment closely to gather lessons learned and make changes to its sampling procedures if needed to address trends or food safety issues. About one year into the assignment, the FDA decided to stop its collection and testing at 825 samples because it had already collected samples on more than one occasion from many of the sprouting operations known to the agency and its state partners. The sample set acquired was sufficient for the FDA to estimate the bacterial prevalences in the commodity with a 95 percent confidence interval of 0% to 2% for a one percent contamination rate.

The FDA tested only domestically grown sprouts for this assignment because virtually all sprouts eaten in the United States are grown domestically due to the commodity’s delicate nature and relatively short shelf-life. Of note, the industry features a preponderance of relatively small operations.

The FDA tested the sprout samples for three pathogens: Salmonella, Listeria monocytogenes and Escherichia coli (E. coli) O157:H7. Based on the test results, the FDA found the prevalence of Salmonella in the finished product sprouts to be 0.21 percent. The agency also found that the prevalence of Salmonella in seeds (2.35%) was significantly higher than in finished product (0.21%) and in spent irrigation water (0.54%). Based on the test results, the FDA found the prevalence of Listeria monocytogenes in the finished product to be 1.28 percent. There was no significant difference in the prevalence of Listeria monocytogenes based on point in the production process. None of the samples tested positive for E. coli O157:H7. The agency did not test seed for E. coli O157:H7 due to limitations associated with the test method.

Among the FDA’s other findings, the agency found most of the positive samples at a small number of sprouting operations. Specifically, the FDA found violative samples at eight (8.5%) of the 94 sprouting operations visited for purposes of this assignment. The fact that the agency found multiple positive samples at some of these operations underscores the need for sprouting operations to comply with the agency’s Produce Safety Regulation (published November 2015), which seeks to prevent outbreaks of foodborne illness and improve sprout safety.

To address the positive samples, the FDA worked with the firms that owned or released the affected product to conduct voluntary recalls or to have their consignees destroy it, and then followed up with inspections. Of particular note, this sampling assignment helped detect and stop an outbreak of listeriosis while it still entailed a small number of cases, as described in the Public Health Impact section of this report (page 14). This assignment also prompted six product recalls.

The FDA will continue to consider microbial contamination of sprouts and how best to reduce it. Such contamination remains a concern to the FDA given the aforementioned outbreak and the recalls initiated. Going forward, the FDA intends to inspect sprouting operations to ensure they are complying, as applicable, with the Produce Safety Rule, which includes new requirements for sprouts growers. The agency has no plans to conduct additional large-scale sampling of sprouts at this time but may sample the commodity in accordance with its longstanding approach to food sampling, which centers on (but is not limited to) the following criteria:

  • A firm has a previous history of unmitigated microbial contamination in the environment (e.g., human illness, recalled or seized product, previous inspectional history, or environmental pathogens without proper corrective actions by the facility), or
  • Inspectional observations that warrant collection of samples for microbiological analyses.

The complete report is available at https://www.fda.gov/downloads/Food/ComplianceEnforcement/Sampling/UCM566981.pdf?source=govdelivery&utm_medium=email&utm_source=govdelivery

Hong Kong fairytales: More Vibrio: Suspected food poisoning outbreak in tour group

The Centre for Health Protection (CHP) of the Department of Health is investigating a suspected outbreak of food poisoning in a tour group, and hence urged the public to maintain good personal, food and environmental hygiene to prevent food-borne diseases.

Because all foodborne illness is caused by poor personal hygiene, and not contaminated product.

Not

The outbreak affected six members of the tour group, comprising two men and four women aged from 44 to 80, who developed abdominal pain, diarrhoea and vomiting 14 to 40 hours after their lunch buffet in a restaurant in a hotel in Macau on August 13 arranged by a travel agent in Hong Kong.

Among them, three sought medical attention in Hong Kong and required no hospitalisation. All affected persons have been in stable condition.

The stool specimen of one patient tested positive for Vibrio parahaemolyticus upon laboratory testing.

 

Raw is risky: US woman battling cancer dies after eating oysters

I don’t eat much raw food.

Too much risk.

A Texas woman who was vacationing with her husband in Mississippi died last Thursday, after eating raw oysters that were contaminated.

Jane White Cunningham, who had battled leukemia since 2016, had several limbs removed prior to her death in an effort to combat the infection, according to the Houston Chronicle.

“There has been a lot of swelling in her extremities and a lot of pain,” David Cunningham, the 56-year-old’s husband, wrote in an Aug. 8 Facebook post. “Today they had to amputate both legs and her left arm in an attempt to save her life as the infection was spreading rapidly.”

Cunningham was being cared for a Gulfort Mississippi Hospital, with health officials pointing to the bacteria Vibrio as a cause of infection, CBS DFW reported.

Rare chicken hooks UK food porn-types, the country that gave the world mushy peas and mad cow disease: It’s a Salmonella/Campy shit-storm waiting to happen

Just when you thought you’d seen every possible bizarre foodie trend on Instagram, a truly stomach-churning craze comes along to surprise you.

Siofra Brennan of the Daily Mail writes people have been sharing images of their ‘juicy and tender’ meals of medium rare chicken, claiming it’s the best possible way to enjoy the meat, but their claims certainly haven’t gone down well with the masses. 

People have described the craze as ‘salmonella waiting to happen’ with one stating that there’s a ‘special place reserved in hell’ for people who don’t cook their chicken properly. 

However, fans are absolutely insistent that it’s the best way to eat the poultry with one declaring that if you’re not having your chicken medium rare, ‘you’re doing it wrong’.  

People seem particularly keen to find out what firebrand chef Gordon Ramsay thinks of the debacle, frantically tweeting him images of the offending dishes to get his opinion.

His thoughts remain, as yet, unknown.  

(Who gives a fuck?)

Earlier this year Australian Morgan Jane Gibbs found worldwide notoriety with a Facebook snap of a plateful of very pink pieces of chicken with the caption: ‘Just made chicken medium rare chicken strips.

‘They’re so good can’t believe I’ve never tried it like this before,’ she said. 

‘Can’t wait to dig into this with my homemade salad and veges. #healthy #newyearsresolution #clean #cleaneating’

Unsurprisingly the post has gained notoriety online as people tried to figure out if Ms Gibbs is being serious with her nauseating dish.

While the post by Ms Gibbs was most likely a joke, the image itself was of a legitimate dish, origination from a blog promoting tourism in the Japanese region of Shizuoka and the recipe for chicken tataki; chicken seared over hot coals and served raw.

Chicken sashimi is another Japanese dish where the bird is served raw, chefs manage to avoid the issue of pesky food poisoning by serving the meat as fresh as possible and raising the chickens in a hygienic environment.

That’s some microbiological poultry manure (check your organic garden).

To avoid the risk of food poisoning, the NHS recommends that chicken must be cooked through so that the meat is ‘no longer pink, the juices run clear and it’s steaming hot throughout.’ 

No wonder the UK is messed up about chicken, the government-types can’t get advice right.

Use a thermometer and stick it in.

Raw is risky: 25 sickened by oysters in Seattle

A foodborne illness outbreak linked to raw oysters has sickened at least 25 people who dined at local restaurants recently, King County reported on Tuesday. The news comes after the county reported last week that a handful of people got sick eating raw oysters at two Seattle restaurants – The Salted Sea and The White Swan Public House.

The restaurants, however, are not the source of the outbreak, King County says. Most likely, the oysters were mishandled or contaminated before reaching local restaurants, although no specific local oyster beds have been connected to the outbreak.

County health officials believe diners have been sickened by Vibrio, a marine bacteria commonly found in oysters.

“Eating undercooked or raw shellfish, especially raw oysters in warm-weather months, is the main risk for acquiring vibriosis from infection with Vibrio parahaemolyticus,” King County said.

Australia still has an egg problem: WA Salmonella infections explode,1500 sick

It is painfully rewarding that the bureautards in Western Australia are finally catching up to what we’ve been saying for years.

Australia has an egg problem.

A table of Australian egg outbreaks is available at http://barfblog.com/wp-content/uploads/2017/05/raw-egg-related-outbreaks-australia-5-1-17.xlsx.

The West Australian reports the area is experiencing an explosion in stomach bug illnesses, with more than 4,000 cases so far this year and many of them caused by food.

 New figures show 4076 cases of gastrointestinal disease have been reported this year — 31 per cent more than at the same time in the previous two years. The bacterial or viral infections are mostly caused by contaminated food and water or poor hygiene. Much of the surge has been fuelled by a rise in salmonella, with many of the 1566 cases this year associated with eating uncooked eggs.

There has been a big increase in other gastroenteric illnesses, with 358 cases of the viral infection rotavirus, which can make young children seriously ill.

Cryptosporidiosis, which is caused by a parasite, has been reported in 335 people — more than double the number at the same time last year. A WA Health Department spokeswoman said though notifications of salmonella gastroenteritis were declining as expected over winter, the increased levels were a concern.

“The department is concerned about food-borne illness rates in WA, including salmonella risks associated with eggs, and is implementing short and long-term reduction strategies,” she said. The department and local government authorities were focusing on safety surveillance across the food industry, from paddock to plate.

“Eggs are a good source of nutrition, but like many other foods they can be contaminated with bacteria, including salmonella,” the spokeswoman said.

“It is important people handle and prepare eggs safely to reduce the food poisoning risk.”

Hepatitis E: Raw pork is main cause of infection in EU

Consumption of raw or undercooked pork meat and liver is the most common cause of hepatitis E infection in the EU, said the European Food Safety Authority.

More than 21,000 cases of hepatitis E infections have been reported in humans over the last 10 years, with an overall 10-fold increase in this period.

Rosina Girones, chair of EFSA’s working group on hepatitis E, said: “Even if it is not as widespread as other foodborne diseases, hepatitis E is a growing concern in the EU. In the past, people thought the main source of infection was drinking contaminated water while travelling outside the EU. But now we know the main source of transmission of the disease in Europe is food.”

Domestic pigs are the main carriers of hepatitis E in the EU. Wild boars can also carry the virus, but meat from these animals is less commonly consumed.

Experts from EFSA’s Panel on Biological Hazards recommend that Member States increase awareness of public health risks associated with raw and undercooked pork meat and advise consumers to cook pork meat thoroughly. They also recommend the development of suitable methods for detecting hepatitis E in food.

This scientific advice builds on a previous scientific opinion on the occurrence and control of foodborne viruses published in 2011.

The European Centre for Disease Prevention and Control (ECDC) has today also published a report on hepatitis E in humans which assesses testing, diagnosis and monitoring methods and reviews available epidemiological data.

Hepatitis E is a liver disease caused by the hepatitis E virus (HEV).

Most people who contract hepatitis E display no or mild symptoms. However, in some cases especially for those with liver damage or patients with a weak immune system, it can lead to liver failure – which can be fatal.

Why I don’t eat raw oysters: Vibrio thrives by attacking the cell’s cytoskeleton

The leading cause of acute gastroenteritis linked to eating raw seafood disarms a key host defense system in a novel way: It paralyzes a cell’s skeleton, or cytoskeleton.

That finding, from UT Southwestern Medical Center, was reported today in PLoS Pathogens. Without a working cytoskeleton, infected cells are unable to produce defensive molecules called reactive oxygen species (ROS) that normally attack bacterial DNA, said Dr. Marcela de Souza Santos, lead author of the study and a postdoctoral researcher in the laboratory of senior author Dr. Kim Orth. Dr. Orth is a Professor of Molecular Biology and Biochemistry at UT Southwestern as well as an Investigator in the prestigious Howard Hughes Medical Institute.

“Vibrio parahaemolyticus bacteria deploy a needlelike apparatus called a Type III Secretion System (T3SS) that injects toxic bacterial proteins, known as effectors, into cells that line the intestine, resulting in severe gastroenteritis,” Dr. de Souza Santos said.

Usually V. parahaemolyticus causes only a few days of gastrointestinal distress in the form of vomiting or diarrhea. On rare occasions, however, particularly in people with chronic health conditions like diabetes or liver disease that compromise the immune system, the bacteria can escape from the gut and enter the bloodstream, causing life-threatening systemic infection.

Of the nearly 80 known Vibrio strains, only about a dozen infect humans. The Centers for Disease Control and Prevention (CDC) estimates Vibrio cause 80,000 illnesses and 100 deaths in the U.S. annually. Of those, an estimated 45,000 people are sickened by V. parahaemolyticus. Another Vibrio strain, V. vulnificus, can cause life-threatening infections in people with open wounds exposed to warm seawater. As with other Vibrio strains, people who are immunocompromised are at highest risk.

“Vibrio parahaemolyticus is the reason for the old saying that you shouldn’t eat oysters in months without an ‘r’ in them, meaning the summer months,” said Dr. Orth, holder of the Earl A. Forsythe Chair in Biomedical Science and a W.W. Caruth, Jr. Scholar in Biomedical Research. “With the warming of the oceans, the risk now starts earlier in the year and the bacteria’s geographical range is spreading.” The CDC’s fact sheet says that 80 percent of U.S. vibriosis infections occur between May and October.

The state of Alaska reported its first V. parahaemolyticus outbreak in July 2004. Another strain of Vibrio sickened more than 80 people exposed to contaminated seawater during a heatwave in Northern Europe in 2014. The first Vibrio strains were identified in the 18th century.

Until recently, it was believed that Vibrio bacteria remained outside cells, doing their damage by shooting effectors into cells. However, in 2012, the Orth laboratory identified a way that V. parahaemolyticus tricks random cells lining the gut into engulfing the bacterium and bringing it inside the cell. The current study indicates how the T3SS protein VopL aids V. parahaemolyticus infection by helping the pathogen secure a niche within the cell for bacterial replication.

It’s a good strategy for a bacterium to infect random cells only, Dr. Orth said. If a pathogen were to infect most of the host’s cells quickly – as is thought to occur with the Ebola virus – the pathogen might kill its host so fast that it could undermine its own survival, she said.

In a study published last month in Science Signaling, the Orth laboratory did something unprecedented: It followed V. parahaemolyticus infection over time – flash freezing samples every 15 minutes – to chart the pathogen’s effect on host signaling. That study identified 398 genes whose expressions were changed by Vibrio infection, said lead author and postdoctoral researcher Dr. Nicole De Nisco.

In the current study, the researchers found that one of V. parahaemolyticus’ many effectors – VopL – paralyzes the cytoskeleton through a novel mechanism. The cellular machinery, or complex, that makes the ROS sits on the cell surface, but the molecules that the cellular factory needs to assemble ROS are created inside the cell. A working, flexible cytoskeleton is necessary to move the molecules to the ROS factory, she explained.

To confirm their observation, the researchers created two V. parahaemolyticus strains, one able to make VopL and another not. Using confocal microscopy, they found that the Vibrio able to produce VopL inactivated the assembly of ROS by gathering the cytoskeleton into nonfunctional filaments. In contrast, the mutant bacterium unable to produce VopL was vulnerable to ROS attack.

This study identifies the virulence factor used by V. parahaemolyticus to suppress host ROS generation and also reveals an unprecedented mechanism used by a microbial pathogen to do so, said Dr. Orth.

“By hijacking the cytoskeleton, VopL prevents the cell from launching one of its major weapons, reactive oxygen species,” said Dr. Orth. “We hope our work will lead to a better understanding of host defense, which, in turn could lead to new ways to undermine the pathogens.”