High-throughput whole-genome sequencing (WGS) is a revolutionary tool in public health microbiology and is gradually substituting classical typing methods in surveillance of infectious diseases. In combination with epidemiological methods, WGS is able to identify both sources and transmission-pathways during disease outbreak investigations.
This review provides the current state of knowledge on the application of WGS in the epidemiology of Campylobacter jejuni, the leading cause of bacterial gastroenteritis in the European Union.
We describe how WGS has improved surveillance and outbreak detection of C. jejuni infections and how WGS has increased our understanding of the evolutionary and epidemiological dynamics of this pathogen. However, the full implementation of this methodology in real-time is still hampered by a few hurdles. The limited insight into the genetic diversity of different lineages of C. jejuni impedes the validity of assumed genetic relationships. Furthermore, efforts are needed to reach a consensus on which analytic pipeline to use and how to define the strains cut-off value for epidemiological association while taking the needs and realities of public health microbiology in consideration.
Even so, we claim that ample evidence is available to support the benefit of integrating WGS in the monitoring of C. jejuni infections and outbreak investigations.
Use of whole-genome sequencing in the epidemiology of Campylobacter jejuni infections: state-of-knowledge
Ahead of print, doi: http://dx.doi.org/10.1101/078550
It’s one of those restaurant things I have fun with.
Any seafood place will proudly declare their fish is wild, not the farmed stuff.
For 15 years, I’ve asked servers, do you have farmed salmon or whatever aquatic delight awaits my tummy.
The server will brag and brag about how all the seafood they serve is wild, and not the nasty farmed stuff.
Wrong answer.
Like raw-egg aioli.
Elizabeth Weise of USA Today writes that farmed fish has gotten a bad rap, but it’s the only way the world is going to feed the additional 2.4 billion people expected to be added to the Earth’s population in the next 34 years, experts told a sustainable food conference.
With the world’s arable land maxed out and wild seafood overfished, aquaculture is the one place we can look to produce enough animal protein for all those extra mouths, said Steve Gaines (left, not exactly as shown), a professor of marine biology at the University of California Santa Barbara and lead investigator for the university’s sustainable fisheries group. He spoke at a conference on sustainable food at the Monterey Bay Aquarium earlier this month.
The rising human population isn’t the only issue. As standards of living rise, people eat more protein and especially more meat. In China, for example, annual meat consumption has risen from 28 pounds per person in 1982 to 138 pounds in 2015.
Growing enough crops to feed more pigs, chickens and cows is a challenge. In most of the world, all the land that can be planted already is planted. Plowing under the marginal land that’s left would only lead to deforestation and land degradation, which only contributes to climate change, said Gaines.
Turning to the world’s oceans doesn’t help. Analysis of global fisheries, even if all were sustainably managed for maximum production, would only take care of between 1% and 5% of the coming demand, Gaines said.
The only option, experts at the Monterey conference said, is aquaculture. Currently just 15% of world animal protein consumption comes from aquaculture but that can quickly be ramped up.
It’s a hard sell in the United States. Panelists blamed part of the U.S. prejudice against aquaculture on NIMBYism (i.e. Not In My Backyard.) Americans were content to eat farmed salmon, shrimp, oysters and other species when they were produced far away, but didn’t want to see fish farms and pens in their pristine waters at home.
There’s also an ongoing negative connotation with fish farming among the more eco-conscious in the United States because of early unsustainable fishery examples, especially farmed salmon and shrimp, in South America and Asia.
Asian seafood producers have been cleaning up their acts but damaging stories about aquaculture there continue to make the rounds, said Kevin Fitzsimmons, a professor of aquaculture at the University of Arizona in Tucson, Az.
He says he frequently hears Americans complain about agricultural leavings and animal waste being used in fish ponds in southeast Asia, a practice that’s actually both sustainable and deeply rooted in the culture, he said.
“In the United States, if somebody puts chicken waste in their garden they’re an organic farmer and it’s wonderful. But if they put it in a fish pond in China, we say they’re trying to kill us,” he said.
Today a wave of innovation and investment has meant that aquaculture overall is much more environmentally friendly and efficient than it once was.
Currently 78% of the salmon Americans eat is farmed, according to research by Oai Li Chen at the University of Washington. However, as a whole, salmon makes up just one-fifth of world aquaculture production, said Peet.
A rodent believed to have been a live rat fell from the ceiling and landed on a woman’s head as she dined at a fancy London restaurant.
The animal, only a baby at three inches long, was killed on impact when it hit the woman and bounced on to the table at expensive Smiths of Smithfield where the woman was eating with a group of friends.
Obviously horrified by what happened, their party started protesting at what had happened, alerting staff to the unwelcome garnish to their food.
‘We were disgusted,’ witness Paul Stubbs, a 56-year-old city worker from Harrow in North West London told the Sun.
‘It was only a baby but still about three inches long. It had obviously fallen from a nest in the open vents.
‘People were pretty horrified. Everybody stayed to finish, though I wouldn’t go back.’
The restaurant reportedly offered the group of 24 a £450 discount from their bill.
Staff allegedly told customers that the small rodent was a mouse – however, pest control experts told the Sun they were ‘fairly convinced’ it was a baby rat.
The restaurant, rated 3.5 stars on TripAdvisor, is situated next to the capital’s only working meat market and is famous for its rare breed steak and prime cuts.
Metro.co.uk has contacted Smiths of Smithfield for a comment on the rat/possibly a baby mouse incident.
A spokesman previously said: ‘At Smiths we pride ourselves on our hygiene and food safety management. We have investigated the matter fully and this is an isolated incident and we confirm that there is no risk to our customers.’
He went on to say the diners ‘were offered what was accepted as reasonable compensation.’
Alejandro Barahona and Ken Alltucker of AZ Central report a Phoenix resident filed a lawsuit against Texas-based Pappas Restaurants Inc. that claims she contracted salmonella last month after eating at the chain’s Phoenix restaurant.
The Maricopa County Department of Public Health confirmed there was an investigation of a salmonella outbreak at Pappadeaux Seafood Kitchen of Phoenix.
The outbreak is over and the county health department is closing its investigation, said Jeanene Fowler, a department spokeswoman.
Because final paperwork that details the outbreak has not been completed, Fowler said, county officials could not confirm the number of people who became ill after eating at the popular seafood restaurant, at 11051 N. Black Canyon Highway.
A manager at Pappadeaux in Phoenix said he could not discuss the outbreak, referring Republic inquiries to the chain’s headquarters in Houston. Officials at the chain’s headquarters did not respond to phone messages and email questions about the county’s investigation or the lawsuit.
Pappas Restaurants has not yet answered the lawsuit, which was filed last Friday at U.S. District Court in Phoenix.
The lawsuit states that on Aug. 14, Phoenix resident Shaina Robinson ate shrimp, tilapia and crab cakes at Pappadeaux Seafood Kitchen of Phoenix. The lawsuit states that two days later, Robinson became “violently ill” with stomach illness. Four days later, she sought treatment at a Scottsdale hospital.
She spent five days at the hospital and tested positive for a strain of salmonella, according to the lawsuit.
She missed two weeks of work and “incurred significant medical bills as a direct and proximate cause of her salmonella infection contracted at Pappadeaux Seafood Resturant,” the lawsuit states.
Robinson is seeking restitution for irreparable emotional distress, medical expenses, bodily injuries, suffering and permanent impairment, among other claims.
The county health department often does not publicly announce restaurants tied to an outbreak unless officials believe it can help prevent people from becoming sick, Fowler said.
She said part of the issue is timing. County health and environmental services inspectors must confirm that an outbreak is ongoing and public disclosure could prevent people from getting sick. Inspectors also must verify an outbreak is tied to a specific restaurant and not a supplier that delivered tainted food to different establishments.
“We don’t wanted to put (restaurants) out of business for something that may have nothing to do with the business,” Fowler said. “We are trying to take that into account.”
But Fowler said that completed reports, whether it’s a routine inspection or investigation of a foodborne illness, are available for public inspection.
“We get hundreds and hundreds of these each year,” Fowler said, referring to foodborne-illness complaints.
Attorney Ryan Osterholm said he believes county health officials should aggressively notify the public during outbreaks.
“The public deserves to know,” Osterholm said. “There should be transparency in anything unless there is a compelling reason not to. … The baseline should be transparency.”
Thirty-six people infected with the outbreak strains of Salmonella Reading or Salmonella Abony were reported from nine states.
Seven ill people were hospitalized. No deaths were reported.
Epidemiologic and traceback evidence indicated that alfalfa sprouts supplied by Sprouts Extraordinaire of Denver, Colorado were the likely source of this outbreak.
On August 5, 2016, Sprouts Extraordinaire recalled alfalfa sprout products from the market due to possible Salmonella contamination.
This outbreak appears to be over. However, sprouts are known to cause foodborne illness and outbreaks
Public health investigators used the PulseNet system to identify illnesses that may have been part of this outbreak. PulseNet, coordinated by CDC, is the national subtyping network of public health and food regulatory agency laboratories. PulseNet performs DNA fingerprinting on Salmonella bacteria isolated from ill people by using techniques called pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). CDC PulseNet manages a national database of these DNA fingerprints to identify possible outbreaks.
Thirty-six people infected with the outbreak strains were reported from nine states. Of those ill people, 30 were infected with Salmonella Reading, 1 was infected with Salmonella Abony, and 5 were infected with both. A list of the states and the number of cases in each can be found on the Case Count Map page.
Illnesses started on dates ranging from May 21, 2016 to September 10, 2016. Ill people range in age from less than 1 year to 72, with a median age of 30. Fifty-six percent of ill people were female. Seven ill people reported being hospitalized, and no deaths were reported.
This outbreak appears to be over. However, sprouts are known to cause foodborne illness and outbreaks.
Epidemiologic and traceback evidence indicated that alfalfa sprouts supplied by Sprouts Extraordinaire of Denver, Colorado were the likely source of this outbreak.
In interviews, ill people answered questions about the foods they ate and other exposures in the week before they became ill. Of the 31 ill people who were interviewed, 18 (58%) reported eating or possibly eating alfalfa sprouts in the week before illness started. This proportion is significantly higher than results from a 2006 survey of healthy people, in which 3% reported eating raw alfalfa sprouts on a sandwich in the week before they were interviewed. Ill people in the current outbreak reported eating raw sprouts on sandwiches from several restaurants.
Federal, state, and local health and regulatory officials performed a traceback investigation from five restaurants where ill people reported eating alfalfa sprouts. This investigation indicated that Sprouts Extraordinaire supplied alfalfa sprouts to all five of these locations.
On August 5, 2016, Sprouts Extraordinaire recalled its alfalfa sprout products from the market due to possible Salmonella contamination. These products were sold in boxes labeled “5-lb Living Alfalfa.” Read the Advice to Restaurants, Retailers and Consumers.
This outbreak appears to be over. However, sprouts are known to cause foodborne illness and outbreaks. More information about steps to reduce your risk of getting sick from eating sprouts is available on the Advice to Restaurants, Retailers and Consumers page.
Sam Stanton of The Sacramento Bee writes the Blue Angels flight team abruptly canceled its performance Saturday afternoon at the California Capital Airshow at Mather Airport after the squadron’s commanding officer came down with a form of food poisoning.
Air show officials announced the cancellation after determining that Cmdr. Ryan Bernacchi “contracted a foodborne ailment and is under the medical supervision of the team’s flight surgeon.”
“Cmdr. Bernacchi will be re-evaluated regularly, as the team is hopeful he will be ready to fly for the final day of the air show,” a statement from organizers stated. “At this time, the Blue Angels are scheduled to perform on Sunday as planned.”
Organizers said people who attended Saturday’s show can have their tickets honored for general admission for Sunday’s show, and parking passes will be honored with proof of purchase from Saturday or a parking stub.
The Blue Angels are the U.S. Navy’s flight demonstration squadron and stars of the two-day event at Mather, which last year drew more than 109,000 attendees to the event at the former Mather Air Force Base.
Members of the squadron were among Capital Airshow performers who participated in a Friday night “block party” in midtown where fans were able to meet air show pilots, the Sacramento Kings Dancers and take part in other entertainment.
Up until about 3 p.m. Saturday, there were no indications of problems. Before noon, the Blue Angels’ Twitter account indicated all systems were go: “Happy October, Fans! Today, we turned up and inspected the jets, making sure they were good to go for today’s California Capital Airshow.”
But word that illness had grounded the team led to fans expressing their disappointment on social media, and to a number of suppositions about the origins.
“No more gas station sushi!” one follower tweeted.
The thing was my tip-sensitive digital thermometer which is always in my backpack, which is always on my back, and the occasion was the annual BBQ at the annual Coffs Harbour 3-on-3 hockey tournament.
With 120 guests to serve, I always arrive packin’.
The meat was safely-temperature-verified-grilled, no bare hand contact was achieved through either tongs or gloves, and cross-contamination was minimal (the parents all know what I do, and they knew I’d be watching).
Amy and I played sous chefs for a couple of hours, prepping onions, tomatoes, cucumbers and watermelon.
Coffs Harbour Big Banana 3-on-3 Skirmish, now in its sixth year, started as a two club match-up between Newcastle North Stars and Southern Stars from Brisbane with Coffs Harbour as the halfway meeting point for the 3-on-3 ice hockey weekend.
The tournament has grown each year to now include nine clubs represented by 26 teams from NSW, QLD and ACT. Some 175 players ranging in age from 5-to-16-years-old in five different age divisions played in 80 games.
I coached, acted as medic, refereed for the first time since completing that 14-hour training and was called upon to be the badass coach when kids got unruly around the pool and BBQ area.
Amy did scorekeeping, merchandizing, and overall hockey mom stuff, like getting Sorenne prepared.
So many other people contributed in similar ways.
Great kids, great parents, it’s our church, but without the god stuff. There’s singing and dancing, but not so much the hymns. More AC/DC.
The U.S. Centers for Disease Control worked with public health and regulatory officials in many states and the U.S. Food and Drug Administration (FDA) to investigate a multistate outbreak of Shiga toxin-producing Escherichia coli (STEC) infections.
Illnesses started on dates ranging from December 21, 2015 to September 5, 2016. Ill people range in age from 1 year to 95, with a median age of 18. Seventy-six percent of ill people were female. Seventeen ill people were hospitalized. One person developed hemolytic uremic syndrome, a type of kidney failure, and no deaths were reported.
Epidemiologic, laboratory, and traceback evidence indicated that flour produced at a General Mills facility in Kansas City, Missouri was the likely source of this outbreak.
In interviews, ill people answered questions about the foods they ate and other exposures in the week before they became ill. Twenty-eight (76%) of 37 people reported that they or someone in their household used flour in the week before they became ill. Nineteen (50%) of 38 people reported eating or tasting raw homemade dough or batter. Twenty-one (57%) of 37 people reported using Gold Medal brand flour. Three ill people, all children, reported eating or playing with raw dough at restaurants.
In an epidemiologic investigation, investigators compared the responses of ill people in this outbreak to those of people of similar age and gender reported to state health departments with other gastrointestinal illnesses. Results from this investigation indicated an association between getting sick with STEC and someone in the household using Gold Medal brand flour.
Federal, state, and local regulatory officials performed traceback investigations using package information collected from ill people’s homes and records collected from restaurants where ill people were exposed to raw dough. These initial investigations indicated that the flour used by ill people or used in the restaurants was produced during the same week in November 2015 at the General Mills facility in Kansas City, Missouri, where Gold Medal brand flour is produced.
On May 31, 2016, General Mills recalled several sizes and varieties of Gold Medal Flour, Gold Medal Wondra Flour, and Signature Kitchens Flour due to possible E. coli contamination. The recalled flours were produced in the Kansas City facility and sold nationwide.
In June 2016, laboratory testing by FDA isolated STEC O121 in open samples of General Mills flour collected from the homes of ill people in Arizona, Colorado, and Oklahoma. WGS showed that the STEC O121 isolates from the flour samples were closely related genetically to the STEC O121 isolates from ill people. The flour collected in Oklahoma was not included in the initial General Mills recall. The other flour samples that were tested came from lots of flour included in the initial recall announced by General Mills. In July 2016, laboratory testing by General Mills and FDA isolated STEC O26 from a sample of General Mills flour. WGS showed that the STEC O26 isolated from the flour sample was closely related genetically to isolates from an ill person in the PulseNet database. The flour tested was not included in the earlier General Mills recalls. As a result of these findings, General Mills expanded its recall on July 1, 2016 and again on July 25, 2016 to include more production dates.
Although the outbreak investigation is over, illnesses are expected to continue for some time. The recalled flour and flour products have long shelf lives and may still be in people’s homes. Consumers who don’t know about the recalls could continue to eat the products and get sick. A list of the recalled products and how to identify them is available on the Advice to Consumers page.
This outbreak is a reminder that is it not safe to taste or eat raw dough or batter, whether made from recalled flour or any other flour. Flour or other ingredients used to make raw dough or batter can be contaminated with STEC and other germs that can make people sick.
Silver Springs Farms, Inc., a Harleysville, Pa. establishment is recalling approximately 740 pounds of ground beef products that may be contaminated with E. coli O157:H7, the U.S. Department of Agriculture’s Food Safety and Inspection Service (FSIS) announced.
The ground beef items were produced on August 19, 2016. The following products are subject to recall:
20-lb cases containing 4 packages of 5-lb ground beef 80/20.
The products subject to recall bear establishment number “EST. 4771” inside the USDA mark of inspection. These items were shipped to a distributor in Virginia.
The problem was discovered during a routine verification sampling performed by Silver Springs Farms, Inc. There have been no confirmed reports of adverse reactions due to consumption of these products.
Officials said that in all 38 people who purchased the cream puffs had sought treatment at several hospitals in 6 districts.
Sakolkrit Sukhawattanakul, manager of the store’s outlets in the North, said a thorough examination would be made of the production process to find out the exact cause of the food poisoning. Production and sale of the eclairs would cease until the matter is cleared up. He would visit the patients and take responsibility for the incident.
This review provides the current state of knowledge on the application of WGS in the epidemiology of Campylobacter jejuni, the leading cause of bacterial gastroenteritis in the European Union.
