‘It’s a super-cool study’ Salmonella took down the Aztecs

Eye herpes is a real thing.

I got it in 1984.

Probably from my ex roomate’s towel.

I was so sick for two weeks, although I did manage to crawl out of bed for a Neil Young show in Toronto (part of the International Harvesters tour) but then felt so sick afterwards I went home to Brantford.

One of my parent’s neighbours was my evy doctor, so I was in for a regular check-up and he detected it immediately.

Put me on some Acyclovir, which had just come out, and I was cured in no time.

Or temporarily. Viruses don’t go away.

We’re all hosts on a viral planet.

Mine has come back, in the form of a cold sore, probably because of the stress of buying a new house in an over-heated real-estate market and not selling ours.
I went to the chemist, got some drugs that aren’t really working, but at least I had that option.

Imagine 600 years ago, when Cortez from Spain dances across the water to what is now Mexico and there’s no chemist down the road.

Ewen Callaway of Nature writes one of the worst epidemics in human history, a sixteenth-century pestilence that devastated Mexico’s native population, may have been caused by a deadly form of salmonella from Europe, a pair of studies suggest.

In one study, researchers say they have recovered DNA of the stomach bacterium from burials in Mexico linked to a 1540s epidemic that killed up to 80% of the country’s native inhabitants. The team reports its findings in a preprint posted on the bioRxiv server on 8 February.

This is potentially the first genetic evidence of the pathogen that caused the massive decline in native populations after European colonization, says Hannes Schroeder, an ancient-DNA researcher at the Natural History Museum of Denmark in Copenhagen who was not involved in the work. “It’s a super-cool study.”

In 1519, when forces led by Spanish conquistador Hernando Cortés arrived in Mexico, the native population was estimated at about 25 million. A century later, after a Spanish victory and a series of epidemics, numbers had plunged to around 1 million.

The largest of these disease outbreaks were known as cocoliztli (from the word for ‘pestilence’ in Nahuatl, the Aztec language). Two major cocoliztli, beginning in 1545 and 1576, killed an estimated 7 million to 18 million people living in Mexico’s highland regions.

“In the cities and large towns, big ditches were dug, and from morning to sunset the priests did nothing else but carry the dead bodies and throw them into the ditches,” noted a Franciscan historian who witnessed the 1576 outbreak.

There has been little consensus on the cause of cocoliztli — although measles, smallpox and typhus have all been mooted. In 2002, researchers at the National Autonomous University of Mexico (UNAM) in Mexico City proposed that a viral haemorrhagic fever, exacerbated by a catastrophic drought, was behind the carnage2. They compared the magnitude of the 1545 outbreak to that of the Black Death in fourteenth-century Europe. 

In an attempt to settle the question, a team led by evolutionary geneticist Johannes Krause at the Max Planck Institute for the Science of Human History in Jena, Germany, extracted and sequenced DNA from the teeth of 29 people buried in the Oaxacan highlands of southern Mexico. All but five were linked to a cocoliztli that researchers think ran from 1545 to 1550.

Ancient bacterial DNA recovered from several of the people matched that of Salmonella, based on comparisons with a database of more than 2,700 modern bacterial genomes.

Further sequencing of short, damaged DNA fragments from the remains allowed the team to reconstruct two genomes of a Salmonella enterica strain known as Paratyphi C. Today, this bacterium causes enteric fever, a typhus-like illness, that occurs mostly in developing countries. If left untreated, it kills 10–15% of infected people.

It’s perfectly reasonable that the bacterium could have caused this epidemic, says Schroeder. “They make a really good case.” But María Ávila-Arcos, an evolutionary geneticist at UNAM, isn’t convinced. She notes that some people suggest that a virus caused the cocoliztli, and that wouldn’t have been picked up by the team’s method.

Krause and his colleagues’ proposal is helped by another study posted on bioRxiv last week, which raises the possibility that Salmonella Paratyphi C arrived in Mexico from Europe.

A team led by Mark Achtman, a microbiologist at the University of Warwick in Coventry, UK, collected and sequenced the genome of the bacterial strain from the remains of a young woman buried around 1200 in a cemetery in Trondheim, Norway. It is the earliest evidence for the now-rare Salmonella strain, and proof that it was circulating in Europe, according to the study. (Both teams declined to comment on their research because their papers have been submitted to a peer-reviewed journal – good for them, dp).

“Really, what we’d like to do is look at both strains together,” says Hendrik Poinar, an evolutionary biologist at McMaster University in Hamilton, Canada. And if more ancient genomes can be collected from Europe and the Americas, it should be possible to find out more conclusively whether deadly pathogens such as Salmonella arrived in the New World from Europe.

Salmonella in deep-fried ice cream sickens 100 in Brisbane: Happy Chinese New Year

Deep-fried ice cream sounds like something from a U.S. state fair, where everything is deep-fried, but in times of relative truths, decreasing skepticism and declining media coverage, the idea that over 100 people in Brisbane are sick from Salmonella, and that I found out about it from a hockey parent rather than public-health types is disturbing.

deep-fried-icecream-112Or the new normal.

We have a paper coming out in April about the importance of going public with health information, so fewer people barf, but that lesson is increasingly lost.

Part of that paper includes a couple of Australian outbreaks: When 264 were sickened at a principals conference in Brisbane because they were fed some raw-egg dip, and when over 100 people were sickened with deep-fried ice cream at Chin-Chins in Brisbane in 2015.

There has been no public reporting that I can find, but at some time, public-health types and bureaucrats will realize they are paid by taxpayers, their job is to prevent people barf, not cover and hide.

According to a hockey parent, 15 teachers are out at their son’s school after dining on deep-fried ice cream in the Sunnybank suburb of Brisbane a week or so ago.

The diagnosis is Salmonella and over 100 are believed to be sickened.

Or maybe it’s just fake news, but everyone has a camera and social media, so these stories spread.

Maybe our public health types, or their bosses, with their supers (RSP) can take some steps to protect public health, rather than their own asses.

A table of Australian egg outbreaks is available at http://barfblog.com/wp-content/uploads/2015/03/raw-egg-related-outbreaks-australia-3-2-15.xlsx=


 

2 dead, 14 sick from Salmonella in Germany

Joe Whitworth of Food Navigator reports Germany has seen a significant increase in Salmonella Stourbridge infection that has not been identified but a past outbreak was linked to unpasteurized goat cheese.

The first case was in July and the most recent had disease onset in late October.

Nine of the 13 cases with available information have been hospitalised and two males have died.

Texas uni develops oral vaccine against Salmonella

Researchers from The University of Texas Medical Branch at Galveston have developed a vaccine against salmonella poisoning designed to be taken by mouth. The findings are detailed in an article published in Frontiers in Cellular and Infection Microbiology.

salm-vaccine-oralIn earlier studies, the UTMB researchers developed potential vaccines from three genetically mutated versions of the salmonella bacteria, that is Salmonella Typhimurium, that were shown to protect mice against a lethal dose of salmonella. In these studies, the vaccines were given as an injection.

However, oral vaccination is simplest and least invasive way to protect people against salmonella infection. Taking this vaccine by mouth also has the added advantage of using the same pathway that salmonella uses to wreak havoc on the digestive system.

“In the current study, we analyzed the immune responses of mice that received the vaccination by mouth as well as how they responded to a lethal dose of salmonella, said Ashok Chopra, UTMB professor of microbiology and immunology. “We found that the orally administered vaccines produced strong immunity against salmonella, showing their potential for future use in people.”

There is no vaccine currently available for salmonella poisoning. Antibiotics are the first choice in treating salmonella infections, but the fact that some strains of salmonella are quickly developing antibiotic resistance is a serious concern. Another dangerous aspect of salmonella is that it can be used as a bioweapon — this happened in Oregon when a religious cult intentionally contaminated restaurant salad bars and sickened 1,000 people.

Salmonella is responsible for one of the most common food-borne illnesses in the world. In the US alone, the Centers for Disease Control and Prevention estimates that there are about 1.4 million cases with 15,000 hospitalizations and 400 deaths each year. It is thought that for every reported case, there are approximately 39 undiagnosed infections. Overall, the number of salmonella cases in the US has not changed since 1996.

Salmonella infection in people with compromised immune systems and children under the age of three are at increased risk of invasive non-typhoidal salmonellosis, which causes systemic infection. There are about one million cases globally per year, with a 25 percent fatality rate.

Other authors include UTMB’s Tatiana Erova, Michelle Kirtley, Eric Fitts, Duraisamy Ponnusamy, Jourdan Andersson, Yingzi Cong, Bethany Tiner and Jian Sha as well as Wallace Baze from the University of Texas M.D. Anderson Cancer Center. The study was supported by UTMB and The National Institutes of Health.

Resistant Salmonella causes 6,200 illnesses a year in US

Chris Dall of the Center for Infectious Disease Research Policy reports the U.S. Centers for Disease Control and Prevention (CDC) has published new estimates of the incidence of antibiotic-resistant Salmonella infections in the United States, putting the burden at about 6,200 cases annually.

ab-res-salmIn a report in Emerging Infectious Diseases, CDC researchers estimate the overall incidence of resistant salmonella infections as roughly 2 for 100,000 persons per year from 2004 to 2012They also determined that clinically important resistance was linked to four specific Salmonella serotyopes: Enteritidis, Newport, Typhimurium, and Heidelberg.

Nontyphoidal Salmonella causes an estimated 1.2 million foodborne illnesses and about 450 deaths each year, according to the CDC. While most people who get Salmonella infections recover within a week and do not require antibiotics, more severe infections are generally treated with either ampicillin, ceftriaxone, or ciprofloxacin. Resistance to these drugs can result in increased hospitalization, invasive illnesses, and death.

The new estimates are based on data from the US Census Bureau and from two surveillance systems the CDC uses to track Salmonella and drug-resistant Salmonella: The National Antimicrobial Resistance Monitoring System (NARMS) and the Laboratory-based Enteric Disease Surveillance (LEDS) system. NARMS monitors resistance in Salmonella by testing isolates from infected individuals and determining the percentage of isolates that show resistance. LEDS collects Salmonella surveillance data, including serotypes, from state and territorial public health labs.

The researchers defined three mutually exclusive categories of resistance for the study: ampicillin-only resistance, ceftriaxone/ampicillin resistance, and ciprofloxacin nonsusceptibility.

According to the LEDS data, there were 369,254 culture-confirmed Salmonella infections from 2004 through 2012. Four primary serotypes—Enteritidis, Typhimurium, Newport, and Heidelberg—accounted for 52% of all fully serotyped isolates. NARMS tested 19,410 isolates from 2004 through 2012, and overall resistance was detected in 2,320 isolates. Ampicillin-only resistance was the most common resistance pattern detected, followed by ceftriaxone/ampicillin resistance and ciprofloxacin nonsusceptibility.

Using these data, the researchers determined that from 2004 to 20012 there were approximately 6,200 resistant culture-confirmed infections annually. Overall incidence was 1.93/100,000 person-years for any clinically important resistance, 1.07 for ampicillin-only resistance, .51 for ceftriaxone/ampicillin resistance, and .35 for ciprofloxacin nonsusceptibility.

The authors note that while Enteritidis, Typhimurium, Newport, and Heidelberg account for only half of all culture-confirmed Salmonella infections, the four serotypes accounted for 73% of the Salmonella infections that involved clinically important resistance.

The predominance of these four serotypes, they write, reflects their ability to persist in food animals, be transmitted through the food system, and cause illness. It also suggests that strategies to reduce Salmonella infections caused by these four serotypes could have an impact on the incidence of resistant infections overall.

“The 4 major serotypes that have been driving the incidence of resistant infections should continue to be high priorities in combating resistance,” the authors write.

The report also notes that two of these serotypes—Typhimurium and Newport—have been associated with outbreaks of drug-resistant Salmonella infections linked to contaminated meat, which highlights the need for NARMS to continue monitoring emerging resistance patterns by serotype.

The authors caution, however, that while this estimate of resistant Salmonella infection incidence will help define the magnitude of the problem and guide prevention efforts, it might be telling only part of the story. That’s because it relies on culture-confirmed infections only.

The CDC has estimated that for every culture-confirmed case of Salmonella, there may as many as 29 undetected cases. That could put the annual US incidence as high as 180,000 cases.

Pigeons: Rats with wings (and Salmonella factories)

Sane New Yorkers regard them as rats with wings, and they make use of the many tools to combat pigeons on their property. But things get complicated when a neighboring property owner doesn’t care that pigeons are emitting toxic piles of excrement in a shared space between buildings.

pigeon-rats-wingsSuch was the case on the Upper West Side, where pigeons set up housekeeping on a grocery store’s outdoor air vents and cooling system. Residents of a co-op that shares a courtyard with the grocery store hired an exterminator, but the nests remain. The store’s management did not respond to calls. What’s a co-op board to do?

“The mere presence of pigeon droppings in the courtyard is an unsanitary condition” and could be grounds for a violation, Kempshall McAndrew, a real estate lawyer at Anderson Kill, tells the New York Times’ Ask Real Estate column. The board should keep the courtyard free of pigeon droppings in case an inspector visits.

Beyond that, McAndrew advises the co-op board to call the Department of Health and Mental Hygiene directly, bypassing 311. The board should photograph the area, documenting the nests as the source of the problem. It should also keep records of calls to the grocery store and of the exterminator’s efforts.

A Tale of Three Outbreaks: ConAgra plea deal reached

A couple of weeks ago I left my cozy bubble of Raleigh and travelled to Wayne County NC for an evening talk at the Farm-City Banquet. As I was driving I thought about Doug and Gord Surgeoner’s mentorship – both instilled the importance of engaging with real people around issues and chatting over dinners.

Research and extension activities need grounding in reality.caddyshack_be_the_ball_small

The morning of the event I wasn’t entirely sure what to talk about – so I asked Schaffner for input during a podcast recording. He suggested ‘A Tale of Two Outbreaks’ – comparing Jensen Farms to PCA. Both tragic outbreaks, both resulting in criminal charges. One was due to an egregious disregard for public health. The other seemed to be a couple of folks who meant well but didn’t quite get microbiology.

Be the bug.

For the next talk I’m gonna add in ConAgra’s Peter Pan/Salmonella outbreak as part of the story.

The Associated Press reports that ConAgra pled guilty and has agreed to pay $11.2 million in fines and other fees as a result of an outbreak a decade ago.

ConAgra admitted to a single misdemeanor count of shipping adulterated food. No individuals at the leading food conglomerate faced any charges in the 2006 outbreak, which sickened at least 625 people in 47 states.

Disease detectives traced the salmonella to a plant in rural Sylvester, Georgia, that produced peanut butter for ConAgra under the Peter Pan label and the Great Value brand sold at Wal-Mart. In 2007 the company recalled all the peanut butter it had sold since 2004.

Leo Knowles, president of ConAgra Grocery Products, offered no testimony as he entered the misdemeanor plea Tuesday on behalf of the Chicago-based corporation’s subsidiary.

“It made a lot of people sick,” federal prosecutor Graham Thorpe said Tuesday as he described ConAgra’s decision to continue shipments from the Georgia plant in late 2006, before corrective actions were completed, despite lab tests that had twice detected salmonella in samples.

“The industry has taken notice of this prosecution,” Thorpe added.

Though the Justice Department called $8 million the heftiest criminal fine ever imposed in a U.S. food safety case, it represents just one-tenth of one percent of ConAgra’s current $8 billion market capitalization. The company also will pay $3.2 million in cash forfeitures to the federal government.

ConAgra said it didn’t know peanut butter was contaminated with salmonella before it was shipped. However, the plea agreement documents noted that ConAgra knew peanut butter made in Georgia had twice tested positive for salmonella in 2004. Problems weren’t all fixed by the time of the outbreak.

The judge noted that others had already received cash from ConAgra in civil settlements, which he said totaled $36 million to 6,810 people.

About 2,000 of them were represented by Bill Marler, a Seattle-based attorney who specializes in food-safety cases. He said the case shows corporations can be prosecuted even when there’s no evidence of intentional criminality. The misdemeanor charge, he said, required only that ConAgra shipped the contaminated food.

“Companies are very concerned, they’re very worried,” Marler said. “They’re very interested in knowing: How can they charge us with a crime even if we don’t mean to do it? People are paying attention to that and hopefully it’s going to drive positive food behavior.”

The folks in the food and agriculture world in Wayne County seemed to pay attention.

Mac and cheese products recalled due to possible salmonella contamination

TreeHouse Foods, Inc. has announced a voluntary recall of certain macaroni and cheese cup products containing cheddar cheese seasoning which may be contaminated with Salmonella.

salm-mac-cheeseThe company said it was notified by its supplier that the milk powder used in the seasoning has the potential for Salmonella contamination.

The following products are affected by the recall:

Big Win Original Macaroni & Cheese Dinner with a UPC number of 001182258403 and a best-by date of 10/25/2017

Cheese Club Express Mac Macaroni & Cheese Dinner with a UPC number of 004149817167 and any of the following best-by dates: 11/3/2017; 11/4/2017; 11/18/2017; 11/22/2017; 10/20/2017; 10/21/2017; 10/23/2017; 10/29/2017; 11/1/2017; 11/2/2017; 11/11/2017; 11/16/2017; 11/17/2017; 11/22/2017; 11/23/2017; or 11/28/2017

Great Value Macaroni & Cheese Original Cups with a UPC number of 007874208249 and any of the following best-by dates: 10/22/2017; 10/19/2017; 10/27/2017; 10/28/2017; 11/3/2017; 11/7/2017; 11/18/2017; 11/20/2017; or 11/21/2017

Consumers who have purchased any of the above products are urged to dispose of or return the products to the place of purchase for a full refund. They were sold at stores nationwide, including Walmart.

No illnesses have been reported to date.

$11.2M settlement: ConAgra finalizes deal in tainted peanut butter case

Russ Bynum of Federal News Radio reports that in November 2006, the U.S. Centers for Disease Control and state health officials began investigating an outbreak of salmonella infections ultimately blamed for sickening at least 625 people in 47 states and killing nine.

peanut-butter-peter-panInvestigators traced the salmonella to jars of Peter Pan and Great Value brand peanut butter produced in Sylvester, Georgia.

ConAgra officials blamed moisture from a leaky roof and a malfunctioning sprinkler system at the Georgia plant for helping salmonella bacteria grow on raw peanuts.

ConAgra launched a huge recall in February 2007, destroying and urging consumers to throw out all of its peanut butter produced since 2004.

Peter Pan peanut butter vanished from store shelves for months. Meanwhile, ConAgra spent $275 million on upgrades at the Georgia plant and adopted new testing procedures to screen peanut butter for contaminants.

Six months later, in August 2007, ConAgra announced it was ready for Peter Pan to return to supermarkets.

Today, ConAgra faces a court hearing to finalize an $11.2 million settlement — including the largest criminal fine ever in a U.S. food safety case — to resolve federal charges in a salmonella outbreak that sickened hundreds who ate tainted Peter Pan peanut butter.

A federal criminal investigation followed the outbreak. More than eight years after the Peter Pan recall, in May 2015, the Justice Department announced charges and a pre-arranged plea deal with ConAgra.

The agreement called for ConAgra Grocery Products Company, a ConAgra subsidiary, to plead guilty to a single misdemeanor charge of shipping adulterated food. No charges were brought against executives of ConAgra, which was based in Omaha, Nebraska, at the time but has since moved its headquarters to Chicago.

ConAgra issued a statement saying the company didn’t know its peanut butter was contaminated with salmonella before it was shipped. However, the plea agreement documents note that ConAgra knew peanut butter made in Georgia had twice tested positive for salmonella in 2004. Prosecutors said the company destroyed the tainted peanut butter and identified likely sources of contamination, but ConAgra had not finished fixing those problems by the time of the 2007 outbreak.

Going public: FDA not liable for $15 million in damages sought by tomato grower for food safety warning error

I remember. I was in Quebec City with a pregnant Amy when all this went down. Doing hour-long iradio interviews where midnight callers asked about aliens and Salmonella.

tomato

Michael Booth of the National Law Journal reports the U.S. Food and Drug Administration cannot be held liable for financial damages suffered by farmers when it issues emergency, but erroneous, food safety warnings, the U.S. Court of Appeals for the Fourth Circuit has ruled.

In its Dec. 2 ruling, the Fourth Circuit refused to allow a South Carolina tomato farmer to seek more than $15 million in damages from the federal government under the Federal Tort Claims Act after the FDA issued a warning that an outbreak of Salmonella Saintpaul was caused by contaminated tomatoes, when it was later determined that the outbreak was caused by contaminated peppers imported from Mexico.

A South Carolina tomato farm, Seaside Farm on St. Helena Island, sued the federal government, claiming that the incorrect warnings issued by the FDA, beginning in May 2008 and later corrected, cost it $15,036,294 in revenue. The Fourth Circuit agreed with a trial court that the FDA was acting within its authority to issue emergency food safety warnings based on preliminary information in order to protect public health.

“We refuse to place FDA between a rock and a hard place,” wrote Judge J. Harvie Wilkinson for the panel, sitting in Richmond.

“One the one hand, if FDA issued a contamination warning that was even arguably overbroad, premature, or of anything less than perfect accuracy, injured companies would plague the agency with lawsuits,” he said.

“On the other hand, delay in issuing a contamination warning would lead to massive tort liability with respect to consumers who suffer serious or even fatal consequences that a timely warning might have averted,” Wilkinson said.

Judges Paul Niemeyer and Dennis Shedd joined in the Dec. 2 ruling.

The medical crisis arose on May 22, 2008, when the New Mexico Department of Health notified the Centers for Disease Control and Prevention (CDC) that a number of residents had been diagnosed as having Salmonella Saintpaul, a strain that causes fever, diarrhea, nausea and, if left untreated, death. Soon after, similar reports came in from Texas.

The CDC determined that a “strong statistical” analysis determined that the illnesses were caused by people eating raw tomatoes. By June 1 of that year, CDC was investigating 87 illnesses in nine states.

tomato-irradiationThe FDA then issued a warning to consumers in New Mexico and Texas. By June 6, 2008, however, reported cases grew to 145 incidents in 16 states. In New Jersey, three people were reported to have been diagnosed with the illness. On June 7, the FDA issued a blanket nationwide warning telling consumers that they should be wary of eating raw tomatoes. (New Jersey tomatoes were not implicated, since they do not ripen until later in the season.)

The warning listed a number of countries and states, including South Carolina, that were not included and were not implicated, but those states were not listed in media reports. Eventually, 1,220 people were diagnosed as having Salmonella Saintpaul.

Raw tomatoes were not the cause of the illnesses, however. The contamination was traced to imported jalapeño and serrano peppers imported from Mexico.

Seaside Farm, which had just harvested a large crop of tomatoes, sued in May 2011. The farm claimed the erroneous FDA warning about tomatoes cost it $15 million-plus damages in revenue.