Predicting zoonotic Salmonella from livestock

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 entericaserotype 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

January 2019

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 

https://wwwnc.cdc.gov/eid/article/25/1/18-0835_article

 

Harvard Biz: How Wegmans became a leader in improving food safety

Notes from a podcast by Ray Goldberg of the Harvard Business School drawn from his case study, Wegmans and Listeria: Developing a Proactive Food Safety System for Produce

The agribusiness program Goldberg developed in 1955 continues to bring business leaders and policy makers from around the world together each year. Throughout his tenure, Ray has written over 100 articles and 24 books on the business of agriculture, including his very latest, Food Citizenship: Food System Advocates in an Era of Distrust.

He was interviewed by podcast host, Brian Kenny: Did you coin the term agribusiness?

Ray Goldberg: I did, together with John Davis. He was the Assistant Secretary of Agriculture under Eisenhower, and he became the first head of the (HBS) Agribusiness Program.

Brian Kenny: The case cites examples of foodborne illness outbreaks in the US. We’re coming on the heels of the recent romaine lettuce issue in the US, which has now occurred, I think, twice in the last few months.

Ray Goldberg: I can describe the romaine lettuce [event], because I talked to the produce manager this morning, and he tells me the cost to the industry was $100 million dollars.

The problem is that romaine lettuce itself, when cold temperatures occur, begins to blister, which make it more susceptible to listeria. When they tried to find the location of that listeria, it came from a dairy herd about 2,000 feet away from where that lettuce was grown. We have a rule that 1,200 feet is far enough, but they actually found listeria a mile away from where that lettuce was concerned, so he feels very strongly that they have to change the rules.

(They seem to be confusing Listeria with E.coli O157 in Romaine, but that’s Haaaaaaaaarvard.)

Brian Kenny: Which gets to another issue that the case raises, which is has the industry done well enough trying to regulate itself? What are some of the things the industry has tried to do?

Ray Goldberg: Under Danny Wegman’s leadership—he was the person in charge of food safety of the Food Marketing Institute that really looked at the whole industry—he got several members of the industry to sit down and create new rules with the FDA, the EPA, the USDA, and CDC, all of them saying we have to have better rules. Produce, as you know in the case, is the most valuable part of a supermarket but also the most susceptible to problems.

Brian Kenny: This gets a little bit to the topic of your book, Food System Advocates in an Era of Distrust. [What[ are the big ideas coming out of your book?

Ray Goldberg: The big ideas are two-fold, that the kind of men and women in the industry have changed from commodity handlers and bargaining as to how cheap they can buy something, or how expensive they can make something, to finally realizing that they have to be trusted. And because they have to be trusted, they have to start working together to create that trust. In addition to that, they realize that the private, public and not-for-profit sectors really need to work together. That’s why I tried to write a book to give people an inkling of the kind of men and women in this industry who really are the change-makers, who are changing it to a consumer-oriented, health-oriented, environmentally-oriented, economic development-oriented industry.

Just cook it doesn’t cut it: Salmonella in veal liver, Quebec

Salmonella enterica is one of the principal causes of foodborne zoonotic enteritis. Among the different serovars, Dublin (S. Dublin) is of particular importance due to its propensity to progress to an invasive infection in humans and due to the high proportion of multi-drug resistant strains in Canada.

Cattle are considered as the main reservoir of S. Dublin. This serotype has emerged since 2011 in the province of Quebec, Canada, in both cattle and human populations. First animal cases have been reported in calf production.

White veal are valued for the quality of their meat, offal and liver. The liver is usually consumed mildly cooked and is considered as a probable source of foodborne exposure to S. Dublin in humans. The objective of this study was to estimate the prevalence of S. Dublin positive liver after slaughtering and the seroprevalence against S. Dublin at the calf level.

Prevalence of salmonella Dublin in veal liver in Quebec, Canada from a public health perspective, February 2019

International Journal of Infectious Diseases vol. 79 pg. 75

C.M. Andela Abessolo, P. Turgeon, P. Fravalo, G. Côté, G. Eyaba, W.P. Thériault, J. Arsenault

DOI: https://doi.org/10.1016/j.ijid.2018.11.191

https://www.ijidonline.com/article/S1201-9712(18)34770-2/abstract

7 sickened with Salmonella linked to Duncan Hines cake mixes

Flour comes from dried wheat that’s milled and not heat treated (because it messes with the gluten). Because wheat is grown in nature, Salmonella or E. coli or other nasties can be present. As Salmonella dries out it gets hardier and survives for months (or longer).

In 1957, Duncan Hines and his wife, Clara, cut a cake at the Duncan Hines test kitchen in Ithaca, N.Y.

From Dec. 2015 to Sept. 2016, pathogenic E. coli (both O121 and O26 serogroups) sickened 56 people in 22 states linked to raw flour.

In Nov. 2018, the U.S. Food and Drug Administration investigated recalled Duncan Hines Cake Mixes potentially linked to seven Salmonella Agbeni illnesses.

On January 14, 2019, the Centers for Disease Control reported the outbreak appeared to be over. The FDA, CDC, public health and regulatory officials in several states worked together to investigate this multistate outbreak of Salmonella Agbeni infections.

The FDA recommends consumers to not bake with or eat the recalled product. Additionally, consumers should not eat uncooked batter, flour, or cake mix powder.

The FDA advised consumers not to bake with or eat any recalled cake mix. If already purchased, consumers should throw it away or return to the place of purchase for a refund.

Consumers should always practice safe food handling and preparation measures. It is recommended that they wash hands, utensils, and surfaces with hot, soapy water before and after handling food.

FDA offers these tips for safe food handling to keep you and your family healthy:

Do not eat any raw cake mix, batter, or any other raw dough or batter product that is supposed to be cooked or baked.

Wash hands, work surfaces, and utensils thoroughly after contact with flour and raw batter or dough products.

Keep raw foods separate from other foods while preparing them to prevent any contamination that may be present from spreading. Be aware that flour or cake mix may spread easily due to its powdery nature.

Australia still has an egg problem, state of New South Wales trying to do something about it

The NSW Food Authority is urging people to check their kitchens for any eggs that are marked with the identifying stamp BEC or BEC115 because they may be contaminated with a particular type of Salmonella.

The stamp BEC or BEC115 will be found on the shell of individual eggs, not on the carton.

NSW Food Authority CEO Dr Lisa Szabo said thanks to mandatory egg stamping required in NSW, the Food Authority has been able to isolate the particular batch of eggs.

“All other eggs are safe to eat, provided people exercise the usual caution required for a special care food like eggs such as washing your hands and avoiding raw egg products particularly if you are a vulnerable population such as the immune compromised, under two or over 70 years of age or pregnant,” Dr Szabo said.

(That means asking at a restaurant or catered meal if the aioli or mayonnaise served with many dishes, especially great Australian seafood, was made with raw or pasteurized eggs, or was commercially purchased.)

“It is important to know that not all eggs are impacted but if you have any stamped with BEC or BEC115 we recommend as a precaution that you discard them.

“We typically see a rise in Salmonella during the warmer summer months, so this is an opportune time to remind people to practice good hygiene generally when preparing food and to always keep their hands, surfaces and utensils clean and dry before and after handling eggs.”

NSW Health data indicates that during January 2019, 412 cases of Salmonella infection have been notified, which is similar to the number notified during January in recent years. Children under 5 years of age account for most cases notified this month, although all age groups are affected.

The NSW Food Authority placed a Prohibition Order on the business that produced the eggs earlier in January preventing them from selling eggs while the possible Salmonella contamination was investigated.

“While it is likely that most affected eggs are no longer in the supply chain, it is possible that people may have purchased them earlier and still have some at home in the fridge or pantry,” Dr Szabo said.

“We’d just like people to check and if they do have any eggs stamped BEC or BEC115 to throw them out to avoid any risk of food poisoning.”

Further information about how to reduce your food safety risk when consuming eggs can be found at www.foodauthority.nsw.gov.au/eggs

An updated table of Australian egg-related outbreaks) is available here.

Jigsaw puzzle: France reports Salmonella poona cases in infants

Outbreak News Today reports that health officials in France are reporting four Salmonella Poona cases in infants whose strains are genetically linked.

The babies, two months to ten months in age, were sickened between the end of August 2018 and the end of December 2018. Three babies were hospitalized for their salmonellosis and all have been released.

Early investigations reveal a common food source with the four infants–powdered milk of the same brand produced by the same factory in Spain.

Investigations are currently being conducted with the Spanish authorities and the manufacturer to define the management measures to be put in place.

Raw is risky: Pet food recalled after Minn. Health finds Salmonella in a human

State officials are notifying consumers of a recall of raw turkey pet food from Woody’s Pet Food Deli. Salmonella contamination was found after the Minnesota Department of Health identified a human case linked to the pet food

The recalled product was sold in 5-pound plastic containers labeled “Woody’s Pet Food Deli Raw Free Range Turkey” and can be identified by the white date sticker on the cover of the pet food container, the state health and agriculture departments said in a statement Monday.

The product was sold at Woody’s Pet Food Deli locations in Minneapolis, St. Paul and Woodbury. The lots recalled have these use-by dates:

– Jan. 10, 2020

– Jan. 12, 2020

– Jan. 15, 2020

No other lots of Woody’s Pet Food Deli products are affected by the recall, the agencies said.

Consumers with the recalled product at home are being told to throw it out or return it to a Woody’s Pet Food Deli for a full refund and not feed the contaminated product to pets, state officials said.

Consumers with questions can contact the Woody’s Pet Food Deli stores directly or email the company at info@woodyspetdeli.com .

Sampling began after the state health department identified a human case of salmonella linked to the pet food as part of the agency’s ongoing, multistate investigation of salmonella infections coordinated by the federal Centers for Disease Control and Prevention.

Norway finds Salmonella outbreaks linked to countries visited

During summer 2016, Norway observed an increase in Salmonella enterica subsp. enterica serovar Chester cases among travellers to Greece.

Our aim was to investigate genetic relatedness of S. Chester for surveillance and outbreak detection by core genome multilocus sequence typing (cgMLST) and compare the results to genome mapping.

We included S. Chester isolates from 51 cases of salmonellosis between 2000 and 2016. Paired-end sequencing (2 × 250 bp) was performed on Illumina MiSeq. Genetic relatedness by cgMLST for Salmonellaenterica subsp. enterica, including 3,002 genes and seven housekeeping genes, was compared by reference genome mapping with CSI Phylogeny version 1.4 and conventional MLST.

Confirmed travel history was available for 80% of included cases, to Europe (n = 13), Asia (n = 12) and Africa (n = 16). Isolates were distributed into four phylogenetic clusters corresponding to geographical regions. Sequence type (ST) ST411 and a single-locus variant ST5260 (n = 17) were primarily acquired in southern Europe, ST1954 (n = 15) in Africa, ST343 (n = 11) and ST2063 (n = 8) primarily in Asia. Part of the European cluster was further divided into a Greek (n = 10) and a Cypriot (n = 4) cluster. All isolates in the African cluster displayed resistance to ≥ 1 class of antimicrobials, while resistance was rare in the other clusters.

Whole genome sequencing of S. Chester in Norway showed four geographically distinct clusters, with a possible outbreak occurring during summer 2016 related to Greece. We recommend public health institutes to implement cgMLST-based real-time Salmonella enterica surveillance for early and accurate detection of future outbreaks and further development of cluster cut-offs.

Whole genome sequencing of Salmonella Chester reveals geographically distinct clusters, Norway, 2000 to 2016

Siira Lotta, Naseer Umaer, Alfsnes Kristian, Hermansen Nils Olav, Lange Heidi, Brandal Lin T. Whole genome sequencing of Salmonella Chester reveals geographically distinct clusters, Norway, 2000 to 2016. Euro Surveill. 2019;24(4):pii=1800186. https://doi.org/10.2807/1560-7917.ES.2019.24.4.1800186

https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2019.24.4.1800186#abstract_content

Stop kissing chicks, stop stroking that hedgehog and stop touching yourself: 11 sick with Salmonella linked to hedgehogs

Every time someone introduces a new pet at the kid’s school, I see a Salmonella factory (summer holidays are over, grade 5 started today for Sorenne).

This isn’t the first time the prickly pest or pet, depending on perspective, like possums, has been linked to Salmonella Typhimurium: From December 2011 to April 2013, 26 people were infected with Salmonella typhimurium. One person died and eight people were hospitalized in that outbreak, the C.D.C. reported.

According to the U.S. Centers for Disease Control, 11 people infected with the outbreak strain of Salmonella Typhimurium have been reported from eight states.

One person has been hospitalized and no deaths have been reported.

Epidemiologic and laboratory evidence indicate that contact with pet hedgehogs is the likely source of this outbreak.

In interviews, 10 (91%) of 11 ill people reported contact with a hedgehog.

Illnesses started on dates from October 22, 2018 to December 25, 2018. Ill people range in age from 2 to 28 years, with a median age of 12. Forty-five percent are female.

The outbreak strain making people sick was identified in samples collected from three hedgehogs in two ill patients’ homes in Minnesota.

Hedgehogs can carry Salmonella germs in their droppings while appearing healthy and clean.

These germs can easily spread to their bodies, habitats, toys, bedding, and anything in the area where they live. People become sick after they touch hedgehogs or anything in their habitats.

Wash your hands

Always wash hands thoroughly with soap and water right after touching, feeding, or caring for a hedgehog or cleaning its habitatAdults should supervise handwashing for young children.

Play safely

Don’t kiss or snuggle hedgehogs, because this can spread Salmonella germs to your face and mouth and make you sick.

Don’t let hedgehogs roam freely in areas where food is prepared or stored, such as kitchens.

Clean habitats, toys, and supplies outside the house when possible. Avoid cleaning these items in the kitchen or any other location where food is prepared, served, or stored.

529 now sick with Salmonella in Canada: Crisp & Delicious brand chicken breast nuggets recalled

Over a decade ago, when I went to Kansas State, me and Chapman and Phebus came up with a project to see how people cooked raw, frozen chicken thingies.

The American Meat Institute funded it.

Some of these chicken thingies are frozen raw, which means they have to be cooked in an oven and temperature verified with a tip-sensitive digital thermometer, and some of these thingies are pre-cooked, so can be thawed in a microwave.

Labelling has changed over the years, but it’s still necessary to know what you’re buying.

Some of the frozen raw products may appear to be pre-cooked or browned, but they should be handled and prepared with caution.

Through whole genome sequencing, health types in Canada had, by Nov. 2, 2018, identified 474 laboratory-confirmed cases of Salmonella linked to 14 national outbreaks involving raw chicken, including frozen raw breaded chicken products.

The Canadian Food Inspection Agency issued food recall warnings for ten products linked to some of these outbreak investigations.

Make that 11 products.

Sofina Foods Inc. is now recalling Crisp & Delicious brand Chicken Breast Nuggets from the marketplace due to possible Salmonella contamination.

As of January 25, 2019, there have been 529 laboratory-confirmed cases of Salmonella illness investigated as part of the illness outbreaks across the country: British Columbia (42), Alberta (81), Saskatchewan (18), Manitoba (25), Ontario (187), Quebec (111), New Brunswick (27), Nova Scotia (17), Prince Edward Island (5), Newfoundland and Labrador (12), Northwest Territories (1), Yukon (1), and Nunavut (2). There have been 90 individuals hospitalized as part of these outbreaks. Three individuals have died; however, Salmonella was not the cause of death for two of those individuals, and it was not determined whether Salmonella contributed to the cause of death for the third individual. Infections have occurred in Canadians of all ages and genders.

All active and future Salmonella outbreak investigations linked to raw chicken, including frozen raw breaded chicken products, and related food recall warnings will be listed in the next section of the public health notice to remind Canadians of the ongoing risk associated with these types of food products.

Active investigations

As of January 25, 2019, there is one active national Salmonella outbreak investigation linked to raw chicken including frozen raw breaded chicken products, coordinated by the Public Health Agency of Canada.

January 25, 2019 (NEW) – Salmonella Enteritidis

  • Currently, there are 54 cases of illness in ten provinces linked to this outbreak: British Columbia (4), Alberta (11), Saskatchewan (1), Manitoba (3), Ontario (20), Quebec (4), New Brunswick (2), Nova Scotia (5), Prince Edward Island (3) and Newfoundland and Labrador (1). None of the ill individuals have been hospitalized. No deaths have been reported. Frozen raw breaded chicken products have been identified as a source of this outbreak.

Product recall on January 25, 2019

  • Crisp & Delicious Chicken Breast Nuggets (1.6kg) with a best before date of July 19, 2019. UPC – 0 69299 11703 5. The product was distributed in British Columbia, Manitoba, Ontario, and Quebec, and may have been distributed in other provinces or territories

Self-reported and observed behavior of primary meal preparers and adolescents during preparation of frozen, uncooked, breaded chicken products
01.nov.09
British Food Journal, Vol 111, Issue 9, p 915-929
Sarah DeDonder, Casey J. Jacob, Brae V. Surgeoner, Benjamin Chapman, Randall Phebus, Douglas A. Powell
http://www.emeraldinsight.com/Insight/viewContentItem.do;jsessionid=6146E6AFABCC349C376B7E55A3866D4A?contentType=Article&contentId=1811820
Abstract:
Purpose – The purpose of the present study was to observe the preparation practices of both adult and young consumers using frozen, uncooked, breaded chicken products, which were previously involved in outbreaks linked to consumer mishandling. The study also sought to observe behaviors of adolescents as home food preparers. Finally, the study aimed to compare food handler behaviors with those prescribed on product labels.
Design/methodology/approach – The study sought, through video observation and self-report surveys, to determine if differences exist between consumers’ intent and actual behavior.
Findings – A survey study of consumer reactions to safe food-handling labels on raw meat and poultry products suggested that instructions for safe handling found on labels had only limited influence on consumer practices. The labels studied by these researchers were found on the packaging of chicken products examined in the current study alongside step-by-step cooking instructions. Observational techniques, as mentioned above, provide a different perception of consumer behaviors.
Originality/value – This paper finds areas that have not been studied in previous observational research and is an excellent addition to existing literature.