Adaptation to life inside cattle may be driving E. coli to develop harmful features

A large-scale study of the genetic differences and similarities among E. coli bacteria from cattle and humans indicates that features causing food poisoning in humans may continuously be emerging in bacteria from cattle as a means to better adapt to their environment.

While E. coli bacteria are one of the most well-known causes of food poisoning, a wide variety of E. coli strains exists, many of which are harmless, permanent residents of our intestines. However, the ingestion of harmful strains of E. coli on contaminated food can lead to severe illness, vomiting, and diarrhea.

“To develop the most effective preventive measures, we need a deep understanding of the source and living conditions of the bacteria,” says Yoshitoshi Ogura, associate professor at Kyushu University’s Department of Bacteriology, who led the research.

“Although cattle have long been thought to be a main source of E. coli that cause food poisoning, why dangerous forms would keep appearing in cattle has been unclear.”

Ogura’s group, in collaboration with researchers across Japan and in France, Belgium, and the United States, set out to help answer this question by investigating the genetics of E. coli bacteria collected from cattle and humans in 21 countries spanning six continents.

“To date, there have been only a limited number of reports of the genome sequences of E. coli from cattle, so we needed to fill that gap,” comments Yoko Arimizu, first author on the paper in Genome Research announcing the new results.

While the largest number of samples was from Japan, strains from other regions exhibited characteristics that were well distributed among those from Japan, indicating a good diversity of the set of samples.

Based on the genetic features of the bacteria, the researchers could generally separate the different strains of E. coli into two groups, with one primarily consisting of bacteria collected from humans and the other of those from cattle.

Applying the same analysis to clinically obtained E. coli that are known to cause illness, the researchers found that most of the strains causing intestinal problems belonged to the group associated with cattle.

Furthermore, many of the samples from cattle exhibited features similar to those causing food poisoning, such as the production of Shiga toxin. While these features generally appear not to cause illness in cattle, their prevalence in the investigated samples suggests that such characteristics are beneficial for life in a cattle’s intestine.

“As long as there is pressure to maintain or strengthen these illness-producing characteristics to better adapt to living in a cattle’s intestine, new variants of E. coli that cause food poisoning are likely to continue appearing,” states Ogura.

The researchers speculate that these characteristics may help E. coli protect itself from bacteria-eating organisms present in cattle intestines, but more work is needed to identify the exact reason.

How dangerous E. coli find the best place to infect

Scientists at the University of Virginia School of Medicine have learned how a foodborne illness takes hold.

They were looking into E.coli and how it seeks out the most oxygen-free parts of the human colon to cause the worst possible infection in the body.

According to a release, this new discovery shows how the pathogen knows where and when to begin colonizing the colon on the way to making a person sick.

E.coli reportedly can recognize the low-oxygen environment of the large intestine, which is where it can give itself the best odds of establishing a robust infection.

“Bacterial pathogens typically colonize a specific tissue in the host. Therefore, as part of their infection strategies, bacterial pathogens precisely time deployment of proteins and toxins to these specific colonization niches in the human host,” said researcher Melissa Kendall, PhD, of the UVA Department of Microbiology, Immunology and Cancer Biology. “This allows the pathogens to save energy and avoid detection by our immune systems and ultimately cause disease. By knowing how bacterial pathogens sense where they are in the body, we may one day be able to prevent E. coli, as well as other pathogens, from knowing where it is inside a human host and allow it to pass through the body without causing an infection.”

Humans naturally have E.coli in the colon, and most strains do not cause harm.

However, there are several strains that can cause cramps, diarrhea, vomiting, kidney failure and even death, especially in children.

Oxygen diffuses from the intestinal tissues into the gut, and the small intestine contains comparably higher levels than the large E.coli.

The pathogen waits until it has reached the lower oxygen large intestine before trying to establish an infection.

E.coli has a vital asset in the form of RNA, which activates particular genes when oxygen levels get low enough.

That is when the infection can become established, at which time, the bacteria begin to manufacture Shiga toxins, which are harmful to people.

It is believed other bacterial pathogens, like Shigella and Salmonella, may use a similar control mechanism, but more research is needed to establish that.

The findings concerning E.coli have been published in the scientific journal PNAS.

E. coli O157: Which typing is better?

Due to the potential of enterohemorrhagic Escherichia coli (EHEC) serogroup O157 to cause large food borne outbreaks, national and international surveillance is necessary.

For developing an effective method of molecular surveillance, a conventional method, multilocus variable-number tandem-repeat analysis (MLVA), and whole-genome sequencing (WGS) analysis were compared. WGS of 369 isolates of EHEC O157 belonging to 7 major MLVA types and their relatives were subjected to comprehensive in silico typing, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) analyses. The typing resolution was the highest in cgSNP analysis. However, determination of the sequence of the mismatch repair protein gene mutS is necessary because spontaneous deletion of the gene could lead to a hypermutator phenotype. MLVA had sufficient typing resolution for a short-term outbreak investigation and had advantages in rapidity and high throughput. cgMLST showed less typing resolution than cgSNP, but it is less time-consuming and does not require as much computer power. Therefore, cgMLST is suitable for comparisons using large data sets (e.g., international comparison using public databases). In conclusion, screening using MLVA followed by cgMLST and cgSNP analyses would provide the highest typing resolution and improve the accuracy and cost-effectiveness of EHEC O157 surveillance.

IMPORTANCE Intensive surveillance for enterohemorrhagic Escherichia coli (EHEC) serogroup O157 is important to detect outbreaks and to prevent the spread of the bacterium. Recent advances in sequencing technology made molecular surveillance using whole-genome sequence (WGS) realistic. To develop rapid, high-throughput, and cost-effective typing methods for real-time surveillance, typing resolution of WGS and a conventional typing method, multilocus variable-number tandem-repeat analysis (MLVA), was evaluated. Nation-level systematic comparison of MLVA, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) indicated that a combination of WGS and MLVA is a realistic approach to improve EHEC O157 surveillance.

Effective surveillance using multilocus variable-number tandem-repeat analysis and whole-genome sequencing for enterohemorrhagic Escherichia coli O157

Applied and Environmental Microbiology

Kenichi Lee, Hidemasa Izumiya, Sunao Iyoda, Makoto Ohnishi and EHEC Working Group

DOI: 10.1128/AEM.00728-19

https://aem.asm.org/content/85/17/e00728-19.abstract?etoc

Good year for Cyclospora bad year for humans: 205 sick linked to Mexican basil in latest outbreak

The U.S. Centers for Disease Control (CDC), public health and regulatory officials in several states, and the U.S. Food and Drug Administration (FDA) are investigating a multistate outbreak of Cyclospora infections linked to fresh basil from Siga Logistics de RL de CV of Morelos, Mexico.

CDC is advising that consumers do not eat or serve any fresh basil from Siga Logistics de RL de CV of Morelos, Mexico. This investigation is ongoing and the advice will be updated when more information is available.

Consumers who have fresh basil from Siga Logistics de RL de CV of Morelos, Mexico, in their homes should not eat it. Throw the basil away, even if some has been eaten and no one has gotten sick.

Do not eat salads or other dishes that include fresh basil from Siga Logistics de RL de CV of Morelos, Mexico. This includes dishes garnished or prepared with fresh basil from Siga Logistics de RL de CV of Morelos, Mexico, such as salads or fresh pesto.

If you aren’t sure the fresh basil you bought is from Siga Logistics de RL de CV of Morelos, Mexico, you can ask the place of purchase. When in doubt, don’t eat the fresh basil. Throw it out.

Wash and sanitize places where fresh basil was stored: countertops and refrigerator drawers or shelves.

The FDA strongly advises importers, suppliers, and distributors, as well as restaurants, retailers, and other food service providers to not sell, serve or distribute fresh basil imported from Siga Logistics de RL de CV located in Morelos, Mexico. If you are uncertain of the source, do not sell, serve or distribute the fresh imported basil.

Two hundred and five people with laboratory-confirmed Cyclosporainfections and who reported eating fresh basil have been reported from 11 states; exposures occurred at restaurants in 5 states (Florida, Minnesota, New York, Ohio, and Wisconsin).

Illnesses started on dates ranging from June 10, 2019 to July 18, 2019.

Five people have been hospitalized. No deaths attributed to Cyclospora have been reported in this outbreak.

Epidemiologic evidence and early product distribution information indicate that fresh basil from Siga Logistics de RL de CV of Morelos, Mexico is a likely source of this outbreak.

2019 Outbreak of Cyclospora infections linked to fresh basil from Mexico

15.aug.19

CDC

https://www.cdc.gov/parasites/cyclosporiasis/outbreaks/2019/weekly/index.html

Outbreak investigation of Cyclospora illness linked to imported fresh basil, July 2019

16.aug.19

FDA

https://www.fda.gov/food/outbreaks-foodborne-illness/outbreak-investigation-cyclospora-illnesses-linked-imported-fresh-basil-july-2019

Canada: Raw frozen chicken thingies outbreaks

We’ve done extensive work on this topic dating back to 2006 (search barfblog.com), but new tools, like whole genome sequencing, mean additional outbreaks have been identified. A summary paper of recent outbreaks has just been published. Abstract below:

Frozen raw breaded chicken products (FRBCP) have been identified as a risk factor for Salmonella infection in Canada. In 2017, Canada implemented whole genome sequencing (WGS) for clinical and non-clinical Salmonella isolates, which increased understanding of the relatedness of Salmonella isolates, resulting in an increased number of Salmonella outbreak investigations. A total of 18 outbreaks and 584 laboratory-confirmed cases have been associated with FRBCP or chicken since 2017. The introduction of WGS provided the evidence needed to support a new requirement to control the risk of Salmonella in FRBCP produced for retail sale.

Outbreak of salmonella illness associated with frozen raw breaded chicken products in Canada 2015-2019

22 August 2019

Epidemiology and Infection vol. 147

  1. K. Morton(a1)A. Kearney(a2)S. Coleman (a3)M. Viswanathan (a1)K. Chau (a4)A. Orr (a5)and A. Hexemer (a1) 

DOI: https://doi.org/10.1017/S0950268819001432

https://www.cambridge.org/core/journals/epidemiology-and-infection/article/outbreaks-of-salmonella-illness-associated-with-frozen-raw-breaded-chicken-products-in-canada-20152019/9F1E5C0D2BF560E540C47BA064E7F713

255 sick from same Salmonella in American beef and Mexican soft cheese

What is already known about this topic?

Decreased susceptibility to azithromycin is rare among Salmonella serotypes that cause human infections in the United States. If antibiotic treatment is indicated, azithromycin is recommended as an oral therapy.

What is added by this report?

During June 2018–March 2019, an outbreak caused by multidrug-resistant Salmonella Newport with decreased susceptibility to azithromycin led to 255 infections and 60 hospitalizations. Infections were linked to Mexican-style soft cheese obtained in Mexico and beef obtained in the United States.

What are the implications for public health practice?

Whole genome sequencing can be used in Salmonella outbreak investigations for rapid prediction of antimicrobial resistance and can link cases to each other and to possible sources of infection.

Outbreak of salmonella Newport infections with decreased susceptibility to azithromycin linked to beef obtained in the United States and soft cheese obtained in Mexico—United States 2018-2019

23.aug.19

CDC

https://www.cdc.gov/mmwr/volumes/68/wr/mm6833a1.htm?s_cid=mm6833a1_e&deliveryName=USCDC_921-DM7382

Radiation exposure in Russia blamed on Fukushima crabs

I’m a sucker for food safety jokes, and the punchline of “it must have been the Fukushima crabs” is a beauty.

According to the Telegraph, doctors in Russia who treated victims of a military test explosion have evidence of being exposed to radioactive materials, with isotopes being found within their muscle tissue.

Officials however are playing the food safety card when trying to explain why cesium-137 is there.

Staff from the Arkhangelsk regional hospital were not informed at first that they were treating irradiated patients, and protective measures were not taken until the next day, they told Russian media this week.

In some cases, staff said they were falsely told patients had been decontaminated.

One doctor was later found to have the isotope Caesium-137 in his muscle tissue. He was told he must have eaten too many “Fukushima crabs” during a trip to Thailand, his colleague told the news outlet Meduza.

In related news, Chernobyl on HBO is excellent.

 

175 now sick with Listeria in Spanish outbreak

Jack Guy of CNN reports Spain’s health ministry has issued an international health warning over a listeria outbreak that has infected 175 people.

The bacteria was detected in a processed meat product manufactured in the city of Seville, in the southern region of Andalucia, according to an alert published Tuesday.

“My priority is to avoid the spread of the outbreak,” said Spain’s acting health minister María Luisa Carcedo, in a video watched by CNN. 

The country has informed the World Health Organization (WHO) and the European Commission about the outbreak. 

It comes during peak tourist season in Spain, with Andalucia a popular destination among visitors.

Fifty people remained in hospital Wednesday, 23 of whom were pregnant women, according to Reuters.

Snot and washing produce

All washing might do is “remove the snot that some 3-year-old blew onto the food at the grocery store,” says the ever-forthright Powell at Kansas State. Washing “lowers the pathogen count a little, but not to safe levels if it’s contaminated.”

I said that in a Feb.15, 2012 interview with USA Today.

And a coupe of days ago a former MS student and friend sent me this:

 

Satire becomes reality: Poop Like a Champion cereal

I miss Phil Hartman, another good Brantford, Ontario (that’s in Canada) boy who lived there until he was10-years-old, when his family moved to the U.S. His third wife shot him to death while he slept in 1998.

He had a satiric advertisement for a cereal called Colon Blow during his Saturday Night Live years (see below).

My Joy Online reports that Poop Like a Champion is an actual cereal that can allegedly get your bowels moving like nothing else.

Advertised as “the ultimate colon cleansing formula” or “the number one high fiber cereal for number 2’s,” Poop Like a Champion cereal is packed full of fibers and designed specifically to help you get those bowels moving.

Its creators aren’t ashamed to admit that it’s not the greatest tasting cereal money can buy, but it’s not meant to blow you away with its amazing flavor, it’s meant to help you go potty, and apparently, it’s very good at doing that.