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.

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

 

Corn-stuff may increase E. coli O157 in cattle

Inclusion of distillers’ grains (DGs) has been associated with
increased prevalence of Escherichia coli O157:H7 in cattle housed in
research settings. Our objective was to quantify the relationship
between inclusion of DGs in commercial feedlot rations and the burden
of E. coli O157.

A convenience sample of 10 feedlots was enrolled based on DG use in finishing diets; 1 cohort included 5 feedlots in which DGs were greater than 15% of the dietary dry matter and the other cohort consisted of 5 feedlots at a concentration less than 8%. 

Sampling occurred at each feedlot on four occasions at ∼6-week
intervals. At each feedlot visit, 4 pens of cattle within 3 weeks of
slaughter were selected and 24 freshly voided fecal pats were sampled.

Ten-gram samples were enriched in 90 mL of modified tryptic soy broth with novobiocin (20 mg/L) for 14 h at 42°C. Enrichments were subjected to immunomagnetic separation, plating onto chromogenic agar with novobiocin (5 mg/L) and potassium tellurite (2.5 mg/L), incubation for 18 h at 37°C, and latex agglutination of morphologically typical colonies. E. coli O157 was recovered from 16.7% of 3840 samples.

Adjusted prevalence was 14.3% after controlling for within-feedlot and
within-pen clustering. Prevalence during each sampling period was
19.9% (round 1), 21.0% (round 2), 14.1% (round 3), and 11.7% (round
4). Prevalence varied between cohorts, but this difference varied over
time (p = 0.06). Among those with greater than 15% of the diet as DGs, prevalence was greater than those with less than 8% inclusion for all rounds of sampling (p < 0.01). Averaged across time, prevalence was 23.9% and 9.4% for those with greater than 15% and those with less than 8% of DGs, respectively. While observational, these data provide real-world support of reports of increased E. coli O157:H7 burden associated with DG use in cattle diets.

Corn-based distillers’ grains in diets for feedlot cattle are associated with the burden of Escherichia coli O157 in feces

Foodborne Pathogens and Disease 15:298-405

Evan Chaney, Rebecca Maloney, Bradley J. Johnson, J. Chance Brooks, Mindy M. Brashears, and Guy H. Loneragan.

I’m known as the flyslayer around the home: More debate on the role of houseflies in E. coli transmission

The ecology of Escherichia coli O157:H7 is not well understood. The aims of this study were to determine the prevalence of and characterize E. coli O157:H7 associated with houseflies (HF).

 Musca domestica L. HF (n = 3,440) were collected from two sites on a cattle farm over a 4-month period and processed individually for E. coli O157:H7 isolation and quantification. The prevalence of E. coli O157:H7 was 2.9 and 1.4% in HF collected from feed bunks and a cattle feed storage shed, respectively. E. coli O157:H7 counts ranged from 3.0 × 101 to 1.5 × 105 CFU among the positive HF. PCR analysis of the E. coli O157:H7 isolates revealed that 90.4, 99.2, 99.2, and 100% of them (n = 125) possessed the stx1, stx2, eaeA, and fliC genes, respectively.

Large populations of HF on cattle farms may play a role in the dissemination of E. coli O157:H7 among animals and to the surrounding environment.

Association of Escherichia coli O157:H7 with houseflies on a cattle farm

July 2018

Applied and Environmental Microbiology vol. 84 no. 14

Muhammad Alam and Ludek Zurek

doi: 10.1128/AEM.70.12.7578-7580.2004

http://aem.asm.org/content/70/12/7578?ijkey=717a5417861fddb53638f51da6eecec048234a81&keytype2=tf_ipsecsha

Tests show NZ beef sector so far free of M. bovis

Emma left this morning.

Emma has always been a special person in our lives, and especially Sorenne’s.

When Amy was pregnant almost 10 years ago at Kansas State University, we talked about getting some early childhood education students to help out, so I could work and Amy could write.

Never had to post the ad.

Emma was a student in one of Dr. Amy’s French classes, noticed she was pregnant, and asked, are you going to need help with that baby?

Emma became one of our helpers.

This was in the U.S., with six weeks maternity leave, rather than Canada, with six months maternity leave (plus a whole bunch more parental leave, in Canada).

Emma now lives in New Zealand with her partner, the veterinarian, and took advantage of the long weekend to have a visit.

To watch Emma and her partner experiment and flourish over the past 10 years has been a delight.

But this story is for the dude, since he works at MPI in New Zealand, whose $3 billion beef export sector seems to be free so far of the serious new cattle disease Mycoplasma bovis.

The Ministry for Primary Industries, which is attempting to contain an outbreak of the disease in dairy cattle by a mass slaughter of more than 22,000 dairy cattle before the beginning of June, said there had been no positive results from its testing of beef animals.

The beef and dairy sectors work closely in New Zealand through dairy calf rearing and dairy grazing with about 80 per cent of premium beef cattle production originating from the dairy herd.

In response to a Herald inquiry, an MPI spokeswoman said the risk profile for M. bovis in beef farming was very different to that of dairying because of how beef is raised in New Zealand.

“Generally beef cattle are farmed extensively in pasture and are not fed risky discarded calf milk.

“We looked into this carefully and determined the beef stock at greatest risk were those that were raised in feed lots – not that common in New Zealand.”

With the support of industry good organisation Beef+Lamb, MPI had carried out some surveillance of cattle in feed lots, mostly in the South Island, the epicentre of the M. bovis outbreak.

“The animals were tested at slaughter in order to take samples … there were no positive results,” the spokeswoman said.

“We also consider that many dairy beef animals were tested in the response as part of our tests on neighbouring farms to infected properties. Again, no positives were found.”
Meanwhile, newly released MPI reports on M. bovis investigations since the first outbreak last July said “confluence of multiple rare events” could have allowed the bacterial disease into New Zealand, possibly as long ago as 2015.

One of the three released reports identifies seven potential pathways for the disease but finds all “improbable – yet one of them resulted in entry”.

The risk pathways investigated were imported embyros, imported frozen bull semen, imported live cattle, imported feed, imported used farm equipment, and other imported live animals. A seventh pathway was redacted from the reports along with all discussion about it, but the Herald can confirm it was imported veterinary medicines and biological products.

MPI has opted to try to contain the disease with a mass cull of cattle on 28 quarantined properties, all but one in the South Island, because it believes it is not yet well established in New Zealand. The first outbreak of the disease was on a large-scale dairying business in the South Island. However, the MPI reports suggest it may have been introduced in mid-2016 or even earlier.

23 sick: Cryptosporidiosis outbreak in Illinois linked to 4-H projects

The Clark and Champaign county health departments say they’re investigating 23 possible cases of cryptosporidiosis linked to dairy calves brought to the region for youth 4-H projects. 

The calves were sold to children.  A Clark County epidemiologist says hydrogen peroxide is the only known disinfectant for killing the parasite. No other information has been released. 

Careful with that cow: 56 sick from Salmonella linked to contact with dairy

The U.S. Centers for Disease Control reports this outbreak investigation is over. Illnesses could continue because people may not know they could get a Salmonella infection from contact with dairy calves or other cattle.

CDC, several states, and the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service (USDA-APHIS) investigated a multistate outbreak of multidrug-resistant Salmonella Heidelberg infections. Epidemiologic and laboratory evidence indicated that contact with dairy calves and other cattle was the likely source of this outbreak.

A total of 56 people infected with the outbreak strains of Salmonella Heidelberg were reported from 15 states.  Illnesses started on dates ranging from January 27, 2015 to November 25, 2017. Of those with available information:

35% of people were hospitalized. No deaths were reported.

35% of people in this outbreak are children younger than 5 years.

Epidemiologic, laboratory, and traceback investigations linked ill people in this outbreak to contact with calves, including dairy calves.

In interviews, ill people answered questions about contact with animals and foods eaten in the week before becoming ill. Of the 54 people interviewed, 34 (63%) reported contact with dairy calves or other cattle. Some of the ill people interviewed reported that they became sick after their calves became sick or died.

Surveillance in veterinary diagnostic laboratories showed that calves in several states were infected with the outbreak strains of multidrug-resistant Salmonella Heidelberg

Information collected earlier in the outbreak indicated that most of the calves came from Wisconsin. Regulatory officials in several states attempted to trace the origin of calves linked to more recent illnesses. A specific source of cattle linked to newer illnesses was not identified.

Antibiotic resistance testing conducted by CDC on clinical isolates from ill people shows that the isolates were resistant to multiple antibiotics.

Antibiotic resistance may be associated with increased risk of hospitalization, development of a bloodstream infection, or treatment failure in patients.

Whole genome sequencing analysis identified predicted antibiotic resistance in outbreak-associated isolates from 48 ill people, in 88 isolates from cattle, and in 13 isolates from animal environments.

These findings match results from standard antibiotic resistance testing methods used by CDC’s National Antimicrobial Resistance Monitoring System (NARMS) laboratory on 10 isolates from 9 ill people and 1 animal. All 10 isolates were resistant to amoxicillin-clavulanic acid, ampicillin, cefoxitin, ceftriaxone, streptomycin, sulfisoxazole, and tetracycline. In addition, nine had reduced susceptibility to ciprofloxacin, nine were  resistant to trimethoprim-sulfamethoxazole, six were resistant to nalidixic acid, four were resistant to chloramphenicol, and one was resistant to gentamicin. All 10 isolates tested were susceptible to azithromycin and meropenem.

Follow these steps to prevent illness when working with any livestock:

Always wash your hands thoroughly with soap and water right after touching livestock, equipment, or anything in the area where animals live and roam. Use dedicated clothes, shoes, and work gloves when working with livestock. Keep and store these items outside of your home.

It is especially important to follow these steps if there are children younger than 5 years in your household. Young children are more likely to get a Salmonella infection because their immune systems are still developing.

Work with your veterinarian to keep your animals healthy and prevent diseases.

It is important to remember that cattle can carry Salmonella and not appear sick. However, in this outbreak, some people did notice illness in their cattle, especially among calves. Livestock handlers should watch for sicknesses in dairy calves and consult their veterinarian if needed.

Woman’s rare eye infection highlights (low) risk of parasite spread by flies

Susan Perry of the Minnesota Post reports an Oregon woman is the first known person to become infected with a tiny parasitic worm that lives in the eyes of cattle, according to a case study report published Monday by researchers at the Centers for Disease Control and Prevention (CDC).

Although common in animals, eye-worm infections in humans are extremely rare. And, if caught and treated early, they don’t cause any permanent damage to the eye.

“This is only the 11th time a person has been infected by eye worms in North America,” lead author Richard Bradbury, who heads the CDC’s Parasite Diagnostics and Biology Laboratory, told CNN. “But what was really exciting it that it is a new species that has never infected people before. It’s a cattle worm that somehow jumped into a human.”

The woman, 28-year-old Abby Beckley, was working on a salmon boat in Alaska two summers ago when her left eye became irritated and inflamed. A week later, when the symptoms didn’t go away, she decided to investigate.

BuzzFeed reporter Nidhi Subbaraman, who interviewed Beckley, describes what happened next:

Standing at the mirror in the galley, [Beckley] plucked at her eyeball, as if extracting a contact lens. 

“I put my fingers in there in kind of a picking motion and I pulled out a worm,” Beckley [said]. “I looked at my finger and it was moving and I was shocked.” 

Beckley said she woke up her bunkmate to show her the worm, a piece of tangled white fluff wriggling at the end of her index finger. “She confirmed I wasn’t crazy,” Beckley said.

Over the course of the next few days she pulled out about a half dozen more worms. “I was living with these things, and I’d just keep pulling them out when I’d feel them,” Beckley said. 

Beckley flew home and went to see specialists at the Oregon Science and Health Laboratory in Portland. They extracted two more worms, and sent one to the CDC for analysis. It was identified as being the nematode Thelazia gulosa, which commonly infects the eyes of cattle, but had never been found in humans.

The case report was published online in the American Journal of Tropical Medicine and Hygiene, where it can be read in full.

Salmonella Dublin is nasty

Salmonella enterica serotype Dublin is a cattle-adapted bacterium that typically causes bloodstream infections in humans.

To summarize demographic, clinical, and antimicrobial drug resistance characteristics of human infections with this organism in the United States, we analyzed data for 1968–2013 from 5 US surveillance systems.

During this period, the incidence rate for infection with Salmonella Dublin increased more than that for infection with other Salmonella. Data from 1 system (FoodNet) showed that a higher percentage of persons with Salmonella Dublin infection were hospitalized and died during 2005–2013 (78% hospitalized, 4.2% died) than during 1996-2004 (68% hospitalized, 2.7% died). Susceptibility data showed that a higher percentage of isolates were resistant to >7 classes of antimicrobial drugs during 2005–2013 (50.8%) than during 1996–2004 (2.4%).

Epidemiology of Salmonella enterica Serotype Dublin infections among humans, United State, 1968-2013

Emerging Infectious Diseases, vol. 23, no. 9, September 2017, R. Reid Harvey, Cindy R. Friedman, Stacy M. Crim, Michael Judd, Kelly A. Barrett, Beth Tolar, Jason P. Folster, Patricia M. Griffin, and Allison C. Brown

https://wwwnc.cdc.gov/eid/article/23/9/17-0136_article

Dehydration and salt toxicity? Cows dying in Saskatchewan

Ann Hui of The Globe and Mail reports that for decades, cattle farmers have sent their livestock to graze on the sprawling Shamrock pasture, about 80 kilometres south of Chaplin in southwest Saskatchewan. Shamrock is where Russ Coward, a fourth-generation cattle farmer, has for years raised nearly a quarter of his cattle. It’s the same place Mr. Coward’s father sent his cattle.

But some time between last Monday and Friday, the cows and calves at Shamrock began to die. It’s not known whether the deaths happened all at once or slowly over the course of the four days. But by the time the manager arrived on Friday afternoon, 200 of the approximately 680 cattle in a single field were dead.

The president of Shamrock Grazing Ltd., Glenn Straub, called Mr. Coward, who raced out to the field. He was met with a gruesome scene. “We seen a tragedy,” he said. “We simply seen a terrible sight.”

Other ranchers soon joined him, about 31 in total who have cows and calves there. “We all had the same feelings – how did this happen? How did this happen?”

Since Friday, provincial authorities as well as the local RCMP have been trying to piece together the mystery. The cause is still being determined, but the prevailing theory is dehydration and salt toxicity.

The area has been subject to drought in recent weeks, said Saskatchewan’s chief veterinary officer, Betty Althouse. Officials believe this may have led to evaporation at the water source, resulting in higher concentrations of salt in the water.

“An analogy would be someone shipwrecked in the ocean,” Dr. Althouse told reporters this week. “They’re thirsty, they’re craving water, so they’re going to drink the water. But ultimately the salt water will kill them.”

Many of the dead cows and calves were found clustered around one “dugout” in particular – the pools of collected rain and runoff where they drink. Investigators at the Western College of Veterinary Medicine in Saskatoon who were called in to assist have collected samples from the dugouts. Results are expected some time this week.