Not your parents wedding: Shotgun metagenomics for STECs in spinach

This from a poster presented at the International Association for Food Protection annual meeting this week in St. Louis.

shotgun_wedding-620x413-300x200Introduction: Consumption of fresh bagged spinach contaminated with Shiga toxin-producing Escherichia coli (STEC) has led to severe illness and death. Since not all STEC strains are considered human pathogens, virulence characterization of STEC strains is important. Shotgun metagenomics may provide a rapid method to detect, obtain virulence gene information, and determine strain identification and phylogenetic relatedness.

Purpose: The objective of this study was to evaluate the comprehensiveness of a metagenomics approach for detection and strain level identification of STEC on bagged spinach using pathogenic STEC strains of a variety of serotypes and Shiga toxin subtypes.

Methods: Bagged spinach was spiked with one of 12 STEC strains at a level of 0.1 CFU/g spinach and processed according to the U.S. FDA BAM protocol. Sequencing data generated from each sample was used to determine molecular serotype and STEC-specific virulence genes by BLAST analysis, identify the microbial communities present in the enriched sample using a discriminative k-mer method, and perform E. coli core gene SNP analysis on de novo assemblies of the metagenomic sequencing data.

Results: Bacterial community analysis determined that E. coli was a major component of the population in most samples, but molecular serotyping using the metagenomic data revealed the presence of indigenous E. coli in some samples. Despite the presence of additional E. coli strains, the serotype and virulence genes of the spiked STEC, including correct Shiga toxin subtype, were detected in 92% of the samples. E. coli core gene SNP analysis of the metagenomic sequencing data correctly placed the spiked STEC in a phylogeny of related strains in cases where the indigenous E. coli did not predominate.

Significance: Utilizing a shotgun metagenomics approach to characterize STEC contaminating bagged spinach may expedite the time necessary to ascertain the risk level to public health and response time during outbreaks.

 Evaluation of the use of shotgun metagenomics sequencing for detection and strain level discrimination of Shiga toxin producing Escherichia coli contamination on fresh bagged spinach

Susan Leonard, U.S. Food and Drug Administration, Laurel, MD, Mark Mammel, U.S. Food and Drug Administration, Laurel, MD, David Lacher, U.S. Food and Drug Administration, Laurel, MD, Christopher Elkins, U.S. Food and Drug Administration, Laurel, MD

https://iafp.confex.com/iafp/2016/webprogram/Paper11398.html

 

At least 30 sick: E. coli strikes Montana town

Aja Goare of KTVQ reports the Dawson County Health Department is investigating an outbreak of E. coli at the Richey Centennial that sickened more than 30 people.

richey.montanaThe event took place the third weekend in July in Richey, which is about 50 miles north of Glendive.

Health officials do not know exactly where the outbreak originated, but they believe it may have originated with a local food vendor present at the event.

According to the DCHD, the vendors have been cooperating with the investigation.

People who attended the event are discouraged from consuming any leftover food they may have from the event and are asked to turn it over to the local health department.

At least six of the people who became ill have been hospitalized.

Visitors from eight different states and six Montana counties have become ill, according to the DCHD.

New cases are still being reported and additional laboratory results are pending.

On a Facebook page created for the event, a Nevada woman who attended reported that her mother had been hospitalized for several days due to the illness.

Poor, poor pitiful me: ‘Social media is killing Chipotle’s recovery’

The Motley Fool writes that Chipotle Mexican Grill’s (NYSE:CMG) food safety crisis has been over for six months. But you wouldn’t know it from the company’s sales results. During the recently ended second quarter, Chipotle’s comparable restaurant sales plunged 23.6%.

chipotle_adThe company can probably blame social media for its slow recovery. The rapid spread of information — and in some cases, misinformation — via social media has made Chipotle’s late 2015 E. coli outbreak much worse for the company than it otherwise would have been.

Social media increased awareness of Chipotle’s food safety problems in the first place, and Chipotle’s food safety issues continued to be the butt of jokes on social media long after the initial outbreak.

In my case, Chipotle was the brunt of social media jokes and taunting going back to 2007.

The lesson for executives in the restaurant industry is clear: The right time to address food safety weaknesses is now. Waiting for food safety lapses to make customers sick is a recipe for disaster.

Linda Ronstadt’s version might be more popular, but the original, by songwriter Warren Zevon, is darker and more apt.

Except with the Springsteen bit. Never a fan.

Cattle be shedding STECs

Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen that can cause hemorrhagic colitis and hemolytic-uremic syndrome. Cattle are the primary reservoir for STEC, and food or water contaminated with cattle feces is the most common source of infections in humans.

beef.cattleConsequently, we conducted a cross-sectional study of 1,096 cattle in six dairy herds (n = 718 animals) and five beef herds (n = 378 animals) in the summers of 2011 and 2012 to identify epidemiological factors associated with shedding.

Fecal samples were obtained from each animal and cultured for STEC. Multivariate analyses were performed to identify risk factors associated with STEC positivity. The prevalence of STEC was higher in beef cattle (21%) than dairy cattle (13%) (odds ratio [OR], 1.76; 95% confidence interval [CI], 1.25, 2.47), with considerable variation occurring across herds (range, 6% to 54%). Dairy cattle were significantly more likely to shed STEC when the average temperature was >28.9°C 1 to 5 days prior to sampling (OR, 2.5; 95% CI, 1.25, 4.91), during their first lactation (OR, 1.8; 95% CI, 1.1, 2.8), and when they were <30 days in milk (OR, 3.9; 95% CI, 2.1, 7.2). These data suggest that the stress or the negative energy balance associated with lactation may result in increased STEC shedding frequencies in Michigan during the warm summer months.

Future prevention strategies aimed at reducing stress during lactation or isolating high-risk animals could be implemented to reduce herd-level shedding levels and avoid transmission of STEC to susceptible animals and people.

STEC shedding frequencies vary considerably across cattle herds in Michigan, and the shedding frequency of strains belonging to non-O157 serotypes far exceeds the shedding frequency of O157 strains, which is congruent with human infections in the state. Dairy cattle sampled at higher temperatures, in their first lactation, and early in the milk production stage were significantly more likely to shed STEC, which could be due to stress or a negative energy balance. Future studies should focus on the isolation of high-risk animals to decrease herd shedding levels and the potential for contamination of the food supply.

Factors associated with Shiga toxin-producing Escherichia coli shedding by dairy and beef cattle

Cristina Venegas-Vargasa*, Scott Hendersona,b, Akanksha Khareb*,Rebekah E. Moscib, Jonathan D. Lehnertb*, Pallavi Singhb,Lindsey M. Ouelletteb*, Bo Norbya, Julie A. Funka, Steven Rustc, Paul C. Bartletta,Daniel Groomsa and Shannon D. Manningb

aDepartment of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA

bDepartment of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA

cDepartment of Animal Science, Michigan State University, East Lansing, Michigan, USA

Applied and Environmental Microbiology, August 2016, Volume 82, Number 16, Pages 5049-5056, doi:10.1128/AEM.00829-16

http://aem.asm.org/content/82/16/5049.abstract?etoc

$1.6 M lawsuit claims Calgary siblings infected with E. coli after eating at Vietnamese restaurant

Kevin Martin of the Calgary Herald reports a $1.6-million lawsuit has been filed on behalf of a Calgary brother and sister who were infected with E. coli, allegedly from eating tainted food at a Vietnamese restaurant.

Chi Lan Vietnamese RestaurantThe lawsuit filed on behalf of minors Hunter and Julia Aloisio said both were infected with E. coli after dining at the Chi Lan Vietnamese Restaurant on July 31, 2014.

It says Hunter Aloisio was impacted most by the infection, developing hemolytic uremic syndrome.

The boy required dialysis to treat the illness and is now susceptible to kidney failure, the lawsuit says.

The claim names the restaurant, as well as its suppliers and “upstream defendants,” unidentified companies “involved in the livestock slaughter and dressing industry, the farming industry and/or the secondary processing industry.”

“The defendants were negligent and breached the standard of care owed to the plaintiffs,” the statement of claim filed on behalf of the siblings says.

“The defendants owed the plaintiffs a duty of care to ensure that their products, including the restaurant food, were safe for consumption and would not expose the plaintiffs to contaminants such as E. coli bacteria,” it says.

Headline of the week: Chipotle’s decision to open a burger joint is ridiculously stupid

Chipotle has fooled so many people for so long it can say and do almost anything.

But when investors sour, shit gets real.

chipotleBrian Sozzi  of The Street wonders what Chipotle is thinking.

The bruised and battered better burrito joint confirmed Thursday that the first Tasty Made burger restaurant will open this fall in Lancaster, Ohio. Chipotle said the Tasty Made menu will be limited to burger, fries and milkshakes.

Here is why Chipotle’s decision to try and play the role of a bootleg Shake Shack is ill-conceived.

The core Chipotle brand is far from fixed.

Chipotle’s well-paid management team should be 1,000% focused on returning its namesake brand to full health in the wake of several high-profile food safety incidents last year. Judging by Chipotle’s second quarter results, efforts to restore large amounts of goodwill among consumers via free food giveaways, intensified marketing and a new rewards program are not working to a sizable degree.

The company’s second quarter earnings nosedived 80% from the prior year to 87 cents a share. Wall Street estimated earnings of 93 cents a share. Revenue fell 16.6% to $998.4 million, missing Wall Street’s $1.05 billion estimate. Same-store sales plunged 23.6% in the quarter, and are down about 21% so far in July.

Hadley Malcolm of USA Today writes the company’s first burger joint, Tasty Made, is set to open in the fall in Lancaster, Ohio. With it, Chipotle will draw on the game plan it’s banked on for years: a simple menu featuring fresh ingredients. The only items diners can order will be hamburgers, french fries and milkshakes. Burgers will be made from fresh, not frozen beef; the buns will be preservative-free.

Adam Chandler of The Atlantic writes that last week, analysts at the financial-services firm Stifel downgraded its recommendation on Chipotle to “sell” and warned that the company could lose half of its value in the coming months.

“Chipotle was really vulnerable because of their heavy reliance on their claims about their food,” Chris Malone, the co-author of The Human Brand, a book on consumers’ connections to companies, told Business Insider last week. The steady refrain of purity and the constant trill of its motto, “Food With Integrity,” left little room for a contaminated supply chain.

16 sick with E. coli O157 linked to blue cheese in Scotland

Health Protection Scotland (HPS) are investigating 16 confirmed cases of the same strain of E. coli O157, which may be associated with eating blue cheese made from unpasteurised milk  in Lanarkshire.

blue.cheeseOf the 16 cases, 14 are in Scotland across seven NHS boards and two are in England.

Food Standards Scotland (FSS) said the company is carrying out a voluntary recall of suspected batches of the blue cheese and advised consumers who have bought the product and still have it in their fridge not to eat it.

Officials are advising anyone who purchased the cheese with batch codes C22 or D14 between mid-May and the end of July to not eat the product. 

Dr Syed Ahmed, clinical director at HPS, said: “Members of the public who purchased Dunsyre Blue cheese and still have the product in their fridges should return it to the retailer where they purchased the product or dispose of it.”

The cases developed symptoms between 2 and 15 July.

The business’ founder, Humphrey Errington, told The Scotsman they were co-operating fully with HPS’ investigation but were shocked by the initial findings.

Mr Errington said: “We don’t know for sure yet if this happened because of our cheese. We’re completely baffled by their (HPS) conclusion it is connected to Dunsyre Blue. We haven’t seen the evidence yet, only circumstantial proof that some of the 16 had eaten the cheese at hotels we supply. We have sent more than 40 samples to testing centres and all tests so far have come back negative for E. coli O157.”

Mr Errington, whose daughter Selina Cairns now runs the company, was concerned of the impact the outbreak could have on the family-run firm.

Tragic: Settlement reached after Canadian boy left disabled by E. coli

Kevin Rollason of the Winnipeg Free Press reports a 14-year-old Winnipeg youth has been awarded more than $2.5 million after eating ground beef tainted with deadly E. coli bacteria and being left to live with multiple disabilities and unable to look after himself for the rest of his life.

ground-beef_350(2)Justice Lori Spivak, of Manitoba Court of Queen’s Bench, approved the settlement in an order last month, which had been reached earlier between the boy’s family, the province’s Public Trustee, grocer Westfair Foods, and meat processor XL Foods.

“The events were quite tragic,” Chris Wullum, the family’s lawyer, said on Thursday.

“The hamburger meat he consumed left catastrophic injuries. The family is pleased that a fair settlement was reached that will allow them to look after him.”

The boy, who is a permanent ward of Metis Child and Family Services, was just two in 2004 when his mother fed him Hamburger Helper with ground beef she had bought at the Superstore on McPhillips Street.

The mother got sick, but her son became severely ill and had to be hospitalized. He needed a kidney transplant and he suffered a massive stroke in his middle cerebral artery, leaving him with severe spastic quadriplegic cerebral palsy and permanent cognitive impairments. Doctors didn’t know if he was going to survive during the first couple of years.

The Canadian Food Inspection Agency launched a recall of ground beef products in August 2004 after two people in Manitoba were poisoned with E. coli bacteria the month before. A Public Health Agency of Canada report later that year said 27 people became ill after consuming beef tainted with the same strain of E. coli.

Court documents said the agency tested frozen ground beef, still in the family’s freezer, and found it was contaminated with that strain of E. coli.

The boy became a permanent ward of Winnipeg Child and Family Services because the mother couldn’t look after him with all of his special needs, but he has since been transferred to Metis CFS and he has been living with his grandparents since 2009.

The settlement also saw XL Foods drop its counter lawsuit against the boy’s mother, in which it claimed she had been at fault for not cooking the ground beef properly.

E. coli O165:H25 in Nebraska cattle

Russ Rice a DVM from Broken Bow, Nebraska, writes in Bovine Veterinarian that a recent experience in a Nebraska feedlot, supported by extensive diagnostic work from veterinarians at the University of Nebraska-Lincoln, indicates Escherichia coli O165:H25, an enterohemorrhagic strain, can cause disease in cattle and potentially poses a food-safety hazard for humans.

Russ RiceNebraska veterinarians whose work on this case proved critical in establishing a diagnosis and analyzing the implications included Bruce Brodersen, DVM, PhD, Dee Griffin, DVM, MS, John D. Loy, DVM, PhD and Rodney A. Moxley, DVM, PhD.

The case report was published in JMM Case Reports in November 2015, in an article titled “Haemorrhagic colitis associated with enterohaemorrhagic Escherichia coli O165:H25 infection in a yearling feedlot heifer.” Authors, in addition to Brodersen, Loy and Moxley, included Zachary R. Stromberg and Gentry L. Lewis from the University of Nebraska School of Veterinary Medicine and Biomedical Sciences, and Isha R. Patel and Jayanthi Gangiredla from the FDA’s Center for Food Safety and Applied Nutrition.

This case began in early January, 2014, with a pen of 170 Iowa-origin heifers, averaging 160 pounds, in a Nebraska feedlot. The 54 mega-calorie ration included dry and high moisture corn, 32% wet distillers’ grains, syrup, roughage, standard supplements and Bovatec.

In February, the feedlot crew began pulling some heifers from the pen for respiratory disease treatment. Crews noted that some bloody stools were present in the pen, and we treated the cattle with amprolium based on a presumptive diagnosis of coccidiosis. Bloody stools persisted though, and one animal died and another showed neurological signs and bloody diarrhea on February 18th. We euthanized that heifer using methods approved by the University of Nebraska Institutional Animal Care and Use Committee, and conducted a necropsy immediately. The gross lesion appeared to be acute inflammation of the cecum and colon. Our differential diagnosis included coccidiosis, salmonellosis, BVD, bovine coronavirus and clostridial enteritis.

We prepared fresh and fixed specimens and sent them to the UNL diagnostic laboratory for analysis. Dr. Loy’s laboratory isolated a strain of E. coli from the colonic mucosal tissue, and Dr. Brodersen noted histopathologic lesions in the colon that were suggestive of infection with a strain of attaching-and-effacing E. coli. He consulted with Dr. Moxley, an E. coli researcher, who requested the gross and fixed tissues for further study. Upon close examination, Dr. Moxley found small erosions in the colonic mucosa which he photographed.  He then had his laboratory conduct other cultures, and had the original E. coli isolate serotyped.  The isolate was determined to be an O165:H25 serotype.  At this point, Dr. Moxley obtained specific antiserum to O165, and had the histology laboratory of the diagnostic lab conduct immunohistochemistry using this antiserum. Dr. Moxley found O165-positive bacteria in lesion sites corresponding to the gross erosions, and it was then that the cause of the lesions was confirmed. He had the isolate tested further by microarray analysis through collaborators at the FDA. It was found to contain virulence genes corresponding to type III secretion system (T3SS) structure and regulation. Microarray analysis of another E. coli strain (serotype O145:H28) isolated from the same tissue by the Moxley laboratory ruled the latter organism out as a pathogen in the case because that strain was found to have a number of mutations that inactivated virulence genes, such as those of the T3SS. Details of the molecular typing are included in the paper published in JMM Case Reports. …

The O165:H25 serotype is similar to E. coli O157:H7, and could be an emerging food-borne pathogen in cattle and beef. The pathogen has been isolated from the feces and beef carcasses of cattle, but has not previously been associated with disease in cattle. UNL scientists note that the serotype has been involved in uncommon, but potentially severe disease in humans. Based on findings in this case, we suggest veterinarians include enterohemorrhagic E. coli in their list of differential diagnoses when they see enteric disease, particularly bloody diarrhea, in feedlot cattle. If EHEC is suspected, veterinarians should work with their diagnostic laboratory to ensure proper collection, handling and submission of appropriate samples for diagnosis.

At the diagnostic laboratory, Drs. Moxley, Brodersen, and Loy indicate that these lesions might not have been seen in samples taken as early as ten minutes of death. Fortunately in this case, in which we euthanized the heifer and were able to collect samples immediately, we were able to verify this unexpected diagnosis. Most of the time, post-mortem changes will occur before we get the opportunity to collect samples.

Several veterinarians have commented to me they may have missed cases of EHEC in the past. I probably have missed these as well. Going forward, I plan to take extra care in collecting samples and communicating this to our clients. This case serves as a good reminder of the public-health risk we face on a daily basis. We all need to emphasize this to our clients and staff.