Whole-genome sequencing detection of ongoing Listeria contamination at a restaurant, Rhode Island, USA, 2014

Infection with Listeria monocytogenes, a foodborne bacterial pathogen, causes listeriosis, which can lead to severe illness, typically among persons with compromised immune systems and pregnant women and their fetuses.

listeria4The pathogen can survive at high salt concentrations and grow at refrigeration temperatures (1). These properties enable the bacteria to persist in food processing and food service establishments for extended periods. Listeriosis has a long incubation period (3–70 days), making exposure recall difficult.

Retail delicatessens are a potential source of L. monocytogenes because they hold ready-to-eat foods at refrigeration temperatures; however, a risk assessment by the United States Department of Agriculture’s Food Safety and Inspection Service suggests that thorough sanitization of food contact surfaces, proper maintenance of equipment and facilities, safe product handling practices, and good employee practices to avoid cross-contamination can help prevent listeriosis cases associated with retail food establishments (2).

Since 1998, PulseNet (http://www.cdc.gov/pulsenet/index.html) has used pulsed-field gel electrophoresis (PFGE) to look at genetic differences in L. monocytogenes subtypes and to identify outbreaks. However, distantly related strains can appear indistinguishable by PFGE; thus, greater differentiation may be needed to distinguish between outbreak and sporadic cases of listeriosis. Whole-genome sequencing (WGS) offers an opportunity to further discriminate between strains and identify outbreaks. WGS has historically been used retrospectively to provide additional insight into outbreak investigations (3). However, since September 2013, WGS has been performed on all clinical L. monocytogenes isolates identified in the United States by the Centers for Disease Control and Prevention (Atlanta, GA) and several state public health laboratories (4). L. monocytogenes is a good candidate for WGS because it causes a relatively rare condition that can result in serious illness, it has a small genome that is relatively easy to analyze, and epidemiologic surveillance and food regulatory program components for the bacterium are strong (5).

Data obtained from WGS has been analyzed using whole-genome multilocus sequence typing (wgMLST), a technique that examines allelic differences from thousands of loci, and ≈96% of L. monocytogenes coding sequences have been identified as loci in the wgMLST scheme (S. Stroika, Centers for Disease Control and Prevention, pers. comm., 2016 Jan 29). To discriminate between strains and identify outbreaks, alleles within the coding sequence (i.e., loci) are compared with ≈178 reference genomes. A unique combination of alleles at each locus specifies the sequence type, which enables comparison of isolates (6); the smaller the number of allelic differences between isolates, the more related they are.

The Rhode Island Department of Health (RIDOH) attempts interviews and, when applicable, conducts environmental investigations for all reports of listeriosis. Each year during 2011–2013, RIDOH received ≈3 reports of listeriosis, most of which were sporadic cases. However, in November 2014, a cluster of cases was detected from laboratory reports and examined using WGS in conjunction with epidemiologic, laboratory, and environmental investigations. Isolates were confirmed to be L. monocytogenes and submitted for PFGE analysis. The Centers for Disease Control and Prevention performed WGS on clinical isolates; the Food and Drug Administration performed WGS on food isolates.

The Investigation

During October 27–November 5, 2014, RIDOH’s Center for Acute Infectious Disease Epidemiology was notified of 3 L. monocytogenes–infected persons residing in the same city. The 3 case-patients were all non-Hispanic white persons >60 years of age; 2 had an immunocompromising condition. Interviews conducted by the Center for Acute Infectious Disease Epidemiology identified a single common restaurant visited by the 3 patients. RIDOH’s Center for Food Protection performed inspections and collected food and environmental samples at the establishment.

listeria.cdc.jul.14PFGE analysis showed that clinical L. monocytogenes isolates from the 3 case-patients shared an identical, common PFGE pattern (Figure). To determine the relationship between the isolates, RIDOH collaborated with federal partners to conduct WGS. Results of wgMLST showed that the isolates were closely related (0–5 allelic differences) (Figure) and a close genetic match (median allelic differences 4) to a clinical isolate from a 2013 patient, who was reinterviewed and reported eating at the same restaurant. A sliced prosciutto sample from the restaurant tested positive for L. monocytogenes, and PFGE patterns for this isolate matched those for isolates from the 2013 and 2014 case-patients. Results of wgMLST showed that the isolate from the prosciutto differed by 0–5 alleles (median 3) from the 2014 clinical samples and by 0–11 alleles (median 4) from the 2013 clinical sample. Sequences for the isolates were uploaded to GenBank (7) (clinical isolates: accession nos. SAMN02400177, SAMN03253348–49, SAMN03253359; isolate from prosciutto: accession no. SAMN03218571).

A total of 10 food and environmental food samples were initially collected from the restaurant. Swab samples were obtained from the food slicer, preparation tables, and walk-in cooler. Environmental investigation of the restaurant identified issues related to control of L. monocytogenes: the temperature of the refrigerated unit that held sliced meat and other food items was elevated (52°F [11°C]), and cleanliness issues were observed with the preparation tables and slicer. An additional 19 environmental samples were later collected from the establishment; however, the refrigerated unit and preparation tables had been replaced, so additional swab samples could not be collected from those surfaces. The sample of sliced prosciutto was the only L. monocytogenes–positive sample identified at the restaurant; however, just 1 of the 2014 case-patients reported eating prosciutto (in an antipasto salad) at the restaurant. Other foods reported included green salad and coleslaw.

RIDOH tested a sample of prosciutto from an unopened package from the establishment and collaborated with the Food Safety and Inspection Service to see if the processing plant had recently tested positive for L. monocytogenes. The sample tested negative, and no positive tests had been reported at the plant in at least 1 year.

Conclusions

Epidemiologic, environmental, and laboratory investigation results implicated a restaurant with sanitation issues and improper sliced meat storage as the likely source of a multiyear listeriosis outbreak. A long incubation period makes WGS an effective technology to use during listeriosis outbreak investigations and to identify outbreak-associated cases originally believed to be sporadic cases. This technology can help overcome difficulties associated with investigating listeriosis cases and can be useful for the investigation of other pathogens. In this investigation, WGS (wgMLST) helped link the 2013 listeriosis case, which was originally believed to be a sporadic case, to the 2014 outbreak. Furthermore, given that the 4 isolates had a common PFGE pattern, this technology increased confidence that the restaurant, which was the only common restaurant among the 4 patients, was the source of the outbreak. The allelic differences observed are consistent with slow, spontaneous mutation occurring over a long period due to persistent contamination.

There is no set number of allelic differences used to determine whether clusters of cases are part of actual outbreaks (8). Thus, WGS is not sufficient by itself to identify outbreaks and must be performed in conjunction with epidemiologic, laboratory, and environmental investigations (8,9). In the investigation we describe, WGS was used in this supporting role. The close relationship that WGS showed between the clinical isolates and the isolate from meat provides additional evidence that the restaurant was the likely source of contamination for the cases in 2013 and 2014.

Our findings support the need to control L. monocytogenes at retail food establishments. Storing meat at <41°F (5°C) can prevent ≈9% of listeriosis cases (2). In addition, retail delicatessens and food establishments can prevent L. monocytogenes–associated illnesses among customers by controlling cross-contamination, cleaning and sanitizing food contact surfaces, and eliminating environmental niches.

Mr. Barkley is a public health epidemiologist at the Center for Food Protection, Rhode Island Department of Health. His research interests include understanding risk factors of foodborne illness associated with retail food establishments.

Acknowledgment

We thank the Rhode Island State Laboratory for performing confirmatory L. monocytogenes testing on clinical and food samples and for coordinating PFGE and WGS testing; the Massachusetts William A. Hinton State Laboratory for performing PFGE testing of the clinical and food samples; and the Centers for Disease Control and Prevention and Food and Drug Administration for performing WGS of clinical and food samples, respectively.

References

  1. Ferreira V, Wiedmann M, Teixeira P, Stasiewicz MJ. Listeria monocytogenespersistence in food-associated environments: epidemiology, strain characteristics, and implications for public health. J Food Prot. 2014;77:150–70.DOIPubMed
  2. United States Department of Agriculture, Food Safety and Inspection Service. Best practices guidance for controllingListeria monocytogenesin retail delicatessens. June 2015 [cited 2016 Feb 1].http://www.fsis.usda.gov/wps/wcm/connect/29d51258-0651-469b-99b8-e986baee8a54/Controlling-LM-Delicatessens.pdf?MOD=AJPERES
  3. Le VT, Diep BA. Selected insights from application of whole-genome sequencing for outbreak investigations. Curr Opin Crit Care. 2013;19:432–9. DOIPubMed
  4. Centers for Disease Control and Prevention. Advanced molecular detection (AMD). AMD projects: learning from Listeria [cited 2015 Oct 23]. http://www.cdc.gov/amd/project-summaries/listeria.html
  5. Jackson B, Jackson K, Tarr C, Evans P, Klimke W, Kubota K, Improving detection and investigation of listeriosis outbreaks using real-time whole-genome sequencing. Presented at: IDWeek 2014; Philadelphia, PA, USA; 2014 Oct 8–12.
  6. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012;50:1355–61. DOIPubMed
  7. Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2015;43:D30–5.DOIPubMed
  8. Jackson B. Everything in sequence: listeriosis outbreak investigations in the era of WGS. Presented at: Integrated Foodborne Outbreak Response and Management (InFORM) 2015 Conference; Phoenix, AZ, USA; 2015 Nov 17–20.
  9. Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM. Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica.PLoS One. 2014;9:e87991. DOIPubMed

Whole-genome sequencing detection of ongoing Listeria contamination at a restaurant, Rhode Island, USA, 2014

Emerging Infectious Diseases, Volume 22, Number 8, August 2016

Jonathan S. Barkley , Michael Gosciminski, and Adam Miller

http://wwwnc.cdc.gov/eid/article/22/8/15-1917_article

Fancy food ain’t safe food: Michelin-starred Japanese restaurant shuts down after 14 diners suffer food poisoning

A Michelin-starred restaurant in Japan has been ordered to shut temporarily after 14 people got food-poisoning on a fancy Japanese-style meal.

Kita Kamakura Saryo GentoanThe Kanagawa Prefectural Government said officials were investigating after six men and eight women complained of diarrhea and stomach pains after eating at Kita Kamakura Saryo Gentoan on June 11.

Among items on their menu were squid, jelly with sea urchin, pumpkin cooked with fish, eel and sweets, according to the prefecture.

A picturesque restaurant among the trees of Kamakura, a coastal town south of Tokyo, it was known for serving meals in quiet Japanese-style rooms.

The restaurant closed on its own on June 14. The prefecture’s order was made June 20 and remains effective until the cause is determined. Usually, such closures last a few days.

Yelp reviews & Anchorage restaurant health reports just a click away

Next time you look up a restaurant on your phone you can find the business in Yelp reviews along with its food inspection report.

ny_rest_inspect_disclosureMonday the city released more information from its “open data” initiative, which aims to make information more easily available on multiple platforms.

Anchorage food inspection results will now be available on Yelp.com and on Muni.org. The city says information is provided with a LIVES (Local Inspector Value-Entry Specification) open data source link to Yelp.

Yelp will also include a summary of the violations for the past three years of inspections.

“You’re already looking for restaurant information why not put the restaurant inspection data there instead of having to go to the muni site, just give you more information where people are looking for it,” said Brendan Babb, from the city’s Chief Innovation Office.

 

E. coli O157 victim sues over outbreak at Vietnamese restaurant in Colorado

The Denver Post reports the family of a 14-year-old Denver boy hospitalized weeks ago after ingesting E.coli-tainted food filed suit Thursday in Arapahoe County against the Vietnamese restaurant where he ate, alleging a pattern of recklessness in how food is prepared and handled.

noah.thompson.pho_.75-1The restaurant, Pho 75 on South Havana Street in Aurora, was allowed to re-open Wednesday, five days after it was shuttered by Tri-County Health Department officials who determined four people — all of them under 18 — were infected with the same strain of E. coli-O157:H7 after eating there sometime between May 24 and June 10.

Officials said the restaurant Tuesday passed an inspection for cleanliness and that employees were trained in proper food handling practices.

The illnesses occurred just three months after health officials cited the restaurant for a number of foodborne safety risks during a routine inspection, then gave Pho 75 employees extensive training on safe-food handling, officials confirmed Thursday.

“Rather than just check the box, we really spent some time in there to teach them,” said Brian Hlavacek, director of environmental health at Tri-County. “We really did quite a bit of teaching and education on the trends we were seeing and we spent the extra time with them.”

But because Colorado is like Canberra, mere mortals who spent their money on a meal at Pho 75 wouldn’t know the restaurant had a history of sucking at safety, because the governor got rid of restaurant inspection disclosure at the door.

Noah Thompson ate there on May 24 with his parents, who also were sickened though not to the extent Thompson suffered, the lawsuit alleges.

Thompson remains hospitalized with complications from hemolytic uremic syndrome, a sometimes-lethal affliction that comes from ingesting E. coli-tainted food. Children and the elderly are the most vulnerable to HUS, for which there is no cure.

Thompson’s father, Marc Thompson, told The Denver Post his son nearly needed a blood transfusion and is finally improving. He said the experience “really scared us and made us think twice about what we’re eating.”

Attorneys for the family said vegetables were the common ingredient in the foods they ate at Pho 75, and that each ordered a different item. Thompson had eaten a noodle bowl, attorneys said.

“From what I see from the (inspection) reports, it’s no surprise there was an outbreak,” said Seattle attorney Bill Marler, who is representing Thompson. “Perhaps the question is why were they still open?”

From the Ministry of Doublespeak: Canberra eateries score worst hygiene result after government ditches food ratings

More Canberra eateries than ever failed hygiene checks in the same year the ACT government ditched its proposal for “scores on doors” restaurant safety ratings.

doublespeakMarkus Mannheim of The Canberra Times writes that in the past year, three in every 10 inspections found failures to comply with public health laws, twice as many as the government’s target maximum failure rate.

The result – the worst the Health Directorate has reported – included inspections of other types of premises, such as pharmacies, but the government said most failures related to unsafe food practices.

It was the fifth consecutive year in which inspection pass rates fell well below the official target of 85 per cent.

However, industry group Restaurants and Catering Australia says the result shows that inspections are now tougher, not that hygiene practices are worse.

Its chief executive, John Hart, said the ACT’s worst food-poisoning cases had involved raw-egg products, such as mayonnaise, which inspections would not have prevented.

It would have prevented them if inspectors told restaurants, don’t be a dumb-ass and use raw eggs in a dish meant for many.

But that would have raised the ire of industry.

Government is no better, with Assistant Health Minister Meegan Fitzharris’s spokeswoman saying some failures were for “smaller things, like a battery not in a thermometer.”

It’s not a useful f*cking thermometer without a battery, but that would depend on someone actually using the thermometer, which the vast majority of Australians don’t.

The government pledged five years ago to crack down on unhygienic restaurants in the wake of Canberra Times reports on laws that prevented dirty eateries from being identified.

However, few changes have been introduced since, other than new requirements for staff training and a register of convictions for the most serious food-safety breaches.

The register lists very few breaches and only identifies the businesses years after an offence, often after the eatery closes or has new owners.

The now-closed Copa Brazilian restaurant in Dickson, for example, where a salmonella outbreak poisoned more than 160 people three years ago, was never listed on the register, as the matter remains before court.

By contrast, several jurisdictions internationally, including British councils, publish all health inspection reports.

However, industry groups – such as the hotels association, ClubsACT and the food and grocery council – opposed the policy and the government abandoned the idea last year. Labor and the Greens had voiced support for the scheme before the 2012 election, while the Liberals had questioned the need for it.

jake_gyllenhaal_rest_inspection_disclosure(6)
Mr Hart, of Restaurants and Catering Australia, said the past year’s poor compliance result was simply the result of tougher inspections following high-profile salmonella outbreaks in recent years, such as at The Copa.

“They’re certainly going to much greater lengths to determine compliance. And I think this [latest result] reflects not a decrease in the standards of food safety but an increase in the penetration of the assessment,” he said.

“So we’re in fact not getting worse; we’re just seeing more technical breaches being considered a non-compliance.”

Restaurant owners in Canberra, your trade organization and governments are failing you, yet they’ll still have jobs if your business is hit with foodborne illness. The best always have, and always will, go beyond the minimal standards of government to inspire confidence, so that consumers might spend money in your shop. Take matters into your own (washed) hands rather than bear witness to the rise of idiocracy.

Will fewer people barf? Ho Chi Minh City plans food safety agency

Ho Chi Minh City authorities are planning to set up a major food safety agency as the number of food poisoning cases has been on the rise.

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The new agency, directly managed by the city’s administration, will have more authority in coordinating with relevant agencies and handling violations, according to the plan.

The current food safety agency of the city, managed by the Department of Health, has limited personnel and authority, the city’s Interior Department said in the plan.

A total of 248 people were hospitalized for food poisoning in the first four months this year, according to the Food Safety Agency. That was nearly equal to the number of patients with food poisoning in 2015. 

Salmonella in raw pistachios

Crescent Specialty Foods, Inc. of Everett, WA is voluntarily recalling 6 oz. bags of Crescent Pistachio Raw, UPC Code: 8 95296 00103 5 because they have the potential to be contaminated with Salmonella.

salm.pistachio.jun.16No illnesses have been reported to date.

The product was distributed to retail stores and on-line stores in Oregon and Washington.

The products are packaged in 6 oz. clear, plastic bag with Crescent Nuts & Dried Fruits Pistachio Raw label attached with UPC code 8 95296 00103 5 and were distributed from October 21, 2015 – May 2, 2016. See photo below.

The recall was as a result of a routine, random sampling program conducted by an FDA third party contracted lab which revealed the recalled product tested positive for Salmonella. The root cause is unknown to date.

Consumers should not consume the product. The consumer should return the product to place of purchase for a refund. Customers with questions may contact the stores where they purchased the product. For further inquiries email us at: info@csf1.com

This recall is being made at the request of the U.S. Food and Drug Administration.

UK restaurant owner fined £10k for food hygiene breaches

The owner of an Italian restaurant has been hit with fines totalling £10,000 after pleading guilty to seven food hygiene breaches.

mediciMehdi Karimian, who runs Medici’s restaurant in North Ferriby, appeared at Beverley Magistrates’ Court yesterday to answer the charges, which related to a routine visit by food safety inspectors last year. The court heard how on July 29 inspectors found an accumulation of “dirt and grease” across the walls, ceiling and floors of the restaurant kitchen.

Structural issues left food at risk of contamination and the inside of a freezer lid was found to have a build-up of mould. The kitchen ceiling was discoloured from an accumulation of grease and a chopping board used to prepare food was found to be “worn and dirty”.

Mr Karimian was not present at the restaurant on the day, but met with inspectors when they visited again the next day. The levels of dirt and grease were deemed to be so deeply ingrained that the owner was advised to close the restaurant temporarily while the premises was professionally cleaned as it was thought to be beyond the capabilities of his staff.

He blamed the shortcomings on his workers and chef, who he had handed over the day-to-day running of Medici’s to as he recovered from a serious operation on his ankle.

Outbreak of something at Lumby Days in Canada

I can’t help but think that Lumby, British Columbia, is named after lumberjacks, but perhaps I’m stereotyping.

Lumby Interior Health is investigating following an outbreak at a Lumby Days’ event left at least two dozen people sick.

lumberjackDr. Silvina Mema, IH medical health officer, said the health authority has received reports of 24 people falling ill after attending the delegates’ luncheon.

She said the event was attended by 75-80 people and more could have been sick, but did not report it.

Among those who fell victim to illness were Vernon Mayor Akbal Mund, Liberal MLA Eric Foster and North Okanagan Regional District board chair Rick Fairbairn.

Mema said officials do not suspect food poisoning, but rather a viral outbreak, possibly norovirus.

People had diarrhea, vomiting and a fever.

“We are thinking it’s a viral disease,” said Mema. “It is quite common and it gets around quite easily. Food poisoning usually develops faster – within a few hours. This was a longer incubation period.” (fail – dp)

Those attending the luncheon will be asked to fill out a questionnaire as officials try to find a common link.

Mema said there were also leftovers that people took home and IH would like to get samples from that food – if any is left – and to speak to anyone who became sick after eating it.

Of course people don’t work when they’re sick: Six Ajuua’s employees test positive for Salmonella, 33 sick in total

Six Ajuua’s Mexican Restaurant employees have tested positive for salmonella, but officials do not know if they contracted the infection before or after the outbreak was caught by Ector County health officials.

ajuua'sEctor County Health Department Director Gino Solla said the tests for the six employees came to the department Monday, and the number of lab-confirmed tests has increased to 10 since the outbreak was confirmed on June 6. The number of probable cases, he added, was now at 23.

Those six employees have not been interviewed by the health department, Solla said, adding that when they do, it was unlikely they would confess to carrying the infection while working. Solla added to see if those employees got sick from the food, they would have to test the food that has already been thrown out.

“Common sense tells us no employee is going to say ‘I was sick,’ ” Solla said. “It’s very unlikely they’re going to fess up.”

Julian Rubio, CEO for Ajuua’s, said the six employees who tested positive do not reflect on the cleanliness of the restaurant, referring to the 97 and 100 restaurant report scores Ajuua’s got on Feb. 4 and April 13 respectively.

Rubio also said he was surprised to have six employees test positive.

“These employees never mentioned any signs of being sick or having any symptoms,” Rubio said. “We thought we were going to get everyone back negative.”

Of those 10 lab-confirmed cases, five are men and the other five are women, with an age range between 36 and 84 years old, Solla said. For the probable cases, 13 are men, seven are women and three are unknown, he added.