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WGS project helps Denmark uncover Campylobacter outbreak

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Fifty people are ill in Denmark from Campylobacter after eating chicken meat but authorities believe the actual number of patients may be much higher.

Statens Serum Institut (SSI), Danish Veterinary and Food Administration (Fødevarestyrelsen) and DTU Food – National Food Institute are investigating the Campylobacter jejuni outbreak.

Campylobacter is the main cause of bacterial intestinal infections in Denmark and more than 4,500 cases were registered in 2018.

The same type of Campylobacter, sequence type 122, identified in patients by whole genome sequencing has also been found in chicken meat from one slaughterhouse, named as HKScan in Vinderup, a town in Northwestern Jutland.

HKScan is a Nordic meat and meals company employing more than 600 people in Denmark at production units in Vinderup and Skovsgaard. The Danish Veterinary and Food Administration is continuing to investigate and officials have been sent to help the company track and eliminate the source of infection.

Looking at sources of Campylobacter

Those sick are 20 women and 30 men aged 14 to 87 with a median age of 49 years old.

As part of a project this year involving the Clinical Microbiology Department (KMA) in Aalborg, the Danish Veterinary and Food Administration and SSI; Campylobacter isolates from patients diagnosed in Aalborg since March 2019 have been collected, sent to SSI and whole genome sequenced.

Campylobacter isolates are not routinely submitted and sequenced so the outbreak has been detected due to the project and may otherwise have gone unnoticed. In the past it has been difficult to detect and solve such outbreaks.

Some isolates also come from other KMA’s as part of the Danish Integrated Antimicrobial Resistance Monitoring and Research Programme (DANMAP) project.

Steen Ethelberg, a senior scientist at SSI, said patients have fallen sick over a couple of months and are still being reported.

“The most recent estimate for how many more cases are in the population relative to the diagnosed laboratory controlled cases is a factor of 12 so there would be more cases that are actually ill in any outbreak,” he told Food Safety News.

“The reason we know about this outbreak is because we are running a project in one part of the country where all the patient isolates are being collected and subjected to whole genome sequencing. Since the outbreak is mainly based on one of the 10 labs only you would expect patients all over the country. It seems likely that there could be more cases and we also have some smaller clusters detected in the project.”

Ethelberg said the project is trying to see how WGS may be helpful in understanding Campylobacter.

“It is about collecting patient isolates from one lab and at the same time analyzing chicken meat and subjecting the Campylobacter isolates in chicken meat to WGS and then comparing the sequences. In the project we are learning about the etiology of Campylobacter but we also see outbreaks in real time. This outbreak is big enough that we thought it should be reported to the public but in a sense it is not so different because we know many people are ill from Campylobacter from poultry products.”

DVFA investigation

The Danish Veterinary and Food Administration has been taking samples for Campylobacter of various cuts of chicken from different stores and these have been sequenced.

Annette Perge, from the agency, told Food Safety News that it was still too early to conclude the outbreak was over.

“The slaughterhouse produces both fresh and frozen products hence we can´t rule out that products may still be on the market or bought and stored frozen at private households. Based on patient interviews it has not been possible to point out specific products, places of purchase or periods of purchase,” she said.

“Furthermore there is no legal requirements stating that Campylobacter is prohibited in poultry meat. However even without legal requirements foods used as intended should not result in illness. The slaughterhouse is a large establishment and their products are sold at all the major Danish retail chains.”

The agency does not yet know if a link was limited to one farm or establishment, according to Perge.

“The link between food isolates and routine samples taken at the slaughterhouse, samples of thigh skin from chickens taken routinely for analyses, and the patient isolates was seen when comparing whole genome sequencing results. However it has not been possible to verify the link through interview with patients.

“We have no indication that this outbreak is due to a contamination persisting in the slaughterhouse. They have been allowed to continue production. They are assisting us in any way possible to solve the case.”

Perge said samples from chickens from a specific farm showed a close resemblance to the patients.

“The farm has been visited by the audit team from the slaughterhouse and corrections to practices have been made. At the moment no chickens are delivered for slaughter as they are not yet old enough. Meat from chickens slaughtered from that farm will be tested for Campylobacter and eventual isolates will be sequenced and compared to the outbreak strain. If the meat contains larger numbers of Campylobacter, the use of the meat will be restricted.”

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