Thank you, WGS: Listeria linked to smoked salmon in Denmark and France

In Denmark, on 23 August 2017, Statens Serum Institut (SSI) identified a genetic cluster of four human Listeria monocytogenes sequence type (ST) 8 isolates by core genome multilocus sequence typing (cgMLST) [1]. The allele calling was performed in BioNumerics (v7.6.2, Applied Maths, Belgium). We initiated an epidemiological investigation and notified the Danish Central Outbreak Management Group (collaboration between the Danish Veterinary and Food Administration (DVFA), the National Food Institute at the Technical University of Denmark (DTU) and SSI). On 25 August, two additional human isolates were found to belong to the same genetic cluster.

A confirmed case was defined as a person clinically diagnosed with listeriosis after 1 January 2017 with laboratory-confirmed L. monocytogenes ST8 clustering using cgMLST (≤ 5 allelic distance, single linkage). Cases diagnosed before 1 January 2017 with an isolate belonging to this cluster were defined as probable cases.

As of 25 August 2017, the genetic cluster comprised six cases; five confirmed and one probable. The age of the cases ranged from 59 to 96 years (median 80 years) and four were women. All patients had underlying illness and no travel history. One patient died within 30 days of diagnosis. Epidemiological investigations including a standard questionnaire on exposures showed that all five confirmed cases had consumed cold-smoked and/or cured salmon in the 30 days before disease onset. Four cases had bought the salmon in retail chain X. No other food-item was reported as consumed in high frequencies among cases. Epidemiological follow-up for the probable case did not include information on fish consumption.

On 29 August 2017, a comparison between the human outbreak isolates and 16 L. monocytogenes ST8 food- and environmental isolates identified in Denmark from 2014 to August 2017 showed that the human isolates clustered with a food isolate from cold-smoked salmon, cut and packaged at company Y in Poland (zero to two allelic differences using cgMLST). L. monocytogenes had been detected on 31 July 2017 at levels of 110 CFU/g (threshold: 100 CFU/g) at the end of shelf life. The product was widely sold in Denmark and had been sampled by the DVFA in retail chain X, as part of a consumer exposure survey (i.e. analyses project on retail packages). Because the L. monocytogenes concentration had been just above the accepted limit and found at the end of the product shelf life a recall of this batch was not conducted. However, due to the positive finding, follow-up sampling had been performed on the 9 and 10 August 2017 from the central storage unit of retail chain X. L. monocytogenes had been isolated from two batches analysed before end of shelf life. In one sample from the same batches, which was also analysed at the end of the shelf life, on 28 August 2017 a L. monocytogenes level of 240 CFU/g was found. Isolates from the follow-up samples had zero to four allelic differences to the human outbreak isolates using cgMLST.

The human outbreak sequences were also compared to all L. monocytogenes ST8 genomes derived from clinical samples in Denmark from 2012 onwards. Although ST8 genomes from Danish patients in the period 2012–2017 showed high diversity, the outbreak isolates clearly formed a distinct cgMLST cluster with 16 allelic differences to the nearest isolates outside the genetic outbreak cluster and a maximum of nine allelic differences within the cluster (Figure 2a). We investigated the relatedness of outbreak isolates further by single-nucleotide polymorphisms (SNP) analysis performed by both SSI and DTU using two analysis pipelines: Northern Arizona SNP Pipeline (NASP) [2] and CSI Phylogeny version 1.4 from Center for Genomics Epidemiology (CGE), DTU [3] leading to the same conclusion.

On 30 August 2017, DVFA advised retail chain X to recall all cold-smoked salmon produced at company Y. This advice was based on the elevated number of L. monocytogenes (240 CFU/g) found in the product at the end of shelf-life and the link to the outbreak. Retail chain X voluntarily recalled both cold-smoked and cured salmon produced at company Y. As part of the recall procedure, retail chain X informed company Y on the situation. Information from company Y, provided by the Polish food authorities via the European Union Rapid Alert System for Food and Feed (RASFF), showed that the implicated batches were exclusively sold via retail chain X and only in Denmark.

The French National Reference Centre (NRC) for Listeria (Institut Pasteur, Paris), compared the sequences of the Danish human isolates against its database, using cgMLST as previously described [1,4]. A human isolate from a French resident belonged to the same cluster (L2-SL8-ST8-CT771) as the Danish isolates. This French probable case, a female patient in her mid-80s, was diagnosed in June 2016. Epidemiological investigations carried out by Santé Publique France were inconclusive, since food consumption history was not available at the time of diagnosis nor could information on travel to Denmark be retrieved, as the person had since died.

On 6 September 2017, an official control by the Ministry of Economy was carried out at a French retailer where a kosher chilled cured salmon was sampled for analysis. The sample was contaminated with L. monocytogenes at the level of 460 CFU/g and the salmon producer was company Y. An isolate was sent to the French NRC for typing and showed to belong to the same cgMLST type as the Danish outbreak. Further investigations on the food product confirmed that it had not been further processed after production in Poland. The product was recalled and no human cases were linked to its consumption as of beginning of December 2017.

The other nine countries that replied to the EPIS-FWD UI-426 notification (Austria, Finland, Germany, Luxembourg, the Netherlands, Norway, Slovenia, Sweden, United Kingdom) did not report any human or food isolates linked to the Danish outbreak. However, after submission of this report, at the end of November, we were informed through EPIS about three genetically linked human isolates in Germany.

Discussion

Here we report on a listeriosis outbreak and highlight the value of rapidly comparing the genomes of human and food/environmental isolates at the national and international levels.

The fact that the contaminated salmon products identified in Denmark and France were from different batches suggests environmental contamination possibly at the production facility at company Y. It is too early to assess whether any measures taken at company Y have been effective in controlling the outbreak. However, experiences from previous investigations suggest that once L. monocytogenes is detected in one product, the whole production site should be subject to a thorough inspection, and sampling with special attention to all the possible contamination/cross contamination issues before implementing corrective measures [5,6]. Moreover, the risk for L. monocytogenes persistent strains in the production environment requires the close monitoring for several years to ensure the elimination of these [7,8].

Since WGS was introduced for routine surveillance in Denmark, a number of listeriosis outbreaks have been detected and solved, including outbreaks involving cold-smoked ready-to-eat sliced fish products [5]. The present investigation further reinforces the suspicion that ready-to-eat fish products are important sources of L. monocytogenes infections in Denmark, as well as in other countries.

Though only involving a low number of isolates, WGS L. monocytogenes surveillance and communication between countries allowed us to detect and rapidly solve this salmon-associated outbreak, leading to food product recall in two European countries. Compared with previous typing methods, WGS has a higher discriminatory power and the ability to determine genetic distance between isolates. The introduction of WGS for surveillance of food-borne infections has shown that it improves outbreak detection and facilitates outbreak investigations and likely helps reduce the number of infections [4,9-16]. The EPIS-FWD communication platforms allowed for the communication to link cases across borders. However, currently cross-border outbreaks are only detected when case numbers in at least one country exceed normal levels and are notified internationally. Therefore, a possible future system for easy exchange of and comparison of WGS data, e.g. by the use of an agreed cgMLST nomenclature, across borders will enable the identification of more dispersed outbreaks as well as cross-border links between food samples and human infections. This report highlights that by the application of cross-disciplinary and real-time cross-border comparison of WGS data, L. monocytogenes infections can be prevented and thereby providing safer food for at-risk groups such as the elderly, immunodeficient individuals and pregnant women.

Cross-border outbreak of listeriosis caused by cold-smoked salmon, revealed by integrated surveillance and whole genome sequencing (WGS), Denmark and France, 2015 to 2017

Schjørring Susanne, Gillesberg Lassen Sofie , Jensen Tenna, Moura Alexandra, Kjeldgaard Jette S, Müller Luise, Thielke Stine, Leclercq Alexandre, Maury Mylene M, Tourdjman Mathieu, Donguy Marie-Pierre, Lecuit Marc, Ethelberg Steen, Nielsen Eva M. Cross-border outbreak of listeriosis caused by cold-smoked salmon, revealed by integrated surveillance and whole genome sequencing (WGS), Denmark and France, 2015 to 2017. Euro Surveill. 2017;22(50):pii=17-00762. https://doi.org/10.2807/1560-7917.ES.2017.22.50.17-00762

https://eurosurveillance.org/content/10.2807/1560-7917.ES.2017.22.50.17-00762

Europe models: Listeria monocytogenes contamination of ready-to-eat foods and the risk for human health in the EU

Here’s an idea: don’t serve cold cuts and raw sprouts to old people.

Duh.

The European Food Safety Authority reports that food safety criteria for Listeria monocytogenes in ready-to-eat (RTE) foods have been applied from 2006 onwards (Commission Regulation (EC) 2073/2005). Still, human invasive listeriosis was reported to increase over the period 2009–2013 in the European Union and European Economic Area (EU/EEA). Time series analysis for the 2008–2015 period in the EU/EEA indicated an increasing trend of the monthly notified incidence rate of confirmed human invasive listeriosis of the over 75 age groups and female age group between 25 and 44 years old (probably related to pregnancies).

A conceptual model was used to identify factors in the food chain as potential drivers for L. monocytogenes contamination of RTE foods and listeriosis. Factors were related to the host (i. population size of the elderly and/or susceptible people; ii. underlying condition rate), the food (iii. L. monocytogenes prevalence in RTE food at retail; iv. L. monocytogenes concentration in RTE food at retail; v. storage conditions after retail; vi. consumption), the national surveillance systems (vii. improved surveillance), and/or the bacterium (viii. virulence).

Factors considered likely to be responsible for the increasing trend in cases are the increased population size of the elderly and susceptible population except for the 25–44 female age group. For the increased incidence rates and cases, the likely factor is the increased proportion of susceptible persons in the age groups over 45 years old for both genders. Quantitative modelling suggests that more than 90% of invasive listeriosis is caused by ingestion of RTE food containing > 2,000 colony forming units (CFU)/g, and that one-third of cases are due to growth in the consumer phase. Awareness should be increased among stakeholders, especially in relation to susceptible risk groups. Innovative methodologies including whole genome sequencing (WGS) for strain identification and monitoring of trends are recommended.

Ready-to-eat meals may be popular but have risks

Eugene Boisvert of Au News writes that more than 40 per cent of ready-to-eat meals tested by South Australian health types contained an unsatisfactory level of bacteria, according to survey results published in the Eastern Health Authority’s annual report this month.

The SA Health survey said one of the tested meals contained 310 times the safe level of Bacillus cereus, and another had almost 13 times the safe level of E. coli, which comes from feces.

Out of 98 meals bought at local supermarkets and shops with a shelf life of 10 or more days, 42 had an unsatisfactory microorganism count.

Eastern Health Authority chief executive Michael Livori said more small businesses were trying to capitalise on the growing popularity of ready-to-eat meals without understanding the health risks involved.

“Most manufacturers who are normally in this business will (understand the risks) but there’s an increase in small businesses or retailers getting into this realm but not without risk,” Mr Livori said.

The SA Health survey and subsequent report, published in June, was sparked by Eastern Health Authority concerns about the standard of manufacturing processes of ready-to-eat meals.

The SA Health report recommended measures to prevent bacteria growing in ready-to-eat meals, including that they be heated to at least 90C for 10 minutes when being cooked.

Meanwhile, the Eastern Health Authority issued 10 businesses with prohibition orders in 2016/17, banning them from preparing, selling or transporting food until they cleaned up their act, compared with three in the previous two financial years.

RTE salad storage temps should be reduced in Sweden

Prepacked ready-to-eat mixed ingredient salads (RTE salads) are readily available whole meals that include a variety of ingredients such as raw vegetables, cooked meat, and pasta.

rte.salad.swedenAs part of a trend toward healthy convenience foods, RTE salads have become an increasingly popular product among consumers. However, data on the incidence of foodborne pathogens in RTE salads are scarce.

In this study, the microbiological safety of 141 RTE salads containing chicken, ham, or smoked salmon was investigated. Salad samples were collected at retail and analyzed using standard methods for Listeria monocytogenes, Shiga toxin–producing Escherichia coli (STEC), pathogenic Yersinia enterocolitica, Salmonella, and Campylobacter spp.L. monocytogenes was isolated from two (1.4%) of the RTE salad samples.

Seven (5.0%) of the samples were positive for the ail gene (present in all human pathogenic Y. enterocolitica isolates) and three (2.1%) of the samples were positive for the Shiga toxin genes stx 1 and/or stx 2. However, no strains of pathogenic Y.enterocolitica or STEC were isolated.

Thus, pathogens were found or suspected in almost 1 of 10 RTE salads investigated, and pathogenic bacteria probably are present in various RTE salads from retail premises in Sweden.

Because RTE salads are intended to be consumed without heat treatment, control of the ingredients and production hygiene is essential to maintain consumer safety. The recommended maximum storage temperature for RTE salads varies among countries but can be up to 8°C (e.g., in Sweden). Even during a short shelf life (3 to 5 days), storage at 8°C can enable growth of psychrotrophs such as L. monocytogenes and Y. enterocolitica. The maximum storage temperature should therefore be reduced.

Foodborne bacterial pathogens in retail prepacked ready-to-eat mixed ingredient salads

Journal of Food Protection®, Number 6, June 2016, pp. 896-1055, pp. 978-985(8)

Söderqvist, Karin; Thisted Lambertz, Susanne; Vågsholm, Ivar; Boqvist, Sofia

http://www.ingentaconnect.com/contentone/iafp/jfp/2016/00000079/00000006/art00011

Sounds a bit militaristic: Seek and destroy Listeria process controls in the ready-to-eat meat and poultry industry

The majority of human listeriosis cases appear to be caused by consumption of ready-to-eat (RTE) foods contaminated at the time of consumption with high levels of Listeria monocytogenes.

listeria4Although strategies to prevent growth of L. monocytogenes in RTE products are critical for reducing the incidence of human listeriosis, control of postprocessing environmental contamination of RTE meat and poultry products is an essential component of a comprehensive L. monocytogenes intervention and control program.

Complete elimination of postprocessing L. monocytogenes contamination is challenging because this pathogen is common in various environments outside processing plants and can persist in food processing environments for years. Persistent L. monocytogenes strains in processing plants have been identified as the most common postprocessing contaminants of RTE foods and the cause of multiple listeriosis outbreaks.

Identification and elimination of L. monocytogenes strains persisting in processing plants is thus critical for (i) compliance with zero-tolerance regulations for L. monocytogenes in U.S. RTE meat and poultry products and (ii) reduction of the incidence of human listeriosis.

The seek-and-destroy process is a systematic approach to finding sites of persistent strains (niches) in food processing plants, with the goal of either eradicating or mitigating effects of these strains. This process has been used effectively to address persistent L. monocytogenes contamination in food processing plants, as supported by peer-reviewed evidence detailed here. Thus, a regulatory environment that encourages aggressive environmental Listeria testing is required to facilitate continued use of this science-based strategy for controlling L. monocytogenes in RTE foods.

Journal of Food Protection®, Number 2, February 2015, pp. 240-476, pp. 436-445(10)

Malley, Thomas J. V.; Butts, John; Wiedmann, Martin

http://www.ingentaconnect.com/content/iafp/jfp/2015/00000078/00000002/art00028

Is it in the sauce? Single pork product responsible for 23 per cent of USDA salmonella-positives

 Pork barbecue with vinegar and pepper-based sauce is the source of 23 per cent of salmonella-positive samples the U.S. Department of Agriculture reviewed from 2005 to 2010. The contamination has not caused any known illnesses.

Exactly what part of the dish is contaminating it with salmonella isn’t clear. FSIS notes that it “may have come from the addition of contaminated ingredients (such as the pepper) to the sauce, or from cross-contamination of the product or sauce in the post lethality processing environment.”

During processing of these products, the pork was cooked first, and the barbecue sauce was added after the cooking step. The lack of a lethality treatment for the sauce or its ingredients could result in contamination of the final product.

Meatingplace.com reports inspectors were told to plan an awareness meeting on the subject, and to ensure that the plants they inspect have a HACCP plan that enables them to determine whether the establishment had a way of evaluating the safety of the ingredients added after the lethality step.