EFSA Panel on Biological Hazards (BIOHAZ). Scientific Opinion on an update on the present knowledge on the occurrence and control of foodborne viruses

Detection of Hepatitis A RNA, Hepatitis E RNA, Human Adenovirus F DNA, and Norovirus RNA in Fresh and Frozen Berry Products at Point of Retail in Ireland

Soft fruits are at particular risk of contamination with enteric viruses such as Hepatitis A virus (HAV), Hepatitis E Virus (HEV), Norovirus (NoV), Human Adenovirus (HAdV) and Sapovirus (SaV). The aim of this study was to investigate, for the first time, the presence of these biological agents in ready to eat (RTE) berries at point of retail in Ireland. A sampling strategy was designed in which RTE fresh and frozen strawberries and raspberries were purchased from five retailers between May and October 2018. Reverse Transcriptase Polymerase Chain Reaction (RT-qPCR) assays for HEV RNA, Nov RNA, SaV RNA, and human Adenovirus species F DNA (HAdV-F) were performed on 239 samples (25g portions). Viral nucleic acid was present in 6.7% (n = 16) of samples tested as follows: HAV RNA (n = 5), HAdV-F DNA (n = 5), HEV RNA (n = 3) and NoV GII RNA (n = 3). Sapovirus RNA was not detected in any product. No significant differences were found between berry type, fresh/frozen status, or supermarket source. This study suggests a risk that exists across all retail outlets however only low levels of nucleic acid ranging from 0 to 16 genome copies/g were present. Although these findings may reflect non-viable/non-infectious virus the continued provision of risk mitigation advice to consumers is warranted and further work is required to ensure control measures to reduce contamination are implemented and enforced.

Evaluation of the Impact of Compliance with Mitigation Strategies and Frequency of Restaurant Surface Cleaning and Sanitizing on Control of Norovirus Transmission from Ill Food Employees Using an Existing Quantitative Risk Assessment Model

ABSTRACT

Reduction of foodborne illness caused by norovirus (NoV) continues to be a focus for the food safety community. Using a previously published quantitative risk assessment model, we evaluated more than 60 scenarios examining the impact of implementation of and compliance with risk management strategies identified in the U.S. Food and Drug Administration Food Code for (a) surface cleaning and sanitizing, (b) hand hygiene, (c) exclusion, or (d) restriction of ill employees. Implementation of and compliance with hand hygiene and ill food employee exclusion strategies had the largest impact on the predicted number of highly contaminated food servings and associated consumer illnesses. In scenarios in which gloves were always worn and hand washing compliance was 90%, the model estimated reductions in the number of highly contaminated food servings and ill consumers to 39 and 43% of baseline estimates (i.e., typical practice), respectively. Reductions were smaller when gloves were never worn. Hand washing compliance after using the restroom strongly impacted predicted numbers of highly contaminated servings and consumer illnesses. Ten percent compliance with removing or excluding ill food employees was predicted to increase the number of highly contaminated food servings and ill consumers to 221 and 213% of baseline estimates, respectively. Ninety-four percent compliance with exclusion of ill food employees was predicted to decrease these numbers to 69 and 71% of baseline estimates, respectively. Surface cleaning in food establishments had a relatively small impact on these measures. Restriction of food employees (removed from contact with food and food contact equipment and utensils) was not effective for reducing NoV illness unless this restriction included additional provisions. The results from this study can help risk managers prioritize mitigation strategies and their implementation for controlling the transmission of NoV and subsequent consumer foodborne illness.

HIGHLIGHTS

Oxidized Forms of Olive Oil Secoiridoids: Semisynthesis, Identification and Correlation with Quality Parameters

Secoiridoids is the prominent chemical class of olive oil polar constituents and are characterized by significant biological properties. They are abundant in different chemical forms and relatively high concentrations compared to other components, while prone to oxidation due to their chemical motif. In recent years, oxidized derivatives of secoiridoids have been reported, either as natural constituents of olive oil or as components which are gradually formed in all stages of its production and storage. The mono-oxidized forms of oleocanthal and oleacein named as the respective acids have been recently isolated from olive oil and unambiguously structurally characterized. Other oxidized forms of elenolic acid or more complex secoiridoids, such as those of oleuropein and ligstroside aglycones are also sporadically mentioned in the literature. No further information is provided since they have not been isolated in pure form in order to be accurately identified. Most of the time, they are generally referred as oxidized forms of the parent compounds and commonly identified based on mass spectrometric data. In the current study, the semi-synthesis of the main oxidized olive oil secoiridoids, i.e., oleocanthalic acid, oleaceinic acid, EDA acid, carboxylic form of elenolic acid, carboxylic form of ligstroside aglycon, and carboxylic form of oleuropein aglycon is described starting from the corresponding aldehydic derivatives, using SeO₂/H₂O₂ as oxidative agents. Furthermore, their presence in a number of Greek olive oils was investigated as well, as possible correlation thereof with quality parameters.

Detection and Genetic Correlation Analysis of Diarrhea Cases and Norovirus in Oysters in Yantai, China

Background

This study aimed to assess the correlation between Norovirus (NoV), diarrhea, and raw oysters from the eastern coastal areas of Yantai, Shandong, China.

Methods

Marine oysters were selected from the three aquatic markets in Laishan district, Yantai City, in March 2019. Meanwhile, 100 fecal samples were collected from patients with diarrhea from the same areas during the same period. Nucleic acids were extracted from these samples and detected by employing reverse transcription polymerase chain reaction (RT-PCR) for NoV GI/GII. The VP1 gene of the coat protein of NoV was amplified by semi-nested RT-PCR and sequenced. Sequence comparison of VP1 was performed with BioEdit software, and the evolutionary tree was constructed with Mega7.0 software.

Results

Of the 151 oysters, 42 (27.8%) were positive for NoV. Among them, 32 (21.2%) were GII-positive, 10 (6.6%) were GI-positive, and one GI VP1 sequence was obtained in the oyster samples. Of 100 fecal samples from patients with diarrhea, 38 were GII-positive and 17 were GI-positive. Totally, 19 GII VP 1 sequences and eight GI VP 1 sequences were obtained. Two G1 VP 1 sequences in two fecal samples showed 98.7% nucleotide sequence identity and 99.1% amino acid sequence identity G1 VP 1 acquired in the oyster sample.

Conclusions

The results suggest that oysters may be responsible for the spread of NoV in Yantai, Shandong province, China.

The efficacy and safety of high-pressure processing of food

High-pressure processing (HPP) is a non-thermal treatment in which, for microbial inactivation, foods are subjected to isostatic pressures (P) of 400-600 MPa with common holding times (t) from 1.5 to 6 min. The main factors that influence the efficacy (log10 reduction of vegetative microorganisms) of HPP when applied to foodstuffs are intrinsic (e.g. water activity and pH), extrinsic (P and t) and microorganism-related (type, taxonomic unit, strain and physiological state). It was concluded that HPP of food will not present any additional microbial or chemical food safety concerns when compared to other routinely applied treatments (e.g. pasteurisation). Pathogen reductions in milk/colostrum caused by the current HPP conditions applied by the industry are lower than those achieved by the legal requirements for thermal pasteurisation. However, HPP minimum requirements (P/t combinations) could be identified to achieve specific log10 reductions of relevant hazards based on performance criteria (PC) proposed by international standard agencies (5-8 log10 reductions). The most stringent HPP conditions used industrially (600 MPa, 6 min) would achieve the above-mentioned PC, except for Staphylococcus aureus. Alkaline phosphatase (ALP), the endogenous milk enzyme that is widely used to verify adequate thermal pasteurisation of cows' milk, is relatively pressure resistant and its use would be limited to that of an overprocessing indicator. Current data are not robust enough to support the proposal of an appropriate indicator to verify the efficacy of HPP under the current HPP conditions applied by the industry. Minimum HPP requirements to reduce Listeria monocytogenes levels by specific log10 reductions could be identified when HPP is applied to ready-to-eat (RTE) cooked meat products, but not for other types of RTE foods. These identified minimum requirements would result in the inactivation of other relevant pathogens (Salmonella and Escherichia coli) in these RTE foods to a similar or higher extent.

Comparison of virucidal efficacy of sodium hypochlorite, chlorine dioxide, peracetic acid, and ethanol against hepatitis A virus by carrier and suspension tests

A carrier (stainless steel disc as a default carrier) testing method is very needed for use in the actual food-processing fields by following the standard guideline. Here, we aimed to compare the virucidal efficacy of four commercial liquid disinfectants, including sodium hypochlorite (NaOCl), chlorine dioxide (ClO₂), and peracetic acid (PAA) against hepatitis A virus (HAV) following the OECD guideline protocol based on the quantitative carrier testing method and compared carrier testing results with the suspension testing results. The OECD method specifies a test for establishing whether a chemical disinfectant or a microbicide has a virucidal activity on hard non-porous surfaces. The antiviral efficacy was evaluated by plaque assays, and disinfectants were considered effective if the virus reduction was greater than or equal to 3 log₁₀ (99.9% decrease) for carrier or 4 log₁₀ (99.99% decrease) for suspension tests. Results indicated that ClO₂ above 500 ppm and 50% ethanol were effective in the carrier test method. In contrast, more than 200 ppm NaOCl and 50 ppm ClO₂ for all exposure times and 70% ethanol with contact for more than 5 min were effective in suspension tests. Treatment with PAA (80-2500 ppm) were not effective in carrier or suspension tests. Therefore, we recommend the use of more than 500 ppm ClO₂ or 50% ethanol with exposure for 10 min to disinfect surfaces that may be contaminated with HAV. Thus, these results could be effective in establishing official antiviral efficacy testing methods and basic data.

Assessment of the Impact on Human Health of the Presence of Norovirus in Bivalve Molluscs: What Data Do We Miss?

In the latest One Health ECDC EFSA technical report, Norovirus in fish and fishery products have been listed as the agent/food pair causing the highest number of strong-evidence outbreaks in the EU in 2019. This review aims to identify data gaps that must be filled in order to increase knowledge on Norovirus in bivalve molluscs, perform a risk assessment and rank the key mitigation strategies for this biological hazard, which is relevant to public health. Virologic determinations are not included in any of the food safety and process hygiene microbiologic criteria reflected in the current European regulations. In addition, the Escherichia coli-based indices of acceptable faecal contamination for primary production, as well as the food safety criteria, do not appear sufficient to indicate the extent of Norovirus contamination. The qualitative risk assessment data collected in this review suggests that bivalve molluscs present a high risk to human health for Norovirus only when consumed raw or when insufficiently cooked. On the contrary, the risk can be considered negligible when they are cooked at a high temperature, while information is still scarce for non-thermal treatments.

Lactic Acid Bacteria - A Promising Tool for Controlling Chicken Campylobacter Infection

Since 2005, campylobacteriosis has been the most common zoonotic disease in Europe. The main reservoir of pathogenic Campylobacter strains is broilers, which makes raw and undercooked poultry meat two major sources of disease. Infection in chicken flocks is most often asymptomatic, despite a high level of colonization reaching 106-109cfu/g in animal ceca. It is widely believed that controlling the level of colonization of the birds' digestive tract by pathogenic strains is a good way to increase food safety. Many treatments have been proposed to combat or at least reduce the level of colonization in animals reservoirs: probiotics, bacteriophages, vaccines, and anti-Campylobacter bacteriocins. This review focuses on the effects of Campylobacter infection on the chicken microbiome and colonization control strategies using probiotics (mostly lactic acid bacteria, LAB), which are live microorganisms included in the diet of animals as feed additives or supplements. Probiotics are not only an alternative to antibiotics, which were used for years as animal growth promoters, but they also constitute an effective protective barrier against excessive colonization of the digestive system by pathogenic bacteria, including Campylobacter. Moreover, one of the many beneficial functions of probiotics is the ability to manipulate the host's microbiota. Recently, there have also been some promising attempts to use lactic acid bacteria as a delivery system of oral vaccine against Campylobacter. Recombinant LAB strains induce primarily a mucosal immune response against foreign antigens, accompanied by at most a low-level immune response against carrier strains. Since the main barrier against the invasion of pathogens in the gastrointestinal tract is the intestinal mucosal membrane, the development of effective oral vaccines to protect animals against enteric infection is very reasonable.

Monitoring of new coronavirus (SARS-CoV-2): Origin, transmission, and food preservation methods

Unfortunately, there is limited research on coronavirus survival of food products and also food processing. The knowledge of the physical and chemical characteristics of coronaviruses mostly comes from the study of SARS-CoV and MERS-CoV physical (i.e., thermal processing, chilling and freezing, microwave irradiation, ultraviolet light, gamma irradiation, high hydrostatic pressure) and chemical (acidification and use of common disinfectants in the food industry like chlorinated derivatives and ozone) are means which could be used to inactive the coronaviruses or reduce the infection. These methods can be applied individually or in combination to act better performance. Thermal processing is one of the most effective methods for inactive coronavirus. Heating at 75°C (15-60 min) and 65°C (1 min) was the best temperature for inactive SARS-CoV and MERS virus, respectively. Among irradiation methods (microwave, UV, and gamma), the most effective one is UVC rays. Moreover, the use of disinfectant like chlorinated derivatives is appropriate way to disinfect food product surfaces.

Novelty impact statement

This review provided updated information on effective strategies for inactive coronavirus that can be used in the food industry. SARS-CoV-2 as a new pandemic coronavirus was initiated from contaminated foods and can be transmitted by close contact, aerosols, and food surfaces. Food preservation (physical and chemical) methods could decrease SARS-CoV-2. Probably, heating and UVC are the most effective approach to inactive SARS-CoV-2. Despite the findings of coronavirus inactivation which were here discussed, much research is still needed for the development of new approaches to overcome the coronavirus.

The Orphan Crop Crassocephalum crepidioides Accumulates the Pyrrolizidine Alkaloid Jacobine in Response to Nitrogen Starvation

Crassocephalum crepidioides is an African orphan crop that is used as a leafy vegetable and medicinal plant. Although it is of high regional importance in Sub-Saharan Africa, the plant is still mainly collected from the wild and therefore efforts are made to promote its domestication. However, in addition to beneficial properties, there was first evidence that C. crepidioides can accumulate the highly toxic pyrrolizidine alkaloid (PA) jacobine and here it was investigated, how jacobine production is controlled. Using ecotypes from Africa and Asia that were characterized in terms of their PA profiles, it is shown that the tetraploid C. crepidioides forms jacobine, an ability that its diploid close relative Crassocephalum rubens appears to lack. Evidence is provided that nitrogen (N) deficiency strongly increases jacobine in the leaves of C. crepidioides, that this capacity depends more strongly on the shoot than the root system, and that homospermidine synthase (HSS) activity is not rate-limiting for this reaction. A characterization of HSS gene representation and transcription showed that C. crepidioides and C. rubens possess two functional versions, one of which is conserved, that the HSS transcript is mainly present in roots and that its abundance is not controlled by N deficiency. In summary, this work improves our understanding of how environmental cues impact PA biosynthesis in plants and provides a basis for the development of PA-free C. crepidioides cultivars, which will aid its domestication and safe use.

Alternaria toxins in tomato products in Northern Italy in the period 2017-2019

The occurrence of tenuazonic acid (TeA), alternariol, alternariol monomethyl and tentoxin in tomato-based products was surveyed over the years 2017-2019. A total of 120 samples were collected from retail outlets and tomato-based food producers located in Northern Italy. After extraction and purification through prepacked columns, the mycotoxins were analysed using LC-MS/MS. A widespread contamination of TeA was found in tomato-based products, particularly in concentrated tomato paste. Other Alternaria toxins were not detected. The incidence of TeA was 78.5%, 47.4%, 55.5%, and 76.9% in concentrated tomato paste (maximum value 5955 µg kg^-1), tomato sauce, tomato pulp, and ketchup, respectively. The mean level was 243 ± 725 µg kg^-1 in concentrated tomato paste and below 30 µg kg^-1 in the other tomato products. The contamination varied from year to year. Alternaria spp strains isolated from fresh tomatoes produced mainly TeA. This study provides further Alternaria toxins occurrence data, useful for future risk assessments.

SARS-CoV-2 transmission via aquatic food animal species or their products: A review

Outbreaks of COVID-19 (coronavirus disease 2019) have been reported in workers in fish farms and fish processing plants arising from person-to-person transmission, raising concerns about aquatic animal food products' safety. A better understanding of such incidents is important for the aquaculture industry's sustainability, particularly with the global trade in fresh and frozen aquatic animal food products where contaminating virus could survive for some time. Despite a plethora of COVID-19-related scientific publications, there is a lack of reports on the risk of contact with aquatic food animal species or their products. This review aimed to examine the potential for Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) contamination and the potential transmission via aquatic food animals or their products and wastewater effluents. The extracellular viability of SARS-CoV-2 and how the virus is spread are reviewed, supporting the understanding that contaminated cold-chain food sources may introduce SAR-CoV-2 via food imports although the virus is unlikely to infect humans through consumption of aquatic food animals or their products or drinking water; i.e., SARS-CoV-2 is not a foodborne virus and should not be managed as such but instead through strong, multifaceted public health interventions including physical distancing, rapid contact tracing, and testing, enhanced hand and respiratory hygiene, frequent disinfection of high-touch surfaces, isolation of infected workers and their contacts, as well as enhanced screening protocols for international seafood trade.

Hepatitis E Virus in the Food of Animal Origin: A Review

Hepatitis E virus (HEV) is a cosmopolitan foodborne pathogen. The viral agent infects humans through the consumption of contaminated food (uncooked or undercooked). Most cases of infection are asymptomatic and for this reason, this pathology is considered underdiagnosed. Domestic and wild animals are considered natural reservoirs: that is, domestic pig, wild boar, sheep, goat, deer, rabbit, and so on. Therefore, various work categories are at risk: that is, veterinarians, farmers, hunters, slaughterhouse workers, and so on. In these last decades, researchers found a high percentage of positivity to the molecular viral detection in several food matrices included: ready-to-eat products, processed meat products, milk, and shellfish. This review aims to provide an international scenario regarding HEV ribonucleic acid (RNA) detection in several foodstuffs. From this investigative perspective, the study aims to highlight various gaps of the current knowledge about technologies treatments' impact on viral loads. The purpose was also to provide an innovative point of view "One Health"-based, pointing out the strategic role of environmental safety.

Molecular characterisation of extended-spectrum β-lactamase-producing Escherichia coli and Salmonella isolated from poultry and poultry products in Egypt

Extended-spectrum β-lactamase (ESBL) producing E. coli and salmonellae have spread rapidly worldwide and pose a serious threat to human and animal health. The present study was conduct-ed to determine the prevalence of ESBL-producing E.coli and salmonellae, to perform molecular characterisation of the ESBL-related bla genes, including blaTEM, blaSHV and blaCTX, and the sus-ceptibilities of these bacteria to various antimicrobial agents. From a total of 300 poultry samples, 25 and 20 samples were recognised as Salmonella and E. coli, respectively by microbiological and molecular methods. All E. coli and Salmonella isolates were positive for an ESBL phenotype. Mo-lecular detection for antibiotic resistance gene revealed blaTEM in all isolates of salmonellae and E. coli (100%), while blaSHV was detected in 5 (20%) and 2 (10%) of salmonellae and E. coli isolates, respectively. None of the isolates contained blaCTX gene. Serotyping of Salmonella spp. in chick-ens revealed that S. enteritidis was the major isolates followed by S. Infantis (21.4%), S. Kentucky (14.2%) and S. Typhimurium, S. Kapemba, S. Newport, S. Vejle and S. Magherafelt were detected at 7.1% respectively. S. Infantis was the major isolate detected in chicks (60%), while in ducks S. Typhimurium and S. Blegdam were identified. In ducklings, S. Sinchew, S. Infantis and S. Sekon-di were equally prevalent. Only S. Newmexico was identified in poultry products. E. coli in chick-en were serotyped into O1, O8, O29, O125, O128 and O157. In chicks, O29 and O126 serotypes were detected. In poultry products only O8 was detected. The results indicate that ESBL frequen-cy has reached an alarming level in poultry isolates in Egypt, with TEM enzymes being the pre-dominant β-lactamases detected.

Inactivation of hepatitis A virus and murine norovirus on surfaces of plastic, steel and raspberries using steam-ultrasound treatment

The leading causes of foodborne viral disease outbreaks are human norovirus and hepatitis A virus (HAV). Their environmental persistence enables contamination of kitchen surfaces and crops often consumed raw, such as berries. Many decontamination procedures are inefficient and unsuitable for surfaces of industrial kitchen environments and soft fruits. In this study, we investigated the efficiency of a novel surface decontamination technology, combining steam and ultrasound (steam-ultrasound). Plastic, steel or raspberry surfaces were spiked with the norovirus surrogate, murine norovirus (MNV), and HAV, and steam-ultrasound treated at 85, 90 and 95 °C for 0-5 s. Post treatment viruses were titrated for survival by plaque assay and for genome stability by real-time quantitative PCR (RT-qPCR) of nucleic acid extracts. Survival of viruses were estimated in a log-linear model and the treatment time requirements for each decimal reduction (D value) in viral survival were calculated. The estimated D values of MNV or HAV were 0.4-0.2 or 1.1-0.8 s on plastic, 0.9-0.7 or 1.4-0.8 s on steel and 1.6-1.7 or 3.2-4.7 s on raspberries. No clear trend of genome reduction was observed with tested treatment parameters. Raspberries treated up to 4 s retained its natural texture and visual appeal similar to untreated controls whilst monitored for 7 days. In conclusion, steam-ultrasound treatment can within seconds reduce the titre of foodborne viruses on surfaces of plastic, steel and raspberries. This may particularly benefit industrial scale production of soft fruits for raw consumption and for swift non-hazardous decontamination of industrial kitchen surfaces.

An Optimised Direct Lysis Method for Viral RNA Extraction and Detection of Foodborne Viruses on Fruits and Vegetables

Detection of norovirus (NoV) and hepatitis A virus (HAV) on fruits and vegetables using current standard methodologies can be inefficient. Method optimisation focussing on ease, rapidity and increased viral RNA recovery is needed for efficient reverse transcription (RT)-qPCR detection of viruses. A simple and quick direct lysis method for RNA extraction was optimised (method A) to achieve increased viral RNA recovery and minimised RT-qPCR inhibition by increasing the volume of lysis buffer and inclusion of pectinase, Plant RNA Isolation Aid and OneStep PCR Inhibitor Removal Kit. Method A and an internal method structurally comparable to the ISO 15216 standard (method B) were compared for their efficiencies to recover viral RNA from the process controls, mengovirus (MC₀) and murine norovirus (MNV), spiked in 13 types of fruits, vegetables, compound foods or seeds/nuts. All extracts (> 61) were also analysed for RT-qPCR inhibition and for natural contamination of NoV and HAV. The overall mean extraction efficiencies of MC₀ and MNV were 36 ± 31 and 44 ± 38%, respectively, for method A and 9 ± 16 and 5 ± 11%, respectively, for method B. Inhibition of RT-qPCR amplification of RNA from NoV genogroup (G)I, NoV GII, and HAV ranged from 5 ± 10 to 13 ± 14% for method A and 34 ± 36 to 48 ± 40% for method B. NoV GII was detected in samples of strawberries and seaweed processed by both methods. In conclusion, the new direct lysis method showed an overall better performance compared to the modified ISO 15216 standard and should be validated for implementation in analysis of viruses in foods of plant origin.

Analysis of the sanitary survey 2015-2017 conducted in the gulf of La Spezia (Italy): Reclassification of the areas of production of live bivalve molluscs

The sanitary survey is aimed at classifying and monitoring the production areas of live bivalve molluscs (LBM) and it is performed using standards that are provided by the Centre for Environment, Fisheries and Aquaculture Science's Guide to Good Practice. In this study, data from the sanitary survey carried out by the Asl5 Spezzino on the production areas of the gulf of La Spezia during the period 2015-2017 were analysed. The number and type of the analysis performed both on the total sampling and on the individual target species, as well as the number and type of found non-compliance (assessed on both mandatory parameters and on parameters fixed by the local monitoring plan) were considered. Data were also compared with those from the sanitary survey 2012-2014. Appropriate statistic tests were used to evaluate data from E. coli and Norovirus monitoring. Overall, 4306 analysis were performed, especially on the species M. galloprovincialis (89%) and they were mostly focused on to the search of biological agents. 160 NC were detected. Most of the NC concerns the Norovirus's positivity (93.75%) in M. galloprovincialis and C. gigas. A correlation between the levels of E. coli and rainfall/ seasonality (higher levels in the colder months) was proved, especially in the sampling points located in the inner part of the dam and in the Portovenere Bay. Class B was reconfirmed for M. galloprovincialis, the production areas of C. gigas were reclassified as A and those of V. verrucosa were definitively closed. The sanitary survey was therefore confirmed as a useful tool for reclassification and for monitoring LBM production areas.

Study on norovirus contamination of live bivalve molluscs using real-time PCR

Foodborne and waterborne viruses are a major cause of human morbidity. Of them, noroviruses are recognised as the leading causative agents of sporadic infections and epidemic outbreaks of acute gastroenteritis in humans. Contaminated food products and water are the main source of infection with noroviruses. The infection of bivalve molluscs with human pathogenic viruses occurs by faecal contamination in the production coastal waters. In this study, 47 samples of live bivalve molluscs, including 15 samples of cultivated mussels (Mytilus galloprovincialis) and 32 samples of wild mussels (Tapes decussatus), collected from the Bulgarian and Mediterranean coasts, respectively, were submitted to RT-real-time TaqMan PCR to detect the presence of noroviruses genotype GI and GII. Norovirus genotype GII was found in 11 (23.4%) of all the samples tested. A single mollusc sample (2.1%) was positive for both norovirus genotypes. Our results demonstrated that shellfish intended for sale on the Bulgarian market might pose a potential risk for acquiring norovirus infection. Thus, food safety quality control of shellfish by optimised and standardised methods for detection of foodborne viruses, including noroviruses, should be urgently implemented in Bulgaria.

Foodborne Norovirus State of Affairs in the EU Rapid Alert System for Food and Feed

The European Union Rapid Alert System for Food and Feed (EU RASFF) database is an invaluable instrument for analyzing notifications involving norovirus in food. The aim of this work was to carry out a thorough research of the alert and border rejection notifications submitted in the RASFF database from its onset until 31 August 2017. Some conclusions of interest were: (i) Denmark, France, Italy, the Netherlands and Norway have contributed the majority of alert notifications as notifying countries, (ii) France and Serbia have been cited more often in alert notifications as countries of origin, (iii) Italy and Spain have submitted the majority of border rejection notifications, (iv) Third Countries implicated more frequently in border rejection notifications for norovirus in bivalve molluscs were Vietnam and Tunisia, whereas in fruits and vegetables were China and Serbia, (v) "risk dispersion" from norovirus-contaminated food was narrow since, in just over half of all alert notifications and all of the border rejection notifications, only up to three countries were involved, and (vi) both raw (oysters and berries) and cooked (mussels) food products can present a health risk to consumers. The information retrieved from the RASFF database on norovirus-contaminated food could prove helpful in the planning of future norovirus risk analysis endeavors.

High Throughput Sequencing for Detection of Foodborne Pathogens

High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic "natural" strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.

Inactivation of Viruses and Bacteriophages as Models for Swine Hepatitis E Virus in Food Matrices

Hepatitis E virus has been recognised as a food-borne virus hazard in pork products, due to its zoonotic properties. This risk can be reduced by adequate treatment of the food to inactivate food-borne viruses. We used a spectrum of viruses and bacteriophages to evaluate the effect of three food treatments: high pressure processing (HPP), lactic acid (LA) and intense light pulse (ILP) treatments. On swine liver at 400 MPa for 10 min, HPP gave log₁₀ reductions of ≥4.2, ≥5.0 and 3.4 for feline calicivirus (FCV) 2280, FCV wildtype (wt) and murine norovirus 1 (MNV 1), respectively. Escherichia coli coliphage ϕX174 displayed a lower reduction of 1.1, while Escherichia coli coliphage MS2 was unaffected. For ham at 600 MPa, the corresponding reductions were 4.1, 4.4, 2.9, 1.7 and 1.3 log₁₀. LA treatment at 2.2 M gave log₁₀ reductions in the viral spectrum of 0.29-2.1 for swine liver and 0.87-3.1 for ham, with ϕX174 and MNV 1, respectively, as the most stable microorganisms. The ILP treatment gave log₁₀ reductions of 1.6-2.8 for swine liver, 0.97-2.2 for ham and 1.3-2.3 for sausage, at 15-60 J cm^-2, with MS2 as the most stable microorganism. The HPP treatment gave significantly (p < 0.05) greater virus reduction on swine liver than ham for the viruses at equivalent pressure/time combinations. For ILP treatment, reductions on swine liver were significantly (p < 0.05) greater than on ham for all microorganisms. The results presented here could be used in assessments of different strategies to protect consumers against virus contamination and in advice to food producers. Conservative model indicators for the pathogenic viruses could be suggested.

Outbreaks and factors influencing microbiological contamination of fresh produce

Fresh fruits and vegetables are nutritionally well-recognised as healthy components in diets. The microbiological foodborne outbreaks associated with the consumption of fresh produce have been increasing. Salmonella spp., Escherichia coli O157:H7, Staphylococcus aureus, Campylobacter spp. and Listeria monocytogenes are the most common pathogens that contaminate fresh produce. This review discusses recent foodborne outbreaks linked to fresh produce, factors that affect microbiological contamination and measures that could be adopted to reduce the foodborne illnesses. © 2016 Society of Chemical Industry.

Regulatory Issues Associated with Preharvest Food Safety: European Union Perspective

Free movement of safe and wholesome food is an essential aspect of any society. This article contains an updated description of the regulatory issues associated with preharvest food safety within the European Union. Salmonella , Campylobacter , Trichinella , antimicrobial resistance, and bovine spongiform encephalopathy are dealt with in detail. Moreover, Cysticercus bovis / Taenia saginata , Toxoplasma , Yersinia , verotoxigenic/shigatoxigenic Escherichia coli , Listeria , and foodborne viruses are briefly covered. The article describes how the focus in the European Union is changing to involve a supply chain view with a focus on cost-effectiveness. The precautionary principle—as well as the use of private standards as an instrument to ensure compliance—is dealt with. In addition, actions in the pipeline are presented and discussed.

Human and Animal Viruses in Food (Including Taxonomy of Enteric Viruses)

In recent years, there has been an increase in the incidence of foodborne diseases worldwide, with viruses now being recognized as a major cause of these illnesses. The most common viruses implicated in foodborne disease are enteric viruses, which are found in the human gastrointestinal tract, excreted in human feces and transmitted by the fecal-oral route. Many different viruses are found in the gastrointestinal tract but not all are recognized as foodborne pathogens. The diseases caused by enteric viruses fall into three main types: gastroenteritis, enterically transmitted hepatitis, and illnesses that can affect other parts of the body such as the eye, the respiratory system and the central nervous system leading to conjunctivitis, poliomyelitis, meningitis and encephalitis. Viral pathogens excreted in human feces include noroviruses, sapoviruses, enteroviruses, adenoviruses, hepatitis A virus (HAV), hepatitis E virus (HEV), rotaviruses, and astroviruses. Most of these viruses have been associated with foodborne disease outbreaks. Noroviruses and HAV are commonly identified as foodborne causes of gastroenteritis and acute hepatitis, respectively.

Viral Contamination of Food

A review of the relevant foodborne viruses is presented. Published data from scientific journals as well as the data presented in official reports and published on the Internet were used for this review. In the review, information is given for the main foodborne viruses, implicated virus species, and food matrices involved, some history data are given, as well as modes of transmission, and sources of the virus presence in food. Results of surveys on the presence of viruses in different kind of foods commodities (fresh produces and shellfish) and in some cases connections to caused outbreaks are presented. Also, possible zoonotic infection and implicated viruses that could be transmitted through food are given. Human Norovirus followed by hepatitis A virus are the most common foodborne viruses, which are transmitted by food consumed raw, such as shellfish, fresh vegetables, and berry fruit. In developed countries, hepatitis E virus is increasingly being recognized as an emerging viral foodborne pathogen that includes zoonotic transmission via pork products. The existing knowledge gaps and the major future expectations in the detection and surveillance of foodborne viruses are mentioned.

Retention of Rotavirus Infectivity in Mussels Heated by Using the French Recipe Moules Marinières

To evaluate the persistence of infectious virus after heating, mussels contaminated with a rotavirus strain were prepared following the French recipe moules marinières (mariner's mussels). Rotavirus was then quantified by real-time quantitative PCR (RT-qPCR) and a cell culture infectivity assay. Results showed the persistence of infectious virus after 3 min of cooking. After 5 min, when no infectious virus could be detected, the RT-qPCR approach showed a 1-log decrease compared with concentrations detected after 1 min of cooking.

Quantitative farm-to-fork risk assessment model for norovirus and hepatitis A virus in European leafy green vegetable and berry fruit supply chains

Fresh produce that is contaminated with viruses may lead to infection and viral gastroenteritis or hepatitis when consumed raw. It is thus important to reduce virus numbers on these foods. Prevention of virus contamination in fresh produce production and processing may be more effective than treatment, as sufficient virus removal or inactivation by post-harvest treatment requires high doses that may adversely affect food quality. To date knowledge of the contribution of various potential contamination routes is lacking. A risk assessment model was developed for human norovirus, hepatitis A virus and human adenovirus in raspberry and salad vegetable supply chains to quantify contributions of potential contamination sources to the contamination of produce at retail. These models were used to estimate public health risks. Model parameterization was based on monitoring data from European supply chains and literature data. No human pathogenic viruses were found in the soft fruit supply chains; human adenovirus (hAdV) was detected, which was additionally monitored as an indicator of fecal pollution to assess the contribution of potential contamination points. Estimated risks per serving of lettuce based on the models were 3×10(-4) (6×10(-6)-5×10(-3)) for NoV infection and 3×10(-8) (7×10(-10)-3×10(-6)) for hepatitis A jaundice. The contribution to virus contamination of hand-contact was larger as compared with the contribution of irrigation, the conveyor belt or the water used for produce rinsing. In conclusion, viral contamination in the lettuce and soft fruit supply chains occurred and estimated health risks were generally low. Nevertheless, the 97.5% upper limit for the estimated NoV contamination of lettuce suggested that infection risks up to 50% per serving might occur. Our study suggests that attention to full compliance for hand hygiene will improve fresh produce safety related to virus risks most as compared to the other examined sources, given the monitoring results. This effect will be further aided by compliance with other hygiene and water quality regulations in production and processing facilities.

Evidence of the internalization of animal caliciviruses via the roots of growing strawberry plants and dissemination to the fruit

Human norovirus (NoV) is the leading cause of foodborne disease in the United States, and epidemiological studies have shown that fresh produce is one of the major vehicles for the transmission of human NoV. However, the mechanisms of norovirus contamination and persistence in fresh produce are poorly understood. The objective of this study is to determine whether human NoV surrogates, murine norovirus (MNV-1) and Tulane virus (TV), can attach and become internalized and disseminated in strawberries grown in soil. The soil of growing strawberry plants was inoculated with MNV-1 and TV at a level of 10(8) PFU/plant. Leaves and berries were harvested over a 14-day period, and the viral titer was determined by plaque assay. Over the course of the study, 31.6% of the strawberries contained internalized MNV-1, with an average titer of 0.81 ± 0.33 log10 PFU/g. In comparison, 37.5% of strawberries were positive for infectious TV, with an average titer of 1.83 ± 0.22 log10 PFU/g. A higher percentage (78.7%) of strawberries were positive for TV RNA, with an average titer of 3.15 ± 0.51 log10 RNA copies/g as determined by real-time reverse transcriptase quantitative PCR (RT-qPCR). In contrast, no or little virus internalization and dissemination were detected when TV was inoculated into bell peppers grown in soil. Collectively, these data demonstrate (i) virally contaminated soils can lead to the internalization of virus via plant roots and subsequent dissemination to the leaf and fruit portions of growing strawberry plants and (ii) the magnitude of internalization is dependent on the type of virus and plant.

Hepatitis A outbreak in Italy, 2013: a matched case–control study

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Occurrence of norovirus and hepatitis A virus in wild mussels collected from the Baltic Sea

The aim of the study was to define the occurrence of human noroviruses of genogroup I and II (NoV GI and NoV GII) and hepatitis A virus (HAV) in the Baltic Sea mussels. The shellfish samples were taken at the sampling sites located on the Polish coast. In total, 120 shellfish were tested as pooled samples using RT-PCR and hybridisation with virus specific probes. NoV GI was detected in 22 (18.3%), NoV GII in 28 (23.3%), and HAV in 9 (7.5%) of the shellfish. The nucleotide sequence analysis of the detected NoV GII strains showed a 97.3-99.3% similarity to GII.4 virus strain. This is the first report describing the NoV and HAV occurrence in wild Baltic mussels and their possible role as bioindicators of seawater contamination with human enteric viruses.

Wipes coated with a singlet-oxygen-producing photosensitizer are effective against human influenza virus but not against norovirus

Transmission of enteric and respiratory viruses, including human norovirus (hNoV) and human influenza virus, may involve surfaces. In food preparation and health care settings, surfaces are cleaned with wipes; however, wiping may not efficiently reduce contamination or may even spread viruses, increasing a potential public health risk. The virucidal properties of wipes with a singlet-oxygen-generating immobilized photosensitizer (IPS) coating were compared to those of similar but uncoated wipes (non-IPS) and of commonly used viscose wipes. Wipes were spiked with hNoV GI.4 and GII.4, murine norovirus 1 (MNV-1), human adenovirus type 5 (hAdV-5), and influenza virus H1N1 to study viral persistence. We also determined residual and transferred virus proportions on steel carriers after successively wiping a contaminated and an uncontaminated steel carrier. On IPS wipes only, influenza viruses were promptly inactivated with a 5-log10 reduction. D values of infectious MNV-1 and hAdV-5 were 8.7 and 7.0 h on IPS wipes, 11.6 and 9.3 h on non-IPS wipes, and 10.2 and 8.2 h on viscose wipes, respectively. Independently of the type of wipe, dry cleaning removed, or drastically reduced, initial spot contamination of hNoV on surfaces. All wipes transferred hNoV to an uncontaminated carrier; however, the risk of continued transmission by reuse of wipes after 6 and 24 h was limited for all viruses. We conclude that cleaning wet spots with dry wipes efficiently reduced spot contamination on surfaces but that cross-contamination with noroviruses by wiping may result in an increased public health risk at high initial virus loads. For influenza virus, IPS wipes present an efficient one-step procedure for cleaning and disinfecting contaminated surfaces.

Bioaccumulation efficiency, tissue distribution, and environmental occurrence of hepatitis E virus in bivalve shellfish from France

Hepatitis E virus (HEV), an enteric pathogen of both humans and animals, is excreted by infected individuals and is therefore present in wastewaters and coastal waters. As bivalve molluscan shellfish are known to concentrate viral particles during the process of filter feeding, they may accumulate this virus. The bioaccumulation efficiencies of oysters (Crassostrea gigas), flat oysters (Ostrea edulis), mussels (Mytilus edulis), and clams (Ruditapes philippinarum) were compared at different time points during the year. Tissue distribution analysis showed that most of the viruses were concentrated in the digestive tissues of the four species. Mussels and clams were found to be more sensitive to sporadic contamination events, as demonstrated by rapid bioaccumulation in less than 1 h compared to species of oysters. For oysters, concentrations increased during the 24-h bioaccumulation period. Additionally, to evaluate environmental occurrence of HEV in shellfish, an environmental investigation was undertaken at sites potentially impacted by pigs, wild boars, and human waste. Of the 286 samples collected, none were contaminated with hepatitis E virus, despite evidence that this virus is circulating in some French areas. It is possible that the number of hepatitis E viral particles discharged into the environment is too low to detect or that the virus may have a very short period of persistence in pig manure and human waste.

Sample preparation prior to molecular amplification: complexities and opportunities

Molecular amplification using Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) is currently considered as the gold standard to detect enteric human pathogenic viruses such as norovirus and hepatitis A virus in food and water. However, the molecular-based detection requires an adequate sampling strategy and a sample preparation specific for viruses. Sampling for enteric human viruses in water and food should not necessarily follow bacterial sampling plans. The development of a reference detection method including sample preparation as proposed in ISO/TS 15216 represents a milestone to facilitate the evaluation of the performance and eventually validation of future virus detection methods. The potential viral infectivity linked to a positive PCR result is a remaining issue and pretreatments allowing the differentiation of infectious viruses would be useful for future risk assessments.

Environmental detection of genogroup I, II, and IV noroviruses by using a generic real-time reverse transcription-PCR assay

Norovirus is the most common agent implicated in food-borne outbreaks and is frequently detected in environmental samples. These viruses are highly diverse, and three genogroups (genogroup I [GI], GII, and GIV) infect humans. Being noncultivable viruses, real-time reverse transcription-PCR (RT-PCR) is the only sensitive method available for their detection in food or environmental samples. Selection of consensus sequences for the design of sensitive assays has been challenging due to sequence diversity and has led to the development of specific real-time RT-PCR assays for each genogroup. Thus, sample screening can require several replicates for amplification of each genogroup (without considering positive and negative controls or standard curves). This study reports the development of a generic assay that detects all three human norovirus genogroups on a qualitative basis using a one-step real-time RT-PCR assay. The generic assay achieved good specificity and sensitivity for all three genogroups, detected separately or in combination. At variance with multiplex assays, the choice of the same fluorescent dye for all three probes specific to each genogroup allows the levels of fluorescence to be added and may increase assay sensitivity when multiple strains from different genogroups are present. When it was applied to sewage sample extracts, this generic assay successfully detected norovirus in all samples found to be positive by the genogroup-specific RT-PCRs. The generic assay also identified all norovirus-positive samples among 157 archived nucleic acid shellfish extracts, including samples contaminated by all three genogroups.

Virus transfer proportions between gloved fingertips, soft berries, and lettuce, and associated health risks

Multiple outbreaks of human norovirus (hNoV) have been associated with fresh produce, such as soft berries and lettuce. Even though food handlers are considered an important source for the introduction of hNoV into food chains, their contribution to public health risks associated with hNoV remains unknown. To assess to which extent food handlers contribute to the introduction and spread of hNoV in fresh produce chains quantitative virus transfer data are needed. We estimated transfer proportions of hNoV GI.4, GII.4, murine norovirus (MNV-1), a culturable surrogate of hNoV, and human adenovirus (hAdV-2), a human pathogen proposed as an indicator for human faecal pollution, between gloved fingertips and raspberries, strawberries, and lettuce, by quantitative RT-PCR and cell culture if applicable. Virus transfer proportions were corrected for virus-matrix specific recoveries, and variability and uncertainty of the parameters were estimated. Virus transfer from gloves to soft berries was generally lower as compared to lettuce, with mean transfer proportions ranging between 0.1 to 2.3% and 9 to 10% for infectious MNV-1 and hAdV-2, respectively. Transfer from produce to glove was mostly greater than transfer from glove to produce, adding to the likelihood of virus transfer due to cross contamination from contaminated produce via food handlers. HNoV GI.4 and hNoV GII.4 showed no significant difference between their mean transfer proportions. Using the estimated transfer proportions, we studied the impact of low and high transfer proportions on the public health risk, based on a scenario in which a food handler picked raspberries with contaminated fingertips. Given the made assumptions, we could show that for a pathogen as infectious as hNoV, low transfer proportions may pose a greater public health risk than high transfer proportions, due to a greater viral spread. We demonstrated the potential of food handlers in spreading hNoV in food chains, showing that prevention of virus contamination on food handlers' hands is crucial for food safety. Nevertheless, complete prevention of virus contamination on fresh produce cannot be achieved in reality, and reliable and effective intervention measures are consequently required. We estimated that, especially for low transfer proportions, a robust one log10-unit reduction of infectious hNoV on contaminated produce, and on food handlers' hands, could lower the public health risk substantially. Using the obtained data in quantitative risk assessment will aid in elucidating the contribution of food handlers in hNoV transmission.

Detection and Typing of Norovirus from Frozen Strawberries Involved in a Large-Scale Gastroenteritis Outbreak in Germany

During September/October 2012, a norovirus gastroenteritis outbreak affecting about 11,000 people occurred in Germany. Epidemiological studies suggested that frozen strawberries represented the vehicle of infection. We describe here the analysis of frozen strawberries for the presence of norovirus. Samples were taken by applying a stratified subsampling scheme. Two different methods for virus extraction from strawberries were compared. First, viruses were eluted from strawberries under alkaline conditions and concentrated using a polyethylene glycol precipitation. Second, ultrafiltration was applied for concentration of viruses rinsed off of the berries. In both cases, RNA was extracted and analyzed by real-time RT-PCR. Application of the ultrafiltration method generally resulted in a lower detection rate. Noroviruses were detected in 7/11 samples derived from the lot of strawberries implicated in the outbreak using the precipitation method. Typing of norovirus revealed three different genotypes including a combination of norovirus genotype II.16 (viral polymerase) and II.13 (viral capsid). This genotype combination was also found in some of the patients that were involved in the outbreak, but that had not been reported in Germany so far. In conclusion, heterogeneously distributed noroviruses in frozen strawberries can be detected by applying an optimized combination of sampling procedures, virus extraction methods, and real-time RT-PCR protocols. The detection of several different genotypes in the strawberries may suggest contamination from sewage rather than from a single infected food handler.