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The European Commission asked EFSA for a scientific opinion on chronic wasting disease in two parts. Part one, on surveillance, animal health risk-based measures and public health risks, was published in January 2017. This opinion (part two) addresses the remaining Terms of Reference, namely, ‘are the conclusions and recommendations in the EFSA opinion of June 2004 on diagnostic methods for chronic wasting disease still valid? If not, an update should be provided’, and ‘update the conclusions of the 2010 EFSA opinion on the results of the European Union survey on chronic wasting disease in cervids, as regards its occurrence in the cervid population in the European Union’. Data on the performance of authorised rapid tests in North America are not comprehensive, and are more limited than those available for the tests approved for statutory transmissible spongiform encephalopathies surveillance applications in cattle and sheep. There are no data directly comparing available rapid test performances in cervids. The experience in Norway shows that the Bio-Rad TeSeE™ SAP test, immunohistochemistry and western blotting have detected reindeer, moose and red deer cases. It was shown that testing both brainstem and lymphoid tissue from each animal increases the surveillance sensitivity. Shortcomings in the previous EU survey limited the reliability of inferences that could be made about the potential disease occurrence in Europe. Subsequently, testing activity in Europe was low, until the detection of the disease in Norway, triggering substantial testing efforts in that country. Available data neither support nor refute the conclusion that chronic wasting disease does not occur widely in the EU and do not preclude the possibility that the disease was present in Europe before the survey was conducted. It appears plausible that chronic wasting disease could have become established in Norway more than a decade ago.

EFSA was requested: to assess the impact of a proposed quantitative real‐time polymerase chain reaction (qPCR) ‘technical zero’ on the limit of detection of official controls for constituents of ruminant origin in feed, to review and update the 2011 QRA, and to estimate the cattle bovine spongiform encephalopathy (BSE) risk posed by the contamination of feed with BSE‐infected bovine‐derived processed animal protein (PAP), should pig PAP be re‐authorised in poultry feed and vice versa, using both light microscopy and ruminant qPCR methods, and action limits of 100, 150, 200, 250 and 300 DNA copies. The current qPCR cannot discriminate between legitimately added bovine material and unauthorised contamination, or determine if any detected ruminant material is associated with BSE infectivity. The sensitivity of the surveillance for the detection of material of ruminant origin in feed is currently limited due to the heterogeneous distribution of the material, practicalities of sampling and test performance. A ‘technical zero’ will further reduce it. The updated model estimated a total BSE infectivity four times lower than that estimated in 2011, with less than one new case of BSE expected to arise each year. In the hypothetical scenario of a whole carcass of an infected cow entering the feed chain without any removal of specified risk material (SRM) or reduction of BSE infectivity via rendering, up to four new cases of BSE could be expected at the upper 95th percentile. A second model estimated that at least half of the feed containing material of ruminant origin will not be detected or removed from the feed chain, if an interpretation cut‐off point of 100 DNA copies or more is applied. If the probability of a contaminated feed sample increased to 5%, with an interpretation cut‐off point of 300 DNA copies, there would be a fourfold increase in the proportion of all produced feed that is contaminated but not detected.

EFSA received an application from the Dutch Competent Authority, under Article 20 of Regulation (EC) No 1069/2009 and Regulation (EU) No 142/2011, for the evaluation of an alternative method for treatment of Category 3 animal by-products (ABP). It consists of the hydrolysis of the material to short-carbon chains, resulting in medium-chain fatty acids that may contain up to 1% hydrolysed protein, for use in animal feed. A physical process, with ultrafiltration followed by nanofiltration to remove hazards, is also used. Process efficacy has been evaluated based on the ability of the membrane barriers to retain potential biological hazards present. Small viruses passing the ultrafiltration membrane will be retained at the nanofiltration step, which represents a Critical Control Point (CCP) in the process. This step requires the Applicant to validate and provide certification for the specific use of the nanofiltration membranes used. Continuous monitoring and membrane integrity tests should be included as control measures in the HACCP plan. The ultrafiltration and nanofiltration techniques are able to remove particles of the size of virus, bacteria and parasites from liquids. If used under controlled and appropriate conditions, the processing methods proposed should reduce the risk in the end product to a degree which is at least equivalent to that achieved with the processing standards laid down in the Regulation for Category 3 material. The possible presence of small bacterial toxins produced during the fermentation steps cannot be avoided by the nanofiltration step and this hazard should be controlled by a CCP elsewhere in the process. The limitations specified in the current legislation and any future modifications in relation to the end use of the product also apply to this alternative process, and no hydrolysed protein of ruminant origin (except ruminant hides and skins) can be included in feed for farmed animals or for aquaculture

Parasites are important food-borne pathogens. Their complex lifecycles, varied transmission routes, and prolonged periods between infection and symptoms mean that the public health burden and relative importance of different transmission routes are often difficult to assess. Furthermore, there are challenges in detection and diagnostics, and variations in reporting. A Europe-focused ranking exercise, using multicriteria decision analysis, identified potentially food-borne parasites of importance, and that are currently not routinely controlled in food. These are Cryptosporidium spp., Toxoplasma gondii and Echinococcus spp. Infection with these parasites in humans and animals, or their occurrence in food, is not notifiable in all Member States. This Opinion reviews current methods for detection, identification and tracing of these parasites in relevant foods, reviews literature on food-borne pathways, examines information on their occurrence and persistence in foods, and investigates possible control measures along the food chain. The differences between these three parasites are substantial, but for all there is a paucity of well-established, standardised, validated methods that can be applied across the range of relevant foods. Furthermore, the prolonged period between infection and clinical symptoms (from several days for Cryptosporidium to years for Echinococcus spp.) means that source attribution studies are very difficult. Nevertheless, our knowledge of the domestic animal lifecycle (involving dogs and livestock) for Echinoccocus granulosus means that this parasite is controllable. For Echinococcus multilocularis, for which the lifecycle involves wildlife (foxes and rodents), control would be expensive and complicated, but could be achieved in targeted areas with sufficient commitment and resources. Quantitative risk assessments have been described for Toxoplasma in meat. However, for T. gondii and Cryptosporidium as faecal contaminants, development of validate

In 2017, EFSA published a ‘simplified’ food safety management system (FSMS) for certain small retail establishments (butcher, grocer, baker, fish and ice cream shop) based on the application of prerequisite programme (PRP) criteria. The aim of this opinion was to develop similar FSMSs for other small retail enterprises including retail distribution centres, supermarkets, restaurants (including pubs and other catering activities) and food donation. The latter presents several novel food safety challenges because donated food may be nearing the end of its shelf‐life and several actors are involved in the food donation chain, each reliant on each other to assure food safety. In this opinion, the simplified approach to food safety management is presented based on a fundamental understanding of processing stages and the activities contributing to increased occurrence of the hazards (biological, chemical (including allergens) or physical) that may occur. Control is achieved using PRP activities as previously described but with a modified ‘temperature control’ PRP and the addition of PRPs covering shelf‐life control, handling returned foods, shelf‐life evaluation for food donation, allocation of remaining shelf‐life, and freezing food intended for donation. Examples of the simplified approach are presented for retail distribution centres, supermarkets, restaurants and food donation.

In April and May of 2016, Norway con firmed two cases of chronic wasting disease (CWD) in a wildreindeer and a wild moose, respectively. In the light of this emerging issue, the European Commissionrequested EFSA to recommend surveillance act ivities and, if necessary, additional animal healthrisk-based measures to prevent the introduction of the disease and the spread into/withi n the EU,specifically Estonia, Finland, Iceland, Latvia, Lithuania, Norway, Poland and Sweden, and consideringseven wild, semidomesticated and farmed cervid species (Eurasian tundra reindeer, Finnish (Eurasian)forest reindeer, moose, roe deer, white-tailed deer, red deer and fallow deer). It was also asked toassess any new evidence on possible public health risks related to CWD. A 3-year surveillance systemis proposed, differing for farmed and wild or semidomesticated cervids, with a two-stage samplingprogramme at the farm/geographically based population unit level (random samp ling) and individuallevel (convenience sampling targeting high-risk animals). The current derogations of CommissionImplementing Decision (EU) 2016/1918 present a risk of introduction of CWD into the EU. Measures toprevent the spread of CWD within the EU are dependent upon the assumption that the disease isalready present; this is currently unknown. The measures listed are intended to contain (limit thegeographic extent of a focus) and/or to contro l (acti vely stabilise/reduce infection rates in an affectedherd or population) the disease where it occurs. With regard to the zoonotic potential, the humanspecies barrier for CWD prions does not appear to be absolute. These prions are present in theskeletal muscle and other edible tissues, so humans may consume infected material in enzootic areas.Epidemiological investigations carried out to date make no association between the occurrence ofsporadic Creutzfeldt–Jakob disease in humans and exposure to CWD prions

EFSA and EMA have jointly reviewed measures taken in the EU to reduce the need for and use of antimicrobials in food-producing animals, and the resultant impacts on antimicrobial resistance (AMR). Reduction strategies have been implemented successfully in some Member States. Such strategies include national reduction targets, benchmarking of antimicrobial use, controls on prescribing and restrictions on use of specific critically important antimicrobials, together with improvements to animal husbandry and disease prevention and control measures. Due to the multiplicity of factors contributing to AMR, the impact of any single measure is difficult to quantify, although there is evidence of an association between reduction in antimicrobial use and reduced AMR. To minimise antimicrobial use, a multifaceted integrated approach should be implemented, adapted to local circumstances. Recommended options (non-prioritised) include: development of national strategies; harmonised systems for monitoring antimicrobial use and AMR development; establishing national targets for antimicrobial use reduction; use of on-farm health plans; increasing the responsibility of veterinarians for antimicrobial prescribing; training, education and raising public awareness; increasing the availability of rapid and reliable diagnostics; improving husbandry and management procedures for disease prevention and control; rethinking livestock production systems to reduce inherent disease risk. A limited number of studies provide robust evidence of alternatives to antimicrobials that positively influence health parameters. Possible alternatives include probiotics and prebiotics, competitive exclusion, bacteriophages, immunomodulators, organic acids and teat sealants. Development of a legislative framework that permits the use of specific products as alternatives should be considered. Further research to evaluate the potential of alternative farming systems on reducing AMR is also recommended. Animals s

Under current European hygiene legislation, food businesses are obliged to develop and implement food safety management systems (FSMS) including prerequisite programme (PRP) activities and hazard analysis and critical control point principles. This requirement is especially challenging for small food retail establishments, where a lack of expertise and other resources may limit the development and implementation of effective FSMS. In this opinion, a simplified approach to food safety management is developed and presented based on a fundamental understanding of processing stages (flow diagram) and the activities contributing to increased occurrence of the hazards (biological, chemical (including allergens) or physical) that may occur. The need to understand and apply hazard or risk ranking within the hazard analysis is removed and control is achieved using PRP activities as recently described in the European Commission Notice 2016/C278, but with the addition of a PRP activity covering ‘product information and customer awareness’. Where required, critical limits, monitoring and record keeping are also included. Examples of the simplified approach are presented for five types of retail establishments: butcher, grocery, bakery, fish and ice cream shop.

EFSA is requested to assess the safety of a broad range of biological agents in the context of notification formarket authorisation as sources of food and feed additives, food enzymes and plant protection products.The qualified presumption of safety (QPS) assessment was developed to provide a harmonised generic pre-assessment to support safety risk assessments performed by EFSA’sscientific Panels. The safety ofunambiguously defined biological agents (at the highest taxonomic unit appropriate for the purpose forwhich an application is intended), and the completeness of the body of knowledge are assessed. Identifiedsafety concerns for a taxonomic unit are, where possible and reasonable in number, reflected as‘qualifications’in connection with a recommendation for a QPS status. The list of QPS recommendedbiological agents was reviewed and updated in the current opinion and therefore becomes the valid list.The 2016 update reviews previously assessed microorganisms including bacteria, yeasts and viruses usedfor plant protection purposes following an Extensive Literature Search strategy. The taxonomic units relatedto the new notifications received since the 2013 QPS opinion, were periodically evaluated for a QPS statusand the results published as Statements of the BIOHAZ Panel.Carnobacterium divergens,Lactobacillusdiolivorans,Microbacterium imperiale,Pasteuria nishizawae,Pediococcus parvulus, Bacillusflexus,Bacillus smithii, Xanthomonas campestrisandCandida cylindraceawere recommended for the QPS list. Alltaxonomic units previously recommended for the 2013 QPS list had their status reconfirmed as well theirqualifications with the exception ofPasteuria nishizawaefor which the qualification was removed. Theexclusion offilamentous fungi and enterococci from the QPS evaluations was reconsidered but monitoringwill be maintained and the status will be re-evaluated in the next QPS Opinion update. Evaluation ofbacteriophages should remain as a case-by-case procedure and should no

Breeding programmes to promote resistance to classical scrapie, similar to those for sheep in existingtransmissible spongiform encephalopathies (TSE) regulations, have not been established in goats. TheEuropean Commission requested a scientific opinion from EFSA on the current knowledge of geneticresistance to TSE in goats. An evaluation tool, which considers both the weight of evidence andstrength of resistance to classical scrapie of alleles in the goatPRNPgene, was developed and appliedto nine selected alleles of interest. Using the tool, the quality and certainty of thefield andexperimental data are considered robust enough to conclude that the K222, D146 and S146 allelesboth confer genetic resistance against classical scrapie strains known to occur naturally in the EU goatpopulation, with which they have been challenged both experimentally and underfield conditions. Theweight of evidence for K222 is greater than that currently available for the D146 and S146 alleles andfor the ARR allele in sheep in 2001. Breeding for resistance can be an effective tool for controllingclassical scrapie in goats and it could be an option available to member states, both at herd andpopulation levels. There is insufficient evidence to assess the impact of K222, D146 and S146 alleleson susceptibility to atypical scrapie and bovine spongiform encephalopathy (BSE), or on health andproduction traits. These alleles are heterogeneously distributed across the EU Member States and goatbreeds, but often at low frequencies (<10%). Given these low frequencies, high selection pressuremay have an adverse effect on genetic diversity so any breeding for resistance programmes should bedeveloped at Member States, rather than EU level and their impact monitored, with particular attentionto the potential for any negative impact in rare or small population breeds

The qualified presumption of safety (QPS) concept was developed to provide a harmonised generic pre-evaluation to support safety risk assessments of biological agents performed by EFSA's scientific Panels. The identity, body of knowledge, safety concerns and antimicrobial resistance of valid taxonomic units were assessed. Safety concerns identified for a taxonomic unit are, where possible and reasonable in number, reflected as ‘qualifications’ which should be assessed at the strain level by the EFSA's scientific Panels. No new information was found that would change the previously recommended QPS taxonomic units and their qualifications. Between the end of September 2016 and March 2017, the QPS notification list was updated with 87 applications for market authorisation. From these, 32 biological agents already had a QPS status, and 37 were not included in the evaluation as they are filamentous fungi or enterococci. Streptomyces species (Streptomyces cinnamonensis, Streptomyces mobaraensis and Streptomyces violaceoruber), Bacillus circulans (three notifications) and Escherichia coli (seven notifications) were re-confirmed not suitable for QPS. Streptomyces rubiginosus and Streptomyces netropsis, not evaluated within the previous mandate, were also not recommended for QPS. Streptomyces spp. and E. coli will be excluded from further QPS evaluations within the current QPS mandate. Hyphomicrobium denitrificans, which has never been evaluated before, was not recommended for the QPS list and for Pseudomonas amyloderamosa, the QPS assessment was not applicable because it is not a validated species. Lactobacillus animalis was a new taxonomic unit recommended to have the QPS status

Sixty bovine spongiform encephalopathy (BSE) cases of Classical or unknown type (BARB-60 cases)were born after the date of entry into force of the EU total feed ban on 1 January 2001. The EuropeanCommission has requested EFSA to provide a scientific opinion on the most likely origin(s) of theseBARB-60 cases; whether feeding with material contaminated with the BSE agent can be excluded asthe origin of any of these cases and, if so, whether there is enough scientific evidence to conclude thatsuch cases had a spontaneous origin. The source of infection cannot be ascertained at the individuallevel for any BSE case, including these BARB-60 cases, so uncertainty remains high about the origin ofdisease in each of these animals, but when compared with other biologically plausible sources ofinfection (maternal, environmental, genetic, iatrogenic), feed-borne exposure is the most likely. Thisexposure was apparently excluded for only one of these BARB-60 cases. However, there isconsiderable uncertainty associated with the data collected through thefield investigation of thesecases, due to a time span of several years between the potential exposure of the animal and theconfirmation of disease, recall difficulty, and the general paucity of documented objective evidenceavailable in the farms at the time of the investigation. Thus, feeding with material contaminated withthe BSE agent cannot be excluded as the origin of any of the BARB-60 cases, nor is it possible todefinitively attribute feed as the cause of any of the BARB-60 cases. A case of disease is classified asspontaneous by a process of elimination, excluding all other definable possibilities; with regard to theBARB-60 cases, it is not possible to conclude that any of them had a spontaneous origin.

Hepatitis E virus (HEV) is an important infection in humans in EU/EEA countries, and over the last 10 years more than 21,000 acute clinical cases with 28 fatalities have been notified with an overall 10-fold increase in reported HEV cases; the majority (80%) of cases were reported from France, Germany and the UK. However, as infection in humans is not notifiable in all Member States, and surveillance differs between countries, the number of reported cases is not comparable and the true number of cases would probably be higher. Food-borne transmission of HEV appears to be a major route in Europe; pigs and wild boars are the main source of HEV. Outbreaks and sporadic cases have been identified in immune-competent persons as well as in recognised risk groups such as those with pre-existing liver damage, immunosuppressive illness or receiving immunosuppressive treatments. The opinion reviews current methods for the detection, identification, characterisation and tracing of HEV in food-producing animals and foods, reviews literature on HEV reservoirs and food-borne pathways, examines information on the epidemiology of HEV and its occurrence and persistence in foods, and investigates possible control measures along the food chain. Presently, the only efficient control option for HEV infection from consumption of meat, liver and products derived from animal reservoirs is sufficient heat treatment. The development of validated quantitative and qualitative detection methods, including infectivity assays and consensus molecular typing protocols, is required for the development of quantitative microbial risk assessments and efficient control measures. More research on the epidemiology and control of HEV in pig herds is required in order to minimise the proportion of pigs that remain viraemic or carry high levels of virus in intestinal contents at the time of slaughter. Consumption of raw pig, wild boar and deer meat products should be avoided.

The qualified presumption of safety (QPS) concept was developed to provide a harmonised generic pre-evaluation to support safety risk assessments of biological agents performed by EFSA's scientific Panels. The identity, body of knowledge, safety concerns and antimicrobial resistance of valid taxonomic units were assessed. Safety concerns identified for a taxonomic unit are, where possible and reasonable in number, reflected as ‘qualifications’ which should be assessed at the strain level by the EFSA's scientific Panels. No new information was found that would change the previously recommended QPS taxonomic units and their qualifications. Between the end of September 2016 and March 2017, the QPS notification list was updated with 87 applications for market authorisation. From these, 32 biological agents already had a QPS status, and 37 were not included in the evaluation as they are filamentous fungi or enterococci. Streptomyces species (Streptomyces cinnamonensis, Streptomyces mobaraensis and Streptomyces violaceoruber), Bacillus circulans (three notifications) and Escherichia coli (seven notifications) were re-confirmed not suitable for QPS. Streptomyces rubiginosus and Streptomyces netropsis, not evaluated within the previous mandate, were also not recommended for QPS. Streptomyces spp. and E. coli will be excluded from further QPS evaluations within the current QPS mandate. Hyphomicrobium denitrificans, which has never been evaluated before, was not recommended for the QPS list and for Pseudomonas amyloderamosa, the QPS assessment was not applicable because it is not a validated species. Lactobacillus animalis was a new taxonomic unit recommended to have the QPS status.

On 22 January 2015, Croatia submitted to the European Commission (EC) a request to revise its bovine spongiform encephalopathy (BSE) monitoring programme. The EC requested the European Food Safety Authority (EFSA) to provide scientific and technical assistance on an assessment of the capacity of the proposed revised monitoring programme in Croatia to allow the detection of BSE, both classical and atypical strains, with a design prevalence of at least one case per 100,000 animals in the adult cattle population of the EU26 group (EU25 and Croatia). Under this revision Croatia would stop testing all healthy slaughtered cattle and would test all ‘at risk’ cattle of active surveillance above 36 months of age. The EC resolved that the EU26 should be considered as a unique epidemiological unit for this assessment. Data related to the EU26 were updated to run the Cattle Transmissible Spongiform Encephalopathies Monitoring Model (C-TSEMM), previously applied to similar assessments. This model allows the estimation of the design prevalence of the same surveillance regime applied by a group of countries. Using data up to 2014, the current EU25 surveillance regime would allow the detection of BSE in the EU25 with a design prevalence of at least 1 per 3,769,555 of the cattle adult population, lower (i.e. more sensitive) than the minimum requirement of 1 case per 100,000. The addition of Croatia to the EU25 epidemiological unit (EU26) assuming the current EU25 surveillance regime resulted in an ability in EU26 to detect BSE with a design prevalence of at least 1 per 3,789,838 of the adult cattle population. It is recommended: [1] to run the C-TSEMM model on an annual basis with updated data; [2] to monitor MS data in order to evaluate the surveillance coverage and [3] to identify any shortcomings affecting the overall sensitivity of the surveillance system.

EFSA was requested to assess the safety of a broad range of biological agents in the context of notifications for market authorisation as sources of food and feed additives, enzymes and plant protection products. The qualified presumption of safety (QPS) assessment was developed to provide a harmonised generic preassessment to support safety risk assessments performed by EFSA's scientific Panels. The safety of unambiguously defined biological agents (at the highest taxonomic unit appropriate for the purpose for which an application is intended) and the completeness of the body of knowledge were assessed. Safety concerns identified for a taxonomic unit are, where possible and reasonable in number, reflected as ‘qualifications’ in connection with a recommendation for a QPS status. A total of 129 biological agents were notified to EFSA between September 2015 and March 2016. From these, 34 biological agents already had a QPS status and did not require further evaluation, and 63 were not included as they are filamentous fungi or enterococci, biological groups which have been excluded from the QPS activities since 2014. Five notifications for species belonging to Streptomyces genus, one for Paenibacillus lentus, four for Escherichia coli and one for one species of Actinomadura were not evaluated for QPS status because these species were recently assessed and considered not suitable for QPS status. Furthermore, it was agreed not to include nine notifications from Pesticides Unit as the respective dossiers (including the literature review) were not yet received. Therefore, there were 12 notifications related to 12 taxonomic units that were evaluated for QPS status. Pediococcus parvulus, Bacillus flexus and Lactobacillus diolivorans may be recommended for the QPS status. Candida rugosa, Cellulosimicrobium cellulans, Geobacillus caldoproteolyticus (Anoxybacilluscaldiproteolyticus), Aeribacillus pallidus (ex-Geobacillus pallidus), ‘Chryseobacterium proteolyticum’, Klebsiella p

The Bacillus cereus group, also known as B. cereus sensu lato, is a subdivision of the Bacillus genus that consists of eight formally recognised species: B. cereus sensu stricto, B. anthracis, B. thuringiensis, B. weihenstephanensis, B. mycoides, B. pseudomycoides, B. cytotoxicus and B. toyonensis. The current taxonomy of the B. cereus group and the status of separate species mainly rely on phenotypic characteristics. Bacillus thuringiensis strains display a similar repertoire of the potential virulence genes on the chromosome as B. cereus sensu stricto strains and it has been shown that these genes can also be actively expressed in B. thuringiensis strains. Bacillus cereus and B. thuringiensis strains are usually not discriminated in clinical diagnostics or food microbiology. Thus, the actual contribution of the two species to gastrointestinal and non-gastrointestinal diseases is currently unknown. Most cases of food-borne outbreaks caused by the B. cereus group have been associated with concentrations above 105 CFU/g. However, cases of both emetic and diarrhoeal illness have been reported involving lower levels of B. cereus. The levels of B. cereus that can be considered as a risk for consumers are also valid for B. thuringiensis. There is no evidence that B. thuringiensis has the genetic determinants for the emetic toxin cereulide. The Panel has recommended the application of whole genome sequencing to provide unambiguous identification of strains used as biopesticides and the detailed characterisation of outbreak strains allowing discrimination of B. thuringiensis from B. cereus. Data gaps include: dose–response and behavioural characteristics of B. cereus group strains and specifically of B. thuringiensis. Field studies after application of B. thuringiensis biopesticides are needed to enable the establishment of pre-harvest intervals.