Scientific Opinion on the revision of the quantitative risk assessment (QRA) of the BSE risk posed by processed animal proteins (PAPs)

Fish feed composition by high-throughput sequencing analysis: Parasite risk assessment

The use of wild small fish species as feed for aquaculture has clearly an economic incentive by speeding the growth of farmed species. Since feed ingredients are sourced from wild fisheries the farmed species could contain natural contaminants which may introduce food safety concerns. In this study, we used High-Throughput Sequencing (HTS) to explore the whole DNA profile of ten dry commercial feeds commonly used by Spanish fish farming companies. The feeds were mainly made of species within the genus Sprattus, Ammodytes and Clupea, and vegetables of the genus Triticum. In the feeds, DNA sequences of parasitic nematodes of fishes (˂1 % total OTUs) were also identified. A taxonomic assignment of query sequences, using a phylogeny-based approach, estimation of pairwise nucleotide identities within and between sequence groups and haplotype network analysis, allow assign short query sequences to the species Phocanema krabbei (Anisakidae) and Hysterothylacium aduncum (Rhaphidascarididae). Both species were identified as ingredient in two and six fish feeds, respectively. This result is of highly concern regarding dietetic recommendations to sensitized patients to anisakids, considering the growing evidence on the possible allergenic potential of both genera, and the recent data on the transfer of anisakid heat-resistant allergens from fishmeal to farm and aquaculture animals.

Hotspots and bottlenecks for the enhancement of the environmental sustainability of pig systems, with emphasis on European pig systems

Although pig systems start from a favourable baseline of environmental impact compared to other livestock systems, there is still scope to reduce their emissions and further mitigate associated impacts, especially in relation to nitrogen and phosphorous emissions. Key environmental impact hotspots of pig production systems are activities associated with feed production and manure management, as well as direct emissions (such as methane) from the animals and energy use. A major contributor to the environmental impacts associated with pig feed is the inclusion of soya in pig diets, especially since European pig systems rely heavily on soya imported from areas of the globe where crop production is associated with significant impacts of land use change, deforestation, carbon emissions, and loss of biodiversity. The "finishing" pig production stage contributes most to these environmental impacts, due to the amount of feed consumed, the efficiency with which feed is utilised, and the amount of manure produced during this stage. By definition therefore, any substantial improvements pig system environmental impact would arise from changes in feed production and manure management. In this paper, we consider potential solutions towards system environmental sustainability at these pig system components, as well as the bottlenecks that inhibit their effective implementation at the desired pace and magnitude. Examples include the quest for alternative protein sources to soya, the limits (perceived or real) to the genetic improvement of pigs, and the implementation of alternative manure management strategies, such as production of biogas through anaerobic digestion. The review identifies and discusses areas that future efforts can focus on, to further advance understanding around the potential sustainability benefits of modifications at various pig system components, and key sustainability trade-offs across the environment-economy-society pillars associated with synergistic and antagonistic effects when joint implementation of multiple solutions is considered. In this way, the review opens a discussion to facilitate the development of holistic decision support tools for pig farm management that account for interactions between the "feed * animal * manure" system components and trade-offs between sustainability priorities (e.g., environmental vs economic performance of pig system; welfare improvements vs environmental impacts).

The use of animal by-products in a circular bioeconomy: Time for a TSE road map 3?

In 2005 and 2010, the European Commission (EC) published two subsequent 'Road Maps' to provide options for relaxation of the bans on the application of animal proteins in feed. Since then, the food production system has changed considerably and demands for more sustainability and circularity are growing louder. Many relaxations envisioned in the second Road Map have by now been implemented, such as the use of processed animal proteins (PAPs) from poultry in pig feed and vice versa. However, some legislative changes, in particular concerning insects, had not been foreseen. In this article, we present a new vision on legislation for increased and improved use of animal by-products. Six current legislative principles are discussed for the bans on animal by-products as feed ingredients: feed bans; categorization of farmed animals; prohibition unless explicitly approved; approved processing techniques, the categorization of animal by-products, and monitoring methods. We provide a proposal for new guiding principles and future directions, and several concrete options for further relaxations. We argue that biological nature of farmed animals in terms of dietary preferences should be better recognised, that legal zero-tolerance limits should be expanded if safe, and that legislation should be revised and simplified.

Detection of chicken DNA in commercial dog foods

BACKGROUND

These days the number of potential food allergens is very large, but chicken is one of the most common allergens in dogs. Elimination diet is one of the clinical tools for the diagnosis of allergies and allergy tests are not very reliable. The restriction diet is most commonly carried out by feeding pet foods, relying on the ingredients on the label to select an elimination diet not containing previously eaten foods. Unfortunately, mislabeling of pet food is quite common. The purpose of this study was to determine the absence or presence of chicken DNA using both qualitative and quantitative polymerase chain reaction (PCR) analysis methods in dry and wet maintenance complete pet foods for adult dogs. Results were used to verify the declared composition on the labels.

RESULTS

Eleven out of fifteen (73%) dog foods were produced as declared by the manufacturer, two of which showed the presence of chicken protein as stated on the label. The remaining nine foods contained amounts of chicken DNA below 1%, consistent with declarations that no chicken was added in the composition. Four of tested dog foods (27%) were not produced consistently with the declaration on the packaging. Two dog foods (one dry and one wet) did not contain the claimed chicken protein. In two foods the addition of chicken DNA was detected at the level of over 2% and almost 6%, respectively.

CONCLUSIONS

In this study, we focused on one of the most commonly undeclared animal species on the label-chicken protein-and performed DNA analyzes to investigate possible contamination and mislabeling. The results showed some inaccuracies. However, most of them are trace amounts below 1%, which proves compliance with the label. Our results showed that undeclared animal species can be as common as missing an animal protein declared on the label. The conducted research indicates that both dry and wet analyzed foods should not be recommended as a diagnostic tool in elimination tests, because it may result in false negative results. Over-the-counter maintenance foods for dogs should not be recommended for the diagnosis and treatment of food hypersensitivity.

Analysis of German BSE Surveillance Data: Estimation of the Prevalence of Confirmed Cases versus the Number of Infected, but Non-Detected, Cattle to Assess Confidence in Freedom from Infection

Quantitative risk assessments for Bovine spongiform encephalopathy (BSE) necessitate estimates for key parameters such as the prevalence of infection, the probability of absence of infection in defined birth cohorts, and the numbers of BSE-infected, but non-detected cattle entering the food chain. We estimated three key parameters with adjustment for misclassification using the German BSE surveillance data using a Gompertz model for latent (i.e., unobserved) age-dependent detection probabilities and a Poisson response model for the number of BSE cases for birth cohorts 1999 to 2015. The models were combined in a Bayesian framework. We estimated the median true BSE prevalence between 3.74 and 0.216 cases per 100,000 animals for the birth cohorts 1990 to 2001 and observed a peak for the 1996 birth cohort with a point estimate of 16.41 cases per 100,000 cattle. For birth cohorts ranging from 2002 to 2013, the estimated median prevalence was below one case per 100,000 heads. The calculated confidence in freedom from disease (design prevalence 1 in 100,000) was above 99.5% for the birth cohorts 2002 to 2006. In conclusion, BSE surveillance in the healthy slaughtered cattle chain was extremely sensitive at the time, when BSE repeatedly occurred in Germany (2000–2009), because the entry of BSE-infected cattle into the food chain could virtually be prevented by the extensive surveillance program during these years and until 2015 (estimated non-detected cases/100.000 [95% credible interval] in 2000, 2009, and 2015 are 0.64 [0.5,0.8], 0.05 [0.01,0.14], and 0.19 [0.05,0.61], respectively).

Updated quantitative risk assessment (QRA) of the BSE risk posed by processed animal protein (PAP)

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.

Mass Spectrometry-Based Immunoassay for the Quantification of Banned Ruminant Processed Animal Proteins in Vegetal Feeds

The ban of processed animal proteins (PAPs) in feed for farmed animals introduced in 2001 was one of the main EU measures to control the bovine spongiform encephalopathy (BSE) crisis. Currently, microscopy and polymerase chain reaction (PCR) are the official methods for the detection of illegal PAPs in feed. However, the progressive release of the feed ban, recently with the legalization of nonruminant PAPs for the use in aquaculture, requires the development of alternative methods to determine the species origin and the source (legal or not). Additionally, discussions about the need for quantitative tests came up, particularly if the zero-tolerance-concept is replaced by introducing PAP thresholds. To address this issue, we developed and partially validated a multiplex mass spectrometry-based immunoassay to quantify ruminant specific peptides in vegetal cattle feed. The workflow comprises a new sample preparation procedure based on a tryptic digestion of PAPs in suspension, a subsequent immunoaffinity enrichment of the released peptides, and a LC-MS/MS-based analysis for peptide quantification using isotope labeled standard peptides. For the very first time, a mass spectrometry-based method is capable of detecting and quantifying illegal PAPs in animal feed over a concentration range of 4 orders of magnitude with a detection limit in the range of 0.1% to 1% (w/w).

Peptidomic Approach to Developing ELISAs for the Determination of Bovine and Porcine Processed Animal Proteins in Feed for Farmed Animals

The European Commission (EC) wants to reintroduce nonruminant processed animal proteins (PAPs) safely into the feed chain. This would involve replacing the current ban in feed with a species-to-species ban which, in the case of nonruminants, would only prohibit feeding them with proteins from the same species. To enforce such a provision, there is an urgent need for species-specific methods for detecting PAPs from several species in animal feed and in PAPs from other species. Currently, optical microscopy and the polymerase chain reaction are the officially accepted methods, but they have limitations, and alternative methods are needed. We have developed immunoassays using antibodies raised against targets which are not influenced by high temperature and pressure. These targets were identified in a previous study based on an experimental approach. One optimized competitive ELISA detects bovine PAPs at 2% in plant-derived feed. The detection capability demonstrated on blind samples shows a good correlation with mass spectrometry results.

Isolation and Analysis of Phospholipids in Dairy Foods

The lipid fraction of milk is one of the most complex matrixes in foodstuffs due to the presence of a high number of moieties with different physical and chemical properties. Glycerolipids include glycerol and two fatty acids esterified in positions sn-1 and sn-2 with higher concentration of unsaturated fatty acids than in the triglyceride fraction of milk. Sphingolipids consist of a sphingoid base linked to a fatty acid across an amide bond. Their amphiphilic nature makes them suitable to be added into a variety of foods and recent investigations show that phospholipids, mainly phosphatidylserine and sphingomyelin, can exert antimicrobial, antiviral, and anticancer activities as well as positive effects in Alzheimer's disease, stress, and memory decline. Polar lipids can be found as natural constituents in the membranes of all living organisms with soybean and eggs as the principal industrial sources, yet they have low contents in phosphatidylserine and sphingomyelin. Animal products are rich sources of these compounds but since there are legal restrictions to avoid transmission of prions, milk and dairy products are gaining interest as alternative sources. This review summarizes the analysis of polar lipids in dairy products including sample preparation (extraction and fractionation/isolation) and analysis by GC or HPLC and the latest research works using ELSD, CAD, and MS detectors.

Investigation of pharmaceuticals in processed animal by-products by liquid chromatography coupled to high-resolution mass spectrometry

There is an on-going trend for developing more sustainable salmon feed in which traditionally applied marine feed ingredients are replaced with alternatives. Processed animal products (PAPs) have been re-authorized as novel high quality protein ingredients in 2013. These PAPs may harbor undesirable substances such as pharmaceuticals and metabolites which are not previously associated with salmon farming, but might cause a potential risk for feed and food safety. To control these contaminants, an analytical strategy based on a generic extraction followed by ultra-high performance liquid chromatography coupled to high resolution mass spectrometry (UHPLC-HRMS) using quadrupole time-of-flight mass analyzer (QTOF MS) was applied for wide scope screening. Quality control samples, consisting of PAP commodities spiked at 0.02, 0.1 and 0.2 mg/kg with 150 analytes, were injected in every sample batch to verify the overall method performance. The methodology was applied to 19 commercially available PAP samples from six different types of matrices from the EU animal rendering industry. This strategy allows assessing possible emergent risk exposition of the salmon farming industry to 1005 undesirables, including pharmaceuticals, several dyes and relevant metabolites.

Identification of Proteins and Peptide Biomarkers for Detecting Banned Processed Animal Proteins (PAPs) in Meat and Bone Meal by Mass Spectrometry

The outbreak of bovine spongiform encephalopathy (BSE) in the United Kingdom in 1986, with processed animal proteins (PAPs) as the main vector of the disease, has led to their prohibition in feed. The progressive release of the feed ban required the development of new analytical methods to determine the exact origin of PAPs from meat and bone meal. We set up a promising MS-based method to determine the species and the source (legal or not) present in PAPs: a TCA-acetone protein extraction followed by a cleanup step, an in-solution tryptic digestion of 5 h (with a 1:20 protein/trypsin ratio), and mass spectrometry analyses, first without any a priori, with a Q-TOF, followed by a targeted triple-quadrupole analysis. Using this procedure, we were able to overcome some of the major limitations of the official methods to analyze PAPs, detecting and identifying prohibited animal products in feedstuffs by the monitoring of peptides specific for cows, pigs, and sheep in PAPs.

Effectiveness of the BSE interventions in Japan

Using a stochastic simulation model, we estimated the effectiveness of the three BSE interventions (SRM removal, post-mortem testing and cohort culling) in Japan, in terms of the amount of bovine ID50 that would be prevented from entering the human food supply and the number of life years that would be saved from resulting vCJD cases. The average reduction of the BSE load on the human food supply under SRM removal was 97% over the period from 2002 to 2009. The average reduction of the BSE load under most-mortem testing was 83% over the period from 2002 to 2007. The risk reducing effect of the three interventions combined was 99%. The maximum number of life years saved by the three interventions combined was 40.84 in 2006.

Sensitive detection of porcine DNA in processed animal proteins using a TaqMan real-time PCR assay

A TaqMan real-time PCR method was developed for specific detection of porcine-prohibited material in industrial feeds. The assay combines the use of a porcine-specific primer pair, which amplifies a 79 bp fragment of the mitochondrial (mt) 12 S rRNA gene, and a locked nucleic acid (LNA) TaqMan probe complementary to a target sequence lying between the porcine-specific primers. The nuclear 18 S rRNA gene system, yielding a 77 bp amplicon, was employed as a positive amplification control to monitor the total content of amplifiable DNA in the samples. The specificity of the porcine primers-probe system was verified against different animal and plant species, including mammals, birds and fish. The applicability of the real-time PCR protocol to detect the presence of porcine mt DNA in feeds was determined through the analysis of 190 industrial feeds (19 known reference and 171 blind samples) subjected to stringent processing treatments. The performance of the method allows qualitative and highly sensitive detection of short fragments from porcine DNA in all the industrial feeds declared to contain porcine material. Although the method has quantitative potential, the real quantitative capability of the assay is limited by the existing variability in terms of composition and processing conditions of the feeds, which affect the amount and quality of amplifiable DNA.