EFSA's Scientific Panels Research Articles

Software for benchmark dose modelling

EFSA Supporting PublicationsVolume 14, Issue 2 1170E External scientific reportOpen Access Software for benchmark dose modelling Machteld Varewyck, Machteld Varewyck Open Analytics NVSearch for more papers by this authorTobias Verbeke, Tobias Verbeke Open Analytics NVSearch for more papers by this author Machteld Varewyck, Machteld Varewyck Open Analytics NVSearch for more papers by this authorTobias Verbeke, Tobias Verbeke Open Analytics NVSearch for more papers by this author First published: 23 February 2017 https://doi.org/10.2903/sp.efsa.2017.EN-1170Citations: 7 Question numbers: EFSA-Q-2016-00419 and EFSA-Q-2016-00420 Disclaimer: The present document has been produced and adopted by the bodies identified above as authors. This task has been carried out exclusively by the authors in the context of a contract between the European Food Safety Authority and the authors, awarded following a tender procedure. The present document is published complying with the transparency principle to which the Authority is subject. It may not be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the authors. AboutPDF ToolsExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat References European Food Safety Authority; 2011. Use of BMDS and PROAST software packages by EFSA Scientific Panels and Units for applying the Benchmark Dose (BMD) approach in risk assessment. EN-113. [190 pp.]. Available online: www.efsa.europa.eu Guidance of the Scientific Committee on a request from EFSA on the use of the benchmark dose approach in risk assessment. The EFSA Journal (2009) 1150, 1– 72. Slob, Wout and Cotton, Richard (2015) proast61.3: Benchmark Dose modelling. R package version 0.0 Wheeler, Matthew W., and A. John Bailer. “Properties of model-averaged BMDLs: a study of model averaging in dichotomous response risk estimation.” Risk Analysis 27.3 (2007): 659– 670. Wheeler, Matthew W., and A. John Bailer. “Model averaging software for dichotomous dose response risk estimation.” Journal of Statistical Software 26.5 (2008): 1– 15. Citing Literature Volume14, Issue2February 20171170E ReferencesRelatedInformation

Statement on the update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 3: Suitability of taxonomic units notified to EFSA until September 2015

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 pre-assessment 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 was 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 49 biological agents were notified to EFSA between March and September 2015. From these, 24 biological agents already had a QPS status and did not require further evaluation, and 16 were not included as they are filamentous fungi or enterococci, biological groups which have been excluded from the QPS activities since 2014. Three notifications for Streptomyces were not included because the genus have already been evaluated in the previous statement of December 2014 and found unsuitable for QPS. Two notifications belonging to the species Escherichia coli were not evaluated for QPS status, because this species was recently re-assessed and considered not suitable for QPS status. Therefore, there were four notifications related to four taxonomic units that were evaluated for QPS status. Pasteuria nishizawae may be recommended for the QPS status to be used in plant protection products to combat cyst nematodiasis. The other three units were not recommended for the QPS list: gen. nov. sp. nov. DSM 11798 of the Coriobacteriaceae family, Chromobacterium subtsugaeand Pseudomonas chlororaphis.

Statement on the update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA. 2: Suitability of taxonomic units notified to EFSA until March 2015

EFSA is 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 pre-assessment 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 are assessed. Identified safety concerns 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 85 biological agents were notified to EFSA between October 2014 and March 2015. From those, 35 biological agents already had a QPS status and were not further evaluated, and 45 were also not included as they are filamentous fungi or enterococci, biological groups which have been excluded from the QPS activities since 2014. Two notifications referred to two taxonomic units which were evaluated for the QPS status, one of which was recommended for the QPS list: Xanthomonas campestris, only for the production of xanthan gum, while the other, Bacillus circulans, was not due to insufficient body of knowledge on a safe history of use in foods and feeds. Three notifications belonging to the genus Streptomyces were not evaluated for the QPS status, because the genus was recently considered not suitable for the QPS approach.

Scientific Opinion on the maintenance of the list of QPS biological agents intentionally added to food and feed (2013 update)

EFSA is 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 pre-assessment 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 are assessed. Identified safety 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 recommended biological agents is reviewed and updated periodically. Therefore, the only valid list is the one in the most recently published scientific opinion. The 2013 update reviews previously assessed microorganisms including bacteria, yeasts, filamentous fungi, oomycetes and viruses used for plant protection purposes. All taxonomic units previously recommended for the QPS list had their status reconfirmed. The new notifications since the last QPS update were reviewed. Gluconobacter oxydans and Alphaflexiviridae were assessed for the first time and were recommended for the QPS list. The information of the previous opinion was updated for the taxonomic units on the QPS list. Qualifications for the taxonomic units included in the QPS recommended list were reviewed and confirmed. Filamentous fungi and enterococci were not recommended for the QPS list following updating and reviewing of current scientific knowledge.

Scientific Opinion on the maintenance of the list of QPS biological agents intentionally added to food and feed (2012 update)

EFSA is 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 for safety risk assessments to provide a harmonised generic pre-assessment to support 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 are assessed. Identified safety concerns for a taxonomic unit are where possible and reasonable in number reflected as ‘qualifications’ with a recommendation for the QPS list. The list of QPS recommended biological agents is reviewed and updated annually. Therefore, the only valid list is the one in the most recently published scientific opinion. The 2012 update reviews microorganisms previously assessed including bacteria, yeasts, filamentous fungi and viruses used for plant protection purposes. The BIOHAZ Panel confirmed all taxonomic units previously recommended for the QPS list. The notifications were reviewed. Bacillus firmus was re-evaluated and not recommended for the QPS list. A new recommendation was made for Leuconostoc pseudomesenteroides. Carnobacterium maltaromaticumwas assessed for the first time and not recommended for the QPS list. Qualifications for the taxonomic units included in the QPS recommended list were reviewed and confirmed. Filamentous fungi and enterococci were not recommended for the QPS list following updating and reviewing of current scientific knowledge. For Enterococcus faeciumrecent data indicate a possible distinction between pathogenic and non-pathogenic strains. This is considered too recent knowledge for a QPS recommendation, considering the recent information on the evolution of the epidemiology of Enterococcus infections in humans.

Risk assessment of biological hazards for consumer protection

EFSA's scientific Panel on Biological Hazards (BIOHAZ Panel) provides independent scientific advice on biological hazards in relation to food safety and food-borne diseases. This covers food-borne zoonoses, food microbiology, food hygiene, antimicrobial resistance (AMR), transmissible spongiform encephalopathies (BSE/TSEs) and associated waste management issues. Most of the activities of the BIOHAZ Panel focus on human health and the whole food chain and on science-based interventions to lower the risk to consumers. In the future, food-borne disease burden estimations are foreseen to become increasingly relevant. The risk assessments done by the BIOHAZ Panel are in line with the EU (European Union) strategy of one health, include a farm to fork approach and in many cases have a high multidisciplinary component. Whenever possible, the Panel applies this risk assessment framework developed by Codex Alimentarius as a basis for their work on food safety. The outcomes of some of the activities during the last three to four years are presented. From these examples of recent BIOHAZ opinions it can be seen that the work covers different approaches, ranging from quantitative risk assessments over structured qualitative risk assessment/risk ranking to opinions with short deadlines summarising existence knowledge from scientific literature. The approach taken depends on both the terms of reference (ToR) as received from the EC (European Commission), the available data and resources, and last but not least the time frame for the work following the risk managers’ needs.

Outcome of the public consultation on the draft EFSA guidance on selected default values to be used by the EFSA Scientific Panels and Committee, and EFSA Units in the absence of actual measured data

Outcome of the public consultation on the draft EFSA guidance on selected default values to be used by the EFSA Scientific Panels and Committee, and EFSA Units in the absence of actual measured data

Scientific Opinion on On‐site treatment of pig carcasses

EFSA's Scientific Panel on Biological Hazards (BIOHAZ) was asked for a scientific opinion on an alternative method for processing Category (Cat) 2 Animal By-Products (ABP). The materials to be treated are placentas and fallen pigs; this implies that the animals died due to a disease, which in most cases was not properly diagnosed. The target parameters are: i) particle size less than 150 mm and ii) heating for 10–12 hours at 100°C. The end-product obtained is mixed with pig slurry and used as an organic fertiliser. According to the legislation in force, before being used as an organic fertiliser, Cat. 2 material should be treated with a sterilisation process (i.e. 133°C / 20 min / 3 bars / 50 mm particle size). The most resistant hazards identified by the applicant as target to demonstrate the risk reduction are spores of pathogenic clostridia. Due to uncertainty on the cause of the animals’ death, the presence of more resistant hazards cannot be considered negligible. The sterilisation process defined in the current legislation is able to minimise the risks due to unidentified agents, such as Bacillus anthracis and TSE agents. The BIOHAZ Panel concluded that the process proposed was not properly validated experimentally under real scale conditions. In theory, it should permit a high degree of reduction of spores of pathogenic clostridia but because of several uncertainties (i.e. water evaporation, fat protective effect and particle size) it is not certain that the values of the parameters used in the theoretical calculations would apply in practice. Moreover, the proposed alternative method cannot be considered equivalent to the sterilisation process defined in the current legislation. This would be particularly relevant in the case of extremely heat resistant spores being present in the material to be treated.

Use of BMDS and PROAST software packages by EFSA Scientific Panels and Units for applying the Benchmark Dose (BMD) approach in risk assessment

Use of BMDS and PROAST software packages by EFSA Scientific Panels and Units for applying the Benchmark Dose (BMD) approach in risk assessment

Scientific Opinion on the maintenance of the list of QPS biological agents intentionally added to food and feed (2010 update)

EFSA is requested to assess the safety of a broad range of biological agents (including microorganisms and viruses) 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) concept was developed by EFSA for its own use to provide a generic risk assessment approach applicable across EFSA's scientific Panels, for biological agents notified for intentional use in the whole food chain. The safety of unambiguously defined biological agents at the highest taxonomic unit that is appropriate for the purpose for which an application is intended are assessed, considering if the body of knowledge is sufficient. Identified safety concerns for a taxonomic unit could be reflected as ‘qualifications’ when considered appropriate for an inclusion on the QPS list. The list of QPS recommended biological agents is reviewed and updated annually. The 2010 update reviews the previously assessed microorganisms including bacteria, yeasts, filamentous fungi and viruses used for plant protection purposes. The recommendations of biological agents of the previous year were confirmed in the current update. Qualifications relating to the agents recommended for QPS were reviewed, clarified and updated where necessary. Specific sections dealing with antibiotic resistance relevant for QPS recommended microorganisms and yeast were included. The methodology used for carrying out the annual review of the list of QPS recommended biological agents was detailed. A list of microbial species from previous notifications and as notified to EFSA, annexed in this opinion, includes information on taxonomic units which are or are not recommended for the QPS list. This list of notifications aims to summarize and maintain important information for future assessments and updates.

Biological Safety of a Process for the Hydrolysis on-Farm of Dead Rabbits - Scientific Opinion of the Panel on Biological Hazards

SUMMARY Following a request from the Spanish Competent Authority, the EFSA Scientific Panel on Biological Hazards (BIOHAZ) was asked to deliver a Scientific Opinion on the biological safety of a specific process for the Hydrolysis on-Farm of Dead Pigs. The application concerns the on-farm treatment of pig carcasses and other pig by-products 2 , which are considered as Category 2 animal by-products according to Reg. (EC) No 1774/2002, through an enzymatic hydrolysis in mesophilic and partially anaerobic conditions within a closed vat for a period of minimum six months. The intended end-use of the processed material is represented by its utilisation as organic fertilizer or soil improver, as composting material, as biogas production material or as a material to be delivered to a waste management unit for disposal. The BIOHAZ Panel concluded that, due to some deficiencies in the provided dossier, it was not possible to assess the safety of the process for the disposal or use of Category 2 animal byproducts. The BIOHAZ Panel does not recommend this process to be applied as an alternative method of disposal or use of Category 2 animal by-products.

Opinion of the Scientific Panel on Plant Health on the pest risk analysis made by EPPO on Lysichiton americanus Hultén & St. John (American or yellow skunk cabbage)

Following a request from the European Commission, the EFSA Scientific Panel on Plant Heath was asked to deliver a scientific opinion on two pest risk analyses made by the European and Mediterranean Plant Protection Organization (EPPO) on invasive alien plants (American skunk cabbage and floating pennywort). The Panel was in particular asked a) whether these organisms can be considered as harmful for the endangered area of the European Community and thus potentially eligible for addition to the list of harmful organisms in the plant health Directive 2000/29/EC, and b) whether the identified management options are appropriate through an evaluation of their efficacy, feasibility and impact. This document presents the opinion of the Panel on Plant Health on the pest risk analysis made by EPPO on Lysichiton americanus Hulten and St. John. L. americanus is a yellow-flowered herbaceous perennial plant known as American skunk cabbage or yellow skunk cabbage. It can be terrestrial, semi-aquatic and even aquatic. It has been introduced into Europe intentionally as an ornamental garden plant. It is naturalised in several European countries including Ireland, Germany, Norway, Sweden, Switzerland and UK. However, invasive behaviour has been reported in parts of Europe, with local species extinction reported in Germany. L. americanus is considered an invasive alien plant by EPPO and is included on the EPPO Action List (pests which EPPO recommend member countries to consider for inclusion in their phytosanitary regulations), with the entire EPPO region considered an endangered area. In delivering this opinion the Panel conducted a detailed review of the EPPO pest risk analysis provided, using the internationally accepted standard for pest risk analysis for quarantine pests ISPM No 11. The available information shows that Lysichiton americanus can be considered an invasive species with potential to cause environmental damage to ecologically vulnerable wetland habitats. However, the factors contributing to invasive behaviour are not well characterised and thus the endangered area cannot be clearly defined. Despite the presence of L. americanus in at least nine European countries, clear evidence of environmental damage has been found only in restricted areas of Germany. A more detailed analysis is required to identify the key factors contributing to invasive behaviour. Although the Panel recognises that invasiveness of a plant in one area can be a signal for its invasiveness elsewhere, it concludes that the information provided in the EPPO document is insufficient to confirm that L. americanus qualifies as a quarantine pest for the EC. The Panel considers that the significant knowledge gaps identified in the pest risk assessment stage of the pest risk analysis preclude a detailed evaluation of management options at this stage. The Panel suggests that further work, including monitoring and surveillance, is needed to address the areas of uncertainty identified in the EPPO document, in order to identify the areas of the European Community at risk and enable management options to be considered. These include: a) the effect of abiotic factors on the establishment, development, reproduction, survival and dispersal of the plant in both the native and introduced range; b) the population dynamics of the plant in areas where it is present but not invasive; c) the volume of trade in L. americanus as an ornamental plant entering and moving within the EC, including further analysis of the pathways through which it can reach natural water bodies; d) the nature and occurrence of areas within the EC where conditions result in invasiveness of the plant, supported by the use of modelling and geographic information system (GIS) tools. the environmental damage caused by the plant in areas where it is invasive.

Risk assessment of biological hazards in the European Union

International, community and national food safety law and any subsequent decision-making practices aim to be based on risk analysis—a process consisting of risk assessment, risk management and risk communication. With the appointment of the European Food Safety Authority as an independent scientific point of reference in risk assessment, there is a clear functional separation between risk assessment and risk management in the European Union food safety context. When a food safety question on microbiological hazards is to be answered – which is under the remit of the EFSA's Scientific Panel on Biological Hazards (BIOHAZ) – extensive dialogue and interactions covering the clarity of the question, the acceptability of the deadline and the availability of all necessary information take place with both the risk managers who ask the question and the stakeholders. During the first mandate of the BIOHAZ Panel (2003–2006), the scientific opinions were mainly based on qualitative and in some cases semi-quantitative microbiological risk assessment. In the second mandate of the BIOHAZ Panel, and as a first step towards developing a European approach on Quantitative Microbiological Risk Assessment (QMRA), EFSA is preparing to carry out a QMRA on Salmonella in pigs, at European level through a consortium of European institutes.