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The qualified presumption of safety (QPS) was developed to provide a harmonised generic pre‐evaluation procedure 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 by ‘qualifications’ which should be assessed at the strain level by the EFSA's Scientific Panels. During the current assessment, no new information was found that would change the previously recommended QPS taxonomic units and their qualifications. The Panel clarified that the qualification ‘for production purpose only’ implies the absence of viable cells of the production organism in the final product and can also be applied for food and feed products based on microbial biomass. Between September 2017 and March 2018, the QPS notification list was updated with 46 microorganisms from applications for market authorisation. From these, 28 biological agents already had QPS status, 15 were excluded of the QPS exercise from the previous QPS mandate (10 filamentous fungi and one bacteriophage) or from further evaluations within the current mandate (two notifications of Streptomyces spp. and one of Escherichia coli), and one was excluded where confirmatory data for the risk assessment of a plant protection product (PPP) was requested (Pseudomonas sp.). Three taxonomic units were (re)evaluated: Paracoccus carotinifaciens and Paenibacillus lentus had been previously evaluated in 2008 and 2014, respectively, and were now re‐evaluated within this mandate, and Yarrowia lipolytica, which was evaluated for the first time. P. carotinifaciens and P. lentus cannot be granted QPS status due to lack of scientific knowledge. Y. lipolytica is recommended for QPS status, but only for production purpose.

The blaESBL and blaAmpC genes are spread by plasmid-mediated integrons, insertion sequences, and transposons, some of which are homologous in food animals and humans. Cephalosporin usage in animal production is an important risk factor; restricting such use would be an effective control option

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 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 57 biological agents were notified to EFSA between the end of April 2016 and the beginning of September 2016. From these, 34 biological agents already had a QPS status and did not require further evaluation, and 10 were not included in the evaluation as they are filamentous fungi or enterococci, biological groups which have been excluded from QPS evaluation since 2014. Three notifications for Streptomyces violaceoruber, one for Streptomyces albus, one for Bacillus circulans and four for Escherichia coli were not evaluated for QPS status because these species were recently assessed and considered not suitable for QPS status. Therefore, only four notifications related to three taxonomic units were evaluated for QPS status. Of these, Arthrobacter ramosus and Pseudomonas fluorescens are not recommended for the QPS list. Bacillus smithii is recommended for the QPS status., This publication is linked to the following EFSA Journal article: http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2017.4664/full, http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2017.e15031/full

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.

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 pneumoniae, Paenibacillus macerans, ‘Protaminobacter rubrum’ and Pullulanibacillusnaganoensis are not recommended for the QPS list.