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      Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 5: suitability of taxonomic units notified to EFSA until September 2016

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      EFSA Panel on Biological Hazards (BIOHAZ), , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,
      EFSA Journal
      John Wiley and Sons Inc.
      safety, QPS, bacteria, yeast, Arthrobacter ramosus, Bacillus smithii, Pseudomonas fluorescens

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          Abstract

          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.

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          Introduction of a Qualified Presumption of Safety (QPS) approach for assessment of selected microorganisms referred to EFSA - Opinion of the Scientific Committee

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            Phylogenomics and systematics in Pseudomonas

            The genus Pseudomonas currently contains 144 species, making it the genus of Gram-negative bacteria that contains the largest number of species. Currently, multilocus sequence analysis (MLSA) is the preferred method for establishing the phylogeny between species and genera. Four partial gene sequences of housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD) were obtained from 112 complete or draft genomes of strains related to the genus Pseudomonas that were available in databases. These genes were analyzed together with the corresponding sequences of 133 Pseudomonas type strains of validly published species to assess their correct phylogenetic assignations. We confirmed that 30% of the sequenced genomes of non-type strains were not correctly assigned at the species level in the accepted taxonomy of the genus and that 20% of the strains were not identified at the species level. Most of these strains had been isolated and classified several years ago, and their taxonomic status has not been updated by modern techniques. MLSA was also compared with indices based on the analysis of whole-genome sequences that have been proposed for species delineation, such as tetranucleotide usage patterns (TETRA), average nucleotide identity (ANIm, based on MUMmer and ANIb, based on BLAST) and genome-to-genome distance (GGDC). TETRA was useful for discriminating Pseudomonas from other genera, whereas ANIb and GGDC clearly separated strains of different species. ANIb showed the strongest correlation with MLSA. The correct species classification is a prerequisite for most diversity and evolutionary studies. This work highlights the necessity for complete genomic sequences of type strains to build a phylogenomic taxonomy and that all new genome sequences submitted to databases should be correctly assigned to species to avoid taxonomic inconsistencies.
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              EDITORIAL

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                Author and article information

                Journal
                EFSA J
                EFSA J
                10.1002/(ISSN)1831-4732
                EFS2
                EFSA Journal
                John Wiley and Sons Inc. (Hoboken )
                1831-4732
                14 March 2017
                March 2017
                : 15
                : 3 ( doiID: 10.1002/efs2.2017.15.issue-3 )
                : e04663
                Author notes
                [*] Correspondence: biohaz@ 123456efsa.europa.eu
                Article
                EFS24663
                10.2903/j.efsa.2017.4663
                7328882
                32625420
                6e9410b9-2c30-481d-a47c-e808659bb4fc
                © 2017 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited and no modifications or adaptations are made.

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                Figures: 0, Tables: 2, Pages: 20, Words: 10099
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                2.0
                March 2017
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.8.4 mode:remove_FC converted:23.06.2020

                safety,qps,bacteria,yeast,arthrobacter ramosus,bacillus smithii,pseudomonas fluorescens

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