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      Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 11: suitability of taxonomic units notified to EFSA until September 2019

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      EFSA Panel on Biological Hazards (BIOHAZ) , , , , , , , , , , , , , , , , , , , , , , , , , ,
      EFSA Journal
      John Wiley and Sons Inc.
      safety, QPS, bacteria, yeast, Aurantiochytrium limacinum, Bacillus velezensis, Corynebacterium stationis, Cupriavidus necator, Hamamotoa singularis, Kodamaea ohmeri, Lactobacillus parafarraginis, Paenibacillus illinoisensis, Pantoea ananatis, Parageobacillus thermoglucosidasius, Protaminobacter rubrum, Rhodococcus aetherovorans, Rhodococcus ruber, Tetraselmis chuii, Zygosaccharomyces rouxii

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          Abstract

          Qualified presumption of safety ( QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance are assessed. Safety concerns identified for a taxonomic unit ( TU) are where possible to be confirmed at strain or product level, reflected by ‘qualifications’. No new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA was updated with 54 biological agents, received between April and September 2019; 23 already had QPS status, 14 were excluded from the QPS exercise (7 filamentous fungi, 6 Escherichia coli, Sphingomonas paucimobilis which was already evaluated). Seventeen, corresponding to 16 TUs, were evaluated for possible QPS status, fourteen of these for the first time, and Protaminobacter rubrum, evaluated previously, was excluded because it is not a valid species. Eight TUs are recommended for QPS status. Lactobacillus parafarraginis and Zygosaccharomyces rouxii are recommended to be included in the QPS list. Parageobacillus thermoglucosidasius and Paenibacillus illinoisensis can be recommended for the QPS list with the qualification ‘for production purposes only’ and absence of toxigenic potential. Bacillus velezensis can be recommended for the QPS list with the qualification ‘absence of toxigenic potential and the absence of aminoglycoside production ability’. Cupriavidus necator, Aurantiochytrium limacinum and Tetraselmis chuii can be recommended for the QPS list with the qualification ‘production purposes only’. Pantoea ananatis is not recommended for the QPS list due to lack of body of knowledge in relation to its pathogenicity potential for plants. Corynebacterium stationis, Hamamotoa singularis, Rhodococcus aetherivorans and Rhodococcus ruber cannot be recommended for the QPS list due to lack of body of knowledge. Kodamaea ohmeri cannot be recommended for the QPS list due to safety concerns.

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          Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov.

          Understanding of the phylogeny and interrelationships of the genera within the order 'Enterobacteriales' has proven difficult using the 16S rRNA gene and other single-gene or limited multi-gene approaches. In this work, we have completed comprehensive comparative genomic analyses of the members of the order 'Enterobacteriales' which includes phylogenetic reconstructions based on 1548 core proteins, 53 ribosomal proteins and four multilocus sequence analysis proteins, as well as examining the overall genome similarity amongst the members of this order. The results of these analyses all support the existence of seven distinct monophyletic groups of genera within the order 'Enterobacteriales'. In parallel, our analyses of protein sequences from the 'Enterobacteriales' genomes have identified numerous molecular characteristics in the forms of conserved signature insertions/deletions, which are specifically shared by the members of the identified clades and independently support their monophyly and distinctness. Many of these groupings, either in part or in whole, have been recognized in previous evolutionary studies, but have not been consistently resolved as monophyletic entities in 16S rRNA gene trees. The work presented here represents the first comprehensive, genome-scale taxonomic analysis of the entirety of the order 'Enterobacteriales'. On the basis of phylogenetic analyses and the numerous identified conserved molecular characteristics, which clearly distinguish members of the order 'Enterobacteriales' and the seven reported clades within this order, a proposal is made here for the order Enterobacterales ord. nov. which consists of seven families: Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov.
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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

            (2007)
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              Scientific Opinion on the update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA (2017–2019)

              Abstract The qualified presumption of safety (QPS) was developed to provide a safety pre‐assessment within EFSA for microorganisms. Strains belonging to QPS taxonomic units (TUs) still require an assessment based on a specific data package, but QPS status facilitates fast track evaluation. QPS TUs are unambiguously defined biological agents assessed for the body of knowledge, their safety and their end use. Safety concerns are, where possible, to be confirmed at strain or product level, and reflected as ‘qualifications’. Qualifications need to be evaluated at strain level by the respective EFSA units. The lowest QPS TU is the species level for bacteria, yeasts and protists/algae, and the family for viruses. The QPS concept is also applicable to genetically modified microorganisms used for production purposes if the recipient strain qualifies for the QPS status, and if the genetic modification does not indicate a concern. Based on the actual body of knowledge and/or an ambiguous taxonomic position, the following TUs were excluded from the QPS assessment: filamentous fungi, oomycetes, streptomycetes, Enterococcus faecium, Escherichia coli and bacteriophages. The list of QPS‐recommended biological agents was reviewed and updated in the current opinion and therefore now becomes the valid list. For this update, reports on the safety of previously assessed microorganisms, including bacteria, yeasts and viruses (the latter only when used for plant protection purposes) were reviewed, following an Extensive Literature Search strategy. All TUs previously recommended for 2016 QPS list had their status reconfirmed as well as their qualifications. The TUs related to the new notifications received since the 2016 QPS opinion was periodically evaluated for QPS status in the Statements of the BIOHAZ Panel, and the QPS list was also periodically updated. In total, 14 new TUs received a QPS status between 2017 and 2019: three yeasts, eight bacteria and three algae/protists.
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                Author and article information

                Contributors
                biohaz@efsa.europa.eu
                Journal
                EFSA J
                EFSA J
                10.1002/(ISSN)1831-4732
                EFS2
                EFSA Journal
                John Wiley and Sons Inc. (Hoboken )
                1831-4732
                03 February 2020
                February 2020
                : 18
                : 2 ( doiID: 10.1002/efs2.v18.2 )
                : e05965
                Author notes
                [*] [* ] Correspondence: biohaz@ 123456efsa.europa.eu
                Article
                EFS25965
                10.2903/j.efsa.2020.5965
                7448003
                d6d3335a-232c-4b3c-bdbc-b44b4dcdf97e
                © 2020 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: 3, Pages: 57, Words: 26077
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                2.0
                February 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.8.7 mode:remove_FC converted:26.08.2020

                safety,qps,bacteria,yeast,aurantiochytrium limacinum,bacillus velezensis,corynebacterium stationis,cupriavidus necator,hamamotoa singularis,kodamaea ohmeri,lactobacillus parafarraginis,paenibacillus illinoisensis,pantoea ananatis,parageobacillus thermoglucosidasius,protaminobacter rubrum,rhodococcus aetherovorans,rhodococcus ruber,tetraselmis chuii,zygosaccharomyces rouxii

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