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CGM-18-001 Perseus Report Update Bacterial Taxonomy Final Errata

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report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly. These lists of bacteria originate from 2011, when COGEM petitioned a research project to evaluate the classifications of bacteria in the former GMO regulation and to supplement this list with bacteria that have been classified by other governmental organizations. The resulting pathogenicity classification lists have subsequently been updated in 2013, 2014 and 2017 with new bacterial species that have been classified. Over the years, the bacterial taxonomy has been subjected to many revisions mainly due to developments in sequencing technology. In the 2017 update of the bacterial pathogenicity classifications, COGEM stated that new insights in taxonomy have not yet been processed in the COGEM listings, and that a taxonomic revision of the list would be conducted at a later stage. The present report builds upon this advice, and contains a thorough taxonomic revision of the lists of pathogenic and non-pathogenic bacteria. The research has been performed by dr. Pascale van Rooij and dr. Patrick Rüdelsheim, who have diligently and meticulously gone through the lists of over 2,000 bacterial species and genera to document any inconsistencies with the current taxonomy. A variety of sources and databases have been accessed and any typographic errors and reclassifications were registered. This research also proves that taxonomic revisions can be ambiguous, and in some cases no consensus is reached on the official nomenclature. Differences between databases can further complicate decisions about naming. In case of such uncertainties, the authors have provided detailed information to facilitate the final decision making by COGEM. Taxonomy is an ever changing field; phenotypic characteristics are no longer the sole defining properties and development of novel molecular techniques creates new insights into the bacterial phylogeny. The supervisory committee is pleased with the research report, and the cooperation was prosperous. The authors have provided an extensive and detailed description of taxonomic changes, which serves as a valuable contribution to the COGEM as a knowledge base of phylogeny and for revision of the pathogenicity classification lists. Prof. dr. J.P.M. van Putten Chair of the Advisory Committee Chair of the Medical Veterinary subcommittee of COGEM 3 | 24 Summary A taxonomic review was performed encompassing all pathogenic and apathogenic bacteria listed in the classification lists of COGEM. This report identifies a substantial amount of cases for which a name change should be considered: 294 out of 1360 studied pathogenic taxa and 192 out of 976 apathogenic taxa. The main rationale for a proposed name change was either a typographical correction of a genus name or epithet, or a reclassification due to new insights into bacterial taxonomy. The report identifies several taxa for which one or more synonyms are being used, due to lack of consensus among bacteriologists about the naming, or because no official authority has as yet indicated the correct name. Furthermore, a limited number of taxa remains with an uncertain nomenclature due to lack of scientific information that would enable proper revision or rigid classification. All nomenclatural changes, proposals for amendment and ambiguities are documented in detail in order to allow final decision-making by the COGEM (Annexes 1a-h and 2a-h). Revised listings of apathogenic and pathogenic bacteria are proposed in Annexes 3 and 4. Finally, some observations on risk classifications are documented. 4 | 24 Samenvatting Een taxonomische doorlichting werd uitgevoerd van alle pathogene en apathogene bacteriën die zijn opgenomen in de classificatielijsten van de COGEM. Dit rapport identificeert een aanzienlijk aantal gevallen waarvoor een naamsverandering dient in overweging te worden genomen: 294 van de 1360 bestudeerde pathogene taxa, en 192 van de 976 apathogene taxa. De voornaamste onderliggende redenen om een naamswijziging voor te stellen zijn ofwel een typografische correctie van een genusnaam of epitheton, of een herclassificatie door een nieuw inzicht in de bacteriële taxonomie. Het rapport identificeert verschillende taxa waarvoor één of meerdere synoniemen in gebruik zijn door een gebrek aan eensgezindheid onder bacteriologen over de naamgeving, of doordat geen officiële autoriteit een formeel besluit neemt over welke de correcte naam moet zijn. Daarnaast zijn er verschillende taxa met een onzekere naamgeving waarvoor de nodige wetenschappelijke informatie ontbreekt voor een grondige herziening of herindeling. Alle naamswijzigingen, voorstellen tot wijziging en onduidelijkheden worden uitvoerig gedocumenteerd om tot een vlotte besluitvorming te komen met de COGEM (Annexen 1a-h en 2a-h). Herziene lijsten van apathogene en pathogene bacteria worden voorgesteld in Annexen 3 en 4. Tot slot, documenteert dit rapport een aantal vaststellingen in verband met de pathogeniteitsclassificatie. 5 | 24 Table of contents FOREWORD ................................................................................................................................... 3 SUMMARY ...................................................................................................................................... 4 SAMENVATTING ............................................................................................................................ 5 TABLE OF CONTENTS .................................................................................................................. 6 ABBREVIATIONS AND SYMBOLS ................................................................................................ 7 INTRODUCTION ............................................................................................................................. 9 1 PURPOSE OF THE STUDY ...................................................................................................... 9 2 METHODS ................................................................................................................................. 9 3 RESULTS ................................................................................................................................ 13 3.1 PATHOGENIC BACTERIA .......................................................................................................... 13 3.1.1 TAXA WITHOUT NAME CHANGE (ANNEX 1A) ........................................................................... 13 3.1.2 TAXA TO BE DELETED AND/OR TRANSFERRED TO OTHER COGEM-LISTINGS (ANNEX 1B) ........ 13 3.1.3 TAXA WITH CORRECTED NAMES (ANNEX 1C) ......................................................................... 13 3.1.4 TAXA WITH TAXONOMIC CHANGES (ANNEXES 1D-G) .............................................................. 14 3.1.5 TAXA WITH UNCERTAIN NOMENCLATURE (ANNEX 1H) ............................................................ 15 3.1.6 OBSERVATIONS ON RISK CLASSIFICATIONS ........................................................................... 15 3.2 APATHOGENIC BACTERIA ........................................................................................................ 16 3.2.1 TAXA WITHOUT NAME CHANGE (ANNEX 2A) .......................................................................... 16 3.2.2 TAXA WITH CORRECTED NAMES (ANNEX 2B) ......................................................................... 16 3.2.3 TAXA WITH TAXONOMIC CHANGES (ANNEXES 2C-G) .............................................................. 16 3.2.4 TAXA WITH UNCERTAIN NOMENCLATURE (ANNEX 2H) ............................................................ 17 3.2.5 OBSERVATIONS ON RISK CLASSIFICATIONS ........................................................................... 17 4 DISCUSSION & RECOMMENDATIONS ................................................................................ 18 5 REFERENCES .......................................................................................................................
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