Emendation of the Genus Auritidibacter Yassin et al. 2011 and Auritidibacter ignavus Yassin et al. 2011 based on features observed from Canadian and Swiss clinical isolates and whole-genome sequencing analysis

is a Gram-stain-positive bacillus derived from otorrhea. Four strains derived from ear discharges in Canada and Switzerland, with features consistent with but distinguishable from IMMIB L-1656 (accession number FN554542) by 16S rRNA gene sequencing (97.5 % similarity), were thought to represent a no...

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Veröffentlicht in:International journal of systematic and evolutionary microbiology 2020-01, Vol.70 (1), p.83-88
Hauptverfasser: Bernard, K A, Pacheco, A L, Burdz, T, Wiebe, D, Beniac, D R, Hiebert, S L, Booth, T F, Jakopp, B, Goldenberger, D, Seth-Smith, H M B, Egli, A, Bernier, A-M
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container_title International journal of systematic and evolutionary microbiology
container_volume 70
creator Bernard, K A
Pacheco, A L
Burdz, T
Wiebe, D
Beniac, D R
Hiebert, S L
Booth, T F
Jakopp, B
Goldenberger, D
Seth-Smith, H M B
Egli, A
Bernier, A-M
description is a Gram-stain-positive bacillus derived from otorrhea. Four strains derived from ear discharges in Canada and Switzerland, with features consistent with but distinguishable from IMMIB L-1656 (accession number FN554542) by 16S rRNA gene sequencing (97.5 % similarity), were thought to represent a novel species of the genus . DSM 45359 (=IMMIB L-1656 ) was acquired to compare with Canadian and Swiss strains by whole-genome sequencing (WGS). Unexpectedly, those isolates were observed to be consistent with DSM 45359 by WGS (ANIb scores >98 %), MALDI-TOF (Bruker), cellular fatty acid analysis and biochemically (some differences were observed). A nearly full 16S rRNA gene sequence could not be readily prepared from DSM 45359 , even after multiple attempts. A 16S rRNA gene chimeric consensus sequence created from the genome assembly of DSM 45359 had only 97.5 % similarity to that of IMMIB L-1656 , implying that 16S rRNA sequence accession number FN554542 could not be replicated. We concluded that our isolates of members of the genus were consistent with DSM 45359 , did not represent a novel species, and that the sequence corresponding to FN554542 was not reproducible. By WGS, DSM 45359 had genome of 2.53×10  bp with a DNA G+C content of 59.34%, while genomes of Canadian and Swiss isolates ranged from 2.47 to 2.59×10  bp with DNA G+C contents of 59.3-59.52 %. NML 100628 (=NCTC 14178=LMG 30897) did not demonstrate a rodcoccus cycle. Emendation of was proposed based on these results.
doi_str_mv 10.1099/ijsem.0.003719
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Four strains derived from ear discharges in Canada and Switzerland, with features consistent with but distinguishable from IMMIB L-1656 (accession number FN554542) by 16S rRNA gene sequencing (97.5 % similarity), were thought to represent a novel species of the genus . DSM 45359 (=IMMIB L-1656 ) was acquired to compare with Canadian and Swiss strains by whole-genome sequencing (WGS). Unexpectedly, those isolates were observed to be consistent with DSM 45359 by WGS (ANIb scores &gt;98 %), MALDI-TOF (Bruker), cellular fatty acid analysis and biochemically (some differences were observed). A nearly full 16S rRNA gene sequence could not be readily prepared from DSM 45359 , even after multiple attempts. A 16S rRNA gene chimeric consensus sequence created from the genome assembly of DSM 45359 had only 97.5 % similarity to that of IMMIB L-1656 , implying that 16S rRNA sequence accession number FN554542 could not be replicated. We concluded that our isolates of members of the genus were consistent with DSM 45359 , did not represent a novel species, and that the sequence corresponding to FN554542 was not reproducible. By WGS, DSM 45359 had genome of 2.53×10  bp with a DNA G+C content of 59.34%, while genomes of Canadian and Swiss isolates ranged from 2.47 to 2.59×10  bp with DNA G+C contents of 59.3-59.52 %. NML 100628 (=NCTC 14178=LMG 30897) did not demonstrate a rodcoccus cycle. 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Pacheco, A L ; Burdz, T ; Wiebe, D ; Beniac, D R ; Hiebert, S L ; Booth, T F ; Jakopp, B ; Goldenberger, D ; Seth-Smith, H M B ; Egli, A ; Bernier, A-M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c335t-390d8a20121603ac4caf409cf860df769815305c506c742088de79c56debefcb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Aged</topic><topic>Bacterial Typing Techniques</topic><topic>Base Composition</topic><topic>Canada</topic><topic>DNA, Bacterial - genetics</topic><topic>Ear - microbiology</topic><topic>Fatty Acids - chemistry</topic><topic>Female</topic><topic>Humans</topic><topic>Male</topic><topic>Micrococcaceae - classification</topic><topic>Middle Aged</topic><topic>Nucleic Acid Hybridization</topic><topic>Phylogeny</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Sequence Analysis, DNA</topic><topic>Switzerland</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bernard, K A</creatorcontrib><creatorcontrib>Pacheco, A L</creatorcontrib><creatorcontrib>Burdz, T</creatorcontrib><creatorcontrib>Wiebe, D</creatorcontrib><creatorcontrib>Beniac, D R</creatorcontrib><creatorcontrib>Hiebert, S L</creatorcontrib><creatorcontrib>Booth, T F</creatorcontrib><creatorcontrib>Jakopp, B</creatorcontrib><creatorcontrib>Goldenberger, D</creatorcontrib><creatorcontrib>Seth-Smith, H M B</creatorcontrib><creatorcontrib>Egli, A</creatorcontrib><creatorcontrib>Bernier, A-M</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>International journal of systematic and evolutionary microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bernard, K A</au><au>Pacheco, A L</au><au>Burdz, T</au><au>Wiebe, D</au><au>Beniac, D R</au><au>Hiebert, S L</au><au>Booth, T F</au><au>Jakopp, B</au><au>Goldenberger, D</au><au>Seth-Smith, H M B</au><au>Egli, A</au><au>Bernier, A-M</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Emendation of the Genus Auritidibacter Yassin et al. 2011 and Auritidibacter ignavus Yassin et al. 2011 based on features observed from Canadian and Swiss clinical isolates and whole-genome sequencing analysis</atitle><jtitle>International journal of systematic and evolutionary microbiology</jtitle><addtitle>Int J Syst Evol Microbiol</addtitle><date>2020-01</date><risdate>2020</risdate><volume>70</volume><issue>1</issue><spage>83</spage><epage>88</epage><pages>83-88</pages><issn>1466-5026</issn><eissn>1466-5034</eissn><abstract>is a Gram-stain-positive bacillus derived from otorrhea. Four strains derived from ear discharges in Canada and Switzerland, with features consistent with but distinguishable from IMMIB L-1656 (accession number FN554542) by 16S rRNA gene sequencing (97.5 % similarity), were thought to represent a novel species of the genus . DSM 45359 (=IMMIB L-1656 ) was acquired to compare with Canadian and Swiss strains by whole-genome sequencing (WGS). Unexpectedly, those isolates were observed to be consistent with DSM 45359 by WGS (ANIb scores &gt;98 %), MALDI-TOF (Bruker), cellular fatty acid analysis and biochemically (some differences were observed). A nearly full 16S rRNA gene sequence could not be readily prepared from DSM 45359 , even after multiple attempts. A 16S rRNA gene chimeric consensus sequence created from the genome assembly of DSM 45359 had only 97.5 % similarity to that of IMMIB L-1656 , implying that 16S rRNA sequence accession number FN554542 could not be replicated. We concluded that our isolates of members of the genus were consistent with DSM 45359 , did not represent a novel species, and that the sequence corresponding to FN554542 was not reproducible. By WGS, DSM 45359 had genome of 2.53×10  bp with a DNA G+C content of 59.34%, while genomes of Canadian and Swiss isolates ranged from 2.47 to 2.59×10  bp with DNA G+C contents of 59.3-59.52 %. NML 100628 (=NCTC 14178=LMG 30897) did not demonstrate a rodcoccus cycle. Emendation of was proposed based on these results.</abstract><cop>England</cop><pmid>31596191</pmid><doi>10.1099/ijsem.0.003719</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0002-4807-424X</orcidid><orcidid>https://orcid.org/0000-0002-9796-2702</orcidid><orcidid>https://orcid.org/0000-0002-3788-3818</orcidid><orcidid>https://orcid.org/0000-0003-1420-8323</orcidid><orcidid>https://orcid.org/0000-0002-6082-5114</orcidid><oa>free_for_read</oa></addata></record>
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source MEDLINE; Microbiology Society; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Alma/SFX Local Collection
subjects Aged
Bacterial Typing Techniques
Base Composition
Canada
DNA, Bacterial - genetics
Ear - microbiology
Fatty Acids - chemistry
Female
Humans
Male
Micrococcaceae - classification
Middle Aged
Nucleic Acid Hybridization
Phylogeny
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Switzerland
title Emendation of the Genus Auritidibacter Yassin et al. 2011 and Auritidibacter ignavus Yassin et al. 2011 based on features observed from Canadian and Swiss clinical isolates and whole-genome sequencing analysis
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