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 wholegenome sequencing analysis

This dataset contains the digitized treatments in Plazi based on the original journal article 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 (2020): 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 wholegenome sequencing analysis. International Journal of Systematic and Evolutionary Microbiology 70 (1): 83-88, DOI: 10.1099/ijsem.0.003719, URL: http://dx.doi.org/10.1099/ijsem.0.003719AbstractAuritidibacter ignavus 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 Auritidibacter ignavus IMMIB L-1656 T (accession number FN554542) by 16S rRNA gene sequencing (97.5% similarity), were thought to represent a novel species of the genus Auritidibacter. Auritidibacter ignavus DSM 45359 T (=IMMIB L-1656 T) was acquired to compare with Canadian and Swiss strains by whole-genome sequencing (WGS). Unexpectedly, those isolates were observed to be consistent with A. ignavus DSM 45359 T 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 A. ignavus DSM 45359 T, even after multiple attempts. A 16S rRNA gene chimeric consensus sequence created from the genome assembly of A. ignavus DSM 45359 T had only 97.5% similarity to that of A. ignavus IMMIB L-1656 T, implying that 16S rRNA sequence accession number FN554542 could not be replicated. We concluded that our isolates of members of the genus Auritidibacter were consistent with A. ignavus DSM 45359 T, did not represent a novel species, and that the sequence corresponding to FN554542 was not reproducible. By WGS, A. ignavus DSM 45359 T had genome of 2.53× 106 bp with a DNA G+C content of 59.34%, while genomes of Canadian and Swiss isolates ranged from 2.47 to 2.59× 106 bp with DNA G+C contents of 59.3–59.52%. A. ignavus NML 100628 (=NCTC 14178=LMG 30897) did not demonstrate a rodcoccus cycle. Emendation of Auritidibacter ignavus was proposed based on these results.Auritidibacter ignavus gen. nov. sp. nov. of the family Micrococcaceae was described in 2011 to encompass a biochemically minimally-reactive, Gram-stain-positive coccus to rod-shaped bacterium recovered from a case of fulminant otitis externa; whole-genome sequencing (WGS) analysis had not been performed on the type strain [1]. Four isolates recovered from 2010 to 2013 from ear infections of patients in Canada and Switzerland had, by 16S rRNA gene sequence analysis 99.8–99.9 % similarity to each other, indicating that these isolates represented a single taxon which was close to, but distinguishable from (97.5% sequence similarity) the type strain of A. ignavus by that method. National Microbiology Laboratory (NML) identifier 100628 from the ear of a 57year old male and NML 120636 isolated from a left mastoid biopsy from a 51 year old female, recovered in 2010 and 2012 respectively, were referred from Vancouver British Columbia Canada (49.2827° N, 123.1207° W), with no other patient information being available. A third Canadian strain isolated in 2012 (NML 120779) was from a 76 year old male from Winnipeg Manitoba (49.8951° N, 97.1384° W) with chronic otitis media and otorrhea who had been repeatedly treated with topical ciprofloxacin. Respective provincial laboratories found these isolates to be unidentifiable using standard methods and so had forwarded isolates to the NML for additional characterization. The fourth isolate was recovered at University Hospital Basel (USB), Switzerland (400516/2013=NML 130574, described below as NML 130574) (47.5596° N, 7.5886° E). The patient was a 30 year old HIV-positive male immigrant from Hungary who had recurrent otitis, with at least one infection per year, and had recurrent tympanoplasties (seven on the left side and one on the right side) resulting in presbycusis. Superinfected chronic otitis perforata after tympanoplasty had been resolved with the use of high doses of ciprofloxacin ear drops, two times per day for seven days.Author affiliations: 1 National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg Manitoba, Canada; 2 Department of Medical Microbiology, University of Manitoba, Winnipeg Manitoba, Canada; 3 Division of Infectious Diseases and Hospital Epidemiology, University Hospital, Basel, Switzerland; 4 Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; 5 Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; 6 Department of Biology, Université de Saint-Boniface, Winnipeg Manitoba, Canada. *Correspondence: K. A. Bernard,kathy.bernard@canada.caKeywords: Auritidibacter ignavus; otitis media; Genus Auritidibacter.Abbreviations: ANIb, average nucleotide identity using BLASTn; CFA, cellular fatty acids; dDDH, digital DNA–DNA hybridization; GGDC, genome to genome distance calculator; HPLC, high-pressure liquid chromatography; MALDI-TOF MS, matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry; MSP, mass spectral profile; NML, National Microbiology Laboratory; USB, University Hospital Basel Switzerland; WGS, wholegenome sequence.†Present address: Infectious Diseases Unit, Katonsspital Aarau, Aarau, Switzerland.The GenBank/EMBL/DDBJ accession numbers for 16S rRNA gene sequences derived in this study are KC669621, KC669622 and KC669623, forNML 100628, NML 120636 and NML 120779, respectively, KF360241 for the Swiss isolate 400516/2013 (=NML 130574) and MK069432 for A. ignavus DSM 45359 T. Illumina Sequencing Reads for strains NML 100628, NML 120636, NML 120779 and A. ignavus DSM 45359 T were assigned the accession numbers SRX4212137, SRX4212136, SRX4212138 and SRX5335920, respectively. Whole-genome sequencing shotgun projects for strains of members of the genus Auritidibacter have been deposited under the accession numbers QHLP00000000 (NML 100628), QHLO00000000 (NML 120636), QHLN00000000, (NML 120779) and CP031746 (400516/2013=NML 130574). The WGS project prepared here for Auritidibacter ignavus DSM 45359 T (=IMMIB L-1656 T) has been deposited under the accession number RDQR00000000.Three supplementary figures and two supplementary tables are available with the online version of this article.The observation of 16S rRNA gene similarity of these isolates to the sequence from the A. ignavus type strain (accession number FN554542) prompted characterization of these four bacteria as representing a single taxon which was thought to possibly represent a novel species of the genus Auritidibacter. Strains were characterized biochemically, for antimicrobial susceptibilities, by cellular fatty acid (CFA) composition, matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI–TOF MS, Bruker Daltronics) and by WGS analyses. Auritidibacter ignavus DSM 45359 T (=IMMIB L-1656 T) was acquired from the Leibniz-Institut DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM) to compare with genomes derived from Canadian and Swiss strains. The methodology and features derived from a complete genome prepared from the Swiss isolate (400516/2013=NML 130574) has been described separately [2].The four clinical isolates were found to be generally consistent with Auritidibacter ignavus IMMIB L-1656 T [1] morphologically after growth on SBA or by Gram-stain appearance [Fig. S1a and Fig. 1b (available in the online version of this article), respectively]. Cell morphology including observation of rod-like forms (at 17 h old) or cocci (at 108 h old) had been previously described for A. ignavus IMMIB L-1656 T [1]. Therefore, NML 100628 was grown in brain–heart infusion broth at 35 °C and evaluated for type of morphology observable at different time intervals. Samples drawn at 0, 7.5, 24, 48, 72 and 96h were tested. Each aliquot was gently mixed with fixative containing buffered 2% glutaraldehyde and 1% paraformaldehyde and was then prepared for transmission electron microscopy as previously described [3]. Length measurements were made using the Image J software package using the free hand line tool and the analyse/measure function [4]. Measurements were made in Image J, collated and analysed using Microsoft Excel. Straight or curved rods were seen at all time intervals and coccoidal forms were not observed after 96 h (interval set of electron micrographs not shown). The rod-like morphology of NML 100628 after 48 h of growth was selected as being typical; it was (N, number of measurements) 1.85±0.45 µm long (N =35) with a width of 0.44±0.05 µm (N =58) (Fig. S1c), dimensions similar to those observed for A. ignavus [1].Phenotypically, the four isolates were consistent with A. ignavus IMMIB L-1656 T [1] except for the following features, also summarized in Table S1. Strains were observed to grow at 42 °C on 5% Columbia blood agar base with 5% sheep blood (SBA) as well as under strictly anaerobic conditions, at 35 °C. Strains were tested by tube motility and by the hanging drop method [5]; strains were non-motile by the tube test but positive by hanging drop. Isolates assimilated substrate at pH 6 but not pH 5 (Biolog), could not reduce nitrite and were negative for acetoin, DNase and starch hydrolysis. Pyrolidonyl arylamidase (PYRa) was detected for two strains. API Coryne (Biomérieux) codes generated were 2110004 (two strains) or 6110004 (two strains), which were associated with poor confidence identification scores to members of the genera Rhodococcus, Arthrobacter or Brevibacterium. Strains were found to be non-reactive with API 50 CH panel substrates. By API Zym (Biomérieux), isolates were reactive for esterase and leuc

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