Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov.

  • Ainsley C. Nicholson
  • Christopher A. Gulvik
  • Anne M. Whitney
  • Ben W. Humrighouse
  • James Graziano
  • Brian Emery
  • Melissa Bell
  • Vladimir Loparev
  • Phalasy Juieng
  • Jarrett Gartin
  • Chantal Bizet
  • Dominique Clermont
  • Alexis Criscuolo
  • Sylvain Brisse
  • John R. McQuiston
Original Paper

Abstract

The genus Elizabethkingia is genetically heterogeneous, and the phenotypic similarities between recognized species pose challenges in correct identification of clinically derived isolates. In addition to the type species Elizabethkingia meningoseptica, and more recently proposed Elizabethkingia miricola, Elizabethkingia anophelis and Elizabethkingia endophytica, four genomospecies have long been recognized. By comparing historic DNA–DNA hybridization results with whole genome sequences, optical maps, and MALDI-TOF mass spectra on a large and diverse set of strains, we propose a comprehensive taxonomic revision of this genus. Genomospecies 1 and 2 contain the type strains E. anophelis and E. miricola, respectively. Genomospecies 3 and 4 are herein proposed as novel species named as Elizabethkingia bruuniana sp. nov. (type strain, G0146T = DSM 2975T = CCUG 69503T = CIP 111191T) and Elizabethkingia ursingii sp. nov. (type strain, G4122T = DSM 2974T = CCUG 69496T = CIP 111192T), respectively. Finally, the new species Elizabethkingia occulta sp. nov. (type strain G4070T = DSM 2976T = CCUG 69505T = CIP 111193T), is proposed.

Keywords

AAI ANI Elizabethkingia MALDI-TOF SNPs Taxonomy 

Notes

Acknowledgements

We thank John McInroy for providing strain JM-87, and the State Health Departments of Wisconsin, Minnesota, Illinois, Michigan, Florida, Arizona, Texas, South Carolina, and California in the USA for providing Elizabethkingia clinical specimens. We also thank Aharon Oren for nomenclature advice, Barry Holmes for supplying phenotypic data on some of the strains included in this study, and Aaron Villarma for technical assistance.

Compliance with ethical standards

Funding

CDC research was supported by the Advanced Molecular Detection (AMD) initiative, and work done at the Institut Pastuer was funded by the French government’s Investissement d’Avenir program Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (Grant ANR-10-LABX-62-IBEID).

Conflict of interest

All authors report that they have no conflicts of interest.

Supplementary material

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Copyright information

© Springer International Publishing AG (outside the USA)  2017

Authors and Affiliations

  • Ainsley C. Nicholson
    • 1
  • Christopher A. Gulvik
    • 1
  • Anne M. Whitney
    • 1
  • Ben W. Humrighouse
    • 1
  • James Graziano
    • 1
  • Brian Emery
    • 1
  • Melissa Bell
    • 1
  • Vladimir Loparev
    • 2
  • Phalasy Juieng
    • 2
  • Jarrett Gartin
    • 1
  • Chantal Bizet
    • 3
  • Dominique Clermont
    • 3
  • Alexis Criscuolo
    • 4
  • Sylvain Brisse
    • 5
    • 6
    • 7
  • John R. McQuiston
    • 1
  1. 1.Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and PathologyCenters for Disease Control and PreventionAtlantaUSA
  2. 2.Division of Scientific ResourcesCenters for Disease Control and PreventionAtlantaUSA
  3. 3.Microbiology Department, Institut PasteurCollection de L’Institut Pasteur (CIP)ParisFrance
  4. 4.Institut Pasteur – Bioinformatics and Biostatistics Hub – C3BIParisFrance
  5. 5.Microbial Evolutionary GenomicsInstitut PasteurParisFrance
  6. 6.CNRSParisFrance
  7. 7.Institut Pasteur, Biodiversity and Epidemiology of Bacterial PathogensParisFrance

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