Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jan;111(1):55-72.
doi: 10.1007/s10482-017-0926-3. Epub 2017 Aug 30.

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  1 , Christopher A Gulvik  2 , Anne M Whitney  2 , Ben W Humrighouse  2 , James Graziano  2 , Brian Emery  2 , Melissa Bell  2 , Vladimir Loparev  3 , Phalasy Juieng  3 , Jarrett Gartin  2 , Chantal Bizet  4 , Dominique Clermont  4 , Alexis Criscuolo  5 , Sylvain Brisse  6   7   8 , John R McQuiston  2
Affiliations

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 et al. Antonie Van Leeuwenhoek. 2018 Jan.

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.

PubMed Disclaimer

Conflict of interest statement

Conflict of interest All authors report that they have no conflicts of interest.

Figures

Fig. 1
Fig. 1
The variability of GGDC predicted DDH (top panel) and ANIb (lower panel) for pairwise comparisons is displayed, categorized based on the taxonomy assignments of each strain as described in this manuscript. Box-plots show the range and median of data for each comparison
Fig. 2
Fig. 2
Core genome ML phylogeny of 1,049,915 variable nucleotide sites from 2259 genes. Only bootstrap values ≥70% are displayed
Fig. 3
Fig. 3
UPGMA based on optical maps. The percentage of restriction sites in common between optical maps of each isolate are indicated under the tree
Fig. 4
Fig. 4
Molecular phylogenetic analysis of positions 1939-3629 from the rpoB gene. The evolutionary history was inferred by using the Maximum Likelihood method based on the JC69 model. The tree with the highest log likelihood is shown, and the percentage of trees in which the associated taxa clustered together is shown next to the branches, based on 100 bootstrap replicates. Bootstrap values greater than 70% are displayed. Branch lengths show the number of substitutions per site. The analysis involved 63 nucleotide sequences, and gaps were eliminated, yielding a total of 1690 nucleotide positions
See this image and copyright information in PMC

References

    1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–3402. - PMC - PubMed
    1. Auch AF, Klenk HP, Goker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Gen Sci. 2010a;2(1):142–148. doi: 10.4056/sigs.541628. - DOI - PMC - PubMed
    1. Auch AF, von Jan M, Klenk HP, Goker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Gen Sci. 2010b;2(1):117–134. doi: 10.4056/sigs.531120. - DOI - PMC - PubMed
    1. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–477. doi: 10.1089/cmb.2012.0021. - DOI - PMC - PubMed
    1. Bloch KC, Nadarajah R, Jacobs R. Chryseobacterium meningosepticum: an emerging pathogen among immunocompromised adults. Report of 6 cases and literature review. Medicine. 1997;76(1):30–41. - PubMed

LinkOut - more resources