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

• Published in: Antonie van Leeuwenhoek Vol. 111; no. 1; pp. 55 - 72
• Main Authors: Nicholson, Ainsley C., Gulvik, Christopher A., Whitney, Anne M., Humrighouse, Ben W., Graziano, James, Emery, Brian, Bell, Melissa, Loparev, Vladimir, Juieng, Phalasy, Gartin, Jarrett, Bizet, Chantal, Clermont, Dominique, Criscuolo, Alexis, Brisse, Sylvain, McQuiston, John R.
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 2018; Springer Nature B.V
• Subjects: Bacterial Typing Techniques; Biomedical and Life Sciences; Computational Biology - methods; Deoxyribonucleic acid; DNA; DNA Barcoding, Taxonomic; DNA, Bacterial; Endophytes; Evolution, Molecular; Flavobacteriaceae - chemistry; Flavobacteriaceae - classification; Flavobacteriaceae - genetics; Gene mapping; Gene sequencing; Genes; Genome, Bacterial; Genomes; Genomics - methods; Hybridization; Life Sciences; Mass spectra; Medical Microbiology; Microbiology; New species; Nucleic Acid Hybridization; Nucleotide sequence; Original Paper; Phenotype; Phylogeny; Plant Sciences; Soil Science & Conservation; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Taxonomic revision; Taxonomy; Whole Genome Sequencing; SNPs; AAI; MALDI-TOF; ANI; Taxonomy; Elizabethkingia
• ISSN: 0003-6072; 1572-9699
• DOI: 10.1007/s10482-017-0926-3

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, G0146 T  = DSM 2975 T  = CCUG 69503 T  = CIP 111191 T ) and Elizabethkingia ursingii sp. nov. (type strain, G4122 T  = DSM 2974 T  = CCUG 69496 T  = CIP 111192 T ), respectively. Finally, the new species Elizabethkingia occulta sp. nov. (type strain G4070 T  = DSM 2976 T  = CCUG 69505 T  = CIP 111193 T ), is proposed.