BackgroundNext-generation sequencing is increasingly used for taxonomic identification of pathogenic bacterial isolates. We evaluated the performance of a newly introduced whole genome-based bacterial identification system, TrueBac ID (ChunLab Inc., Seoul, Korea), using clinical isolates that were not identified by three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems and 16S rRNA gene sequencing.MethodsThirty-six bacterial isolates were selected from a university-affiliated hospital and a commercial clinical laboratory. Species was identified by three MALDI-TOF MS systems: Bruker Biotyper MS (Bruker Daltonics, Billerica, MA, USA), VITEK MS (bioMérieux, Marcy l'Étoile, France), and ASTA MicroIDSys (ASTA Inc., Suwon, Korea). Whole genome sequencing was conducted using the Illumina MiSeq system (Illumina, San Diego, CA, USA), and genome-based identification was performed using the TrueBac ID cloud system (www.truebacid.com).ResultsTrueBac ID assigned 94% (34/36) of the isolates to known (N=25) or novel (N=4) species, genomospecies (N=3), or species group (N=2). The remaining two were identified at the genus level.ConclusionsTrueBac ID successfully identified the majority of isolates that MALDI-TOF MS failed to identify. Genome-based identification can be a useful tool in clinical laboratories, with its superior accuracy and database-driven operations.
A Gram-stain-negative, non-spore-forming, rod-shaped, aerobic and diffusible yellow-coloured bacterial strain, designated strain ECD12 was isolated from a seaweed, Ecklonia cava. The isolate required sea salts for growth. Catalase-positive and oxidase-negative. A phylogenetic tree based on 16S rRNA gene sequences showed that strain ECD12 formed an evolutionary lineage within the radiation enclosing the members of genera Spongiibacterium and Flagellimonas sharing the highest similarity to Flagellimonas eckloniae DOKDO007 (96.8 % 16S rRNA gene sequence similarity) followed by Spongiibacterium pacificum SW169 (96.4 %) and Spongiibacterium flavum DSM 22638 (96.1 %). The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The new isolate contained MK-6 as the only isoprenoid quinone and phosphatidylethanolamine, two unidentified amino lipids and two unidentified lipids as the major polar lipids. The genomic DNA G+C content is 39 mol%. A number of phenotypic characteristics such as the production of diffusible pigment distinguished strain ECD12 from the related species. On the basis of the evidence presented in this study, a novel species, Flagellimonas aquimarina sp. nov., is proposed for strain ECD12 (=KCTC 52351=JCM 32292). Based on the sequence similarity, phylogenetic relationship and common morphological, physiological and chemical characters among the members of the genera Spongiibacterium and Flagellimonas, it is recommended that the two genera are combined into a single genus. Thus, transfer of S. flavumYoon and Oh 2012 and S. pacificum Gao et al. 2015 to the genus FlagellimonasBae et al. 2007 as Flagellimonas flava comb. nov. and Flagellimonas pacifica comb. nov., respectively, is also proposed.
The DDBJ/ENA/GenBank accession numbers for 16S rRNA gene and genome sequences of strain GH4-78 T are MG905440 and SMSE00000000, respectively. The version of the genome sequence described in this paper is version SMSE01000000. Three supplementary figures and three supplementary tables are available with the online version of this article.
A non-motile, pink-coloured and rod-shaped bacterium, designated strain POA9, was isolated from a wastewater treatment facility, Republic of Korea. Cells were Gram-reaction-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were C16 : 1ω5c, iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and anteiso-C15 : 0. The strain contained MK-7 as the only isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine. The DNA G+C content was 57 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain POA9 forms a distinct evolutionary lineage within the radiation enclosing the members of the genus Hymenobacter, sharing the highest similarity with Hymenobacter actinosclerus CCUG 39621 (95.5 % sequence similarity) followed by Hymenobacterseoulensis 16F7G (95.5 %), Hymenobactertibetensis XTM003 (95.4 %), Hymenobacterrutilus K2-33028 (95.4 %) and Hymenobacter psychrotolerans Tibet-IIU11 (94.9 %). A number of phenotypic characteristics distinguished strain POA9 from the related members of the genus Hymenobacter. On the basis of the evidence presented in this study, a novel species, Hymenobacter defluvii sp. nov., is proposed for strain POA9 (=KCTC 52270=JCM 31658).
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