Ann Lab Med.  2021 May;41(3):323-327. 10.3343/alm.2021.41.3.323.

A Novel Species of the Genus Arsenicicoccus Isolated From Human Blood Using Whole-Genome Sequencing

• Jeong JH
• Kweon OJ
• Kim HR
• Kim TH
• Ha Sm
• Lee MK

• KMID: 2512691
• DOI: http://doi.org/10.3343/alm.2021.41.3.323

Abstract

Whole-genome sequencing (WGS) is an easily accessible and valuable tool in clinical microbiology, which can be used for identifying novel and rare species. We isolated grampositive cocci from the blood of a pediatric patient, which could not be phenotypically identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) (BioMérieux, Marcy-l’Étoile, France). We could not identify the isolate to the species level using 16S ribosomal RNA (rRNA) sequencing. WGS was performed using the Illumina MiSeq platform (Illumina, San Diego, CA, USA); however, the subsequent genomic sequence database search using the TrueBac ID-Genome system (ChunLab, Inc., Seoul, Korea) did not yield any hits with an average nucleotide identity value > 95.0%, which is the cut-off for species-level identification. Phylogenetic analysis suggested that the isolate belonged to a new Arsenicicoccus species, forming a subcluster with Arsenicicoccus bolidensis. Our data demonstrate that WGS allows a more accurate annotation of microbial genomes than other clinical microbiology tools, such as MALDITOF MS and 16S rRNA sequencing. This is the first report of the isolation of a novelArsenicicoccus species from a clinical sample.

Keyword

Novel Arsenicicoccus species; 16S rRNA sequencing; Whole-genome sequencing

Figure

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  Fig. 1 Subculturing of the isolate on blood (A, B, C) and chocolate (D, E, F) agar plates. G. Gram staining of the isolate.

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  Fig. 2 Phylogenetic analysis based on (A) 16S rRNA sequences using the neighbor-joining method or (B) whole-genome sequencing combined with unweighted pair group and arithmetic mean clustering methods as well as average nucleotide identity values. The isolated pathogen (MKL-02) is underlined. Abbreviation: rRNA, ribosomal RNA.

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