Whole-Genome Sequence of Streptococcus tigurinus Strain osk_001, Isolated from Postmortem Material

GENOME ANNOUNCEMENT

Streptococcus tigurinus was recently described as a novel species, originally identified by Zbinden et al. Some strains of S. tigurinus are highly virulent and cause serious invasive infections, with or without bacteremia, such as infective endocarditis, meningitis, spondylodiscitis, and necrotizing fasciitis (1–3). Diene et al. reported that specific and unique genetic elements are contained in highly virulent strains of S. tigurinus (4). We recently diagnosed a severe soft-tissue infection at the Osaka Prefectural Medical Examiner’s Office and detected S. tigurinus in a necropsy sample. The isolate was cultured and designated S. tigurinus strain osk_001. When performing postmortem microbiology during an autopsy or necropsy, microorganisms isolated from a cadaver’s tissue should be carefully analyzed to determine whether they are truly pathogenic and causative of the diagnosed infection (5). Therefore, we performed whole-genome sequencing of the S. tigurinus strain osk_001 to characterize and confirm the virulence in this case.

Complete genome sequencing of S. tigurinus strain osk_001 was performed using a combination of the MiSeq (Illumina) and PacBio RS II (Pacific Biosciences) platforms. Genomic DNA of S. tigurinus was extracted from cultured cells using a PowerSoil DNA isolation kit (Mo Bio). For MiSeq sequencing, 500 ng of genomic DNA was sheared to about 600 bp, the library was prepared using KAPA library preparation kits (KAPA Biosystems), and then paired-end sequencing (251 bp × 2) was performed. For PacBio RS II sequencing, 2 μg of genomic DNA was sheared to about 15 kb, the library was prepared using a DNA template prep kit (version 1.0), and sequencing was performed. PacBio reads were de novo assembled to a contig using HGAP (6). In order to correct sequence errors, MiSeq reads were mapped onto the assembled PacBio contig using CLC Genomics Workbench version 9.5.3 (CLC bio/Qiagen). This contig was trimmed and circularized into the final complete genome of S. tigurinus osk_001, which comprised 1,889,005 bp with a G+C content of 41.15%. A total of 1,831 predicted coding DNA sequences, 12 rRNAs, and 59 tRNAs were annotated with MiGAP.

Whole-genome sequencing revealed that S. tigurinus strain osk_001 included some of the same genetic elements present in highly virulent strains. We concluded that S. tigurinus strain osk_001 is not a low-virulent strain and that this bacterium may be pathogenic and causative of severe soft-tissue infections. Whole-genome sequencing appears to be a useful tool for confirming whether the microorganisms detected by postmortem microbiology are truly pathogenic and causative of diagnosed infections.