Complete Genome Sequence of Streptococcus mitis Strain SVGS_061 Isolated from a Neutropenic Patient with Viridans Group Streptococcal Shock Syndrome

Abstract

Streptococcus mitis frequently causes invasive infections in neutropenic cancer patients, with a subset of patients developing viridans group streptococcal (VGS) shock syndrome. We report here the first complete genome sequence of S. mitis strain SVGS_061, which caused VGS shock syndrome, to help elucidate the pathogenesis of severe VGS infection.

GENOME ANNOUNCEMENT

Among the different species comprising viridans group streptococci (VGS), Streptococcus mitis, which is closely related to Streptococcus pneumoniae, is the most frequent cause of bacteremia in neutropenic cancer patients (1). The clinical presentation of S. mitis bacteremia in neutropenic patients can vary from mild to severe, for example, VGS shock syndrome. Moreover, invasive S. mitis strains are often multidrug resistant (2), which increases the risk of adverse patient outcomes (3). Despite the increasing clinical relevance of S. mitis infections, little is known about their pathogenesis.

Here, we report the complete genome sequence of the multidrug-resistant S. mitis strain SVGS_061, which was isolated from the bloodstream of a neutropenic-acute myelogenous leukemia patient with VGS-shock syndrome. SVGS_061 was resistant to moxifloxacin (MIC, 4 µg/ml) and tetracycline (MIC, 16 µg/ml) and had intermediate resistance to penicillin (MIC, 1 µg/ml). The SVGS_061 genome was determined using the PacBio SMRT technology (4). A total of 68,561 reads were assembled using the Hierarchical Genome Assembly Process for de novo genome assembly. MiSeq short reads were then used to confirm the 2,167,922-bp circularized genome assembly, with 151× average sequencing depth. The assembled genome was annotated with RASTtk (5), which identified 1,986 coding sequences, 59 tRNAs, and a host of intergenic repeat unit of pneumococcus (RUP) (n = 15), SPRITE (n = 18), and BOX (n = 81) repeats that are typically present in S. pneumoniae genomes in high density and likely regulate gene expression (6, 7). A putative 96-kb (genome coordinates 1076140 to 1172058) Tn5253-like integrative and conjugative element (ICESVGS_061) was identified and was most similar to ICESpn22664 from S. pneumoniae (99% identity over 48% nucleotide overlap). ICESVGS_061 contained several hallmark proteins, including site-specific integrases, type IV secretion, conjugation protein homologs, and Tn5252 and Tn916 open reading frames (ORFs) (8, 9). Moreover, the SVGS_61 integrative and conjugative element (ICE) contains mef (locusID_AXK38_05275), tetM (locusID_AXK38_05320), and cat (locusID_AXK38_05440) genes that confer macrolide, tetracycline, and chloramphenicol resistance, respectively. Furthermore, combined CARD (10) and BLAST analyses identified mutations known to confer high-level fluoroquinolone resistance in GyrA (Ser81Phe) (locusID_AXK38_06150) and ParC (Ser79Ile) (locusID_AXK38_06460) (11–13); the genome also harbored the pmrA (locusID_AXK38_03855) efflux gene, which is associated with fluoroquinolone resistance (14). Mutations associated with increased penicillin resistance in penicillin-binding protein 1a (PBP 1a) (Val408Leu) (locusID_AXK38_08480), PBP 2b (Gln628Glu) (locusID_AXK38_02845), and PBP 2x (Asn417Lys, Leu510Thr, and Thr513Asn) (locusID_AXK38_08630) were also identified (15).

Homologs of a number of S. pneumoniae virulence-associated proteins, such as the capsular proteins encoded by the cps operon, cell wall synthesis-associated proteins, lyase (NanA), and amidase (LytC), were identified via the VFDB database (16) search. The capsule is a crucial virulence factor for S. pneumoniae. Capsular proteins of SVGS_061 are most closely related to serotype 4F and are most similar to the capsular proteins of S. pneumoniae TIGR4 (96% identity over 56% nucleotide overlap). OrthoMCL analysis (17) identified 1,509 orthologs in the S. pneumoniae TIGR4 genome. Exotoxins similar to those causing toxic shock in staphylococci or β-hemolytic streptococci were not identified in SVGS_061. The availability of the complete genome sequence of SVGS_061 should help facilitate a better understanding of the VGS shock syndrome resulting from S. mitis invasive infection.

Nucleotide sequence accession number.

The complete genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession no. CP014326. The version described in this paper is the first version.