Complete Genome Sequence of Streptococcus suis Serotype 3 Strain ST3

Abstract

Streptococcus suis is a zoonotic pathogen causing economic loss in the swine industry and is also a threat to human health. To date, the mechanism of pathogenesis is not fully understood. Here, we report the complete genome sequence of S. suis strain ST3 of serotype 3, which provides opportunities to reveal genetic basis of infection of S. suis non-serotype 2 strains.

GENOME ANNOUNCEMENT

Streptococcus suis is an important swine pathogen and causes various diseases, such as meningitis, pneumonia, arthritis, etc. (8). Moreover, S. suis is an emerging zoonotic agent and can lead to human infection. Among the 33 serotypes of S. suis (types 1 to 31, 33, and 1/2), serotype 3 is more prevalent than the others, in addition to serotype 2 strains (6, 14). For further understanding on the genetic background of the serotypic diversity and pathogenic potential of serotype 3 strains, S. suis ST3, isolated from a pig with pneumonia in Hubei province, China, was chosen for genome sequencing.

The genome sequence was determined by an Illumina genome analyzer at Beijing Institute of Genomics. The assembly that was produced by SOAPdenovo1.04 was based on 23,334,073 paired-end reads with a read length of 79 bp and an average insertion size of 500 bp. The resulting 73 large contigs were aligned to the published genome of S. suis 05ZYH33 using MUMmer3 (10) to obtain linkage information. Gaps were closed by primer walking and sequencing of PCR products. Glimmer 3.02 (5) and GeneMarkS (2) were used to predict open reading frames (ORFs) (results were amalgamated). Annotation was performed by comparing ORFs with those in nonredundant-protein databases (the KEGG and COG databases). tRNAs and rRNAs were predicted by tRNAscan-SE 1.21 (12) and RNAmmer 1.2 (11), respectively.

The genome of strain ST3 is composed of one circular chromosome of 2,028,815 bp, with a GC content of 41.29%. There are 2,031 protein-coding sequences (CDSs) that account for 87.8% of the genome, with an average length of 877 bp, 54 tRNAs, 4 rRNA loci, and 28 insertion (IS) elements.

There are many genes unique to ST3 compared to other sequenced S. suis strains, including a MATE efflux family protein, two transcriptional regulators, and several ABC transporter proteins. Moreover, several genes that located in the cps locus, such as genes encoding a glycosyl transferase family 2 protein and a cps synthesis protein, also share poor homology with that of other S. suis strains and may reveal a distinct role in capsular structure determination for this serotype. Other genes unique to ST3 were characterized by hypothetical protein or phage protein.

The previously identified 89K pathogenicity island region in S. suis (3) was not found in ST3, but several virulence-associated genes were included in it, such as pgdA, which can result in escaping of recognition and increased resistance to lysozyme by modification of peptidoglycan (7), and fbps, which plays a role in colonization of the organs (4). Also, srtA, which encodes an enzyme involved in protein sorting and adherence to host epithelial cells thus associated with bacterial pathogenesis (13), was also present. However, some others were defined as pseudogenes due to frameshift mutations, such as CDSs for muramidase-released protein, serum opacity factor, and a putative IgA-specific zinc metalloproteinase. In addition, extracellular factor and suilysin (1, 9) were found absent in this strain. These results suggest a distinct gene spectrum and the living condition that it encountered, and this genome will provide a foundation for understanding this prevalent serotype.

Nucleotide sequence accession number.

The complete genome sequence of the S. suis strain ST3 has been assigned GenBank accession number CP002633.