Complete Genome Sequence of Streptococcus agalactiae GD201008-001, Isolated in China from Tilapia with Meningoencephalitis

Abstract

This work describes a whole-genome sequence of Streptococcus agalactiae strain GD201008-001, a pathogen causing meningoencephalitis in cultural tilapia in China. The genome sequence provides opportunities to understand the piscine GBS pathogenicity and its genetic basis associated with host tropism.

GENOME ANNOUNCEMENT

Streptococcus agalactiae, referred to as group B streptococcus (GBS), has a broad host range that includes mammals and fish. However, most studies have been focused on S. agalactiae isolated from humans and cows. Since 2009, an outbreak of serious GBS infectious disease in tilapia cultural farms in the south of China has occurred, causing high mortalities and large economic losses (1). S. agalactiae strain GD201008-001 was isolated from moribund cultural tilapia with meningoencephalitis in the Guangdong province of China in 2010 and belongs to serotype Ia, multilocus sequence type 7 (ST7). For a further understanding of the genetic background of the pathogenicity of piscine GBS, strain GD201008-001 was chosen for genome sequencing.

Whole-genome sequencing was performed using the 454 genome sequencer FLX system and an Illumina Solexa Genome Analyzer IIx sequencer with the paired-end protocol. In total, 181,797 raw reads were assembled into 93 contigs with 31.3-fold sequence coverage. Gap filling was based on the conservation of the gene order of the published genome sequence of S. agalactiae A909 (CP000114.1). Gaps between contigs were closed by PCR and subsequent Sanger sequencing using an ABI 3730 capillary sequencer. The results of complete-genome sequencing were analyzed using GLIMMER3 (2), tRNAscan-SE (5), and RNAmmer (4). The functions of encoding genes were annotated by using the NCBI nr, COG, and KEGG databases.

The complete genome of GD201008-001 is composed of a 2,063,112-bp single circular chromosome with a GC content of 35.65%. A total of 1,964 protein-encoding genes, 77 tRNA genes, and 7 5S-16S-23S rRNA operons are found to be located in this chromosome. In addition, the chromosome harbors 1 prophage-like element and 1 putative clustered regularly interspaced short palindromic repeat (CRISPR).

As an invasive and virulent strain, GD201008-001 contains most of known virulence-associated factors, such as β-H/C, CAMP factor, Fbs, SodA, Lmb, BibA, and IagA (7), except for C5a peptidase. Interestingly, there are 10 copies of the self-splicing group II intron, also named reverse transcriptase and maturase, distributed in the GD201008-001chromosome. Group II introns are often located within other DNA mobile elements near potential virulence genes in both Bacteria and Archaea, which could help them to act as carriers during vertical and horizontal distribution (8). The GBS group II intron was first described in human GBS in 2001 (3), and between 0 and 3 copies can be present in human isolates (6). Meanwhile, a previously novel genomic island (10 kb) is integrated after one group II intron in GD201008-001. This unique 10-kb cluster is not found in human strains and has been found only in piscine GBS strains ZQ00910 (AKAP01000000) and GD201008-001. It is likely that this 10-kb cluster contributes to the diversification of the bacterial genome architecture and enhanced piscine GBS survival and virulence in fish.

Nucleotide sequence accession number.

The genome sequence of S. agalactiae strain GD201008-001 reported in this paper has been deposited in the GenBank database under accession number CP003810.