Streptococcus iniae SF1: Complete Genome Sequence, Proteomic Profile, and Immunoprotective Antigens

Abstract

Streptococcus iniae is a Gram-positive bacterium that is reckoned one of the most severe aquaculture pathogens. It has a broad host range among farmed marine and freshwater fish and can also cause zoonotic infection in humans. Here we report for the first time the complete genome sequence as well as the host factor-induced proteomic profile of a pathogenic S. iniae strain, SF1, a serotype I isolate from diseased fish. SF1 possesses a single chromosome of 2,149,844 base pairs, which contains 2,125 predicted protein coding sequences (CDS), 12 rRNA genes, and 45 tRNA genes. Among the protein-encoding CDS are genes involved in resource acquisition and utilization, signal sensing and transduction, carbohydrate metabolism, and defense against host immune response. Potential virulence genes include those encoding adhesins, autolysins, toxins, exoenzymes, and proteases. In addition, two putative prophages and a CRISPR-Cas system were found in the genome, the latter containing a CRISPR locus and four cas genes. Proteomic analysis detected 21 secreted proteins whose expressions were induced by host serum. Five of the serum-responsive proteins were subjected to immunoprotective analysis, which revealed that two of the proteins were highly protective against lethal S. iniae challenge when used as purified recombinant subunit vaccines. Taken together, these results provide an important molecular basis for future study of S. iniae in various aspects, in particular those related to pathogenesis and disease control.

Comparative genome analysis of Streptococcus iniae DX09 reveals new insights into niche adaptation and competitive host colonisation ability

“…This finding was in agreement with data from a previous study on the CRISPR/Cas systems of S.iniae SF1 [19].…”

“…By 2015, eight available genomes of S. iniae were recorded on the NCBI database: YSFST01-82, SF1, 9117, CAIM 527, ISET0901, IUSA1, KCTC 11634BP and ISNO (Table 1). While the complete genome sequence of S. iniae SF1 has been reported [19], comparative genomic analysis of closely related S. iniae species is yet to be conducted. In this study, we have reported the complete genome sequence of S. iniae DX09, a strain isolated from cultured catfish (Ictalurus punctatus) (Supplementary Figure 1) in the Guangxi region of China, for the first time and compared it to all known S. iniae genomes available in the NCBI database.…”

Role of complement proteases in Streptococcus pathogenesis in fish

“…The putative C3-degrading protease was published in the complete genome sequence of S. iniae SF1 isolated from fish by Zhang et al (GenBank ID AGM99589.1) (Zhang et al, 2014). However in the two later complete sequences of S.iniae from Tilapia i.e.…”

“…(AHY18370.1 and AHY16506.1) (Pridgeon et al, 2014a, b) although it has 99-100% identity to C3-degrading protease of Zhang et al, (2014) by BLAST, which warrants further investigation. The protease coding gene cppA was also found in other Streptococci such as S. dysgalactiae subsp.…”

“…Interestingly, the corruption of the complement system by the interference from a C5a peptidase and a C3-degrading protease has been demonstrated in Streptococci of group A, B, G in their pathogenesis in mammals (Cleary et al, 2004;Hostetter et al, 2004;Ji et al, 1996). Genes encoding these proteins are retained in fish pathogenic streptococci, including Streptococcus iniae (Baiano and Barnes, 2009;Locke et al, 2008;Zhang et al, 2014). Could manipulation of the complement system play a role in the meningeal pathology that results from these infections?…”