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

Abstract

Streptococcus iniae is a significant pathogen in a variety of marine and freshwater cultured fish species. Previous investigations on S. iniae have been limited to a single virulence gene or genome. However, different strains are associated with varying pathogenicity and niche adaptation properties. For comprehensive characterization of the genetic variations in S. iniae, whole-genome sequencing of S. iniae DX09 (isolated from diseased catfish) was performed and comparative genome analysis with eight S. iniae strains conducted to determine the virulence evolution patterns. Comparative analysis of all sequenced S. iniae revealed genome-genome variations, mainly in two plasticity zones, within genes encoding specific functions, such as the Ess/type VII secretion system and phosphoenolpyruvate-carbohydrate phosphotransferase system, reflecting adaptation to colonisation of specific host habitats. The plasticity zones analyzed in the S. iniae genome may be a paradigm rather than a unique combination of horizontal gene transfer and underlie the emergence of pathogenic Gram-positive bacteria.

Improving the diagnosis of Streptococcus iniae using a novel probe‐based qPCR assay combined with an enrichment step

“…The different phylogenetic clustering of S. iniae sequences found in this study raises questions about the diversity of S. iniae isolates from different fish host and geographic location. Interestingly, the comparative genome analysis of S. iniae had identified specific genomic regions that may be responsible for the bacteria's adaptation to different host niches (Liu et al, 2014). Further research on the genomic features of the bacteria and their virulence in fish might be necessary to answer these questions.…”

Streptococcal Infections in Marine Mammals

“…Virulence mechanisms include a capsule with antiphagocytic function [ 127 ], the cytotoxin ß-hemolysin streptolysin S [ 128 ], an extracellular nuclease and s secreted nucleotidase that play an important role in immune evasion [ 129 ], a polysaccharide deacetylase involved in adherence, invasion, lysozyme resistance and survival in fish blood [ 130 ], and M-like protein [ 131 ]. Comparative genomics revealed genetic differences between strains from different hosts including I. geoffrensis and identified two plasticity zones that reflect adaptation to specific host environments [ 132 ]. Furthermore, the dolphin isolates differed from the fish and human isolates in lacking a capsule, forming denser and thicker biofilms, increased ability to withstand oxidative stress and were genetically highly divergent to the other isolates [ 133 ].…”