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

Tao Liu,Kaiyu Wang,Yajun Wang

doi:10.18632/oncotarget.23198

Abstract

// Tao Liu 1, 2, * , Yajun Wang 1, 4, * and Kaiyu Wang 1, 3 1 Department of Basic Veterinary, Veterinary Medicine College, Sichuan Agricultural University, Sichuan, Chengdu 611134, P.R. China 2 Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Sichuan, Chengdu 611134, P.R. China 3 Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Sichuan 611134, Cheng’du, P.R. China 4 Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangzhou 510380, Guangdong, P.R. China * These authors contributed equally to this work Correspondence to: Kaiyu Wang, email: kywang1955@126.com Keywords: Streptococcus iniae; whole-genome sequencing; comparative genome analysis; pathogenic Received: September 22, 2017      Accepted: December 01, 2017      Published: December 08, 2017 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.

Highlights

Streptococcus iniae, a Gram-positive bacterium, was initially isolated from freshwater Amazon dolphin (Inia geoffrensis) in the 1970s [1]
The ability to survive intracellularly after invasion of fish cells is important for pathogenic S. iniae
Our results disclosed a 1.98 Mb chromosome with an average GC content of 36.6%, which represents the smallest genome among all sequenced Streptococcus iniae so far

Summary

Introduction

Streptococcus iniae, a Gram-positive bacterium, was initially isolated from freshwater Amazon dolphin (Inia geoffrensis) in the 1970s [1]. 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. 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.

Results

Conclusion