Complete genome sequence and characterization of virulence genes in Lancefield group C Streptococcus dysgalactiae isolated from farmed amberjack (Seriola dumerili)

Abstract

Lancefield group C Streptococcus dysgalactiae causes infections in farmed fish. Here, the genome of S. dysgalactiae strain kdys0611, isolated from farmed amberjack (Seriola dumerili) was sequenced. The complete genome sequence of kdys0611 consists of a single chromosome and five plasmids. The chromosome is 2,142,780 bp long and has a GC content of 40%. It possesses 2061 coding sequences and 67 tRNA and 6 rRNA operons. One clustered regularly interspaced short palindromic repeat, 125 insertion sequences, and four predicted prophage elements were identified. Phylogenetic analysis based on 126 core genes suggested that the kdys0611 strain is more closely related to S. dysgalactiae subsp. dysgalactiae than to S. dysgalactiae subsp. equisimilis. The genome of kdys0611 harbors 87 genes with sequence similarity to putative virulence‐associated genes identified in other bacteria, of which 57 exhibit amino acid identity (>52%) to genes of the S. dysgalactiae subsp. equisimilis GGS124 human clinical isolate. Four putative virulence genes, emm5 (FGCSD_0256), spg_2 (FGCSD_1961), skc (FGCSD_1012), and cna (FGCSD_0159), in kdys0611 did not show significant homology with any deposited S. dysgalactiae genes. The chromosomal sequence of kdys0611 has been deposited in GenBank under Accession No. AP018726. This is the first report of the complete genome sequence of S. dysgalactiae isolated from fish.

Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae

“…Recently, Nishiki et al 7 sequenced the first SD isolate from fish, and reported a closer resemblance to SDSD than SDSE. However, their result was influenced by the inclusion S. equi in the phylogenetic analysis, reducing the basis of the comparison to 126 core genes.…”

“…Rosinski-Chupin et al 27 revealed a reductive evolution to be the most notable in fish-adapted S. agalactiae variants, primarily comprising deletion and inactivation of several metabolic functions. In piscine SD isolates, disruption of the emm -gene operon and pilus island1 by insertion sequences has been reported 7 . Similarly, we observed insertion sequences affecting other virulence factors in SD, including the deletion of the emm -gene in most swine associated SD isolates and the Streptolysin S operon in all SDSD isolates (Figure S2 ).…”

“…Although several studies have involved whole genome sequencing of SDSE, very few studies have sequenced SDSD 6 , 7 . Genomic investigations of SDSD to reveal factors associated with virulence, persistence in the environment and host specificity can contribute to enhancing our understanding of pathogenicity and transmission.…”

Infectious diseases and treatment solutions of farmed greater amberjack Seriola dumerili with particular emphasis in Mediterranean region

“…The same study also described moderate‐to‐severe non‐purulent encephalomyelitis in infected fish. The complete genome sequence and characterization of virulence genes of S. dysgalactiae isolated from farmed greater amberjack were recently described (Nishiki et al, 2019). A possible misdetection problem could occur with L. garvieae , which exhibits clinical similarities (Nomoto et al, 2004).…”

Group C Streptococcus dysgalactiae infection in fish

“…Recently, the whole‐genome sequence of GCSD strain (kdys061) isolated from farmed amberjack ( Seriola dumerili ) was reported (Nishiki, Yoshida, & Fujiwara, 2019). The complete genome sequence consists of a single chromosome and five plasmids.…”