Complete Genome Sequence of Shewanella sp. Strain TH2012, Isolated from Shrimp in a Cultivation Pond Exhibiting Early Mortality Syndrome

Abstract

Here, we present the complete genome sequence of a Shewanella isolate, TH2012, from a shrimp pond in which shrimp exhibited early mortality syndrome (EMS)/acute hepatopancreatic necrosis disease (AHPND). The complete genome of TH2012 has a prophage-like element and a number of potential virulence factors, making TH2012 a possible contributing factor to EMS outbreaks.

Shewanella khirikhana sp. nov. – a shrimp pathogen isolated from a cultivation pond exhibiting early mortality syndrome

“…This was supported by differential morphological and physiological characteristics (Table and Supporting information). Recently, an independent phylogenomic analysis of our published TH2012 T genome sequence (Wechprasit et al , ) also supported this erection of a new species within the genus (Thorell et al , ). Thus, we propose the name Shewanella khirikhana to indicate that TH2012 T originated from Prachuap Khirikhan Province, Thailand.…”

“…In addition, the TH2012 T genome contains a putative prophage (Fig. ) (Wechprasit et al , ) and some virulence genes found in some Shewanella isolates (Paździor, ; Yousfi et al , ) such as putative haemolysins, chitinases and proteases (Wechprasit et al , ).…”

“…Multiple sequence alignments were performed with MUSCLE (Edgar, ) using concatenated multilocus sequence alignment with genes in the order of 16S rRNA, atpA, mreB and rpoA genes, and phylogenetic trees were constructed with the neighbour‐joining, minimum evolution, maximum‐likelihood and maximum parsimonious algorithms (all with Jukes–Cantor distance) in MEGA 7 (Kumar et al , ). Complete genomes of TH2012 T (Wechprasit et al , ) and S. amazonensis SB2B T (Accession: NC_008700) were used to calculate digital DNA:DNA hybridization (dDDH) similarities by the Genome‐to‐Genome Distance Calculator version 2.1 formula 2 (http://ggdc.dsmz.de (Meier‐Kolthoff et al , )) as well as to calculate average nucleotide identity (ANI) scores in IMG/MER (Chen et al , ). GIPSy (Soares et al , ) was used to detect pathogenicity islands and resistance islands by using the genome sequence of TH2012 T as a query against the whole genome sequence of S. amazonensis SB2B T (NC_008700) as a reference.…”

“…DNA-DNA relatedness. Using complete genomes of TH2012 T (Wechprasit et al, 2019) and S. amazonensis SB2B T to calculate dDDH similarities (see Experimental Procedures), it was found that the dDDH value was 25.2% (model 95% C.I. 22.9-27.7%).…”

“…Thus, in a continued effort to test the hypothesis, we have been screening other bacterial isolates that have been obtained from EMS/AHPND ponds. Recently, we reported the complete genome of one such Thai isolate TH2012 T with a high similarity of 16S rRNA to those of species in the genus Shewanella (Wechprasit et al , ). Here, we demonstrate that TH2012 T itself is lethal to juvenile Pacific whiteleg shrimp Penaeus (Litopenaeus) vannamei in laboratory challenges, and we reveal by full genome analysis that it is a new species of the genus Shewanella with a number of potential virulence factor genes.…”