Genome Based Species Delineation of Pseudomonas Sp. Ps-23 Isolate Recovered From Farmed Trout

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Satıcıoğlu İ. B.


  • Basıldığı Şehir: Baku
  • Basıldığı Ülke: Azerbaycan
  • Sayfa Sayıları: ss.203


Numerous Pseudomonas species can cause diseases in humans, animals, and aquatic organisms. Pseudomonas species have been considered one of the most common bacterial infectious agents among cultured fish species and are considered to cause stress-related diseases of freshwater fishes, especially under culture conditions. In this study, Pseudomonas sp. Ps-23 isolate was recovered from rainbow trout (40g), exhibiting clinical signs such as lethargy, inappetence, and exophthalmia at the beginning of winter. It was aimed to determine genome-based identification of the Ps-23 and determine genomic features such as virulence and antimicrobial resistance genes (AMR) genes. Samples were taken from the kidney and cultured on Tryptic Soy Agar (TSA) agar 25°C for 24-48h. Identification and sequence analysis was done with 27F and 1492R universal 16S rRNA primers. Next-generation genome sequencing of the Ps-23 isolate was performed on an Illumina NovaSeq 6000 platform as paired-end (PE) 2x250 base reads with a 1000-cycle MiSeq reagent kit. The high-quality reads of the Ps-23 were assembled into contigs by de novo assembly using the SPAdes assembler 3.13.0. Genome-based species delineation of the Ps-23 was done with Type Strain Genome Server ( and Automated Multi-Locus Species Tree (autoMLST, AMR and virulence genes in the Ps-23 genome were identified using the Virulence Factor Database (VFDB) and NCBIreference antimicrobial resistance genes database. If multiple virulence factors and AMR genes overlapped at the same locus in the genome, only the best-aligned gene was retained. The 16S rRNA sequence of the Ps-23 isolate has similarities with the Pseudomonas brenneri (99.47%) in GenBank. The genome structure of the Ps-23 was found a total of 29.907.130 sequences and assembled in 6.351.950 base. According to genome-based species delineation, the Ps-23 isolate was found as a Pseudomonas brenneri. Based on the autoMLST results, it was determined that the PS-23 isolate was similar to the strains isolated from water and soil in England. 14 virulence and eight putative AMR genes were detected in the genome of the Ps-23 strain. It has been determined that these genes encode resistance to many classes of antimicrobials such as aminoglycoside, nitrofuran, macrolide, tetracycline, and fluoroquinolone. Also, the detected virulence genes were responsible for antiphagocytosis, serum resistance, biofilm production, and motility. The genomic data have been deposited in the DDBJ/ENA/GenBank databases under the accession number JADODS000000000. The next studies aim to determine the pathogenicity in rainbow trout of P. brenneri strain Ps-23 isolate by experimental infection. Thus we will determine the correlation of genomic and phenotypic data.