Whole Genome Sequence Analysıs And Genomıc Characterızatıon Of Lactococcus Petaurı Ksub4 Isolated From Raınbow Trout

Yıl 2025, Cilt: 4 Sayı: 1, 1 - 10, 30.06.2025

Ebru Gültekin , Ertan Emek Onuk , Izzet Burcin Saticioglu , Esra Demirbaş

Öz

Lactococcosis is one of the significant bacterial infectious diseases observed in fish worldwide. Etiologically, this disease is primarily associated with Lactococcus garvieae and, more recently, the newly identified species L. petauri. Traditionally, L. garvieae has been recognized as the most important and best-characterized pathogen of this disease. However, recent studies have revealed that the role of L. petauri in the epidemiology of the disease is increasingly significant. In this study, an isolate (KSUB4) obtained from a trout farm in the Black Sea region in 2022 and confirmed as Lactococcus sp. by Polymerase Chain Reaction (PCR) was identified using Whole Genome Sequencing (WGS) analysis. The genome sequencing of the isolate was performed on the Illumina HiSeqX platform, and the raw sequence reads were assembled using the Unicycler v0.4.8 software after undergoing quality control processes. Annotation of the genome was carried out through the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAP). Species-level identification of the isolate was performed using the Type Strain Genome Server (TYGS; https://tygs.dsmz.de/) platform. Virulence factors and antimicrobial resistance (AMR) genes were identified using the Virulence Factor Database (VFDB) and the Comprehensive Antibiotic Resistance Database (CARD), respectively. The analyses revealed that the genome of the KSUB4 isolate was 2,014,614 base pairs (bp) in length with a G+C content of 38.13%. Species identification analyses demonstrated that the KSUB4 isolate exhibited 51% digital DNA-DNA hybridization (dDDH) similarity with L. garvieae ATCC 49156T and 85.6% dDDH similarity with L. petauri 159469T. In the KSUB4 genome, 46 virulence genes with 35-71% similarity and 12 AMR genes with 53-95% similarity were detected. These findings shed light on the genetic potential of L. petauri in fish pathogenicity and provide significant insights into the antimicrobial resistance profile of this species.

Anahtar Kelimeler

Lactococcus petauri, Whole Genome Sequencing, Virulence Genes, Antibiotic Resistance, Aquaculture

Destekleyen Kurum

This study was supported by the TUBITAK 2209-A University Students Research Projects Support Program (Project No: 1919B012217594).

Proje Numarası

1919B012217594

GÖKKUŞAĞI ALABALIĞINDAN İZOLE EDİLEN LACTOCOCCUS PETAURİ KSUB4'ÜN TÜM GENOM SEKANS ANALİZİ ve GENOMİK KARAKTERİZASYONU

Öz

Laktokokkozis, dünya çapında balıklarda görülen önemli bakteriyel enfeksiyon hastalıklarından biridir. Bu hastalık, etiyolojik açıdan başlıca Lactococcus garvieae ve yakın zamanda tanımlanan L. petauri türleri ile ilişkilendirilmektedir. Geleneksel olarak, L. garvieae bu hastalığın en önemli ve en iyi karakterize edilmiş patojeni olarak kabul edilmektedir. Bununla birlikte, son yıllarda yapılan çalışmalar, L. petauri'nin hastalığın epidemiyolojisindeki rolünün giderek arttığını ortaya koymuştur. Bu çalışmada, 2022 yılında Karadeniz bölgesindeki bir alabalık işletmesinden izole edilen ve PCR ile Lactococcus sp. olarak doğrulanan bir izolat (KSUB4), Tüm Genom Sekans Analizi (WGS) kullanılarak tanımlanmıştır. İzolatın genom dizilemesi, Illumina HiSeqX platformunda gerçekleştirilmiş ve ham sekans okumaları kalite kontrol işlemlerinden geçirildikten sonra Unicycler v0.4.8 yazılımı kullanılarak birleştirilmiştir. Genomun anotasyonu, NCBI Prokaryotik Genom Otomatik Anotasyon Sistemi (PGAP) aracılığıyla yapılmıştır. İzolatın tür düzeyinde tanımlanması, Type Strain Genome Server (TYGS; https://tygs.dsmz.de/) platformu kullanılarak gerçekleştirilmiştir. Virülans faktörleri ve antimikrobiyal direnç (AMR) genlerinin belirlenmesi için sırasıyla Virulence Factor Database (VFDB) ve Comprehensive Antibiotic Resistance Database (CARD) veri tabanları kullanılmıştır. Analizler sonucunda, KSUB4 izolatının genomunun 2.014.614 baz çifti (bp) uzunluğunda ve %38,13 G+C içeriğine sahip olduğu belirlenmiştir. Tür tanımlama analizleri, KSUB4 izolatının L. garvieae ATCC 49156^T suşu ile %51, L. petauri 159469T suşu ile ise %85,6 dijital DNA-DNA hibridizasyon (dDDH) benzerliği gösterdiğini ortaya koymuştur. KSUB4 genomunda, %35-71 benzerlik oranına sahip 46 virülans geni ve %53-95 benzerlik oranına sahip 12 AMR geni tespit edilmiştir. Bu bulgular, L. petauri'nin balık patojenitesindeki genetik potansiyeline ışık tutmakta ve bu türün antimikrobiyal direnç profili hakkında önemli bilgiler sağlamaktadır.

Anahtar Kelimeler

Lactococcus petauri, Tüm Genom Sekans Analizi, Virülens Genleri, Antibiyotik Direnci, Akuakültür

Proje Numarası

1919B012217594

Kaynakça

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