Koi (Cyprinus carpio carpio) Balığından İzole Edilen Nocardia takedensis’in Genom Temelli Karakterizasyonu: Yeni Konak Bildirimi

Öz

Çevresel bir izolat olarak tanımlanan ve zamanla fırsatçı bir insan patojeni olarak değerlendirilmeye başlanan Nocardia takedensis’in balıklardan izole edildiğine dair bugüne kadar literatürde herhangi bir bulguya rastlanmamıştır. Bu çalışmanın amacı, Türkiye’de tatlı su süs balığı olan koi (Cyprinus carpio carpio) balığından izole edilen N. takedensis NTD01 izolatının Oxford Nanopore teknolojisi kullanılarak genom temelli ilk moleküler karakterizasyonunu gerçekleştirmektir. Elde edilen uzun okuma verileri Flye algoritması ile de novo olarak birleştirilmiş, taksonomik doğrulama dijital DNA-DNA hibridizasyonu (dDDH) ve ortalama nükleotid kimliği (ANI) analizleriyle yapılmıştır. İzolatın olası virülansla ilişkili özellikleri ve direnç profili, kapsamlı Antibiyotik Direnç Veri Tabanı (CARD), Virülens Faktörleri Veri Tabanı (VFDB) ve Antibiyotik ve Sekonder Metabolit Analiz Aracı (antiSMASH) kullanılarak genotipik düzeyde incelenmiştir. Analizler sonucunda 8,96 Mb büyüklüğündeki genomun, N. takedensis tip suşu ile %86,6 dDDH ve %99,18 ortalama nükleotid kimliği temelinde hesaplanan nükleotid benzerliği (ANIb) gösterdiği tespit edilmiştir. Genomda rifamisin ve glikopeptid direnciyle ilişkili dört antimikrobiyal direnç geni saptanırken, klasik virülens faktörlerine rastlanmamıştır. Buna karşın, demir kazanımında rol oynayan nocobactin benzeri metallofor kümeleri de dahil olmak üzere 33 biyosentetik gen kümesi (BGC) belirlenmiştir. Sonuç olarak, bu çalışma, bilgimiz dahilinde, bir koi balığından N. takedensis’in izolasyonunu ve genom temelli karakterizasyonunu belgeleyen ilk rapordur. Bununla birlikte, bu türün sucul ortamlardaki ekolojik dağılımını, patojenik önemini ve potansiyel konak ilişkisini netleştirmek için daha kapsamlı sürveyans çalışmaları ve deneysel araştırmalar gereklidir.

Anahtar Kelimeler

• Cyprinus carpio carpio
• Nocardia takedensis
• süs balığı
• tüm genom dizileme
• yeni konak

Teşekkür

Bu çalışmada analiz edilen Nocardia takedensis izolatı, Ondokuz Mayıs Üniversitesi Bilimsel Araştırma Projeleri Koordinasyon Birimi tarafından finanse edilen ve Türkiye Cumhuriyeti Tarım ve Ormancılık Bakanlığı Samsun Veteriner Kontrol Enstitüsü Hayvan Deneyleri Yerel Etik Kurulu’ndan alınan etik onay (no. 2020/10) kapsamında yürütülen PYO.VET.1904.21.027 numaralı proje kapsamında elde edilmiştir. Orijinal tez projesi akvaryum balıklarında mikobakteriyel ajanların belirlenmesine odaklanmış olsa da, elde edilen Nocardia izolatı bu çalışmanın birincil kapsamı dışında değerlendirildi ve bu nedenle mevcut araştırmada ayrı olarak karakterize edildi.

Genome-based Characterization of Nocardia takedensis Isolated from Koi (Cyprinus carpio carpio): A Novel Host Report

Öz

Nocardia takedensis, defined as an environmental isolate and increasingly recognized as an opportunistic human pathogen, has no prior record in the literature regarding its isolation from fish. The aim of this study is to perform the first genome-based molecular characterization of the N. takedensis isolate NTD01, isolated from a koi carp (Cyprinus carpio carpio), a freshwater ornamental fish, in Türkiye, using Oxford Nanopore technology. The obtained long-read data were assembled de novo using the Flye algorithm, and taxonomic validation was performed through digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses. The putative virulence-associated features and resistance profile of the isolate were examined at the genotypic level using the Comprehensive Antibiotic Resistance Database (CARD), Virulence Factors Database (VFDB), and the Antibiotics and Secondary Metabolite Analysis SHell (antiSMASH). The analyses revealed that the 8.96 Mb genome exhibited a nucleotide similarity (ANIb) of 99.18% and a dDDH value of 86.6% with the N. takedensis type strain. While four antimicrobial resistance genes associated with rifamycin and glycopeptide resistance were identified in the genome, no classical virulence factors were detected. In contrast, 33 biosynthetic gene clusters (BGCs) were identified, including nocobactin-like metallophore clusters involved in iron acquisition. Consequently, this study represents, to the best of our knowledge, the first report documenting the isolation and genome-based characterization of N. takedensis from koi fish. However, broader surveillance studies and experimental investigations are required to clarify the ecological distribution, pathogenic significance, and potential host association of this species in aquatic environments

Anahtar Kelimeler

• Cyprinus carpio carpio
• Nocardia takedensis
• novel host
• ornamental fish
• whole-genome sequencing

Teşekkür

The Nocardia takedensis isolate analyzed in this study was obtained within the scope of project no. PYO.VET.1904.21.027, funded by the Scientific Research Projects Coordination Unit of Ondokuz Mayıs University and conducted with ethical approval (no. 2020/10) from the Local Ethics Committee for Animal Experiments of the Republic of Türkiye Ministry of Agriculture and Forestry, Samsun Veterinary Control Institute. Although the original thesis project focused on the determination of mycobacterial agents in aquarium fish, the recovered Nocardia isolate was considered outside the primary scope of that study and was therefore characterized separately in the present research.

Kaynakça

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