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Flavobacterium psychrophilum , the causative agent of bacterial cold‐water disease (BCWD) and rainbow trout fry syndrome (RTFS), remains one of the most important bacterial pathogens affecting salmonid aquaculture. In this study, 24 F. psychrophilum isolates recovered during a 12‐month surveillance programme from two rainbow trout farms in Türkiye were characterized using phenotypic, serological, antigenic, phylogenomic and experimental infection approaches. Phylogenomic analyses showed that most isolates belonged to CC‐ST10, whereas four isolates were assigned to the CC‐ST90/ST108 lineage, representing the first report of this lineage in Türkiye. Comparative genomic analysis revealed extensive conservation of virulence‐associated loci, with only FP0006 and FP0506 showing variable distribution among isolates. Notably, FP0506 was absent exclusively from ST108/CC‐ST90 isolates. Experimental immersion challenge assays demonstrated that all selected isolates were able to induce mortality in rainbow trout under the conditions tested. However, isolate‐dependent differences in survival were not statistically significant in the standard immersion model and became more evident following H ₂ O ₂ pre‐treatment, with the FP1 group showing the lowest survival. These findings suggest that in vivo pathogenicity may be influenced by host barrier status and cannot be fully predicted by phylogenomic lineage, serotype or in vitro virulence‐associated phenotypes alone. Phenotypic serotyping identified Th as the predominant serotype, although discrepancies were observed between phenotypic and genome‐based serotype classifications. Whole‐cell protein profiling and Western blot analyses revealed both antigenic heterogeneity and conserved immunoreactive structures across phylogenetically distinct isolates. Antimicrobial susceptibility testing showed a high proportion of non‐wild‐type phenotypes for oxytetracycline, florfenicol and enrofloxacin; however, no acquired antimicrobial resistance genes were detected by genome‐based screening. Collectively, these findings demonstrate that Turkish F. psychrophilum populations are phylogenomically diverse but retain largely conserved virulence‐associated loci and immunoreactive antigenic structures. This study provides the first evidence of the CC‐ST90/ST108 lineage in Türkiye and highlights the value of integrating genomic, serological, phenotypic, antigenic and experimental infection data for understanding the population structure, serotype heterogeneity and pathogenic potential of F. psychrophilum in rainbow trout aquaculture.

Bu çalışma, Avrupa Birliği (AB)'nin 2016/429 sayılı Hayvan Sağlığı Kanunu (Animal Health Law – AHL) öncesi ve sonrası dönemlerde sucul hayvan sağlığı mevzuatında yaşanan normatif dönüşümü analiz ederek, Türkiye mevzuatıyla karşılaştırmalı bir değerlendirme sunmaktadır. AHL’nin kabulüyle birlikte AB, direktif temelli ve parçalı yapıdan uzaklaşarak; risk-temelli, kanıta dayalı ve dijital yönetişim esasına dayanan bütüncül bir normatif çerçeveye geçmiştir. Türkiye mevzuatı ise büyük ölçüde 91/67/EC ve 2006/88/EC direktifleri ve ikincil mevzuatlarının idari izin temelli yaklaşımını sürdürmektedir. Bu bağlamda, çalışmada 13 temel normatif alan kapsamında yapılan karşılaştırmalı analiz, Türkiye mevzuatının AHL sonrası AB sistemiyle uyum sağlayamadığını göstermektedir. Özellikle dijital izlenebilirlik, risk-temelli sürveyans, dinamik sağlık statüsü yönetimi ve antimikrobiyal direnç (AMR) yönetişimi gibi alanlarda yapısal, işlevsel ve yönetişimsel boşluklar tespit edilmiştir. Çalışma sonucunda, Türkiye için önerilen yol haritası, yeni mevzuat üretiminden ziyade mevcut düzenlemelerin AHL sonrası AB normatif yapısıyla işlevsel uyumunun güçlendirilmesidir.

Aquarium fish are increasingly being recognized as reservoirs of zoonotic pathogens, with Aeromonas species posing a notable risk because of their environmental resilience and opportunistic pathogenicity. This study presents the most comprehensive genome-based investigation to date of Aeromonas diversity in aquarium fish, aiming to characterize their taxonomic distribution, population structure, and genomic features. A total of 64 Aeromonas isolates were collected from various aquarium fish species. Wholegenome sequencing was conducted on all isolates to facilitate comparative genomic analyses. Key approaches included multilocus sequence typing (MLST), pairwise Digital DNA-DNA hybridization (dDDH), and the construction of a phylogenomic tree for species-level classification. Furthermore, a population structure analysis was performed to explore genomic diversity and evolutionary trends among the isolates. The results identified 14 distinct Aeromonas species, with A. veronii, A. caviae, and A. hydrophila being the most common. Importantly, several isolates exhibited taxonomic ambiguity, indicating the possible presence of new species or subspecies lineages. Furthermore, antimicrobial resistance gene profiles and virulence factor distributions varied significantly across clades, indicating genomic plasticity. This study highlights the underappreciated genomic complexity of Aeromonas populations in aquarium environments and raises concerns about the public health implications of pathogen reservoirs in ornamental fish.

Co-infections are increasingly recognized as drivers of disease in ornamental fish, yet their genomic underpinnings and zoonotic implications remain underexplored compared to farmed species. Leveraging a One Health perspective, we investigated an acute mortality event in koi carp and characterized a co-infection by opportunistic aquatic bacteria that are also implicated in human disease. We isolated Aeromonas veronii and Shewanella sp. from a moribund koi using culture, biochemical assays, and MALDI-TOF MS, then generated draft genomes and performed orthology (OrthoVenn3), pathway annotation (KEGG BlastKOALA/Mapper), secondary-metabolite mining (antiSMASH), and virulence/resistome screening (VFDB/CARD), complemented by antimicrobial susceptibility testing. Clinically, affected fish showed dropsy/ascites, scale loss, abnormal buoyancy, and reduced activity. Phylogenomics positioned A. veronii Koi-2 within the A. veronii complex near species thresholds (ANI ~96.1%; dDDH ~70.2%), while Shewanella sp. Koi-1 formed a distinct lineage below accepted cut-offs relative to S. seohaensis (ANI ~95.9%; dDDH ~67.6%). The virulome comprised 194 loci in A. veronii Koi-2 and 152 in Shewanella sp. Koi-1 is enriched for adhesion, secretion, iron uptake, and immune-evasion functions. Genotype–phenotype agreement was high for multidrug resistance: Shewanella sp. encoded OXA-436 and rsmA, matching β-lactam resistance and reduced fluoroquinolone/phenicol susceptibility, whereas A. veronii carried tet(A), OXA-1157, cphA3, sul1, and aadA3 consistent with tetracycline, β-lactam, sulfonamide, and aminoglycoside resistance profiles. In conclusion, genome-resolved diagnostics confirmed a mixed Aeromonas–Shewanella co-infection with broad virulence potential and convergent resistance mechanisms, supporting the routine use of genomics to distinguish single- versus mixed-agent disease and to guide dual-coverage, mechanism-aware therapy in ornamental fish medicine while informing zoonotic risk mitigation.

Avrupa’da 1970’li yıllarda, hayvanlar üzerinde yürütülen araştırmalarda etik ilke ve standartların denetlenmesi için etik kurullar oluşturulmaya başlanmıştır. Türkiye’de 6 Haziran1996 tarihinde Marmara Üniversitesi Tıp Fakültesinde deney hayvanı kullanımına yönelik faaliyete geçen ilk Etik Kurulu, 10 Temmuz 1996 tarihinde Ankara Üniversitesi Veteriner Fakültesinde oluşturulan Etik Kurul ve diğerleri izlemiştir. Gıda Tarım ve Hayvancılık Bakanlığının 2011, Orman ve Su İşleri Bakanlığının 2014 yılında yayımladığı iki Yönetmelikle bilimsel amaçlı kullanılan hayvanların korunması ile ilgili hukuki çerçeve oluşturulmuştur. Avrupa Birliğinin 2010 yılında çıkarttığı Direktifi (2010/63/EU) dayanak alan bu Yönetmelikler ile deney hayvanlarının üretileceği, deneylerin yapılacağı kuruluşların ve hayvan refahından sorumlu etik kurulların taşıması gereken nitelikler belirlenmiştir. Çalışmada, sucul omurgalı canlıların bilimsel amaçlı kullanımına yönelik 2019 yılında yürürlüğe giren Yönetmelik, konuyla ilgili mevzuatla karşılaştırmalı olarak değerlendirilmiştir. Değerlendirme sonucunda: Yönetmeliğin halen yürürlükte olan benzer amaç ve faaliyet alanına sahip Yönetmeliklerle uyuşmazlık gösterdiği ve dayanak aldığı uluslararası ve ulusal mevzuata aykırı hükümler içerdiği belirlenmiştir. Ayrıca, Yönetmeliğin hayvan sağlığı ve refahı gibi konularda veteriner hekimliği hizmetlerinin yerine getirilmesine yönelik görev ve yetki karışıklığı doğurduğu ortaya konulmuştur. Bu yetki karışıklığının deneysel süreçlerin bilimsel ve sağlıklı yürütülmesine engel oluşturacağı vurgulanan çalışmada, ulusal mevzuat kapsamında Yönetmeliğin yeniden bütüncül olarak değerlendirilmesinin gerektiği sonucuna ulaşılmıştır.

Piscine lactococcosis poses a significant threat to a wide range of cultured and wild fish populations worldwide, typically presenting as acute haemorrhagic septicemia with high morbidity and mortality. Although Lactococcus garvieae was historically considered the sole causative agent of piscine lactococcosis, recent studies have identified L. petauri and L. formosensis as additional, highly pathogenic species. In this study, we developed a novel TaqMan‐based multiplex qPCR assay for the simultaneous detection and differentiation of L. garvieae , L. petauri and L. formosensis , following a pangenome analysis of the publicly available genomes of these bacterial species. The assay demonstrated high sensitivity and specificity across 156 bacterial isolates obtained from various cultured fish species and geographical locations between 2008 and 2024, as well as against a panel of non‐target bacteria. It also successfully detected target pathogens in 146 field tissue samples, including tissues preserved in 70% ethanol, formalin‐fixed paraffin‐embedded (FFPE) tissues and tissues fixed on FTA cards. Compared to classical bacteriology, the multiplex qPCR assay yielded higher detection rates and enabled precise identification of the causative species of piscine lactococcosis. Overall, the multiplex qPCR assay developed in this study provides a reliable, rapid, highly sensitive and species‐specific molecular approach for diagnosing piscine lactococcosis, contributing to better surveillance and management of the disease in aquaculture.

Flavobacterium psychrophilum, a devastating fish pathogen, is responsible for bacterial cold‐water disease (BCWD), also known as rainbow trout fry syndrome. F. psychrophilum is the main causative agent of outbreaks in rainbow trout farms, especially at early live stages. In the present study, we aimed to characterize F. psychrophilum Turkish isolates. Eighteen isolates were retrieved from BCWD outbreaks between 2014 and 2021. In vitro phenotypic characterization showed gelatin and casein hydrolysis capacities and in vitro adhesion for all isolates, whereas elastinolytic activity was present for 16 of 18 isolates. We used complete genome sequencing to infer MLST‐type, serotype and phylogenetic reconstruction. Strikingly, one strain isolated from Coruh trout (FP‐369) belongs to ST393, a previously undescribed ST, and is phylogenetically distant from the other isolates. However, all strains retrieved from rainbow trout belong to the well‐characterized clonal complex CC‐ST10, 12 of 17 were tightly connected in a single cluster. Several serotypes (Types ‐1, ‐2 and ‐3) were represented among isolates, but no correlation was observed with geographic origins. This analysis suggests a regional dissemination of an epidemic, disease‐producing bacterial population. This study provides a basis for epidemiological surveillance of isolates circulating in Turkey and phenotypic data for future molecular studies of virulence traits of this important fish pathogen.

Two yellow-coloured strains, F-29T and F-340T, were isolated from fish farms in Antalya and Mugla in 2015 and 2017 during surveillance studies. The 16S rRNA gene sequence analysis showed that both strains belong to the genus Flavobacterium. A polyphasic approach involving a comprehensive genome analysis was employed to ascertain the taxonomic provenance of the strains. The overall genome-relatedness indices of digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) between the strains and the other members of the genus Flavobacterium were found to be well below the established thresholds of 70 and 95 %, respectively. The whole-genome-based phylogenetic analysis revealed that strain F-29T is closely related to Flavobacterium granuli (dDDH 39.3 % and ANI 89.4 %), while strain F-340T has a close relationship with the type strain of Flavobacterium pygoscelis (dDDH 25.6 % and ANI 81.5 %). Both strains were psychrotolerant with an optimum growth temperature of 25 °C. The chemotaxonomic characteristics of the strains were typical of the genus Flavobacterium. Both strains had phosphatidylethanolamine, aminolipids and unidentified lipids in their polar lipid profile and MK-6 as the isoprenoid quinone. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The genome size of the strains was 3.5 Mb, while G+C contents were 35.3 mol% for strain F-29T and 33.4 mol% for strain F-340T. Overall, the characterizations confirmed that both strains are representatives of two novel species within the genus Flavobacterium, for which the names Flavobacterium acetivorans sp. nov. and Flavobacterium galactosidilyticum sp. nov. are proposed, with F-29T (JCM 34193T=KCTC 82253T) and F-340T (JCM 34203T=KCTC 82263T) as the type strains, respectively.

Outbreaks of bacterial infections in aquaculture have emerged as significant threats to the sustainable production of rainbow trout (Oncorhynchus mykiss) worldwide. Understanding the dynamics of these outbreaks and the bacteria involved is crucial for implementing effective management strategies. This comprehensive review presents an update on outbreaks of bacteria isolated from rainbow trout reported between 2010 and 2022. A systematic literature survey was conducted to identify relevant studies reporting bacterial outbreaks in rainbow trout during the specified time frame. More than 150 published studies in PubMed, Web of Science, Scopus, Google Scholar and relevant databases met the inclusion criteria, encompassing diverse geographical regions and aquaculture systems. The main bacterial pathogens implicated in the outbreaks belong to both gram‐negative, namely Chryseobacterium, Citrobacter, Deefgea Flavobacterium, Janthinobacterium, Plesiomonas, Pseudomonas, Shewanella, and gram‐positive genera, including Lactococcus and Weissella, and comprise 36 new emerging species that are presented by means of pathogenicity and disturbance worldwide. We highlight the main characteristics of species to shed light on potential challenges in treatment strategies. Moreover, we investigate the role of various risk factors in the outbreaks, such as environmental conditions, fish density, water quality, and stressors that potentially cause outbreaks of these species. Insights into the temporal and spatial patterns of bacterial outbreaks in rainbow trout aquaculture are provided. Furthermore, the implications of these findings for developing sustainable and targeted disease prevention and control measures are discussed. The presented study serves as a comprehensive update on the state of bacterial outbreaks in rainbow trout aquaculture, emphasizing the importance of continued surveillance and research to sustain the health and productivity of this economically valuable species.