Izzet Burcin Saticioglu

Introduction: We investigated seven-year temporal trends in fosfomycin resistance among Klebsiella pneumoniae bloodstream isolates and characterized resistant isolates phenotypically and molecularly. Methods: We included 198 non-duplicate bloodstream isolates collected from hospitalized adults during 2017–2023. Fosfomycin MICs were determined by agar dilution and evaluated using the 2023 EUCAST intravenous clinical breakpoint, FDA susceptibility test interpretive criteria (STIC), and current EUCAST (T)ECOFF. Temporal trends were assessed by logistic regression. Phenotypic evidence of FosA-like enzyme production was assessed by PPF disk testing, acquired fosA variants by PCR and Sanger sequencing, and two representative isolates by Oxford Nanopore WGS. Results: Using the 2023 EUCAST breakpoint, 25.3% of isolates were resistant, with a significant annual increase in resistance odds (OR 1.22, 95% CI 1.04–1.44; p = 0.019). Using FDA STIC, 12.6% were resistant, with a significant temporal increase (OR 1.43, 95% CI 1.13–1.81; p = 0.003). According to the EUCAST (T)ECOFF, 6.1% were non-WT, with a non-significant trend (OR 1.36, 95% CI 0.99–1.86; p = 0.057). Among 47 viable resistant isolates, 36.2% were PPF-positive. No acquired fosA, fosA2, fosA3, or fosA4 genes were detected. Published fosA4 primers showed non-specific amplification. WGS identified chromosomal fosA5 in both sequenced isolates. Conclusions: Fosfomycin resistance increased significantly according to the 2023 EUCAST breakpoint and FDA STIC, whereas the ECOFF-based non-WT trend was not significant. The absence of common acquired fosA variants and non-specificity of published fosA4 primers highlight the need for careful molecular validation.

Effective water quality management is a fundamental component of disease prevention, fish welfare, and sustainable production in finfish aquaculture. As aquaculture continues to expand to meet increasing global food demand, maintaining biosafe aquatic environments has become increasingly challenging due to production intensification, climate change, emerging pathogens, and the spread of antimicrobial resistance. While conventional approaches such as mechanical filtration, biofiltration, ultraviolet disinfection, ozonation, and water exchange remain central to water prophylaxis, increasing attention is being directed toward technologies that support earlier pathogen detection, improved risk assessment, and more targeted intervention strategies. This review examines water prophylaxis and biosafety through an integrated framework that links water quality, microbial ecology, pathogen surveillance, antimicrobial resistance, and preventive interventions. First, the biological and environmental mechanisms through which water quality influences disease susceptibility, microbiome stability, pathogen persistence, and antimicrobial resistance are evaluated. Conventional water-treatment technologies are then assessed alongside emerging approaches, including environmental DNA/environmental RNA monitoring, probiotics, phage therapy, biosensors, smart sensors, microfluidic platforms, and droplet-based molecular diagnostics. Emphasis is placed on their practical applicability, technological readiness, and suitability for different finfish production systems. The review highlights that effective biosafety management depends increasingly on integrating environmental monitoring with molecular diagnostics, risk assessment, and targeted interventions rather than relying solely on water-quality control or reactive disease treatment. Emerging technologies differ substantially in readiness, ranging from established and pilot-stage approaches to experimental technologies that require further validation before routine implementation. To support practical decision-making, the review synthesizes these technologies within an integrated water-prophylaxis and biosafety framework that links monitoring, diagnostics, risk assessment, intervention strategies, and reassessment pathways. Overall, sustainable finfish aquaculture will depend on combining conventional water-treatment infrastructure with advanced surveillance technologies and preventive biological interventions within coordinated biosafety programs. Such integration offers considerable potential to improve fish health, reduce environmental impacts, support responsible antimicrobial use, and enhance the long-term resilience of aquaculture production systems.

1. This study isolated Campylobacter jejuni, Listeria spp., and Salmonella spp. from faecal samples of wild birds, and determined the antibiotic susceptibilities and genotypes of the recovered C. jejuni isolates.2. A total of 575 faecal samples were collected from wild birds. Recovered isolates were identified using phenotypic tests, serological testing, MALDI-TOF mass spectrometry (MS), and polymerase chain reaction (PCR). The susceptibilities of isolates to six different antibiotics were determined by the disk diffusion method, while genotyping was performed using enterobacterial repetitive intergenic consensus (ERIC)-PCR.3. The prevalence of C. jejuni and Salmonella spp. was 9.2% and 0.2%, respectively. Listeria spp. were not found. For antibiotic susceptibility testing, the highest resistance to amoxycillin-clavulanic acid (30.2%) and tetracycline (15.1%) was seen in the C. jejuni isolates and the rate of multidrug resistance was determined as 7.5%. The ERIC-PCR results for C. jejuni isolates showed a total of 21 different forms.4. The detection of enteropathogenic, antibiotic-resistant and heterogeneous genetic diversity bacteria suggests that wild birds pose a potential health risk.

Outbreaks of vibriosis caused by Vibrio anguillarum are a persistent constraint on rainbow trout ( Oncorhynchus mykiss ) aquaculture. However, information on the population structure of field strains in Turkey has been lacking. Here, we report the first systematic serotypic, proteomic, and genomic characterization of 23 V. anguillarum isolates collected over 10 years from rainbow trout farms located in six major aquaculture regions of Turkey. Serological analyses based on microagglutination, supported by ELISA characterization of hyperimmune sera, identified a clear predominance of serotype O1, whereas isolate V12 exhibited a non‐agglutinating, atypical O‐antigen profile. Protein profiling (SDS‐PAGE) and immunoblotting showed largely conserved whole‐cell protein patterns among the isolates, but distinct immunogenic bands at 14, 18, and 40 kDa were detected in isolates V18 and V21. Long‐read whole‐genome sequencing revealed that most Turkish isolates grouped within the global O1 clade, while V12, V25, and V28 isolates occupied more distant branches. Comparative genomics demonstrated a conserved core virulence gene set (RTX toxins, siderophore and iron‐uptake systems, motility and adhesion factors, Type VI secretion system), with strain‐dependent variation in accessory loci such as anguibactin and T6SS‐I. Experimental infections of rainbow trout demonstrated significant differences in virulence among isolates ( p < 0.05), with the V18 isolate showing high, the V15 intermediate, and the V12 low‐mortality rates. By elucidating the relationship among the serotype, immunogenic protein profiles, virulence gene repertoires, and in vivo pathogenicity, this study provides a comprehensive overview of the antigenic and genomic diversity of Vibrio anguillarum isolates from Turkey. Notably, the identification of V18 and V21 as promising candidate strains for further vaccine evaluation, characterized by high virulence and unique immunogenic features, provides a scientific foundation for the development of serotype‐specific vaccination strategies to mitigate vibriosis‐associated losses in aquaculture.

Edwardsiella tarda is a facultatively anaerobic, Gram-negative bacterium that is widely distributed in aquatic environments. With the increasing interactions between aquatic animals and humans, E. tarda has become an important pathogen with significant implications for global public health. In this study, we characterized strain ET-1, isolated from an aquarium housing Pangasius pangasius, to evaluate its ecological presence, antimicrobial resistance, and pathogenic potential using a combination of phenotypic and genome-based approaches. Biochemical characteristics were determined using the API 20E system. Antimicrobial susceptibility was evaluated using MIC testing to determine resistance to clinically relevant antibiotics. Whole-genome sequencing using Oxford Nanopore Technologies revealed a genome size of 3.76 Mb with a GC content of 57.12%. Genome-based identification using digital DNA–DNA hybridization (dDDH, 86.6%) confirmed the classification as E. tarda. Several virulence-associated genes (flgG – flagellar basal body-rod protein; etfC – electron transfer flavoprotein subunit C) and antimicrobial resistance determinants (qnrS1 – quinolone resistance protein S1; efflux pump genes such as kpnH and kpnF) were identified. Pathogenic potential analysis via PathogenFinder2 indicated a high likelihood of human pathogenicity. Additionally, 16S rRNA-based profiling revealed the widespread environmental and host-associated presence of ET-1-like sequences. These results underscore the zoonotic and environmental significance of E. tarda ET-1 and support its relevance for public health surveillance within the One Health framework.

In this study, we comparatively assessed short-read (Illumina), long-read (Oxford Nanopore Technologies, ONT), and hybrid (Illumina + ONT) sequencing strategies for bacterial genome analysis using the aquaculture-derived isolate 160P. Genomic DNA was extracted and sequenced on Illumina paired-end and ONT long-read platforms, and de novo assemblies were generated using SPAdes, Canu, Flye, and Unicycler under short-read-only, long-read-only, and hybrid workflows, followed by evaluation with QUAST assembly metrics. Among the tested approaches, the hybrid Unicycler assembly provided the highest contiguity, yielding seven contigs and a dominant 4.55 Mb contig consistent with near-complete chromosomal representation. Downstream analyses included functional genome annotation and in silico screening of antimicrobial resistance determinants (CARD), virulence-associated genes (VFDB), and secondary metabolite biosynthetic gene clusters (antiSMASH). Comparative genomic relatedness based on Average Nucleotide Identity (ANI) and digital DNA–DNA Hybridization (dDDH) indicated that 160P is most closely related to Aeromonas sobria CECT 4245^T yet falls below commonly applied species-level thresholds, supporting its placement as a genomically distinct lineage warranting further taxonomic investigation. Collectively, these findings underscore the value of hybrid sequencing for improving assembly continuity, enhancing annotation completeness, and strengthening taxonomic resolution in bacterial pathogen genomics.

The canine ear microbiota plays an important role in ear health, and dysbiosis is associated with otitis externa (OE) and antimicrobial resistance (AMR). This study aims to investigate the ear microbiota of dogs with healthy ears and OE using bacterial culture-based methods and shotgun metagenomic sequencing, and to screen for AMR and virulence-associated genetic signatures. Ear swab specimens from 100 healthy and 100 OE-affected dogs were analyzed. The isolates obtained via bacterial culture were identified by MALDI-TOF MS and 16S rRNA sequencing. Metagenomic analysis was performed via Illumina shotgun sequencing. The most commonly defined species in healthy dogs in culture were Staphylococcus pseudintermedius (24.5%) and Staphylococcus epidermidis (5.7%); in dogs with OE, the most commonly defined species were S. pseudintermedius (30.5%), and Clostridium perfringens (4.5%). In healthy samples, metagenomic analysis revealed higher relative abundances of Bacteroides fragilis (15.8%) and Ezakiella coagulans (8.2%), while S. pseudintermedius (38.7%) dominated in OE. AMR profiling demonstrated diverse resistance determinants, including efflux pump systems and methicillin resistance-associated genes. In conclusion, the present study shows that S. pseudintermedius is a predominant member of canine ear microbiota, with higher presence in OE highlighting microbial shifts, and demonstrates that combining culture and metagenomic analyses provides a concise view of microbial communities and clinical relevance.

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

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.