Person: ALTUN, SONER
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ALTUN
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Publication Pseudomonas piscium sp. nov., Pseudomonas pisciculturae sp. nov., Pseudomonas mucoides sp. nov. and Pseudomonas neuropathica sp. nov. isolated from rainbow trout(Microbiology Soc, 2021-01-01) Duman, Muhammed; Mulet, Magdalena; Altun, Soner; Satıcıoğlu, İzzet Burçin; Gomila, Margarita; Lalucat, Jorge; Garcia-Valdes, Elena; DUMAN, MUHAMMED; ALTUN, SONER; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-7707-2705; 0000-0001-9096-875X; T-1697-2019; AAG-8518-2021Six Gram negative, motile bacteria were isolated from rainbow trout (Oncorhynchus mykiss). The 16S rRNA sequence similarity values grouped them in the Pseudomonas mandelii (strains P49, P50(T), 154a(T) and P154b), Pseudomonas fluorescens (strain P115(T)) and Pseudomonas koreensis (strain P155(T)) phylogenetic subgroups in the genus Pseudomonas. The DNA G+C content ranged from 58.5 to 60mol%. The strains were characterized phenotypically using API 20NE and Biolog GENIII tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. Multi-locus sequence analysis with four housekeeping gene sequences (rpoD, rpoB, gyrB and 16S rRNA) together with genome comparisons by average nucleotide identity and genome-to-genome distance calculations were performed. Results showed that the similarity values of these strains to known species type strains were lower than the thresholds established for species in the genus Pseudomonas. Based on these data, we concluded that strains P49, P50(T), P115(T), P154a(T), P154b and P155(T) belonged to four novel species. The names proposed are: Pseudomonas piscium sp. nov. for strains P49 and P50(T) with P50(T) (=CECT 30175(T)=CCUG 74871(T)) as the type strain; Pseudomonas pisciculturae sp. nov. for strain P115(T) (CECT 30173(T)=CCUG 74873(T)); Pseudomonas mucoides sp. nov. for strains P154a(T) and P154b with P154a(T) (=CECT 30177(T)=CCUG 74874(T)) as the type strain; and Pseudomonas neuropathica sp. nov. for strain P155(T) (=CECT 30178(T)=CCUG 74875(T)).Publication Detection of The First QnrS gene positivity in Aquatic Aeromonas spp. Isolates in Turkey (vol 49, pg 114, 2015)(Ankara Microbiology Society, 2015-04-01) Onuk, Ertan Emek; Caycl, Yeliz Tanrıverdi; Çoban, Ahmet Yılmaz; Çiftçi, Alper; Balta, Fikri; Didinen, Behire Işıl; Pekmezci, Gökmen Zafer; Altun, Soner; Ünlü, Mehtap Söğüt; Deveci, Aydın; ALTUN, SONER; 0000-0001-9096-875X; AAG-8518-2021Publication Population genetic and evolution analysis of vibrio isolated from Turkish fish farms(Elsevier, 2022-08-27) Bujan, Noemi; Romalde, Jesus L.; DUMAN, MUHAMMED; Altun, Soner; ALTUN, SONER; Satıcıoğlu, İzzet Burçin; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi.; Bursa Uludağ Üniversitesi/Keleş Meslek Yüksekokulu.; 0000-0001-7707-2705; 0000-0003-4786-4773; 0000-0002-2721-3204; T-1697-2019; AAD-4156-2019The genus Vibrio includes important pathogenic species for human and aquatic organisms such as Vibrio cholera, V. parahaemolyticus, V. vulnificus, V. anguillarum or V. harveyi. At present, Vibrionaceae family consists of > 190 described species, classified into nine genera. Vibrio are widespread in shellfish, finfish and marine ecosystems and show resourceful ecologies, which recognized as one of the most diverse bacterial groups for illuminating the genome evolution. In the present study, to clarify the relationship among aquatic species in the genus, a multilocus sequence analysis (MLSA) and typing (MLST) approach was applied to characterize 51 Vibrio isolates from Turkish fish farms, 146 strains deposited in the PubMLST database and 59 type strains from GenBank. For all studied isolates (n = 256), diversity analysis, population structure, determination of recombination, demographic history and gene flow were performed based on the MLST scheme. Vibrio isolates, subjected to the study, showed a high diversity within the Vibrio population and also genetic interactions into the genus. We found 17 new described sequence types by MLST analysis that were isolated from rainbow trout, sea bream and sea bass in Turkish fish farms, which clearly indicate that the genes underwent recombination frequently. While predominant sequence types were found in the presented study, differences of genotypes need to be evaluated in a disease situation or preventing measurements. The findings about genetic recombination possibly helps to understand differences of Vibrio infections in fish. Furthermore, elucidating of genetic variability within species shed light on providing effective measurements in aquaculture by vaccine production and drug applications.Publication A comprehensive perspective on a Vagococcus salmoninarum outbreak in rainbow trout broodstock(Elsevier, 2021-07-20) Satıcıoğlu, İzzet Burçin; Yardımcı, Banu; Altun, Soner; Duman, Muhammed; ALTUN, SONER; DUMAN, MUHAMMED; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-9096-875X ; 0000-0001-7707-2705; AAG-8518-2021 ; T-1697-2019Streptococcus species are of major concern for both warm-water and cold-water salmonid species, and have zoonotic importance. While Lactococcus garvieae, associated with warm-water streptococcosis, causes thousands of tons of mortalities, Vagococcus salmoninarum, the causative agent of cold-water streptococcosis, leads to chronic disease and devastating mortality in broodstock. In the present study, five bacterial samplings were performed from outbreaks that occurred between winter 2019 and summer 2020 in rainbow trout broodstock. The isolates were comprehensively characterized by phenotypic tests, using the API 20 Strept, Rapid ID 32 Strept and BIOLOG GENIII test kits. The antimicrobial susceptibilities of the strains were compared by the disk diffusion method, according to the guidelines of the Clinical & Laboratory Standards Institute (CLSI), additionally on commonly used media such as mueller-hinton agar and tryptic soy agar. Following a genomic approach, we analyzed the VS-1 strain by whole-genome sequencing. Virulence genes and correlation data were supported with the histopathological examination of the affected organs and tissues. The genome of the VS-1 strain included 69 virulence genes and 31 antimicrobial resistance genes. This study is one of the most comprehensive researches on V. salmoninarum, and elucidates the phenotypic, genotypic, antimicrobial resistance and virulence characteristics of this species.Publication Shewanella oncorhynchi sp. nov., a novel member of the genus shewanella, isolated from rainbow trout (oncorhynchus mykiss)(Microbiology Soc, 2022-01-01) Ay, Hilal; ALTUN, SONER; Duman, Muhammed; DUMAN, MUHAMMED; Satıcıoğlu, İzzet Burçin; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi.; Bursa Uludağ Üniversitesi/Keleş Meslek Yüksekokulu.; 0000-0001-7707-2705; 0000-0002-2721-3204; T-1697-2019; AAG-8518-2021 ; AAD-4156-2019A strain, S-1(T) was isolated from rainbow trout (Oncorhynchus mykiss) exhibiting clinical symptoms of lens atrophy, inappetence, visual impairment and growth retardation. The strain was identified as representing a member of the genus Shewanella on the basis of the results of 16S rRNA gene sequence analysis. The neighbor-joining phylogenetic tree based on 16S rRNA gene sequences indicated that S-1(T) clustered with Shewanella putrefaciens JCM 20190(T), Shewanella profunda DSM 15900(T), and Shewanella hafniensis P010(T), sharing 99.3, 98.8 and 87.7% 16S rRNA gene similarities, respectively. A polyphasic taxonomic approach including phenotypic, chemotaxonomic, and genomic characterization was employed to ascertain the taxonomic position of S-1(T) within the genus Shewanella. The overall genome relatedness indices (OGRI) for S-1(T) compared with the most closely related type strains S. hafniensis ATCC BAA-1207(T), Shewanella baltica NCTC 10735(T), S. putrefaciens ATCC 8071(T) and S. profunda DSM 15900(T) were calculated as 40.8, 40.1, 28.5 and 27.3% for digital DNA-DNA hybridization (dDDH), and 91.6, 91.0, 86.3 and 85.1% for average nucleotide identity (ANI), respectively. OGRI values between S-1(T) and its close neighbours confirmed that the strain represents a novel species in the genus Shewanella. The DNA G+C content of the strain is 45.2%. Major fatty acids were C-17:1.8 omega 8c, C(15:0)iso, and summed feature 3 (C-16:1 omega 6c and/or C-16:1 omega 7c). The predominant polar lipids were phosphatidylethanolamine, phospholipid, amino-phospholipid and unidentified lipids. The major respiratory quinones were ubiquinone-8, ubiquinone-7 and menaquinone-7. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Shewanella oncorhynchi sp. nov. is proposed, with S-1(T) as the type strain (JCM 34183(T)= KCTC 82249(T)).Publication Pseudomonas arcuscaelestis sp. nov., isolated from rainbow trout and water(Microbiology Society, 2021-01-01) Mulet, Magdalena; Saticioglu, Izzet Burcin; Gomila, Margarita; Matthijs, Sandra; Lalucat, Jorge; Garcia-Valdes, Elena; Altun, Soner; ALTUN, SONER; Duman, Muhammed; DUMAN, MUHAMMED; Bursa Uludağ Üniversitesi/Veteriner Fakültesi.; 0000-0001-7707-2705; T-1697-2019Cells of strains P66(T), V1 and W15Feb18 are Gram-stain-negative short rods and motile by one polar flagellum. Strain P66(T) was isolated from rainbow trout (Oncorhynchus mykiss) cultivated at a fish farm in Turkey. Strain V1 was isolated from sand of an intertidal shore on the Galicia coast in Spain and strain W15Feb18 was isolated from water collected at the Woluwe River in Belgium. Based on 16S rRNA sequence similarity values, the strains were grouped under the genus Pseudomonas and the Pseudomonas putida phylogenetic group of species. The DNA G+C content ranged from 58.5 to 58.9 mol%. The strains were characterized phenotypically by the API 20NE and Biolog GEN III tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. The absence of the hydrolysis of gelatin and the assimilation of arabinose. mannose and mannitol differentiated these strains from the closest species, Pseudomonas alkylphenolica. The major fatty acid components were C-16:0 (29.91-31.68%) and summed feature 3 (36.44-37.55%). Multilocus sequence analysis with four and 83 housekeeping gene sequences and a core proteome analysis showed that these strains formed a phylogenetic cluster in the P putida group of species. Genome comparisons by the average nucleotide identity based on BLAST and the Genome-to-Genome Distance Calculator demonstrated that the three strains belonged to the same genomic species and were distant from any known species, with similarity values lower than the thresholds established for species in the genus Pseudomonas. These data permitted us to conclude that strains P66(T), V1 and W15Feb18 belong to a novel species in the genus Pseudomonas, for which the name Pseudomonas arcuscaelestis sp. nov. is proposed. The type strain is P66(T) (=CECT 30176(T)=CCUG 74872(T)). The other strains have been deposited in the CECT with the corresponding collection numbers: V1 (=CECT 30356) and W15Feb18 (=CECT 30355).Publication A review of bacterial disease outbreaks in rainbow trout (Oncorhynchus mykiss) reported from 2010 to 2022(Wiley, 2023-10-30) Duman, Muhammed; Altun, Soner; Satıcıoğlu, İzzet Burçin; Romalde, Jesus L.; DUMAN, MUHAMMED; ALTUN, SONER; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-7707-2705; 0000-0002-2721-3204; AAD-4156-2019; AAG-8518-2021; T-1697-2019Outbreaks 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.Publication Description of lens atrophy caused by Shewanella sp. strain S-1, a putative novel species isolated from cultured rainbow trout(Elsevier, 2021-04-13) Satıcıoğlu, İzzet Burçin; İsbilir, Fatma; Yavaş, Özkan; Avcı, Zehra; Özdemir, Burak; Süzer, Bayram; Altun, Soner; Duman, Muhammed; İŞBİLİR, FATMA; YAVAŞ, ÖZKAN; Avcı, Zehra; SÜZER, BAYRAM; ALTUN, SONER; DUMAN, MUHAMMED; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Anatomi Anabilim Dalı.; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Patoloji Anabilim Dalı.; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0002-2687-1221; 0000-0001-7707-2705; 0000-0001-9096-875X; HJI-5667-2023; KHD-4075-2024; X-2000-2019; GLV-3407-2022; T-1697-2019; EZZ-5951-2022; CCJ-5608-2022; AAG-8518-2021In the present study, we describe a pathogenic incidence of Shewanella sp. S-1 infection in cultured rainbow trout (Oncorhynchus mykiss, Walbaum, 1792), as evidenced by lens atrophy, inappetence, visual impairment, and growth retardation. Strain S-1 was identified using basic microbiological tests, the BD PhoenixTM rapid diagnostic kit, the MALDI-TOF MS system, and whole-genome analysis. This strain's pathogenicity was assessed based on the histopathological examination of the eyes, lens, muscle, brain, liver, kidney, spleen, and gills. The lens, brain, and eyes of the fish were also examined morphologically. According to genome-based delineation, strain S-1 was determined to belong to the genus Shewanella and was considered a putative novel Shewanella species. While we determined that the lens had atrophied at a level ranging from 30% to 40%, no severe lesion was detected in other organs. Fish that hatched in the same period were bred under uniform feeding and management conditions for a month. Monitoring data revealed that, at the end of this 1-month period, the growth rate and feed conversion rate of the diseased fish were significantly lower than those of the healthy group. Based on microbiological and pathological findings, we concluded that Shewanella sp. S-1 caused lens atrophy in the rainbow trout.Publication Tentative epidemiological Cut-Off values and distribution of resistance genes in aquatic pseudomonas species isolated from rainbow trout(Springer, 2023-05-01) Duman, Muhammed; Woo, Soo-Ji; Altun, Soner; Satıcıoğlu, İzzet Burçin; DUMAN, MUHAMMED; ALTUN, SONER; SATICIOĞLU, İZZET BURÇİN; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-7707-2705; 0000-0002-2721-3204; AAD-4156-2019; T-1697-2019; AAG-8518-2021Epidemiological cut-off value (ECV) analysis for commonly used antimicrobials in aquaculture have not been established for many aquatic pathogens, including Pseudomonas. This study was the first to examine the categorization of 92 aquatic Pseudomonas isolates by calculating seven antimicrobials ECVs using two analytical methods: normalized resistance interpretation and ECOFFinder. Pseudomonas spp. isolates had decreased sensitivity to all antimicrobials examined except for doxycycline and ciprofloxacin. The PCR analysis of the 91 isolates of Pseudomonas spp. detected the tetracycline genes are predominant with the count of 41 genes, including tetA, tetC, tetD, tetM, tetS and tetH, following sulfonamide genes are in 21 isolates including sul1 and sul2, floR gene in 15 isolates and ermA gene in three isolates. Our findings provide an understanding of the antimicrobial categorization of Pseudomonas species, which are significant groups, subgroups, and species for aquaculture due to insufficiently defined breakpoints or cut-off values reported in CLSI and/or EUCAST.Publication Pseudomonas anatoliensis sp. nov and Pseudomonas iridis sp. nov. isolated from fish(Elsevier Gmbh, 2021-03-09) Duman, Muhammed; Mulet, Magdalena; Altun, Soner; Satıcıoğlu, İzzet Burçin; Gomila, Margarita; Lalucat, Jorge; Garcia-Valdes, Elena; DUMAN, MUHAMMED; ALTUN, SONER; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-9096-875X ; 0000-0001-7707-2705; T-1697-2019; AAG-8518-2021In a study carried out between 2013 and 2018 in fish farms in Turkey, several putative novel species were isolated. The 16S rRNA nucleotide sequences of fourteen strains of Gram-negative rods, which were isolated from asymptomatic and symptomatic rainbow trouts (Onchorhynchus mykiss), placed them under the genus Pseudomonas. The similarity values of the concatenated nucleotide sequences of the rpoD, rpoB, gyrB and 16S rRNA genes clustered these isolates into the P. fluorescens phylogenetic group of species and into the Pseudomonas koreensis subgroup, close to Pseudomonas helmanticensis and Pseudomonas baetica. An isolate of a totally different origin, strain CCUG 67011, clustered with these isolates. Phenotypic characterization, together with the chemotaxonomic data, whole-cell MALDI-TOF MS and fatty acids methyl esters analyses were performed. The DNA G + C content was 58.7 mol% for isolate P9(T) and 58.8 mol% for isolate P42(T). The phylogenomic analysis and whole genome nucleotide sequences of four of these isolates confirmed that the isolates P9(T), P25 and P141, represent a novel species for which the name Pseudomonas anatoliensis sp. nov. is proposed, with P9(T) as the type strain (=CCUG 74755(T) = CECT 3172(T)). The isolates P1, P2, P10, P27, P30, P24a, P42(T), P117, P139, P152 and CCUG 67011 represent another novel secies, for which the name Pseudomonas iridis sp. nov. is proposed, with P42(T) as the type strain (=CCUG 74870(T) = CECT 3174(T)). (C) 2021 Elsevier GmbH. All rights reserved.
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