Browsing by Author "Duman, Muhammed"
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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.Item Antimicrobial resistance and molecular characterization of Pantoea agglomerans isolated from rainbow trout (Oncorhynchus mykiss) fry(Elsevier, 2018-04-12) Satıcıoğlu, İzzet Burçin; Duman, Muhammed; Altun, Soner; Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-9096-875X; 0000-0001-7707-2705; AAG-8518-2021; T-1697-2019; 55568071100; 56269221600Aquaculture has become an important candidate as an animal protein source through its growth over the last decade. Based upon a report from the Food and Agriculture Organization of the United Nations, it is the fastest growing sector of the food industry, yet the pathogenicity of many biological agents involved in aquaculture is still unknown. In this study, we isolated Pantoe agglomerans from diseased rainbow trout on several occasions and also attempted to determine their phenotypic and genotypic characteristics, including antimicrobial resistance, of four bacterial isolates. In the present study, P. agglomerans was isolated from diseased rainbow trout as a pathogenic agent. The identification of the P. agglomerans isolates from the rainbow trout was performed through biochemical tests and 16S rRNA sequence analysis. These isolates were predominately biochemically homogeneous, although some features were different, such as seen in methyl-red, mannose and lipase activity tests. All four studied isolates were identified as 99% identical to P. agglomerans based on sequence analysis. The isolates were compared through a phylogenetic analysis with P. agglomerans sequences recovered from 16 other countries and accessed from the GenBank database. All isolates in our study were at least 98.2% similar to sequences from GenBank. Furthermore, the phenotypic antimicrobial susceptibility of the isolates in this study was analyzed through both disc diffusion and broth micro dilution minimum inhibitory concentration (MIC) tests. Although there were some differences between two phenotypic antimicrobial tests, all studied isolates were found susceptible to different antimicrobials. In addition genotypic antimicrobial resistance characteristics were assessed by the presence of antimicrobial resistance genes (ARGs), in which qnrS and sul2 were detected for the first time in P. agglomerans.Item Antimicrobial resistance and resistance genes in Flavobacterium psychrophilum isolates from Turkey(Elsevier, 2019-10-15) Smith, Peter; Wiklund, Tom; Satıcıoğlu, İzzet Burçin; Duman, Muhammed; Altun, Soner; Brusa Uludağ Üniversitesi/Veteriner Fakültesi/Su Ürünleri Hastalıkları Bölümü.; 0000-0001-9096-875X; 0000-0001-7707-2705; AAG-8518-2021; T-1697-2019; 56269221600; 55568071100The antimicrobial susceptibilities of Turkish F. psychrophilum isolates were investigated using a Clinical and Laboratory Standards Institute (CLSI) standard microdilution testing protocol. The significance of the minimum inhibitory concentrations was determined by applying empirically and statistically determined epidemiological cut-off values calculated by normalized resistance analysis. Twenty-five F. psychrophilum isolates made over four years from three different trout species in five different regions were examined. All isolates were fully susceptible to amoxicillin and florfenicol, but 88% of our isolates were categorized as having reduced susceptibility to the two quinolones, oxolinic acid, and enrofloxacin. Eighty percent of the isolates were categorized as showing reduced susceptibility to oxytetracycline. Sequence analysis demonstrated that the reduced susceptibility to the quinolones was associated with chromosomal mutations in the gyrA and parE genes. PCR analysis demonstrated that the genes tetA, tetB, tetC, tetE, tetH, tetL, and tetM were not associated with the reduced susceptibility to oxytetracycline and the significance of this observation is discussed. PCR analysis also showed the presence of sul2 in six isolates and floR in one isolate. This study is the first report of these genes in F. psychrophilum. It was noted, however, that the floR was detected in an isolate categorized as fully susceptible to florfenicol, but the reasons for its lack of expression in the phenotype was not investigated. It is argued that the Turkish trout industry, in common with those of many countries world-wide, is critically dependent on the continued susceptibility of F. psychrophilum to florfenicol.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.Item Determination biochemical differences and rapid ıdentification of yersinia ruckeri and lactococcus garvieae ısolated from aquaculture(Uludağ Üniversitesi, 2018-03-19) Satıcıoğlu, İzzet Burçin; Duman, Muhammed; Altun, Soner; Uludağ Üniversitesi/Veteriner Fakültesi.Aquaculture has growing much more than 100% at the last decade. Rainbow trout is the most economically important fish among the aquatic species. Bacterial agent, especially, Yersinia ruckeri and Lactococcus garvieae have limited freshwater fish production all over the world. There are many reports about identification of bacterial pathogens in aquaculture but most of them should not supported with detailed biochemical features. Therefore, we aimed in this study, determination of biochemical differences and identify two bacteria in a short time by using rapid test kits. 30 isolates of each Y. ruckeri and L. garvieae that are represent different regions of Turkey were used and biochemical characteristics were determined by conventional microbiologic test and API RAPID test kits. Y. ruckeri is the more heterogenetic biochemical structure comparing to L. garvieae. All isolates were successfully identified within 5-7 hours with rapid test kits while there are some differences between each other. The comprehensive biochemical differences of Y. ruckeri and L. garvieae were shown in the present studyItem The determination of antimicrobial susceptibility by MIC and epidemiological cut-off values and the detection of resistance genes inAeromonasspecies isolated from cultured fish(Oxford University, 2020-11) Satıcıoğlu, İzzet Burçin; 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-8518-2021; 55568071100; 57194590388The present study was aimed at determining antimicrobial susceptibility by a CLSI standard microdilution testing protocol and detecting the resistance genes of motileAeromonasspecies isolated from cultured fish. The importance of the minimum inhibitory concentrations was assessed based on statistically determined epidemiological cut-off values calculated by normalized resistance analysis. Unfortunately, CLSI epidemiological cut-off values are available only forAeromonas salmonicida, and there is no further detailed data onAeromonasisolated from aquatic animals. The antimicrobial susceptibilities of pre-identified motileAeromonasspecies to florfenicol, tetracycline and sulfamethoxazole were determined by calculating epidemiological cut-off values with fully automated and freely available Excel spreadsheets, applying the normalized resistance interpretation (NRI) method. Furthermore, the presence of the antimicrobial resistance genesfloR,tetA,tetB,tetC,tetD,tetE,tetH,sulI,sulII andsulIII was detected by PCR analysis and confirmed by sequence analysis. The presence of up to six different genes (multiple antimicrobial resistance) was determined in theAeromonasisolates. Significance and Impact of the Study Significance and Impact of the Study:In this study, we investigated phenotypic and genotypic antimicrobial resistance characteristics by a novel method based on epidemiological cut-off values. This is the second comprehensive study on the antimicrobial susceptibility characteristics ofAeromonasspecies using NRI and epidemiological cut-off values. The present research is related to our previous researches focussed on the identification of motile Aeromonads, their prevalence in relation to different fish lengths, seasons and regions, and covered the investigation ofLactococcus garvieae,Yersinia ruckeri, Flavobacteriumspp.,Enterobacterspp. andCitrobacterspp.Item Determination of opportunistic pathogens and antimicrobial resistance characterization Isolated from Rainbow trout in Turkey(Bursa Uludağ Üniversitesi, 2020-10-29) Satıcıoğlu, İzzet Burçin; Duman, Muhammed; Özdemir, Burak; Ajmi, Nihed; Altun, Soner; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-7707-2705; 0000-0001-9096-875XAquaculture, by modern and technological methods, ensures effectual means for healthy fish production under “controllable” conditions. However, fish have disease problems due to a lack of imbalance with microbiota or opportunistic pathogen in culture systems. In the pres- ent study, we identified the opportunistic pathogens and some members of microbiota, which were obtained from our culture collection by culturable methods and characterized biochemically in addition to molecular analysis. We identified the isolates by partial gene sequencing and confirmed taxonomically in the bacterio.net database. The isolates were characterized based on antimicrobial susceptibilities by broth microdilution method analysis, and the resistance gene determinants were screened by PCR analysis. A total of 14 species were identified with high genetic similarity in the GenBank database. MIC results showed that bacteria have heterogeneous characteristics for the susceptibility of an agent into the genus, and species have high MIC values for sulfamethoxazole, trimethoprim, and ampicillin comparing to other agents. A total of 13 different resistance genes were determined in the bacteria, and some of them have multiple resistance genes up to five genes.Item Determination of phenotypic, serotypic and genetic diversity and antibiotyping of Yersinia ruckeri isolated from rainbow trout(Kafkas Üniversitesi, 2013) Onuk, Ertan Emek; Çiftçi, Alper; Altun, Soner; Duman, Muhammed; Büyükekiz, Ayşe Gül; Uludağ Üniversitesi/Veterinerlik Fakültesi/Su Ürünleri Hastalıkları Bölümü.; 0000-0001-7707-2705; 0000-0001-9096-875X; T-1697-2019; AAG-8518-2021; 56269221600; 55568071100; 55567777200In this study, 15 Yersinia ruckeri isolates that had been isolated from rainbow trout farms and 2 reference strains (serotype 1 and serotype 2) were examined in terms of phenotypic, serotypic and genotypic characteristics. Conventional microbiological and API 20 E tests were used to determine phenotypic characteristics of Y. ruckeri isolates and it was determined that the Y. ruckeri showed significantly homogenous profile by microagglutination test performed by using serotype 1 and serotype 2 immunsera, and 11 of 15 isolates were serotyped as serogroup 1 while the rest 4 were serotyped as serogroup 2. In Random Amplified Polymorphic DNA (RAPD) analysis, Y. ruckeri isolates were genotyped within 2 separate clusters according to 70% similarity coefficient index and it was detected that first cluster includes 2 genotypes (YR1 and YR2) and second cluster includes 3 genotypes (YR3, YR4 and YR5). Furthermore, antibiotic resistance profiles of Y. ruckeri strains were determined and it was found that they were resistance to florfenicol, erythromycin, oxytetracycline and trimethoprim-sulphamethoxazole which have been licensed for fish health in Turkey. It is considered that findings obtained will form a basis to develop diagnosis kit and/or vaccination for Y. ruckeri.Item The determination of the infectious status and prevalence of motile Aeromonas species isolated from disease cases in rainbow trout (Oncorhynchus mykiss) and aquarium fish(Blackwell Publishing, 2018-09-21) Satıcıoğlu, İzzet Burçin; Janda, J. Michael; Duman, Muhammed; Altun, Soner; Uludağ Üniversitesi/Veterinerlik Fakültesi/Su Hayvanları Hastalıkları Bölümü.; 0000-0001-7707-2705; 0000-0001-9096-875X; T-1697-2019; AAG-8518-2021; 55568071100; 56269221600The aims of this study were to determine the prevalence and phylogenetic relationship of motile Aeromonas spp. that might be pathogenic species for rainbow trout in infected/mix infection cases (based upon different outbreaks on fish farms). A total of 99 motile Aeromonas isolates (and three reference strains) were analysed that were isolated from four different fish species in different sizes of fish (0.1-3,000 g), different months and water temperatures (6.1-21.2 degrees C). The biochemical characteristics of the isolates were determined using conventional tests and a rapid test kit. Additionally, molecular identification was performed using the gyrB housekeeping gene region and with glycerophospholipid-cholesterol acyltransferase polymerase chain reaction (GCAT-PCR). The sequencing results obtained from the gyrB gene region were deposited in the GenBank database, and phylogenetic relationships were determined with the BioNumerics 7.6 database. Nearly half of the Aeromonas isolates that were isolated from rainbow trout showing signs of disease were determined to be possible infectious agents. Aeromonas species exhibit biochemical variability for many characters, so some Aeromonas species tested negative for GCAT-PCR despite that this test was created especially for Aeromonas identification. The phylogenetic tree based upon gyrB contained 10 different phylogroups that were based on 96% cut-off value in gyrB gene region.Item Effect of rainbow trout (Oncorhynchus mykiss) seminal plasma on the post-thaw quality of ram semen cryopreserved in a soybean lecithin-based or egg yolk-based extender(Elsevier, 2015-11-15) Üstüner, Burcu; Alcay, Selim; Toker, M. Berk; Nur, Zekariya; Gökce, Elif; Sonat, Füsun Ak; Gül, Zülfiye; Duman, Muhammed; Cenize, Cafer; Uslu, Aydın; Saığrkaya, Hakan; Soylu, Mustafa Kemal; Uludağ Üniversitesi/Veteriner Fakültesi/Üreme ve Suni Tohumlama Anabilim Dalı.; Uludağ Üniversitesi/Veteriner Fakültesi/Fizyoloji Anabilim Dalı.; Uludağ Üniversitesi/Tıp Fakültesi/Farmakoloji Anabilim Dalı.; Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-7707-2705; 0000-0002-1438-221X; 0000-0002-8872-0074; 0000-0002-7678-3289; AAH-2635-2021; T-1697-2019; AAH-8821-2021; AAF-9939-2020; AAG-7238-2021; 18937724600; 56099810300; 56480349200; 6508060684; 56779799700; 26428428000; 56086542900; 55568071100; 57070339500; 57069822700; 6602400461; 7003293300The aim of the current study was to evaluate the effects of different concentrations of rainbow trout seminal plasma (RTSP) (0.1%, 1% and 10%) in extenders containing either egg yolk or lecithin for use in Awassi ram semen cryopreservation. Pooled sperm were diluted in a two-step dilution method to a final concentration of 1/5 (semen/extender) in egg yolk or lecithin extender containing no RTSP, 0.1%, 1% or 10% RTSP (v/v). Semen samples were assessed for sperm motility, plasma membrane integrity [hypoosmotic swelling test (HOST) and Hoechst 33258] and defective acrosomes [FITC-conjugated Pisum sativum agglutinin (PSA-FITC)] at the following five time points: after dilution with extender A; after equilibration; and post-thaw at 0 h, 3 h and 5 h. Malondialdehyde (MDA) was examined only after thawing. Freezing and thawing procedures (dilution, equilibration and post-thaw incubation at Oh, 3 h and 5 h) negatively affected the motility (P<0.001) and acrosome integrity (P<0.001). Additionally, freezing and thawing negatively affected the plasma membrane integrity, as determined by the HOST and Hoechst 33258 (P<0.001). The extender group affected the motility (P<0.001) and the HOST results (P<0.001). Levels of MDA in the egg yolk extender with 1% RTSP group were significantly lower than in the lecithin control group (P<0.05). In conclusion, the egg yolk extender groups that were supplemented with 10% and 1% RTSP provided greater cryoprotective effects for semen survivability during 5 h incubation than the other extender groups.Item Epidemiology, genotypic diversity, and antimicrobial resistance of Lactococcus garvieae in farmed rainbow trout (Oncorhynchus mykiss)(Iranian Fisheries Research Organization, 2020) Satıcıoğlu, İzzet Burçin; Duman, Muhammed; Büyükekiz, Ayşe Gül; Cengiz, Murat; Şahintürk, Pınar; Altun, Soner; Uludağ Üniversitesi/Veteriner Fakültesi/Klinik Öncesi Bilimler Bölümü.; Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; Uludağ Üniversitesi/Veteriner Fakültesi/Farmakoloji ve Toksikoloji Anabilim Dalı.; 0000-0001-7707-2705; 0000-0001-9096-875X; T-1697-2019; CGY-6379-2022; ABE-5935-2020; DPN-8375-2022; AAG-8518-2021; 55568071100; 16635026700; 55567777200; 55342852700; 56269221600Bacterial agents must be genotypically analyzed for vaccinations, effective control programs, and antimicrobial resistance genes that could transfer from aquaculture settings to terrestrial ecosystems and humans. Therefore, we investigated the prevalence, genotypic characterization, and antimicrobial resistance of Lactococcus garvieae for two years at aquaculture sites throughout Turkey. A total of 137 L. garvieae isolates were obtained from rainbow trout (Oncorhynchus mykiss) farms in different regions of Turkey, and three reference strains were used. The isolates were confirmed genotypically using species specific primer sets. All isolates were genotyped with RAPD-PCR using M13 primers. Five different genogroups were determined, and the reference strains were found to differ from all the isolates. Some isolates were compared with the GeneBank database and most isolates were within the same European, Asian, Australian, and South African genogroups. Isolates showed differing levels of resistance to most of the commonly used antimicrobials. The ermB, ermA, tetM, and tetS genes were identified and confirmed, whereas the floR, sulI, sulII, sulIII, tetA, tetB, and tetE genes were not detected. The identification of antimicrobial resistance genes in rainbow trout fry (weight 0.5 g) showed that genes for antimicrobial resistance could be spread during any stage of the fishes’ life, thereby facilitating transmission of resistance to humans and other animals. The investigation of antimicrobial resistance genes in phenotypically susceptible isolates revealed that it is insufficient to investigate only phenotypic resistance in antimicrobial resistance studies.Publication Flavobacterium bernardetii sp. nov., a possible emerging pathogen of farmed rainbow trout (Oncorhynchus mykiss) in cold water(Elsevier, 2021-04-08) Satıcıoğlu, İzzet Burçin; Ay, Hilal; Altun, Soner; Şahin, Nevzat; Duman, Muhammed; ALTUN, SONER; DUMAN, MUHAMMED; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı; 0000-0001-7707-2705; 0000-0001-9096-875X; T-1697-2019; AAG-8518-2021Identification of novel Flavobacterium species from fish samples has growing importance due to their notorious effects on freshwater fish species. During the course of studying farmed rainbow trout (Oncorhynchus mykiss, Walbaum, 1792) samples exhibiting clinical signs in Rize, Turkey, two isolates were recovered, and their taxonomic positions were revealed based on a genome-based polyphasic taxonomy approach. Pairwise sequence analyses of the 16S rRNA genes confirmed that strains F-372T and F-408 belonged to the genus Flavobacterium. Strain F-372T exhibited the highest identity level of 98.37% with Flavobacterium terrigena DSM 17934T (=KCTC 12761T) while the 16S rRNA gene sequence identity between strain F-372T and F-408 was 99.8% A polyphasic taxonomy approach including phenotypic characterization as well as genomic and chemotaxonomic analyses was employed to confirm the novelty of the strains in the genus Flavobacterium. The major fatty acids were isoC15:0 and C15:1 omega 6c for both strains while their predominant menaquinone was MK-6. Both strains have genome size of 3.3 Mb. The genomic DNA G + C content of the strains was 30.89 mol%. In addition, strain F-372T was found to carry 68 high confidence (HC) functional genes encoding AMR and virulence factors implying a possible correlation between those factors and mortality in the rainbow trout. Phylogenomic analysis and whole genome nucleotide sequences confirmed that the isolates represent a new species for which the name Flavobacterium bernardetii sp. nov. is proposed, with F-372T as the type strain (=JCM 34204T = KCTC 82264 T).Publication Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout(Microbiology Soc, 2021-01-01) Duman, Muhammed; Ay, Hilal; Altun, Soner; Şahin, Nevzat; Satıcıoğlu, İzzet Burçin; DUMAN, MUHAMMED; ALTUN, SONER; Uludağ Üniversitesi/Veteriner Fakültesi/Su Ürünleri Hastalıkları Anabilim Dalı; 0000-0001-7707-2705; 0000-0001-9096-875X; AAG-8518-2021; T-1697-2019Two yellow-pigmented isolates, F-60(T) and F-392, were isolated from the internal organs of an apparently healthy rainbow trout (Oncorhynchus mykiss). The strains were identified as members of the genus Flavobacterium based on the results of 16S rRNA gene sequence analysis. Strains F-60(T) and F-392 had the highest 16S rRNA gene sequence identity level of 97.4% to the type strain of Flavobacterium crassostreae LPB0076(T). A polyphasic taxonomic approach including phenotypic, chemotaxonomic and genomic characterization was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity based on BLAST (ANIb) values for strains F-60(T) and F-392 were calculated as 100%. However, dDDH and ANI analyses between the strains and their close neighbours confirmed that both strains represent a novel species in the genus Flavobacterium. The strains shared the highest dDDH and ANIb levels of 23.3 and 77.9%, respectively, with the type strain of Flavobacterium frigidarium DSM 17623(T) while those values for F crassostreae LPB0076(T) were obtained as 21.4-21.5% and 76.3%. The DNA G+C content of the strains was 34.5 mol%. Chemotaxonomic and phylogenomic analyses of these isolates confirmed that both strains are representatives of a novel species for which the name Flavobacterium muglaense sp. nov. is proposed, with F-60(T) as the type strain (=JCM 34196(T) =KCIC 82256(T)).Publication Flavobacterium turcicum sp. nov. and Flavobacterium kayseriense sp. nov. isolated from farmed rainbow trout in Turkey(Elsevier, 2021-02) Satıcıoğlu, İzzet Burçin; Ay, Hilal; Altun, Soner; Duman, Muhammed; Şahin, Nevzat; ALTUN, SONER; DUMAN, MUHAMMED; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Su Ürünleri Hastalıkları Anabilim Dalı; 0000-0001-9096-875X; 0000-0001-7707-2705; AAG-8518-2021; T-1697-2019During a study on culturable microorganisms from fish farms, four yellow-pigmented gram negative, rod shaped isolates, F-47(T), F-339(T), F-380 and F-400, were recovered from rainbow trout samples exhibiting clinical signs. Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genus Flavobacterium. Strains F-47(T) and F-380 shared the highest 16S rRNA gene sequence identity level of 97.6% with the type strain of Flavobacterium frigoris DSM 15719(T) while strains F-339(T) and F-400 shared the highest identity level of 97.6% with the type strain of F. caseinilyticum AT-3-2(T). A polyphasic taxonomic approach including phenotypic and genomic characterization as well as whole-cell MALDI-TOF mass spectrometry analyses was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains F-47(T), F-339(T) and their close neighbours F. frigoris DSM 15719(T) and F. caseinilyticum AT-3-2(T), respectively, confirmed that both strains represent novel species in the genus Flavobacterium. The DNA G+C contents of the strains F-47(T) and F-339(T) are 34.3% and 35.3%, respectively. It can be concluded on the basis of polyphasic characterization as well as pairwise genome comparisons that the strains F-47(T) and F-339(T) represent two novel species within the genus Flavobacterium, for which Flavobacterium kayseriense sp. nov. F-47(T) (=JCM 34195(T)=KCTC 82255(T)) and Flavobacterium turcicum sp. nov. F-339(T) (=JCM 34202(T)=KCTC 82262(T)) are proposed, respectively.Publication Genome analysis and antimicrobial resistance characteristics of Chryseobacterium aquaticum isolated from farmed salmonids(Elsevier, 2021-01-05) Satıcıoğlu, İzzet Burçin; Duman, Muhammed; Altun, Soner; 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-8518-2021Fish diseases caused by bacterial genera belonging to the family Flavobacteriaceae, especially Tenacibaculum, Flavobacterium, and Chryseobacterium, are responsible for losses in wild and farmed fish around the world. In the last decade, the genus Chryseobacterium has rapidly grown in parallel with numerous novel Chryseobacterium species described from systemic infections of fish. Members of the family Flavobacteriaceae, isolated from fish, the environment, and clinical samples, have been reported to show low susceptibility to a broad range of antimicrobials. In this study, seventy C. aquaticum strains were isolated from diseased salmonids in Turkey. The phylogenetic analysis of all C. aquaticum strains, together with the reference strains in GenBank, which were obtained from different sources, including fish, plants, soil, water, and other animals, was performed by 16S rRNA gene sequence analysis. The antimicrobial susceptibility of each C. aquaticum strain was determined by a minimum inhibitory concentration (MIC) test. The isolate with the highest level of antimicrobial resistance, strain C-174, underwent a more detailed whole-genome sequence analysis for virulence and antimicrobial resistance genes (AMR) genes, genome size, and guanine-cytosine (GC) content.Phylogenetically, the 70 strains isolated from Turkey were assigned to three genogroups. Strains previously recovered from the rainbow trout, brown trout, and Siberian sturgeon were genetically very close to our strains. Most of the strains isolated in this study grew even in the presence of high concentrations of the tested antimicrobials, excluding enrofloxacin. Strain C-174 carried 74 putative functional genes encoding AMR and virulence. The number of putative AMR genes detected in the genome of strain C-174 was 46. The regulatory mechanisms of these genes involve antibiotic efflux (13), antibiotic target alteration (17), antibiotic inactivation (7), antibiotic target replacement (3), and antibiotic target protection (6). AMR genes confer resistance to multiple antibiotic groups, including among others, macrolides, fluoroquinolones, beta-lactams, tetracyclines, phenicols, sulphonamides, and diaminopyrimidines. We concluded that antimicrobial resistance could be of intrinsic nature. Furthermore, we detected three putative virulence genes in the genome of strain C-174 that have not been reported for C. aquaticum before. The results of this study demonstrated a strong correlation between these genes in the genome of C-174 and mortality in the rainbow trout.Item Genotyping and antimicrobial resistance genes of Yersinia ruckeri isolates from rainbow trout farms(Inter-Research, 2017-04-12) Duman, Muhammed; Altun, Soner; Cengiz, Murat; Büyükekiz, Ayşe Gül; Şahintürk, Pınar; Satıcıoğlu, İzzet Burçin; Uludağ Üniversitesi/Veteriner Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; Uludağ Üniversitesi/Veteriner Fakültesi/Farmakoloji ve Toksikoloji Anabilim Dalı.; 0000-0001-7707-2705; 0000-0001-9096-875X; 0000-0002-2721-3204; 0000-0003-2124-9406; T-1697-2019; AAG-8518-2021; ABE-5935-2020; 55568071100; 56269221600; 16635026700; 57194590388; 55567777200; 55342852700In this study, we compared 142 Yersinia ruckeri isolates collected between 2013 and 2016 from 6 different regions in Turkey. A total of 18 different genogroups were found, though most of the isolates clustered into the same genogroup as serotype O1. As immunization of fish with inactivated Y. ruckeri by injection, immersion, or feeding provide minimal protection against Y. ruckeri infection in Turkey, many fish producers use antimicrobials unrestrictedly, resulting in antimicrobial resistance in aquatic pathogens. Accordingly, we investigated resistance to the antimicrobials most commonly used to treat yersiniosis. More than 80% of the Y. ruckeri isolates were susceptible to sulfamethoxazole- trimethoprim (SXT), florfenicol (FFC), and tetracycline, whereas none were susceptible to sulfamethoxazole. The most commonly used antimicrobials (SXT and FFC) can be effectively administered because the resistance levels to these drugs are the lowest among those reported for agents used to control enteric red mouth disease (12.6 and 14.7%, respectively). In conclusion, to the best of our knowledge, this study is the first characterization of the antimicrobial resistance genes floR, sulI, tetC, tetD, and tetE in Y. ruckeri isolates from aquaculture. Additionally, we detected the sulII gene but not the tetA, tetB, tetM, tetS, or sulIII genes.Item Goat semen cryopreservation with rainbow trout seminal plasma supplemented lecithin-based extenders(Wiley, 2020-05) Alçay, Selim; Üstüner, Burcu; Aktar, Ahmet; Mülkpınar, Emine; Duman, Muhammed; Akkaşoğlu, Mustafa; Çetinkaya, Bilge Mehmet; Bursa Uludağ Üniversitesi/Veterinerlik Fakültesi/Dölerme ve Suni Tohumlama Anabilim Dalı.; Bursa Uludağ Üniversitesi/Veterinerlik Fakültesi/Su Hayvanları Hastalıkları Anabilim Dalı.; 0000-0001-7707-2705; CBC-7350-2022; AAG-7238-2021; HTU-9909-2023; FQU-5575-2022; T-1697-2019; EMD-6376-2022; HPR-5459-2023; 56099810300; 18937724600; 57215218367; 57207740686; 55568071100; 57215219417; 7006266820The objective of this study was to determine the optimum concentrations of rainbow trout seminal plasma (RTS) supplemented extenders for goat semen quality at post-thaw and after incubation. Five sexually mature Saanen goat (Capra aegagrus hircus) were used for semen collection. Pooled semen was diluted with soybean lecithin-based extender without RTS (control) or supplemented with different concentrations of RTS (1%, 2%, 4% or 8%), at a final concentration of 150 x 10(6) spermatozoon/ml. Sperm motility, plasma membrane functional integrity (HOST), damaged acrosome (PSA-FITC), mitochondrial activity (rhodamine123) and DNA integrity (TUNEL) were evaluated. Spermatological parameters were evaluated at post-thaw and after 6 hr incubation. RTS8 group preserved sperm motility, acrosomal integrity, plasma membrane functional integrity and mitochondrial function better than the control group (p < .05). The study demonstrated that RTS supplemented lecithin-based extenders have useful effects on goat spermatozoa. In addition, the results of the current study represented the positive effect of using 8% RTS supplemented extender.Item Gökkuşağı alabalıklarında görülen Motil aeromonas (Aeromonas hydrophila, A. sobria, A. caviae), Yersinia ruckeri ve Lactococcus garvieae bakterilerinin antimikrobiyal duyarlılıkları ve duyarlılıkta rol oynayan genlerin tespiti(Uludağ Üniversitesi, 2017-08-24) Duman, Muhammed; Altun, Soner; Uludağ Üniversitesi/Sağlık Bilimleri Enstitüsü/Su Ürünleri Anabilim Dalı/Hastalıklar Bilim Dalı.Bu araştırmada, farklı kökenlere sahip Motil Aeromonas spp. (Aeromonas hydrophila, A. sobria, A. caviae), Yersinia ruckeri ve Lactococcus garvieae izolatlarının moleküler karakterizasyonu, antimikrobiyal duyarlılıkları ve antimikrobiyal direnç gelişiminde rol oynayan genlerin tespiti yapılmıştır. Çalışmada hareketli Aeromonas, Y. ruckeri ve L. garvieae izolatlarının biyokimyasal özelliklerinin belirlenmesinde klasik mikrobiyolojik testler (gram boyama, hareketlilik, oksidaz, katalaz, O/F vb.) ve hızlı teşhis kitleri (API 20NE, API 32 STREPT ve API 32E) kullanılmıştır. Hareketli Aeromonas türlerinin identifikasyonu gyrB bölgesinin dizi analizi ile Y. ruckeri ve L. garvieae izolatlarının identifikasyonu ise sırasıyla YER8-YER10, pLG primerleri kullanılarak PCR analizi ile gerçekleştirilmiştir. Y. ruckeri ve L. garvieae izolatlarının genotiplendirilmesi RAPD-PCR, hareketli Aeromonas izolatlarının genetik yakınlıkları ise gyrB bölgesinin dizi analizi ile (Bionumerics 7.0 yazılımı kullanılarak) yapılmıştır. Ayrıca çalışmada kullanılan tüm izolatların sulfanomid, tetrasiklin, florfenikol ile sulfamethoksazol-trimetoprim antimikrobiyallerinde minimum inhibitör konsantrasyonları (MİK) ve bu antimikrobiyallere karşı geliştirdikleri direnç genleri (PCR ve dizi analiziyle) tespit edilmiştir. Araştırmada 6 adedi ülkemizde ilk bildirim olmak üzere toplam 13 motil Aeromonas türü, 18 farklı Y. ruckeri ve 5 farklı L. garvieae genotipi belirlenmiştir. Hareketli Aeromonas türlerinin yaygın olarak sulfanomid ve florfenikole; Y. ruckeri izolatlarının sulfanomid ve tetrasiklin'e; L. garvieae izolatlarının ise sulfonamid ve florfenikol'e direnç geliştirmiş olduğu görülmüştür. Ayrıca Aeromonas türlerinde sulI, tetA, tetE, flor; Y. ruckeri izolatlarında sulI; L. garvieae izolatlarında ise ermA ve tetS genlerinin yaygın olduğu tespit edilmiştir.Item Infectious pancreatic necrosis virus (IPNV) serotype Sp is prevalent in Turkish rainbow trout farms(Wiley, 2018-01) Hansen, E. F.; Markussen, T.; Rimstad, E.; Büyükekiz, Ayşe Gül; Altun, Soner; Satıcıoğlu, İzzet Burçin; Duman, Muhammed; Uludağ Üniversitesi/Veterinerlik Fakültesi/Su Hayvanları Hastalıkları Bölümü.; 0000-0001-9096-875X; 0000-0002-2721-3204; 0000-0001-7707-2705; JIH-9655-2023; AAG-8518-2021; AAD-4156-2019; T-1697-2019; 55567777200; 56269221600; 57194590388; 55568071100Infectious pancreatic necrosis virus (IPNV) is a common pathogen of rainbow trout (Oncorhynchus mykiss) in Turkey. We found that 455 of 1,676 sample pools tested were IPNV positive. Positive samples were found in all geographical regions where sampling was conducted. Sequence and phylogenetic analyses of VP2 from 30 isolates representing all regions showed that the viruses were highly similar in sequence and grouped within Genogroup 5 (serotype Sp-A2). No correlations between sequences, sampling sites or geographical origins were identified. Although clinical disease was evident in several farms, analyses of the amino acid sequence of VP2 showed that all virus strains harboured the P217T221 motif, assumed to be associated with low virulence. We conclude that IPNV is prevalent in Turkish rainbow trout farms and that the viruses are very homogenous and likely to be of European origin. Frequent exchange of eggs and live fish within the farming industry may explain the homogeneity of the IPNV.Item Isolation of Citrobacter braakii from rainbow trout (Oncorhynchus mykiss)(Israeli Journal of Aquaculture-Bamidgeh, 2013) Karataş, Süheyla; Turgay, Emre; Altun, Soner; Duman, Muhammed; Büyükekiz, Ayşe Gül; Özyiǧit, Musa Özgür; Uludağ Üniversitesi/Veterinerlik Fakültesi/Su Hastalıkları Anabilim Dalı.; Uludağ Üniversitesi/Veterinerlik Fakültesi/Patoloji Anabilim Dalı.; 0000-0001-9096-875X; 0000-0001-7707-2705; AAG-8518-2021; T-1697-2019; AAR-6478-2021; AAH-2873-2021; 56269221600; 55568071100; 55567777200; 6507338060About 100 moribund rainbow trout fry (2-3 g) were brought to the laboratory for examination after an epizootic of citrobacteriosis on a farm in Bursa Province, northwest Turkey, in late March 2012. The dominant bacterium was identified by biochemical, API 20E, and VITEK II rapid tests. Colonies grown on xylose lysine deoxycholate (XLD) agar were yellow with an intensive yellow center and a surrounding zone of yellow precipitation. The fish displayed hyperemia of the mouth, dark color, bilateral exophthalmia, pale liver, and necrotic kidney symptoms. The possible etiologic agent was identified by 16S rRNA gene sequencing as Citrobacter braakii (GenBank accession number JX518488). Histopathological examination of the diseased fish revealed vacuolar degeneration in the liver epithelium, round and limited focal necrotic areas in the liver, desquamation in the intestine epithelium and glands that settled in the propria mucosa, and vacuolar degeneration of the intestinal epithelium. According to ATB VET and antibiogram disc diffusion, the isolated C. braakii strain was sensitive to apramycin, cefoperazone, chloramphenicol, colistin, gentamicin, nitrofurantoin, spectinomycin, and streptomycin but resistant to amoxicillin, amoxicillin/clavulanic acid, cefalotine, cotrimoxazole, enrofloxacin, erythromycin, florfenicol, flumequine, fusidic acid, kanamycin, lincomycin, metronidazole, neomycin, oxacilline, oxolinic acid, oxytetracycline, penicillin, pristinamycin, rifampicin, sulfamethizole, sulfamethoxazole-trimethoprim, tetracycline, and tylosin. We found the bacteria sensitive to 4 mg/l doxycycline in the ATB VET test strip but resistant to 30 mu g/l doxycycline in the antibiogram disc diffusion test.