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© 2022, The Author(s), under exclusive licence to Springer Nature Switzerland AG.The strain M-43T was isolated from the Oncorhynchus mykiss from a fish farm in Mugla, Turkey. Pairwise 16S rRNA gene sequence analysis was used to identify strain M-43T. The strain was a member of the genus Myroides sharing the highest 16S rRNA gene sequence identity levels of 98.7%, 98.3%, and 98.3% with the type strains of M. profundi D25T, M. odoratimimus subsp. odoratimimus CCUG 39352T and M. odoratimimus subsp. xuanwuensis DSM27251T, respectively. A polyphasic taxonomic approach including whole genome-based analyses was employed to confirm the taxonomic provenance of strain M-43T within the genus Myroides. The overall genome relatedness indices (OGRI) for strain M-43T compared with its most closely related type strains M. odoratimimus subsp. xuanwuensis DSM 27251T, M. profundi D25T, and M. odoratimimus subsp. odoratimimus ATCC BAA-634T, were calculated as 25.3%, 25.1%, and 25% for digital DNA-DNA hybridization (dDDH), 83.3%, 83.6%, and 83.4% for average nucleotide identity (ANI) analyses, respectively. The OGRI values between strain M-43T and its close neighbors confirmed that the strain represents a novel species in the genus Myroides. The DNA G + C content of the strain is 33.7%. The major fatty acids are iso-C15:0 and summed feature 9 (iso-C17:1ω9c and/or 10-methyl C16:0). The predominant polar lipids are phosphatidylethanolamine, an amino-lipid and five unidentified lipids. The major respiratory quinone is MK-6. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Myroides oncorhynchi sp. nov. is proposed, with M-43T as the type strain (JCM 34205T = KCTC 82265T).

The common guitarfish (Rhinobatos rhinobatos) is an endangered species and included in the red list of the International Union for Conservation of Nature as "critically endangered, cr." Although guitarfish are displayed and protected in public aquaria, only limited information is available on the external and internal anatomy of this species and dissection methods applicable to it. In this study, common guitarfish kept in a public aquarium were dissected with an appropriate method and the internal and external organs of the fish were identified. The general examination of the external organs showed that the animals had the typical anatomical structure of guitarfish. The internal organs, including the stomach, intestines, spleen, liver, gall bladder, epigonal organ, testicles, brain, cerebellum, optic lobes and heart were also observed.

The isolation of Pseudomonas haemolytica from different habitats as well as its distribution over a wide geographical area, possible reservoir role for antibiotic resistance and zoonotic potential, all require the detailed characterization of P. haemolytica strains. In the present study, we describe 18 phenotypically similar strains isolated from the rainbow trout, Oncorhynchus mykiss (Walbaum, 1792). The strains were collected from seemingly healthy, symptomatic or moribund rainbow trout of all sizes, from fry to broodstock. The strains were morphologically, phenotypically (API20 NE and VITEK 2) and chemotaxonomically characterized by their methyl-fatty acid content (FAME), and mass spectrometry (MALDI-TOF) by their protein profiles. The 16S rRNA sequence similarity values grouped them into the Pseudomonas fluorescens phylogenetic group of species. The 18 strains were compared to 6 other previously described P. haemolytica strains, 2 of which were isolated from milk products and 4 from chicken products. A multilocus sequence analysis was performed for all strains. Strain P45 was selected to represent the 18 new isolates for genomic comparisons by ANIb, and GGDC was used to confirm the identification at species level. The presence of genes related to antimicrobial resistance, secretion systems and virulence was also assessed using comparative genomic analyses. This is the first comprehensive report on P. haemolytica strains isolated from fish., The research was supported by TUBITAK under project number: 118O420.

A strain, S-1T 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-1T clustered with Shewanella putrefaciens JCM 20190T, Shewanella profunda DSM 15900T, and Shewanella hafniensis P010T, 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-1T within the genus Shewanella . The overall genome relatedness indices (OGRI) for S-1T compared with the most closely related type strains S. hafniensis ATCC BAA-1207T, Shewanella baltica NCTC 10735T, S. putrefaciens ATCC 8071T and S. profunda DSM 15900T 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-1T 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 C17 : 1ω8c, C15 : 0iso, and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). 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-1T as the type strain (JCM 34183T= KCTC 82249T).

Modern aquaculture enables effective means for intensive aquaculture production under “controllable” conditions. This rapidly growing industry, however, has experienced relatively severe disease problems owing to a lack of control of the microbiota in rearing systems. In the present study, we identified the opportunistic pathogens and some members of natural microbiota, which were obtained from our culture collection by culturable methods and characterized biochemically in addition to molecular analysis. All isolates were identified by gene sequence analysis and confirmed taxonomically in the bacterio.net database. The isolates were characterized by means of 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.

The present study was aimed at determining antimicrobial susceptibility by a CLSI standard microdilution testing protocol and detecting the resistance genes of motile Aeromonas species 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 for Aeromonas salmonicida, and there is no further detailed data on Aeromonas isolated from aquatic animals. The antimicrobial susceptibilities of pre-identified motile Aeromonas species 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 genes floR, tetA, tetB, tetC, tetD, tetE, tetH, sulI, sulII and sulIII was detected by PCR analysis and confirmed by sequence analysis. The presence of up to six different genes (multiple antimicrobial resistance) was determined in the Aeromonas isolates. 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 of Aeromonas species 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 of Lactococcus garvieae, Yersinia ruckeri, Flavobacterium spp., Enterobacter spp. and Citrobacter spp.

In the present study, we sampled sea bream and sea bass, weighing 400-450g, for routine microbiological, hematological, macroscopical and histopathological examinations. Samples were taken from seemingly healthy fish, which displayed increased feed conversion rates, signs of cold shock and slow movement. Routine bacteriological analyses included basic microbiological analyses for oxidase and catalase activity, Gram staining and O/F fermentation using API test kits. Furthermore, 16S rRNA gene sequencing was performed for identification. Serum biochemical and hematological values were determined using a Vetscan®VS2 analyzer and blood smears. Internal organs were examined by routine histopathological techniques. Hepatic fat accumulation and necrosis were noted, and liver damage was observed to be associated with significant alterations in liver enzymes. Due to multi-organ dysfunction and serious hematological disorders, primarily Vibrio alginolyticus also Alteromonas and Pseudoalteromonas species were isolated from the affected fish and co-infections were detected., Bu çalışmada rutin mikrobiyolojik, hematolojik, makroskopik ve histopatolojik incelemeler için 400-450 gr ağırlığında çipura ve levrek balıkları örneklenmiştir. Örnekler morfolojik olarak sağlıklı görünen ancak artan yem dönüşüm oranı, hasat sırasında şoklanma (soğuk şoku) sorunu gösteren ve hareketlerde yavaşlık gibi semptom gösteren balıklardan örnekler alınmıştır. Gram boyama, hareketlilik, oksidaz-katalaz aktivitesi ve O/F fermentasyonu gibi rutin bakteriyolojik analizler ve API test kitleri kullanılarak temel mikrobiyolojik analizlerle bakterilerin mikrobiyolojik teşhisleri yapılmıştır. Ön teşhisi yapılan türler16S rRNA gen bölgesi sekans analizi ile tür bazında identifiye edilmiştir. Serum biyokimyasal ve hematolojik değerleri, Vetscan® VS2 cihazı ve kan yayma frotileri kullanılarak analiz edilmiştir. Hastalıktan etkilenen iç organların incelenmesi için rutin histopatolojik incelemeler yapılmıştır. Hepatik yağ birikimi ve nekroz görünen en belirgin bulgulardan olmuştur ve karaciğer enzimlerinde önemli değişikliklerin karaciğer hasarıyla ilişkili olduğu tespit edilmiştir. Etkilenen balıklardan çoklu organ yetmezliği ve hematolojik bozukluklar nedeniyle başta Vibrio alginolyticus olmak üzere Alteromonas ve Pseudoalteromonas türleri izole edilmiş ve hastalık belirtileri gösteren balıkların bakteriyel koenfeksiyon taşıdığı tespit edilmiştir.

Two yellow-pigmented isolates, F-60Tand F-392, were isolated from the internal organs of an apparently healthy rainbow trout (Oncorhynchus mykiss). The strains were identified as members of the genusFlavobacteriumbased on the results of 16S rRNA gene sequence analysis. Strains F-60Tand F-392 had the highest 16S rRNA gene sequence identity level of 97.4 % to the type strain ofFlavobacterium crassostreaeLPB0076T. A polyphasic taxonomic approach including phenotypic, chemotaxonomic and genomic characterization was employed to ascertain the taxonomic position of the strains within the genusFlavobacterium. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity based onblast(ANIb) values for strains F-60Tand 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 genusFlavobacterium. The strains shared the highest dDDH and ANIb levels of 23.3 and 77.9%, respectively, with the type strain ofFlavobacterium frigidariumDSM 17623Twhile those values forF. crassostreaeLPB0076Twere 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 nameFlavobacterium muglaensesp. nov. is proposed, with F-60Tas the type strain (=JCM 34196T=KCTC 82256T).

Cells of strains P66T, V1 and W15Feb18 are Gram-stain-negative short rods and motile by one polar flagellum. Strain P66T 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 C16:0 (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 P66T, 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 P66T (=CECT 30176T=CCUG 74872T). The other strains have been deposited in the CECT with the corresponding collection numbers: V1 (=CECT 30356) and W15Feb18 (=CECT 30355)., TUBITAK (Award 118O420).

In 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 P9T and 58.8 mol% for isolate P42T. The phylogenomic analysis and whole genome nucleotide sequences of four of these isolates confirmed that the isolates P9T, P25 and P141, represent a novel species for which the name Pseudomonas anatoliensis sp. nov. is proposed, with P9T as the type strain (=CCUG 74755T = CECT 3172T). The isolates P1, P2, P10, P27, P30, P24a, P42T, P117, P139, P152 and CCUG 67011 represent another novel sècies, for which the name Pseudomonas iridis sp. nov. is proposed, with P42T as the type strain (=CCUG 74870T = CECT 3174T)., This research was supported by the Scientific and Technological Research Council of Turkey (TUBITAK) [No: 118O420]. We are thankful to Bursa Uludag University for providing additional support.

In the present study, we describe a pathogenic incidence ofShewanellasp. 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 Phoenix™ 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 genusShewanellaand was considered a putative novelShewanellaspecies. 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 thatShewanellasp. S-1 caused lens atrophy in the rainbow trout.

The prevalence of Pseudomonas species in freshwater fish and water from aquaculture farms in Turkey was determined on a monthly basis, in the period covering 2013–2017 and two seasons of 2018. The farms included in the study were located in six different regions of Turkey. A total of 90 Pseudomonas strains were isolated from water and diseased and healthy fish, and were classified under 20 species. The phenotypic characterization of the strains was based on oxidase and catalase activities, haemolysis, tolerance to temperature and sodium chloride, the production of fluorescent pigments and antibiotic resistance spectra. The phylogenetic identification of the 90 isolates was performed by a 4-gene multilocus sequence analysis, based on the partial sequencing of the 16S rRNA, gyrB, rpoB and rpoD genes. This is the first report on the isolation of several Pseudomonas species, namely, P. brenneri, P. defensor, P. haemolytica, P. lactis, P. lundensis, P. lurida, P. mandelii, P. meridiana, P. migulae, P. proteolytica, P. simiae, and P. weihenstephanensis, from freshwater salmonid fish. Two of these species, P. haemolytica and P. lactis have been isolated for the first time from fish farms, an environment quite different from their original isolation source, raw milk. Furthermore, seven putative new Pseudomonas species were isolated from water and farmed rainbow trout. During the 2013 to 2018 period, several Pseudomonas species were detected to have spread from the Aegean and Central Anatolia regions to the Eastern Anatolia and Black Sea regions., This research was supported by the Scientific and Technological Research Council of Turkey (TUBITAK) [No: 118O420], and approved by the Local Ethics Commission (report 2012-14-04).

Çalışmamızda iştahsızlık, ekzoftalmus, renkte kararma ve sırt yüzgeci erozyonu belirtileri gösteren 1-4 gram ağırlıkları arasında gökkuşağı alabalıklarından izole edilen oniki izolat kullanılmıştır. Konvansiyonel mikrobiyolojik testlerin yanı sıra Biolog GENIII mikroplate kullanılarak geniş kapsamlı fenotipik karakterizasyon yapılmıştır. 16S rRNA bölgesi kullanılarak moleküler identifikasyon ve karakterizasyon yapılmıştır. Çalışmada kullanılan izolatların antimikrobiyal duyarlılıkları disk difüzyon yöntemi kullanılarak belirlenmiştir. 16S rRNA bölgesine dayalı dizi analizi ile yapılan moleküler identifasyonda izolatlarımız %99 oranında Chryseobacterium piscicola olarak tanımlanmıştır. İzolatlarımız, Amerika, Şili ve Finlandiya’daki üç farklı konakçıdan elde edilen izolatlarla yapılan filogenetik analizde yüksek benzerlik oranı ile beş farklı genogrup belirlenmiştir. Finlandiya, Şili ve ABD'den izole edilen izolatlar ve C-316 (Türkiye) izolatı aynı genogrupta bulunmuştur. 16S rRNA bölgesi ile oluşturulan filogenetik analizin bakterinin izole edildiği konakçı ayrımının yapamadığı görülmüştür. Filogenetik analize göre seçilen altı temsili izolatın fenotipik özellikleri Biolog GENIII mikroplakası ile belirlenmiştir. Temsili izolatların Biolog GENIII sonuçlarına göre, 94 testin 40'ının sonuçlarının değişken olduğu bulunmuştur. Bu sonuçla, C. piscicola izolatlarının fenotipik olarak homojen bir yapıda olmadığı görülmüştür. Ayrıca çalışmamızda izolatlarımızın florfenikol, enrofloksasin ve sülfametoksazol/trimetoprime karşı oluşan zon çaplarının diğerlerine göre daha yüksek olduğu ve C-41’in en dirençli izolat olduğu bulunmuştur., Twelve isolates recovered from rainbow trout weighing 1-4 grams showing signs of anorexia, exophthalmos, darkening, and dorsal fin erosion were used in our study. In addition to conventional microbiological tests, comprehensive phenotypic characterization has been performed using the Biolog GEN III microplate. Molecular identification and characterization were performed using the 16S rRNA region. Antimicrobial susceptibilities of the isolates were determined using the disk diffusion method. Our isolates were identified as Chryseobacterium piscicola in molecular identification performed by sequence analysis based on the 16S rRNA region. In a phylogenetic analysis of our isolates, obtained from three different hosts in America, Chile, and Finland, five genogroups were determined with high similarity rate. Isolates from Finland, Chile, the United States, and Turkey (only C-316) were found in the same genogroup. It was determined that the phylogenetic analysis created with the 16S rRNA region could not distinguish the host from which the bacteria was isolated. The phenotypic characterization of six representative isolates selected according to phylogenetic analysis, was determined with the Biolog GENIII microplate. Based on the Biolog GENIII results of the representative isolates, the results of 40 out of 94 tests were found to be variable. With this result, it was found that C. piscicola isolates were not phenotypically homogeneous. Besides, it was found that the zone diameters of our isolates against florfenicol, enrofloxacin, and sulfamethoxazole/trimethoprim were higher than the other isolates, in addition to that C-41 was the most resistant isolate.

Son yıllarda Chryseobacterium cinsinde bulunan türler, birçok ülkede balıklarda ölümlere neden olabilen fırsatçı balık patojenleri olarak ortaya çıkmaktadır. Yalnızca son on yılda C. aahli, C. oncorhynchi, C. chaponense ve C. pis-cicola’nın balıklarda sistemik enfeksiyonlara neden olduğu bildirilmiştir. Bu çalışmada, Chryseobacterium sp. C-204, anormal yüzme, sırt lezyonu, renkte koyulaşma ve iki taraflı egzoftalmi gibi klinik belirtiler gösteren 1 gram ağırlığındaki gökkuşağı alabalığından izole edildi. C-204'ün 106 farklı testi içeren fenotipik özellikleri API 20NE ve BIOLOG GEN III sistemi ile karakterize edildi. C-204'ün antimikrobiyal duyarlılığı, su ürünleri yetiştiriciliğinde yaygın olarak kullanılan beş farklı antimikrobiyal ajana karşı broth mikrodilüsyon yöntemiyle belirlendi. Dizi analizi bazlı tür tanımlama, 27F ve 1387R primerleri kullanılarak yapıldı. C-204'ün tüm genom analizinde, yeni nesil dizilime sistemi kullanıldı ve toplam 24195304 okuma elde edildi. Bu okumalar birleştirilerek 4012452 baz uzunluğunda taslak genom elde edildi. C-204'ün genoma dayalı tür tanımlaması, 100 farklı korunmuş gen bölgesi ve en yakın 50 Chryseobacterium türü ile autoMLST sisteminde (https://automlst.ziemertlab.com) yapıldı. C-204 genomundaki antimikrobiyal direnç genleri (AMR) ve virülans genleri, NCBI referans antimikrobiyal direnç genleri veritabanı ve Virülans Faktör Veritabanı (VFDB) kullanılarak tanımlandı. C-204 izolatının 16S rRNA gen bölgesinin, GenBankta C. aquaticum ile %99.65 ve C. green-landense ile %98.95 oranında benzerliklere sahip olduğu belirlenmiştir. Ortak yapılmış olan 19 biyokimyasal testte, C-204 izolatı nitrat indirgeyebilmesi ve glikozdan asit üretememesi testleri ile diğer tip suşlardan ayrılabildiği belirlenmiştir. Antimikrobiyal duyarlılıkla ilgili olarak, C-204 izolatının yüksek antimikrobiyal konsantrasyonlarında bile üreyebildiği tespit edilmiştir. Genom bazlı tür tanımlamasına göre, C-204 izolatı, Chryseobacterium aquaticum subsp green-landense olarak tanımlandı. Ayrıca, C-204 suşunun genomunda 13 virülans ve sekiz AMR geni tespit edildi. Çalışmamızda sonuç olarak, C-204 izolatının 106 biyokimyasal özellik içeren detaylı fenotipik ve tüm genom dizi ana-lizine dayalı genom yapısı belirlenmiştir., In recent years, species in the Chryseobacterium genus have emerged as opportunistic fish pathogens that can cause death in fish in many countries. In the last decade, C. aahli, C. oncorhynchi, C. chaponense, and C. piscico-la have been reported to cause systemic infections in fish. In the present study, Chryseobacterium sp. C-204 was iso-lated from 1g weight rainbow trout showing clinical signs such as abnormal swimming, dorsal skin ulceration, darkening in color, and bilateral exophthalmos. The detailed phenotypic characteristics of the C-204 were characterized by API 20NE, and the BIOLOG GEN III system includes 106 phenotypes. Antimicrobial susceptibility of the C-204 was also determined by the broth microdilution method against five antimicrobial agents commonly used in the Aquaculture. Sequence-based identification was done using 16S rRNA genome sequencing. The genome structure of the C-204 was revealed by using next-generation genome sequencing with reading a total of 24195304 bases and assembled in 4012452 base. Genome-based species delineation of C-204 was done 100 different housekeeping gene regions and 50 the closest Chryseobacterium species with Automated Multi-Locus Species Tree (autoMLST, https://automlst.ziemertlab.com). Antimicrobial resistance genes (AMR) and virulence genes in the C-204 genome were iden-tified using the Virulence Factor Database (VFDB) NCBI-reference antimicrobial resistance genes database. The 16S rRNA sequence of C-204 isolate had similarities with the C. aquaticum (99.65%) and C. greenlandense (98.95%) in GenBank. In parallel 19 biochemical tests, C-204 isolate can be differentiated from the closest type strains by nitrate reduction and inability to produce acid from glucose. With regard to antimicrobial susceptibility, the C-204 isolate can grow even at high antimicrobial concentrations determined for Flavobacteriaceae. According to genome-based species delineation, the C-204 isolate was identified as Chryseobacterium aquaticum subsp greenlandense. 13 virulence and eight AMR genes were detected in the genome of the C-204 isolate. Conclusively, the detailed phenotypic characteris-tic includes 106 biochemical test and genome structure of C-204 isolate by whole genome sequencing were deter-mined.

A study of 91 isolates from fish farms in Turkey showed that isolates P7T, P11, P24b, P29, P72, P73 and P158 belonged to the genus Pseudomonas according to 16S rRNA nucleotide sequence analysis. The analysis of the sequences of the RNA polymerase sigma factor gene (rpoD) located these strains in the Pseudomonas fluorescens lineage of species within the P. fluorescens subgroup, close to the cluster composed of the species Pseudomonas grimontii, Pseudomonas marginalis and Pseudomonas panacis. Based on similarities in the 16S rRNA and rpoD gene sequences of three previously isolated strains from other origins (CCUG 57209, CCUG 62357 and W5.2-93) linked them to the same cluster. A polyphasic taxonomic approach including phenotypic characterization, fatty acid composition, and multilocus sequence analysis, together with whole-cell MALDI-TOF data, corroborated this assumption. The genome G+C mol% contents were 59.48 and 59.71, respectively. The average nucleotide indices based on BLAST analysis and the genome-to-genome distance calculation for the P7T and CCUG 57209 strains with their closest relative, P. grimontii, were 88.16–88.29% and 38.10–38.20%, respectively. These data confirm that isolates P7T, P11, P24b, P29, P72, P73, P158, CCUG 57209, CCUG 62357 and W5.2-93 represent a new species for which the name Pseudomonas sivasensis is proposed, with P7T as a type strain (=CCUG 74260T= and CECT30107T)., This research was supported by the Scientific and Technological Research Council of Turkey (TUBITAK) [No: 118O420]. We are thankful to Bursa Uludag University for additional support.

Fecal contaminants are a major public concern that directly affect human health in the fish production industry. In this study, we aimed to determine the fecal coliform, spoilage bacteria, and antimicrobial-resistant bacterial contamination in rainbow trout (Oncorhynchus mykiss) farms. Fish were sampled from rainbow trout farms that have a high production capacity and are established on spring water, stream water, and dammed lakes in six different regions of Turkey. A total of seven Enterobacter subspecies, two strains of Pseudomonas spp., and one isolate each of Morganella and Stenotrophomonas were characterized based on biochemical and molecular methods, including the 16S rRNA and gyrB housekeeping gene regions. The sequencing results obtained from the 16S rRNA and gyrB gene regions were deposited in the GenBank database and compared with isolates from different countries, which were registered in the database. Resistance to 10 different antimicrobial compounds was determined using the broth microdilution method, and molecular resistance genes against florfenicol, tetracycline, and sulfamethoxazole were identified by PCR. All detected resistance genes were confirmed by sequencing analyses. E. cloacae, E. asburiae, Pseudomonas spp., S. maltophilia, and M. psychrotolerans were identified using the gyrB housekeeping gene, while isolates showed different biochemical characteristics. All isolates were found to be phenotypically resistant to sulfamethoxazole, and some isolates were resistant to tetracycline, florfenicol, amoxicillin, and doxycycline; the resistance genes of these isolates included floR, tetC, tetD, and tetE. We showed that fecal coliforms, spoilage bacteria, and antimicrobial resistant bacteria were present in farmed rainbow trout, and they pose a threat for human health and must be controlled in the farming stage of fish production.

The aim of this study was to determine the immunostimulant effects of geophyte plant extract on non-specific defence mechanisms of rainbow trout (Oncorhynchus mykiss). For this purpose, Muscari comosum was collected in Muğla region and extracted in ethanol. Then, The plant extract applied into fish by intraperitonal injection in two different concentrations (0.5mg/ fish and 2.0 mg/fish). The average fish weight was 140 g. Following the injection on the 1st, 7th, 14th, 21st, 28th days the blood and serum samples were collected from fish in each group and examined for various parameters including percentage of hematocrit, the counts of nitroblue tetrazolium (NBT) positive neutrophils, total leukocyte counts, percentage of white blood cells and serum lysozyme activity. The results indicated that the counts of NBT (+) neutrophils, percentage of monocyte and neutophil and total leukocyte counts increased in the group with injected 0.5mg plant extract /fish compared to control group (P

Correcciones al abstract del artículo original., The authors regret the incorrect publication of strain collection number in the original article In the original article, there is an error regarding the strain collection number in the Abstract. The strain designation for Pseudomonas anatoliensis sp. nov. in the CECT Bacteria Collection should be CECT 30172 instead of CECT3172.

Infectious 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 P217 T221 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.

The rainbow trout production increased more than 100% in the last decade and total rainbow trout production was shown as 107.013 tonsaccording to 2016 statics. According to Federation of European Aquaculture Producer, Turkey was determined as the biggest rainbow troutproducer into the European Countries in 2016. Together with high production capacity, a number of outbreaks were reported causing L.anguillarum (Vibriosis). The pathogenesis of L. anguillarum which were experimentally infected in rainbow trout were examined during 15days in our study. Spreading of agent that was injected with intraperitoneally into tissue and organs were studied by using histopathologicalmethods. The mortality rate of agent was determined above 70% and deaths were seen in 2-3th days of experiment. In addition of these, liver,spleen, kidney and gills were determined as the most affected organs and tissues. In the present study was obtain for original pathologicalfindings of L. anguillarum.

Identification 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 ω6c 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).

© 2021 Elsevier GmbHDuring a study on culturable microorganisms from fish farms, four yellow-pigmented gram negative, rod shaped isolates, F-47T, F-339T, 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-47T and F-380 shared the highest 16S rRNA gene sequence identity level of 97.6% with the type strain of Flavobacterium frigoris DSM 15719T while strains F-339T and F-400 shared the highest identity level of 97.6% with the type strain of F. caseinilyticum AT-3-2T. 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-47T, F-339T and their close neighbours F. frigoris DSM 15719T and F. caseinilyticum AT-3-2T, respectively, confirmed that both strains represent novel species in the genus Flavobacterium. The DNA G+C contents of the strains F-47T and F-339T 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-47T and F-339T represent two novel species within the genus Flavobacterium, for which Flavobacterium kayseriense sp. nov. F-47T (=JCM 34195T=KCTC 82255T) and Flavobacterium turcicum sp. nov. F-339T (=JCM 34202T=KCTC 82262T) are proposed, respectively.

© 2021 Elsevier B.V.Fish 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.

The 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. Ministry of Food, Aqriculture and Animal Husbandry (TAGEM/14/AR-GE/26)

Turkey was the largest rainbow trout producer of the European countries in 2016, and the reason for this production is mainly attributed to its egg and fry production. Flavobacterium psychrophilum cause the highest rates of mortality in the starting to feeding stages of the fish. In the present study, twenty-five F. psychrophilum isolates recovered from rainbow trout, coruh trout and brook trout were analysed by RAPD-PCR, ERIC-PCR, REP-PCR and PCR-RFLP, including 16S rRNA, gyrA and gyrB gene regions and PCR-based serotyping method. The PCR-based molecular analysis showed that the isolates could not be differentiated exactly according to isolation source and geographical region. Most isolates were of type-1 and type-2, and some of them were of type-0 and type-3; in addition, one isolate showed a unique serotype. The combined analysis results showed that F. psychrophilum isolates discriminated as five different genotypes and all isolates were successfully discriminated based on host.

Aquaculture 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.

Bu çalışmada, gökkuşağı alabalıklarından izole edilen altı L. anguillarum izolatı ve bir referans suş fenotipik ve genotipik özellikler açısından incelendi. İzolatların fenotipik özelliklerinin belirlenmesinde klasik mikrobiyolojik testler ve API 20 E strip testi kullanıldı. İzolatların moleküler identifikasyonu amiB genine dayanan L. anguillarum tür spesifik PCR uygulaması ve sonrasında aynı bölgenin sekans analizinin yapılmasıyla gerçekleştirildi. İzolatların dokuz farklı antibiyotiğe karşı antimikrobiyel aktiviteleri disk difüzyon yöntemiyle belirlendi. Ayrıca izolatlar arasındaki olası klonal ilişkiler Rastgele Amplifiye Edilmiş Polimorfik DNA (RAPD) metodu ile ortaya konuldu. API 20 E testlerinde izolatlar arasında ?-Galaktosidaz, arginin dihidrolaz, sitrat, sorbitol, amygdalin ve arabinoz testlerinde farklıklar görülmüştür. Tüm izolatların L. anguillarum spesifik 429 bp’lik bant verdiği saptanmış ve bu sonuç sekans analizi ile doğrulanmıştır. L. anguillarum izolatlarının çalışmada kullanılan dokuz farklı antibiyotiğe karşı değişik düzeyde antimikrobiyal aktiviteye sahip oldukları belirlendi. En yüksek direnç oranı neomisin ve linkomisin’e (% 100), en düşük direnç oranı ise doksisklin’e (% 14,2) karşı gözlendi. RAPD analizi sonucunda L. anguillarum izolatları % 60 benzerlik katsayısına göre bir unique tip ve beş alt türden oluşan bir küme (cluster) içerisinde gruplanmıştır. Bu çalışmanın balık kökenli L. anguillarum izolatlarının fenotipik ve genotipik özelliklerinin belirlenmesi ile ilgili ileride yapılacak çalışmalara temel oluşturabileceği düşünülmektedir. Ayrıca elde edilen sonuçlar, balık hastalıklarının tedavisinde uygun antimikrobiyal ajanların seçilmesinin önemini ortaya koymaktadır. In this study, six L. anguillarum isolates obtained from rainbow trout and one reference strains were examined in terms of phenotypic and genotypic characteristics. Conventional microbiological and API 20E tests were used to determine phenotypic characteristics of isolates. Molecular identification of isolates was carried out by applying the L. anguillarum specific PCR method based on the amiB gene followed by sequence analysis of the analysis of amplified product with the same primer pairs. Antimicrobial activity of isolates was determined by disk diffusion method against the nine different antibiotics. Additionally, possible clonal relationships between isolates were demonstrated by the RAPD-PCR method. There were differences between strains in terms of ?-galactosidase, arginine dihydrolase, citrate, sorbitol, amygdalin and arabinose tests in API 20E system. In L .anguillarum specific PCR assay all of isolates gave the final PCR product of 429 bp and this result was confirmed by sequence analysis. L. anguillarum isolates were found to have different levels of antimicrobial activity against nine different antibiotics used in the study. There was a high incidence of resistance to neomycine and lincomycine (84%), and a low incidence of resistance to doxycycline (14.2%). In RAPD method, L. anguillarum isolates were grouped into one unique type and one cluster including five subtypes according to 60% similarity coefficient index. The present study was considered to may provide a basis for further studies on phenotypic and genotypic characterization of L. anguillarum isolates from fishes. Moreover the present results showed the importance of choosing appropriate antimicrobial agents for treatment of fish diseases.

In 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. Gıda Tarım ve Hayvancılık Bakanlığı- TAGEM/14/AR-GE/26

Aim: Over the last decade, Citrobacter species have been responsible for infections in fish and many species and also new Citrobacter species have been identified. In this study, molecular identifications and the phenotypic and genotypic antimicrobial-resistance characteristics of atypical and typical Citrobacter species were determined. Materials and methods: Seven Citrobacter isolates were investigated from rainbow trout of different lengths with signs of disease. Biochemical characteristics were determined using conventional tests and rapid test kits; moreover, molecular identifications were conducted with 16S rRNA and the gyrB housekeeping gene region. The sequencing results obtained from the gyrB gene region were deposited in the GenBank database and compared with isolates from different countries that were registered in the database. Resistances to florfenicol, sulfonamides, and tetracycline antimicrobials were determined using the broth micro dilution method, and molecular resistance genes against these antimicrobials were identified. All detected resistance genes were confirmed by sequence analyses. Results: It was determined that three of the Citrobacter species with biochemical characteristics were atypical and showed oxidase-positive reactions. All the Citrobacter species were identified as Citrobacter sp. using the 16S rRNA gene; three isolates were identified as Citrobacter gillenii and four as Citrobacter sp. based on gyrB gene sequence analysis. Some isolates were found in the same group as other countries' isolates in the GenBank database, while isolates with high identities were found in different genogroups. All isolates were found to be phenotypically resistant to sulfamethoxazole and susceptible to tetracycline; these isolates' resistance genes included sulI, tetA, tetB, and tetD. Gıda Tarım ve Hayvancılık Bakanlığı - TAGEM/14/AR-GE/26 Scientific Researcher Department through KUAP(V)-2014/7

The antimicrobial susceptibilities of TurkishF. psychrophilumisolates 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-fiveF. psychrophilumisolates 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 thegyrA andparE genes. PCR analysis demonstrated that the genestetA,tetB,tetC,tetE,tetH,tetL, andtetM were not associated with the reduced susceptibility to oxytetracycline and the significance of this observation is discussed. PCR analysis also showed the presence ofsul2 in six isolates andfloR in one isolate. This study is the first report of these genes inF. psychrophilum.It was noted, however, that thefloR 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 ofF. psychrophilumto florfenicol.

Aksoy, Abdurrahman/0000-0001-9486-312X WOS: 000380923000006 PubMed: 27144782 Aeromonas hydrophila is known to be causative agent of an infection named as Bacterial haemorrhagic septicaemia or red pest in freshwater fish. The aim of this study was to develop and validate the glycoprotein-based fish vaccine against Aeromonas hydrophila. For this aim, after identification and characterization of A. hydrophila isolates from fish farms, one A. hydrophila isolate was selected as vaccine strain. Antigenic glycoproteins of this vaccine strain were determined by Western blotting and glycan detection kit. The connection types of these glycoproteins were examined by glycoprotein differentiation kit. Two glycoproteins, molecular weights of 19 and 38 kDa, with SNA connection type were selected for use in vaccination trials. After their purification by SNA-specific lectin and size-exclusion chromatography, protection studies with purified proteins were performed. For challenge trials, four experimental fish groups were designated: Group I (with montanide), Group II (with montanide and ginseng), Group III [with Al (OH) 3] and Group IV [with Al(OH) 3 and ginseng]. The survival ratings of fish were determined, and protection was calculated as 21.56%, 29.41%, 69.83% and 78.88% in groups I, II, III and IV, respectively. In conclusion, A. hydrophila glycoproteins with Al(OH) 3 and ginseng could be used as a safe and effective vaccine for fish. Scientific and Technological Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [111O806] This study was supported by the Scientific and Technological Research Council of Turkey (TUBITAK) (Project No: 111O806).

WOS: 000350946600012 PubMed: 25706737 Aeromonas spp. are oxidase positive, gram-negative, facultative anaerobic bacilli that are widely distributed in aquatic environments. A.hydrophila, A.sobria and A.bestiarum may cause severe infections in both human and cold-blooded animals. Environmental persistance of quinolones that are widely used in both human and veterinary medicine plays an important role in the selection of resistant mutants. Plasm id-mediated resistance is one of the main mechanisms involved in quinolone resistance, and qnr, qepA, aac(6')-Ib-cr, oqxAB genes are identified as resistance determinants. Determination of various types of qnr gene in different bacteria mainly in Enterobacteriaceae, suggests that they are widely distributed in nature. Recently, plasmid-mediated quinolone resistance was defined among Aeromonas species isolated from water. The aim of this study was to investigate the presence of qnr genes among aquatic Aeromonas spp. in Turkey. A total of 45 Aeromonas strains isolated from water and fishes collected from three different geographical regions (Aegean, Mediterranean and Blacicsea) in Turkey, were included in the study. The isolates were identified at species level by the use of 16S rDNA-RFLP (Restriction fragment length polymorphism) analysis and multiplex polymerase chain reaction (M-PCR). Among the isolates, 20 were identified as A.sobria, 10 as A.hydrophila, nine as A.salmonicida, four as A.bestiarum and two as A.veronii. The plasmid-mediated quinolone resistance determinants, qnrA, qnrB, qnrC and qnrS genes, were investigated by M-PCR, and sequence analysis was performed for nine qnr-positive isolates. According to the sequence analysis of the genes, qnr genes were characterized in six A.sobria, in two A.bestiarum and in one A.hydrophila isolate (9/45; 20%). When the sequence was compared with GenBank database, this gene was found as qnrS2. All qnrS-positive Aeromonas spp. isolates were ciprofloxacin-susceptible, while five of them were resistant to nalidixic acid. This study is the first research about the plasmid-mediated quinolone resistance and the presence of qnrS2 genes among Aeromonas spp. isolated from fishes and water in Turkey. In conclusion, various resistance genes of aquatic bacteria may constitute a potential risk for the transmission of those genes to other bacteria as well as clinical isolates.

In the present study, the etiological agent that caused mortality in goldfish at an aquarium company located in Bursa in northwestern Turkey was identified. Diseased fish were lethargic, displaying a loss of appetite, ascites, and exophthalmia. Internal examination revealed that the kidney was surrounded by exudate and that the spleen and liver were pale. Microbiological examination showed that the kidney, spleen, and liver were infected by gramnegative, cytochrome oxidase, catalase, and H2S positive rod-shaped bacteria identified as Shewanella putrefaciens. Identification of the bacteria was confirmed by 16S rRNA gene sequencing. Histopathological examination of the kidney, spleen, and liver revealed necrosis in kidney tubules and the presence of hepatocytes and hemosiderin in melanomacrophages. According to the disk diffusion method, isolates were sensitive to enrofloxacin (5 µg), florfenicol (30 µg), gentamycin (120 µg), and sulfamehoxazole+ trimethoprim (25 µg). The IJA appears exclusively as a peer-reviewed on-line open-access journal at http://www.siamb.org.il. To read papers free of charge, please register online at registration form. Sale of IJA papers is strictly forbidden.

Duman, Muhammed/0000-0001-7707-2705 WOS: 000321750600003 In this study, phenotypic and genotypic features of 10 L. garvieae strains isolated from rainbow trout farms were examined with 3 reference strains (Spain, England and ATCC 43921) comperativly. Rapid 32 STREP and conventional microbiologic tests were used for determining phenotipic features of L. garvieae strains. Altough there are differences, in Rapid 32 STREP system, between strains in terms of beta-Glucuronidase, D-ribose, sorbitol, lactose, raffinose, alanyl-phenylalanyl-proline arylamidase, pyrrolidonyl arylamidase, hippurate hydrolysis, urease tests, all strains have been confirmed as L. garvieae by API web. In RAPD PCR analysis, in which ERIC 2 primer is used, L. garvieae isolates were genotyped within 3 separate clusters according to similarity coefficient index of 70%, and it was detected that a vast majority of isolates with Turkey-origin (8 isolates) belongs to predominant type LG1 genotype. In addition to this, antimicrobial tests of L. garvieae strains shows that there are resistance against gentamycin, neomycin, lincomycin, sulfamethoxazole-trimethoprim, oxytetracycline, erythromycin, amoxicillin, florfenicol and doxycycline, which are frequently used on fish in our country. Scientific Research Administration of Uludag UniversityUludag University [UAP (V) 2009/13] This study was supported by Scientific Research Administration of Uludag University (UAP (V) 2009/13)

In 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. Bu çalışmada gökkuşağı alabalığı işletmelerinden izole edilmiş olan 15 adet Yersinia ruckeri izolatının 2 adet referans suşla (serotip 1 ve serotip 2) karşılaştırmalı olarak fenotipik, serotipik ve genotipik özellikleri bakımından incelenmesi amaçlanmıştır. Y. ruckeri izolatlarının fenotipik özelliklerinin belirlenmesinde klasik mikrobiyolojik ve API 20 E testleri kullanılmış ve bu testlerde bakterinin oldukça homojen bir yapı gösterdiği belirlenmiştir. Serotip 1 ve serotip 2 immunserumlar kullanılarak yapılan mikroaglütinasyon testinde ülkemizden izole edilmiş olan 15 suştan 11’nin serotip 1, 4’ünün ise serotip 2 özellikte olduğu belirlenmiştir. Rastgele Çoğaltılmış Polimorfik DNA (RAPD) analizinde Y. ruckeri izolatları %70 benzerlik katsayısına göre 2 ayrı küme içerisinde gruplanmış, kümelerden birincisinin 2 (YR1 ve YR2), ikincisinin ise 3 genotip (YR3, YR4 ve YR5) içerdiği saptanmıştır. Ayrıca bu çalışmada Y. ruckeri izolatlarının antibiyotik duyarlılıkları belirlemiş ve bu izolatların ülkemizde balıklarda ruhsatlı olan florfenikol, eritromisin, oksitetrasiklin ve trimetoprimsulfamethoxazole karşı direnç geliştirmiş oldukları saptanmıştır. Çalışma sonucunda elde edilen bulguların Y. ruckeri için teşhis kiti ve/veya aşı geliştirme çalışmalarına temel teşkil edeceği düşünülmektedir.

The aim of the study was the phenotypic and molecular characterization of Yersinia (Y) ruckeri strains, the causative agent of Enteric Redmouth Disease (ERM), by antibiotyping, random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) and sodium dodecylsulphate-polyacrylamide gel electrophoresis (SDS-PAGE) patterns of whole cell proteins. For this aim, a total of 97 Y ruckeri isolates were analyzed. The isolates were distinguished into ten antibiotypes and six phenotypes according to their resistance properties and whole cell protein profiles, respectively. Also, a glycoprotein band of approximately 25.5 kDa was observed in all Y ruckeri strains tested. In all strains, six different RAPD types were observed. In conclusion, Y ruckeri strains isolated from rainbow trout of fish farms in Turkey showed variation according to their phenotypic and genotypic characteristics, and the use of these three typing techniques in double and triple combinations could be more useful for discriminating the strains.

Arastirmada, ulkemizin farkli cografik bolgelerinde bulunan gokkusagi alabaligi isletmelerinden izole edilmis olan 19 adet Yersinia ruckeri susunun 2 adet referans susla (serotip 1 ve serotip 2) karsilastirmali olarak fenotipik ve serotipik ozellikleri incelenmistir. Yersinia ruckeri suslarinin fenotipik ozelliklerinin belirlenmesinde geleneksel mikrobiyolojik ve API 20 E testleri kullanilmistir. Geleneksel mikrobiyolojik ve API 20 E testlerinde bakterinin oldukca homojen (API 20 E testinde suslar arasinda jelatin hidrolizi, voges proskauer reaksiyonu, sitrat kullanimi testleri yonunden farkliliklar olmakla birlikte) bir yapi gosterdigi belirlenmistir. Shotts-Waltman medium (SWM) ve Riboz Ornitin Dezoksikolat (ROD) selektif besiyerlerinde Y. ruckeri suslarinin spesifik koloniler olusturdugu saptanmistir. Serotip 1 ve serotip 2 immunserumlar kullanilarak yapilan mikroaglutinasyon testinde ise ulkemizden izole edilmis olan 19 sustan 18’inin serotip 1, geri kalan 1 susun ise serotip 2 ozellikte oldugu gorulmustur. Bu sonuclar, ulkemizde Serotip 1 ozellikteki Yersinia ruckeri suslarinin yaygin oldugunu gostermistir.

The effectiveness of vaccine mixtures against lactococcosis was tested in rainbow trout (Oncorhynchus mykiss). The M1 strain of Lactococcus garvieae, isolated from a recent outbreak of lactococcosis at a rainbow trout farm in Turkey, was used in a trial comparing five immuniza- tion treatments: (a) formalin inactivated bacterin (vaccine), (b) the above bacterin together with Freund’s Incomplete Adjuvant (FIA), (c) the bacterin combined with β-glucan, (d) β-glucan only, and (e) phosphate buffered saline-PBS (control). Fish were given intrapritoneal injections and challenged by exposure to the bacteria 30, 75, or 125 days after vaccination. In fish exposed to the bacteria 30 days after injection, the relative percent survival (RPS) was 88.89% in the group that received only bacterin and 100% in the group that received the bacterin combined with FIA. Immunity remained high in the bacterin+FIA group, as the RPS in this group remained 100% in fish challenged at 75 days, significantly higher than in all other groups. In fish exposed to the bacteria 125 days after vaccination, the RPS was 54.55% in fish vaccinated with the bacterin only and 84.84% in fish vaccinated with bacterin+FIA. In the group that received only β-glucan, immunity did not improve after vaccination. Micro-agglutination tests of serums showed that immunized fish produced antibodies at high titers within 30 days. In short, the formalin-inacti- vated M1 strain provided longer lasting protection against Lactococcus garvieae in rainbow trout when combined with FIA than when administered alone or with β-glucan.

The aims of this study were to determine differences with respect to immunogenic potency in the antigenic profiles of nine Lactococcus garvieae strains from Turkey, Spain, and England, to develop a bacterin, and to examine the immunological response of rainbow trout to the bacterin. The strains had identical Western blot patterns with 30, 37, 40, 46, 52, and 66 kDA mw protein bands. After culturing the bacteria, proteins were separated by SDS-PAGE and transferred to Immobilon membranes. The membranes were incubated with hyperimmune rabbit sera obtained by immunizing a rabbit against L. garvieae. One group of 50 fish was immunized with formalin- killed bacterin prepared from the most immunogenic strain of L. garvieae. A second group of 50 fish served as an unimmunized control. Four weeks after vaccination, both groups were chal- lenged intraperitoneally with a homologous strain. The protection rate of the bacterin was judged by the relative percent survival (RPS) of the groups. A significantly high level of protection was achieved in the vaccinated group (88.8% RPS).