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Yersinia ruckeri İzolatlarının Genotiplendirilmesinde PCR Tabanlı DNA Fingerprinting Tekniklerinin Karşılaştırmalı Analizi

Year 2019, Volume: 15 Issue: 3, 262 - 271, 15.09.2019
https://doi.org/10.22392/actaquatr.503853

Abstract



Bu
çalışmanın amacı, Türkiye'nin farklı coğrafi bölgelerinden elde edilmiş olan Y. ruckeri izolatlarını
tiplendirilmesinde farklı PCR tabanlı DNA fingerprinting metotlarını değerlendirmektir.
Gökkuşağı
alabalıklarından izole edilmiş on sekiz Y.
ruckeri
izolatı ERIC2 primerinin kullanıldığı enterobacterial repetitive
intergenic consensus (ERIC) PCR metodu, P5, P6 ve M13 primerlerinin
kullanıldığı randomly amplified polymorphic (RAPD) DNA PCR metodu ve (GTG)5
primerinin kullanıldığı (GTG)5 PCR metodu ile karakterize edildi. Test edilen tüm primerlerin doğru bir analiz
için kullanılabilir amplifikasyon ürünü oluşturduğu belirlendi. Kluster ve
ayrım gücü analizi sonuçlarına göre, Y
ruckeri
'nin moleküler tiplendirmesi için en uygun primerin ERIC2 primeri
olduğu, bunu P5, P6, M13 ve (GTG) 5 primerinin takip ettiği belirlendi. ERIC
PCR DNA fingerprinting metodu Y. ruckeri’nin
epidemiyolojik sürveyansının belirlenmesinde güçlü bir genotipik araç olarak
düşünülebileceği sonucuna ulaşılmıştır.




References

  • Altun, S., Onuk, E.E., Çiftçi, A., Duman, M. & Büyükekiz, A.G. (2013). Determination of phenotypic, serotypic and genetic diversity and antibiotyping of Yersinia ruckeri isolated from Rainbow trout. Kafkas Üniversitesi Veteriner Fakültesi Dergisi, 19(2), 225-232.
  • Avendano-Herrera, R., Rodrıguez, J., Magarinos, B., Romalde, J.L. & Toranzo, A.E. (2004). Intraspecific diversity of the marine fish pathogen Tenacibaculum maritimum as determined by randomly amplified polymorphic DNA-PCR. Journal of Applied Microbiology, 96, 871-877.
  • Bastardo, A., Bohle, H., Ravelo, C., Toranzo, A.E. & Romalde, J.L. (2011a). Serological and molecular heterogenetity among Yersinia ruckeri strains isolated from farmed Atlantic salmon Salmo salar in Chile. Diseases Aquatic Organisim, 93, 207-214.
  • Bastardo, A., Ravelo, C. & Romalde, J.L.(2012). Multilocus sequence typing reveals high genetic diversity and epidemic population structure for the fish pathogen Yersinia ruckeri. Environmental Microbiology, 14(8), 1888-1897.
  • Bastardo, A., Sierralta, V., Leon, J., Ravelo, C. & Romalde, J.L. (2011b). Phenotypical and genetic characterization of Yersinia ruckeri strains isolated from recent outbreaks in farmed rainbow trout Oncorhynchus mykiss (Walbaum) in Peru. Aquaculture, 317, 229-232.
  • Çagırgan, H. & Yüreklitürk, O. (1991). First isolation of Yersinia ruckeri from rainbow trout in Turkey. Fifth International Conference, Disease of Fish and Shellfish Book of Abstracts, 131.
  • Davies, R.L. & Frerichs, G.N. (1989). Morphological and biochemical differences among isolates of Yersinia ruckeri obtained from wide geographical areas. Journal of Fish Diseases, 12, 357-365.
  • Duman, M., Altun, S., Cengiz, M., Saticioglu, I.B., Buyukekiz, A.G. & Sahinturk, P. (2017). Genotyping and antimicrobial resistance genes of Yersinia ruckeri isolates from rainbow trout farms. Diseases of Aquatic Organisms, 125, 31-44.
  • Durmaz, R. (2008). Bakteri tiplendirme çalışmaları niçin gerekli?, XXXIII. Türk mikrobiyoloji kongresi, İstanbul, Kongre Kitabı, s, 27-30.
  • Ewıng, W.H., Ross, A.J., Brenner, D.J. & Fanning, G.R. (1978). Yersinia ruckeri sp. nov., the Red Mouth (RM) Bacterium, International Journal of Systematic Bacteriology, 28, 37-44.
  • Fidanboylu, A. (2010). Gram negatif bakterilerin moleküler tiplendirilmesinde bazı pcr tabanlı yöntemlerin karşılaştırılması. Ege Üniversitesi Sağlık Bilimleri Enstitüsü, Yüksek Lisans Tezi, İzmir.
  • Foschino, R., Nucera, D., Volponi, G., Picozzi, C., Ortoffi, M. & Bottero, M.T. (2008). Comparison of Lactococcus garvieae strains isolated in northern Italy from dairy products and fishes through molecular typing. Journal of Applied Microbiology, 105(3), 652-62.
  • Grundmann, H.J., Towner, K.J., Dijkshoorn, L., Gerner-Smidt, P., Mahmer, M., Seifert, H. & Vaneechoutte, M. (1997). Multicenter study using standardized protocols and reagents for evaluation of reproducibility of PCR-based fingerprinting of Acinetobacter spp. Journal of Clinical Microbiology, 35, 3071-7.
  • Horne, M.T. & Barnes, A.C. (1999). Enteric Red Mouth Diseases (Yersinia ruckeri) In: Fish Diseases and Disorders Volume 3. Viral, Bacterial and Fungal Infections. Ed.: P.T.K. Woo, D.W. Bruno, CAB International, New York, USA. p, 455-479.
  • Huang, Y., Runge, M., Michael, G.B., Schwarz, S., Jung, A. & Steinhagen, D. (2013). Biochemical and molecular heterogeneity among isolates of Yersinia ruckeri from rainbow trout (Oncorhynchus mykiss, Walbaum) in north west Germany. BMC Veterinary Research, 9, 215
  • Köksal, F. (1999). Moleküler tiplendirme yöntemlerinin hastane infeksiyonlarıda kullanımı. Hastane İnfeksiyonları Dergisi, 3, 189-95.
  • Kumar, G., Menanteau-Ledouble, S., Saleh, M. & El-Matbouli, M. (2015). Yersinia ruckeri, the causative agent of enteric redmouth disease in fish. Veterinary Research, 46, 103
  • Li, W., Raoult, D. & Fournier, P.E. (2009). Bacterial strain typing in the genomic era. FEMS Microbiology Reviews, 33, 892-916.
  • Mancuso, M., Avendano-Herrera, R., Zaccone, R., Toranzo, A.E. & Magarinos, B. (2007). Evaluation of different DNA-based fingerprinting methods for typing Photobacterium damselae ssp. piscicida. Biological Research, 39, 71-82.
  • Olive, D.M. & Bean, P. (1999). Principles and applications of methods for DNA-based typing of microbial organisms. Journal of Clinical Microbiology, 37(6), 1661-1669.
  • Onuk, E.E., Çiftçi, A., Fındık, A., Çiftçi, G., Altun, S., Balta, F., Özer, S. & Çoban, A.Y. (2011). Phenotypic and Molecular characterization of Yersinia ruckeri isolates from Rainbow Trout (Oncorhynchus mykiss, Walbaum, 1792) in Turkey. Berliner und Münchener Tierärztliche Wochenschrift, 124(7-8), 320-328.
  • Özer, S., Bulduklu, P., Dönmez, E., Koyuncu, E., Serin, M.S., Aslan, G., Tezcan, S., Aydin, E. & Emekdas, G. (2008). Phenotypic and genetic homogeneity of Yersinia ruckeri strains isolated from farmed rainbow trout, Oncorhynchus mykiss (Walbaum), in Mersin Province, Turkey. Bulletin of the European Association of Fish Pathologists, 28(3), 97-104.
  • Öztürk, R.Ç. & Altınok, İ. (2014). Bacterial and viral fish diseases in Turkey. Turkish Journal of Fisheries and Aquatic Sciences, 14, 275-297.Romalde, J.L., Margarinos, B., Barja, J.L. & Toranzo, A.E. (1993). Antigenic and molecular characterization of Yersinia ruckeri: proposal for a new intraspecies classification. Systematic and Applied Microbiology, 16, 411-419.
  • Tobback, E., Decostere, A., Hermans, K., Haesebrouck, F. & Chiers, K. (2007). Yersinia ruckeri infections in salmonid fish, Journal of Fish Diseases, 30, 257-268.
  • Versalovic, J., Koeuth, T. & Lupski, R. (1991). Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Research, 19(24), 6823-6831.
Year 2019, Volume: 15 Issue: 3, 262 - 271, 15.09.2019
https://doi.org/10.22392/actaquatr.503853

Abstract

References

  • Altun, S., Onuk, E.E., Çiftçi, A., Duman, M. & Büyükekiz, A.G. (2013). Determination of phenotypic, serotypic and genetic diversity and antibiotyping of Yersinia ruckeri isolated from Rainbow trout. Kafkas Üniversitesi Veteriner Fakültesi Dergisi, 19(2), 225-232.
  • Avendano-Herrera, R., Rodrıguez, J., Magarinos, B., Romalde, J.L. & Toranzo, A.E. (2004). Intraspecific diversity of the marine fish pathogen Tenacibaculum maritimum as determined by randomly amplified polymorphic DNA-PCR. Journal of Applied Microbiology, 96, 871-877.
  • Bastardo, A., Bohle, H., Ravelo, C., Toranzo, A.E. & Romalde, J.L. (2011a). Serological and molecular heterogenetity among Yersinia ruckeri strains isolated from farmed Atlantic salmon Salmo salar in Chile. Diseases Aquatic Organisim, 93, 207-214.
  • Bastardo, A., Ravelo, C. & Romalde, J.L.(2012). Multilocus sequence typing reveals high genetic diversity and epidemic population structure for the fish pathogen Yersinia ruckeri. Environmental Microbiology, 14(8), 1888-1897.
  • Bastardo, A., Sierralta, V., Leon, J., Ravelo, C. & Romalde, J.L. (2011b). Phenotypical and genetic characterization of Yersinia ruckeri strains isolated from recent outbreaks in farmed rainbow trout Oncorhynchus mykiss (Walbaum) in Peru. Aquaculture, 317, 229-232.
  • Çagırgan, H. & Yüreklitürk, O. (1991). First isolation of Yersinia ruckeri from rainbow trout in Turkey. Fifth International Conference, Disease of Fish and Shellfish Book of Abstracts, 131.
  • Davies, R.L. & Frerichs, G.N. (1989). Morphological and biochemical differences among isolates of Yersinia ruckeri obtained from wide geographical areas. Journal of Fish Diseases, 12, 357-365.
  • Duman, M., Altun, S., Cengiz, M., Saticioglu, I.B., Buyukekiz, A.G. & Sahinturk, P. (2017). Genotyping and antimicrobial resistance genes of Yersinia ruckeri isolates from rainbow trout farms. Diseases of Aquatic Organisms, 125, 31-44.
  • Durmaz, R. (2008). Bakteri tiplendirme çalışmaları niçin gerekli?, XXXIII. Türk mikrobiyoloji kongresi, İstanbul, Kongre Kitabı, s, 27-30.
  • Ewıng, W.H., Ross, A.J., Brenner, D.J. & Fanning, G.R. (1978). Yersinia ruckeri sp. nov., the Red Mouth (RM) Bacterium, International Journal of Systematic Bacteriology, 28, 37-44.
  • Fidanboylu, A. (2010). Gram negatif bakterilerin moleküler tiplendirilmesinde bazı pcr tabanlı yöntemlerin karşılaştırılması. Ege Üniversitesi Sağlık Bilimleri Enstitüsü, Yüksek Lisans Tezi, İzmir.
  • Foschino, R., Nucera, D., Volponi, G., Picozzi, C., Ortoffi, M. & Bottero, M.T. (2008). Comparison of Lactococcus garvieae strains isolated in northern Italy from dairy products and fishes through molecular typing. Journal of Applied Microbiology, 105(3), 652-62.
  • Grundmann, H.J., Towner, K.J., Dijkshoorn, L., Gerner-Smidt, P., Mahmer, M., Seifert, H. & Vaneechoutte, M. (1997). Multicenter study using standardized protocols and reagents for evaluation of reproducibility of PCR-based fingerprinting of Acinetobacter spp. Journal of Clinical Microbiology, 35, 3071-7.
  • Horne, M.T. & Barnes, A.C. (1999). Enteric Red Mouth Diseases (Yersinia ruckeri) In: Fish Diseases and Disorders Volume 3. Viral, Bacterial and Fungal Infections. Ed.: P.T.K. Woo, D.W. Bruno, CAB International, New York, USA. p, 455-479.
  • Huang, Y., Runge, M., Michael, G.B., Schwarz, S., Jung, A. & Steinhagen, D. (2013). Biochemical and molecular heterogeneity among isolates of Yersinia ruckeri from rainbow trout (Oncorhynchus mykiss, Walbaum) in north west Germany. BMC Veterinary Research, 9, 215
  • Köksal, F. (1999). Moleküler tiplendirme yöntemlerinin hastane infeksiyonlarıda kullanımı. Hastane İnfeksiyonları Dergisi, 3, 189-95.
  • Kumar, G., Menanteau-Ledouble, S., Saleh, M. & El-Matbouli, M. (2015). Yersinia ruckeri, the causative agent of enteric redmouth disease in fish. Veterinary Research, 46, 103
  • Li, W., Raoult, D. & Fournier, P.E. (2009). Bacterial strain typing in the genomic era. FEMS Microbiology Reviews, 33, 892-916.
  • Mancuso, M., Avendano-Herrera, R., Zaccone, R., Toranzo, A.E. & Magarinos, B. (2007). Evaluation of different DNA-based fingerprinting methods for typing Photobacterium damselae ssp. piscicida. Biological Research, 39, 71-82.
  • Olive, D.M. & Bean, P. (1999). Principles and applications of methods for DNA-based typing of microbial organisms. Journal of Clinical Microbiology, 37(6), 1661-1669.
  • Onuk, E.E., Çiftçi, A., Fındık, A., Çiftçi, G., Altun, S., Balta, F., Özer, S. & Çoban, A.Y. (2011). Phenotypic and Molecular characterization of Yersinia ruckeri isolates from Rainbow Trout (Oncorhynchus mykiss, Walbaum, 1792) in Turkey. Berliner und Münchener Tierärztliche Wochenschrift, 124(7-8), 320-328.
  • Özer, S., Bulduklu, P., Dönmez, E., Koyuncu, E., Serin, M.S., Aslan, G., Tezcan, S., Aydin, E. & Emekdas, G. (2008). Phenotypic and genetic homogeneity of Yersinia ruckeri strains isolated from farmed rainbow trout, Oncorhynchus mykiss (Walbaum), in Mersin Province, Turkey. Bulletin of the European Association of Fish Pathologists, 28(3), 97-104.
  • Öztürk, R.Ç. & Altınok, İ. (2014). Bacterial and viral fish diseases in Turkey. Turkish Journal of Fisheries and Aquatic Sciences, 14, 275-297.Romalde, J.L., Margarinos, B., Barja, J.L. & Toranzo, A.E. (1993). Antigenic and molecular characterization of Yersinia ruckeri: proposal for a new intraspecies classification. Systematic and Applied Microbiology, 16, 411-419.
  • Tobback, E., Decostere, A., Hermans, K., Haesebrouck, F. & Chiers, K. (2007). Yersinia ruckeri infections in salmonid fish, Journal of Fish Diseases, 30, 257-268.
  • Versalovic, J., Koeuth, T. & Lupski, R. (1991). Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Research, 19(24), 6823-6831.
There are 25 citations in total.

Details

Primary Language Turkish
Subjects Structural Biology
Journal Section Research Articles
Authors

Seda Köstereli This is me

Ertan Emek Onuk

Publication Date September 15, 2019
Published in Issue Year 2019 Volume: 15 Issue: 3

Cite

APA Köstereli, S., & Onuk, E. E. (2019). Yersinia ruckeri İzolatlarının Genotiplendirilmesinde PCR Tabanlı DNA Fingerprinting Tekniklerinin Karşılaştırmalı Analizi. Acta Aquatica Turcica, 15(3), 262-271. https://doi.org/10.22392/actaquatr.503853