Significance of RAPD method for the detection of filogenetic relation between virulence factors identified E. coli strains isolated from extraintestinal infections.

TEZ12346Tez (Yüksek Lisans) -- Çukurova Üniversitesi, Adana, 2016.Kaynakça (s. 55-62) var.XII, 63 s. :_res. (bzs. rnk.), tablo ;_29 cm.İntestinal ekosistemin kommensal üyesi olmakla birlikte her türlü çevre şartına karşı yüksek rekombinasyon-mutasyon yeteneği ile büyük bir uyum gösteren E. coli suşları, yüksek GC oranına sahip olmakla birlikte ilginç şekilde genomik plastisite özelliğine sahiptir. Diğer taraftan bu özelliklerinin yanı sıra klasik besiyerlerinde hızlı üreme yeteneğini koruyan E. coli, prokaryotlardaki spontan DNA transfer olaylarının açıklanması için iyi bir modeldir. Genomda kodlanan yapısal genlerin yanı sıra, patojenite adaları (PI), plazmidler, bakteriyofajlar ve transpozonlar gibi mobil genetik elemanlarda kodlanan, esasen mikroorganizmaların içinde bulundukları mikro çevre şartlarına uyum sağlamasında rol oynayan ancak bazen mikroorganizmaya farklı virülans özellikler de kazandıran proteinlerin kodlandığı, genlerin transferi ile kendilerinde olmayan yeni virülans özellikler de kazanabilirler. İntestinal kaynaklı ExPEC suşlarının özel genotiplerin mutasyonu sonucumu oluştuğu yoksa rastgele mutasyonlarınmı ExPEC suşlarını oluşturduklarının bilinmesi bu suşların toplumdaki hareketlerinin izlenmesi ve enfeksiyon kontrol protokollerinin oluşturulabilmesine imkan sağlayacaktır. Bu amaçla yapılacak epidemiyolojik sürveyans da klinik ile ilişkisine dayalı patotipleme, fizyolojik özellikler, (MLEE) veya antibiyotik duyarlılık kalıplarının tespiti gibi düşük ayırım gücüne sahip fenotipik yöntemlerin yerine veya yanında genomdaki spesifik dizileri tanıyan nükleik asit amplifikasyon bazlı ve/veya restriksiyon enzimlerinin de kullanıldığı, filotipleme, PCR, PCR-RFLP, PFGE ve (MLST) gibi sekanslama yöntemlerine ihtiyaç bulunmaktadır. Bu çalışmada extra intestinal sistemden izole edilen ve bazı virülans genleri gösterilmiş ExPEC izolatlarının muhtemel klonal ilişkilerini tespit amacı ile, üç farklı kısa oligonükleotid dizisinin kullanıldığı RAPD ve XbaI-PFGE yöntemlerinin ayırım güçlerini tespiti amaçladık. Çalışmada farklı klinik örneklerden izole edilen 155 ExPEC suşu kullanılmıştır.The importance of RAPD method in the investigation of filogenetic relation of E.coli strains isolated from Extraintestinal infections and virulence factors of which are determined. E. coli strains which are the commensal members of intestinal ecosystem and which are adapted to any environmental condition due to its great recombination mutation ability have not only high potential of GC but also an interesting genomic plasticity feature. In addition to these features, E. coli which can rapidly grow in classic medium is a good model accounting for DNA transfer cases. In fact, they may gain new virulence features which do no exist in them with the gene transfer in which proteins playing a role in the adaption of microorganism to any micro environment, yet providing microorganism with different virulence are coded. Whether intestinal ExPEC strains are developed as a result of special genotype mutation or random mutation developed ExPEC strains is of great importance for the tracking the signs of these strains in the society and for the infections control protocols. Thus instead of together of with fenotypic methods which have a low level of differenciation such as clinical patotypes, physiological features multilocus enzyme electrophoresis phylotypic, such methods as PCR, PCR-RFLP, PFGE and Multilocus Sequence Typing (MLST) sequencing which are based on nucleic acid amplification and can determine specific sequence and/or in which restriction enzymes are used are needed. In this study; We aimed at investigating the determination power of RAPD and XbaI-PFGE in which three different short oligonucleotide sequences were used in order to determine the possible clonal relation ExPEC isoates some virulence genes of which were shown in the the strains isolated from extra intestinal system. In the study, 155 ExPEC strains isolated from various clinical samples were used.Bu çalışma Ç.Ü. Bilimsel Araştırma Projeleri Birimi tarafından desteklenmiştir. Proje No: TYL-2015-5188

Comparative analysis of selected cagPAI genes and different vacA genotypes in Iranian and Turkish H. pylori-positive patients suffering from gastric adenocarcinoma and active chronic gastritis

Background/aim: Helicobacter pylori is a pathogen that colonizes a majority of the world’s population. Genetic diversity within the virulence genes of bacteria such as cagPAI and vacA may have a modified effect on the pathogenic potential of the bacteria. This study aimed to investigate which genes can be suggested as potentially related virulence factors for H. pylori-associated active chronic gastritis and stomach adenocarcinoma in the northwest of Iran and south of Turkey. Materials and methods: Formalin-fixed, paraffin-embedded stomach biopsy tissue samples were obtained from Iranian and Turkish patients from selected geographical regions. The prevalence of selected cagPAI genes and vacA genotypes were studied in H. pyloripositive samples by using polymerase chain reaction and specific primers. Results: Out of 320 patients, H. pylori was detected in 28.43% of patients. We found that the vacAs1, vacAm2, and cagA genes with mean prevalences of 82.41%, 71.42%, and 69.23%, respectively, were dominant in Iranian and Turkish patients. Conclusion: In the south of Turkey and northwest of Iran the studied genes were homogeneous and there were no significant differences in bacterial genetics. The results of this study indicate that cagA and vacAs1 are dominant genes in people with gastric disorders in our selected geographical regions.Background/aim: Helicobacter pylori is a pathogen that colonizes a majority of the world’s population. Genetic diversity within the virulence genes of bacteria such as cagPAI and vacA may have a modified effect on the pathogenic potential of the bacteria. This study aimed to investigate which genes can be suggested as potentially related virulence factors for H. pylori-associated active chronic gastritis and stomach adenocarcinoma in the northwest of Iran and south of Turkey. Materials and methods: Formalin-fixed, paraffin-embedded stomach biopsy tissue samples were obtained from Iranian and Turkish patients from selected geographical regions. The prevalence of selected cagPAI genes and vacA genotypes were studied in H. pyloripositive samples by using polymerase chain reaction and specific primers. Results: Out of 320 patients, H. pylori was detected in 28.43% of patients. We found that the vacAs1, vacAm2, and cagA genes with mean prevalences of 82.41%, 71.42%, and 69.23%, respectively, were dominant in Iranian and Turkish patients. Conclusion: In the south of Turkey and northwest of Iran the studied genes were homogeneous and there were no significant differences in bacterial genetics. The results of this study indicate that cagA and vacAs1 are dominant genes in people with gastric disorders in our selected geographical regions