Farklı Salmonella Typhimurium kökenlerinin taşıdıkları patojenite adası ve direnç genlerinin in silico analizi

Öz

Salmonella Typhimurium, dünyada en sık izole edilen Salmonella serotiplerinden birisidir. Tüm genom analizi gibi yeni moleküler yöntemlerin gelişmesi ile, antibiyotik direnci ve farklı genlerin karşılaştırmalı analizleri daha kolay yapılabilmektedir. Çalışmamızda farklı S. Typhimurium kökenlerine ait genomik verilerin, taşıdıkları patojenite adaları, MLST, seqserotipleri ve direnç genleri açısından karşılaştırmalı in silico analizini gerçekleştirmeyi amaçladık. Çalışmamıza genomik verileri NCBI’da yer alan 15 farklı S. Typhimurium kökenini dahil edildi. Kökenlerin birbirleri ile evrimsel olarak yakınlıkları CSI filogeni ile antimikrobiyal direnç belirteçlerinin varlığı ise ResFinder yazılımı ile gerçekleştirildi. Salmonella kökenlerine ait patojenite adaları, MLST ve serotip tespiti için sırasıyla SPIFinder, MLST ve SeqSero yazılımları kullanıldı. Çalışmamıza dahil edilen 15 S. Typhimurium kökeninin birbirlerine %97 ve üstünde genomik benzerlik gösterdikleri tespit edildi. MLST analizlerine göre 9 köken (%60) ST19 olarak bulundu. Tüm kökenlerin SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-12, SPI-13, SPI-14 patojenite adalarını taşıdıkları gözlenirken, SGI1 patojenite adası sadece 3 kökende tespit edildi. Aminoglikozid direnci ile ilişkili aac(6')-Iaa geni tüm kökenlerde saptandı. Yeni nesil dizileme tekniklerinin gelişimi, S. Typhimurium gibi önemli enfeksiyon etkenlerine ait yeni moleküler epidemiyolojik veriler elde edilmesini sağlamaktadır. Bu verilerin karşılaştırmalı in silico analizleri ile enfeksiyonlarda kullandıkları virülans genlerinin analizleri ve moleküler patogenez mekanizmalarının aydınlatılması sağlanabilecektir.

Anahtar Kelimeler

• direnç genleri
• in silico analiz
• salmonella patojenite adası
• Salmonella Typhimurium

In silico analysis of pathogenicity island and resistance genes carried by different Salmonella Typhimurium strains

Öz

Salmonella Typhimurium is one of the most frequently isolated Salmonella serotypes in the world. With the path of the new strategy of analysis like the whole genome, comparative analyzes of weaknesses and different genes can be done more easily. In our study, S. Typhimurium has different origins, it is aimed for different purposes to analyze genomic data, calculus pathogens islands, belonging MLST, seqs types, and silico genes. Our study included 15 different S. Typhimurium strains whose local data were obtained in NCBI. Evolutionary affinities of origins with C. Pathogenicity islands of Salmonella origin, SPIFinder, MLST, and SeqSero software for MLST. It was determined that Typhimurium origins showed 97% and more genomic similarity. According to MLST analysis, origin 9 (60%) was found to be ST19. While all were observed to carry pathogenicity islands SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-12, SPI-13, SPI-14, only 3 were detected in the SGI1 pathogenicity island. The aminoglycoside-related aac(6')-Iaa gene was detected in all strains. It would seem that the course of sequencing techniques such as the next generation is to obtain a new epidemiological route for owners of S. Typhimurium. With these data comparative analyzes, virulence genes that can be applied and the analyzes that can be corrected can be elucidated.

Anahtar Kelimeler

• resistance genes
• in slico analyses
• Salmonella Typhimurium.
• salmonella pathogenicity island
• salmonella pathogenicity island,

Kaynakça

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