Development of diagnosis panel for common bacteria using bi̇oi̇nformatics tools and mass spectroscopy

Nowadays, food security and sustainable livestock are two of very important concepts with growing world population. Infections are one of threatening facts of these concepts. Infections can cause significant economic losses in livestock, leading to yield loss in dairy and meat production, even it may cause deaths if it is left untreated. Additionally these pathogens can infect humans and cause significant illness. In taken samples from patients who carries expected symptoms, detection and diagnosis of these bacteria has got key importance for determining the subsequent treatment. Nowadays, the most common methods for the diagnosis of this bacterium are culture, serological, biochemical and molecular methods. Although being cheap and easy, giving results in a long time, not allowing to species level diagnosis and low sensitivity are significant limitations of serological and culture-based methods. Molecular based methods also do not allow to analyze the multiple samples as a group and this situation increases the workloads. In this thesis, it is aimed that developing a panel for the diagnosis of 26 pathogens in multiple samples with high accuracy. For this purpose, 208 SNPs (single nucleotide polymorphisms) that designated first time in this thesis, have been identified from two gene region of 26 different pathogen. 17 of species-specific SNPs that have been determined by the bioinformatics of these pathogens have been chosen and analyzed by MALDI-TOF MS / iPLEX genotyping system and that shof the feasibility of system. In this thesis, a user friendly diagnostic have designed panel that have got features like; reducible or expandable number of target species as user needs, independent from source, identify capable in multi sample with high accuracy. Species-specific diagnosis of these 26 microorganisms in single panel, performing optimization and validation studies, before presenting to commercial use, species-specific diagnosis of these microorganisms and also shed light to the new researches with other microorganisms