Investigation of the evolutionary structure and antimicrobial resistance profile of Salmonella Infantis
Salmonella species, including the zoonotic agent Salmonella Infantis, are significant pathogens that cause substantial economic losses in poultry and foodborne infections in humans, leading to diseases such as gastroenteritis, enteric fever, and septicemia. Despite extensive research, Salmonella Infantis remains a prevalent non-host-specific serotype isolated from humans, necessitating continued efforts in protection and control measures. Molecular methods, especially whole genome sequencing, play a crucial role in these endeavours by providing high-resolution genomic data essential for detailed analyses. This study aims to determine the antimicrobial resistance (AMR) profiles and evolutionary developments of S. Infantis strains isolated from Turkish poultry houses over the last five years using whole genome sequencing. Additionally, it seeks to construct an accurate phylogenetic tree based on the alignment of similar regions in the AMR gene sequences of each isolate, examining the phylogenetic relationships among isolates from diverse locations. Furthermore, this study aims to develop a bioinformatics analysis method that will not only standardize future bioinformatic analyses but also serve as a model for subsequent research. Through these objectives, the study will help to understand S. Infantis's antimicrobial resistance and evolutionary dynamics, offering insights into its control and prevention.