Diversity of salmonella typhi-phages in Dhaka city through whole genome sequencing

Abstract

Bacteriophages and their hosts form a vast ecosystem, with bacteria evolving diverse defense mechanisms against phage infection while phages simultaneously develop strategies to overcome these defenses. Limited data on Salmonella Typhi phages hampers understanding of their genomics, evolution, and interactions with bacterial hosts. This dissertation aims to study Salmonella Typhi phages in the environmental water sources of Dhaka city, focusing on their genomic characterization and structure. Phage DNA was sequenced using a combination of propagation experiments, genomic DNA extraction, and sequencing library preparation. Computational tools, including Pharokka and Kraken2, were employed to analyze the genetic makeup and taxonomical classification of these phages. A phylogenetic tree was generated using tail fiber protein sequences to explore evolutionary relationships with mid-20th-century phages. Recent findings indicate the circulation of three phage genera, with Kayfunavirus being dominant, followed by Teseptimavirus and Macdonaldcampvirus. The generated genome map revealed gene structures and arrangements, highlighting annotated proteins required by the phages and further denoted large sequences of hypothetical proteins that can be crucial for phage survival and host interaction. These insights contribute to understanding pathogen behavior, the spread of antibiotic-resistant genes, and environmental survival mechanisms, underscoring the importance of phages in microbial ecology.