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Genomics and Infectious Diseases: Susceptibility, Resistance, Response, and Antimicrobial Therapy 

Genomics and Infectious Diseases: Susceptibility, Resistance, Response, and Antimicrobial Therapy
Chapter:
Genomics and Infectious Diseases: Susceptibility, Resistance, Response, and Antimicrobial Therapy
Author(s):

Michaela Fakiola

, Wei Lu

, Sarra E. Jamieson

, and Christopher S. Peacock

DOI:
10.1093/med/9780199896028.003.0037
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date: 30 October 2020

The genomic era continues to revolutionise the manner in which infectious disease research is being undertaken, both from the point of view of the human host and the infecting pathogen. The generation of new and exciting discoveries progress at a phenomenal rate with the real possibility of translational outcomes in the clinical setting. The ongoing development of genome-wide technologies will continue to support large-scale, high-throughput projects that allow both human and pathogen genomes and transcriptomes to be considered in their entirety, and will eventually allow them to be considered together. With respect to human susceptibility to infectious disease, the ongoing development and reducing costs of NGS sequencing technologies will shortly allow the human genome to be fully sequenced in large enough sample sizes within the scope of a research project. In conjunction with large-scale projects such as the 1KGP this will allow the role of rare genetic variation, as well as common variation, in susceptibility to infectious disease to be determined. Reducing costs, of both NGS and high-throughput SNP arrays, will allow much larger cohort sizes (>10,000) to be investigated and will eventually allow researchers to start untangling the complex genetic interactions that exist between genes (gene x gene interactions) and the environment (gene x environment interactions). Not only will this provide valuable information about the pathways involved in susceptibility to infectious disease, but will hopefully lead to the development of novel therapies, diagnostics and allow the more targeted application of appropriate drug therapies. A decade ago, the availability of a representative complete genome sequence for microbial pathogens was seen as the breakthrough required for completely interpreting the pathogen genome resulting in a new era of novel therapies against infectious diseases. It has become apparent that the rapid evolutionary rate of microbes, their ability to exchange genomic material within communities and the increasing emergence of novel pathogens means that we must continue to sequence isolates from all pathogens just monitor outbreaks. The ability to now be able to sequencing of the microbiome has also improved our understanding of just how important our relationship is with the microbial environment. This knowledge is leading to an increasing emphasis on the benefits of promoting a healthy microbiome to prevent chronic disease. While the advent of next generation sequencing heralded a new era of non-hypothesis driven science, the 3rd generation of sequencing machines is likely to herald a new era, one that may make this technology indispensable in the routine clinical environment.

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