Thoughts about Genome Distance Analysis for Pathogen Outbreak Isolates

Contributed by Carol Huang

The recent work on bioinformatics analysis of pathogen strains from outbreaks made me consider the aspects that can be used for this type of analysis. When we are facing a pathogen outbreak, the first thing we need to do is to identify the source and genetic variation. Understanding evolutionary dynamics and the route of transmission of the pathogens is the key to developing effective preventive strategies.

Whole genome sequencing has the potential of answering most of the key questions of related evolutionary questions. To answer these key questions, different strains of the same species were collected from different resources then sequenced with the Illumina NGS platform.   Draft de novo assemblies then were further analyzed for genome-to-genome distance calculation, which blast each individual genome against all genomes in the group. This analysis will help to determine the phylogeny of these genomes and geological association. On this aspect, it should include as many relevant strains to be representative and accurate ie: having a big enough inclusive population. Further genetic phenotypic characterization like SNP antibiotic resistance ability will enable us to develop more effective strategies.

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