Extending the Microbial Forensic Toolkit Through Whole Genome Sequencing and Statistical Phylogenomics

Microbes have also developed a number of elaborate mechanisms for generating natural genetic diversity, including high mutation and recombination rates as well as the horizontal transfer of gene(s). One major goal of microbial forensics is to use this genetic diversity to identify the source of a pathogen used to commit a crime. While phylogenetic analysis of nucleotide variation within a small number of genes has been used in past forensic studies to assess relationships among pathogens, a large fraction of those genomes remain uncharacterized, ignoring useful information contained in the presence or absence of different genes and other structural variation. Recent advances in next generation sequencing (NGS) technologies and phylogenetic analysis of complete genomes (phylogenomics) have the potential to significantly alter the technological approaches used in characterizing case samples. This proposal seeks to expand our existing scientific work on HIV forensic studies by developing a robust "pathogen toolkit" for source identification across a range of biological agents. ca/ncf