Pathogen Genomic Sequencing

The forensic detection of disease-causing (pathogenic) bacteria is facilitated by knowledge of target sequences of the genome of the particular organism. Sequencing of some pathogens has been undertaken by organizations such as the Institute for Genomic Research. In the national interest, the United States has embarked on a genomic sequencing program of pathogens that will have forensic applications.

The Pathogen Genomic Sequencing program initiated by the Defense Advanced Research Project Agency (DARPA) in 2002 focuses on characterizing the genetic components of pathogens in order to develop novel diagnostics, treatments, and therapies for the diseases they cause. In particular, the program will collect an inventory of genes and proteins that are specific to pathogens and then to look for patterns among these molecules.

This information will facilitate the development of tools for identifying pathogens in a variety of vectors. It will also provide a foundation for engineering antibodies to identify pathogens. Initially, one representative strain of the bacteria that cause a variety of diseases (or their close relatives) are being studied for this program: Brucella suis (brucellosis), Burkholderia mallei (melioidosis), Clostridium perfringens (botulism), Coxiella burnetti (Q fever), Franciscella tularensis (tulareremia), and Rickettsia typhi (Rocky Mountain spotted fever).

As part of the Pathogen Genomic Sequencing project, a website focusing on orthopox viruses has been created. Known as the Poxvirus Bioinformatics Resource, this website serves as a repository for genetic sequence data for orthopox viruses. It currently contains sequence data for 35 viral pathogens including the virus that causes smallpox. In addition, the website contains data-mining and sequence analysis software and a poxvirus literature resource. The goals of the Poxvirus Bioinformatics Resource are the development of novel therapies for human diseases caused by orthopox viruses, the ability to detect orthopox viruses in the environment and the development of quick diagnostic tools for detecting pox diseases.