cine and manufacturing” (AAM, 2009b). Gene sequencing, WGS, and the techniques these make possible are moving microbiology forward more rapidly than ever before. They also have given rise to new tools—genomics, proteomics, metabolomics, transcriptomics, molecular phylogeny, and others—that now are available to scientists studying the relationships among microbes, their pathogenicity mechanisms, and their metabolic potential (AAM, 2009b). The AAM report went on, however, to note that a “major effort in functional annotation to understand the DNA sequence we already have” is needed (2009b:16). “Annotation is a critical part of making genome sequences into resources, but it represents a huge bottleneck.” It also called for the implementation of a set of standard annotation platforms and a central annotation resource “with defined methods and standards, and guidelines for people to use the resource” (2009b:16).
THE INTERPLAY BETWEEN SEQUENCING AND BIOINFORMATICS
Dr. Jongsik Chun of Seoul National University in South Korea believes that WGS provides the ultimate information for both epidemiology and microbial forensics. As an illustration of the power of WGS, he pointed to its use in tracking the transmission of carbapenem-resistant K. pneumoniae among individuals during the NIH Clinical Center’s 2011 outbreak (Snitkin et al., 2012). WGS is superior to all other identification methods if cost, time, and bioinformatics are not issues. However, using genomic information is the area of microbial forensics in which the application of bioinformatics is most needed. Chun sought to provide an understanding of the scope of microbial knowledge that is lacking and the uses to which the data that are available could be applied with better tools. He reviewed the challenges faced in assembling and curating databases, as well as in developing bioinformatics to efficiently and effectively exploit the data.
Chun, who is a trained taxonomist, reminded the workshop participants that the traditional concept of species is “groups of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups” (Mayr, 1942). But in the bacterial world, this definition falls short because there is no “sex” or “breeding,” per se. Instead, bacteria may exchange genetic information through lateral transmission both within species and among different species, allowing for high genetic diversity. For bacteria the fundamental concept of a species is actually based on how similarity between strains is measured. Bacte-