Microbial Genomics and Pathogen Discovery*

In recent years, our understanding of microbial diversity has grown tremendously as many previously unidentified bacterial, archaeal, and viral species have been discovered and sequenced. In the era of the human microbiome and metagenomics (chapter 15), large-scale DNA sequencing projects and advances in bioinformatics have yielded abundant data regarding human-associated microbes. As human microbiology rapidly expands beyond its past framework of cultured pathogens in the medical microbiology laboratory, opportunities for detection and identification of novel human pathogens associated with infectious diseases abound. In this chapter, we focus on specific or defined sets of pathogens associated with human infections, in contrast to microbial components of disease and microbial ecology. We begin with an overview of historical methodologies, followed by a brief description of the evolution of nucleic acid sequencing technologies. Finally, we describe how microarrays, nucleic acid sequencing technologies, and mass spectrometry are profoundly reshaping strategies aimed at pathogen discovery and identification.