High-throughput sequencing in the population analysis of bacterial pathogens of humans.
High-throughput nucleotide sequence determination technologies present new opportunities for studies of bacterial pathogens by enabling the accumulation of large volumes of biodiversity information from isolate collections. Population studies, which combine these data with epidemiological, phylogenetic, and evolutionary concepts, provide insights into the behaviour of pathogens that are unavailable from other approaches as they address questions of relevance to pathogenesis from the perspective of the infectious organism rather from that of the host. Hypothesis-driven analyses applied to these data permit the determination of microbial population diversity and structure, the identification of the mechanisms of genetic change in bacterial populations, and the generation of models of pathogen evolution. The nucleotide sequence-based population studies performed to date demonstrate a spectrum of nucleotide sequence diversity, population structure, and evolutionary mechanisms among pathogenic bacteria. The rapid development of nucleotide sequence determination and analysis techniques provides the tools necessary for the prosecution of population studies on an increasing number of bacterial pathogens.