Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics

The development of next-generation sequencing as a cost-effective technology has facilitated the analysis of bacterial population structure at a whole-genome level and at scale. From these data, phylogenic trees have been constructed that define population structures at a local, national, and global level, providing a framework for genetic analysis. Although still at an early stage, these approaches have yielded progress in several areas, including pathogen transmission mapping, the genetics of niche colonization and host adaptation, as well as gene-to-phenotype association studies. Antibiotic resistance has proven to be a major challenge in the early 21st century, and phylogenetic analyses have uncovered the dramatic effect that the use of antibiotics has had on shaping bacterial population structures. An update on insights into bacterial evolution from comparative genomics is provided in this review. The growth of next-generation sequencing has facilitated the analysis of bacterial population structures at a local, national, and global level. Here, Klemm and Dougan review how the burgeoning field of bacterial phylogenomics is providing insights into many aspects of pathogen biology, including transmission, niche colonization, and host adaptation.