title: Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics.
abstract: 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 21(st) 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.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Klemm
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. Electronic address: gd1@sanger.ac.uk.
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods; D006801:Humans; D010802:Phylogeny
chemical_list: D004269:DNA, Bacterial