title: Bacterial genomics in infectious disease and the clinical pathology laboratory.
abstract: BACKGROUND
  Throughout history, technologic advancements have fueled the engine of innovation, which, in turn, has driven discovery. Accordingly, recent advancements in DNA sequencing technology are revolutionizing bacterial genomics.
  
  
  OBJECTIVE
  To review important developments from the literature. The current state of bacterial genomics, with an emphasis on human pathogens and the clinical pathology laboratory, will be discussed.
  
  
  METHODS
  A comprehensive review was performed of the relevant literature indexed in PubMed (National Library of Medicine) and referenced medical texts.
  
  
  CONCLUSIONS
  Many important discoveries bearing on infectious disease research and pathology laboratory practice have been achieved through whole-genome sequencing strategies. Bacterial genomics has improved our understanding of molecular pathogenesis, host-pathogen interactions, and antibiotic-resistance mechanisms. Bacterial genomics has also facilitated the study of population structures, epidemics and outbreaks, and newly identified pathogens. Many opportunities now exist for clinical pathologists to contribute to bacterial genomics, including in the design of new diagnostic tests, therapeutic agents, and vaccines.
authors.affiliation: Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX 77030, USA. RJOlsen@tmhs.org
authors.forename: Randall J
authors.initials: RJ
authors.lastname: Olsen
authors.forename: S Wesley
authors.initials: SW
authors.lastname: Long
authors.forename: James M
authors.initials: JM
authors.lastname: Musser
mesh_terms: D001419:Bacteria / Q000145:classification / Q000187:drug effects / Q000235:genetics / Q000821:virology; D001424:Bacterial Infections / Q000453:epidemiology / Q000382:microbiology*; D004196:Disease Outbreaks; D024881:Drug Resistance, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D023281:Genomics / Q000639:trends; D006801:Humans; D007753:Laboratories / Q000639:trends; D010338:Pathology, Clinical / Q000639:trends; D010802:Phylogeny; D014774:Virulence / Q000235:genetics