title: Within-host evolution of bacterial pathogens.
abstract: Whole-genome sequencing has opened the way for investigating the dynamics and genomic evolution of bacterial pathogens during the colonization and infection of humans. The application of this technology to the longitudinal study of adaptation in an infected host--in particular, the evolution of drug resistance and host adaptation in patients who are chronically infected with opportunistic pathogens--has revealed remarkable patterns of convergent evolution, suggestive of an inherent repeatability of evolution. In this Review, we describe how these studies have advanced our understanding of the mechanisms and principles of within-host genome evolution, and we consider the consequences of findings such as a potent adaptive potential for pathogenicity. Finally, we discuss the possibility that genomics may be used in the future to predict the clinical progression of bacterial infections and to suggest the best option for treatment.
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College, London W2 1PG, UK.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.affiliation: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
authors.forename: A Sarah
authors.initials: AS
authors.lastname: Walker
authors.affiliation: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
authors.forename: Tim E
authors.initials: TE
authors.lastname: Peto
authors.affiliation: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.|National Infection Service, Public Health England, London SE1 8UG, UK.
authors.forename: Derrick W
authors.initials: DW
authors.lastname: Crook
authors.affiliation: Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.|Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Wilson
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001419:Bacteria / Q000235:genetics* / Q000254:growth & development; D001424:Bacterial Infections / Q000188:drug therapy / Q000382:microbiology*; D024881:Drug Resistance, Bacterial; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions / Q000235:genetics*; D006801:Humans
chemical_list: D000900:Anti-Bacterial Agents