title: Rapid pneumococcal evolution in response to clinical interventions.
abstract: Epidemiological studies of the naturally transformable bacterial pathogen Streptococcus pneumoniae have previously been confounded by high rates of recombination. Sequencing 240 isolates of the PMEN1 (Spain(23F)-1) multidrug-resistant lineage enabled base substitutions to be distinguished from polymorphisms arising through horizontal sequence transfer. More than 700 recombinations were detected, with genes encoding major antigens frequently affected. Among these were 10 capsule-switching events, one of which accompanied a population shift as vaccine-escape serotype 19A isolates emerged in the USA after the introduction of the conjugate polysaccharide vaccine. The evolution of resistance to fluoroquinolones, rifampicin, and macrolides was observed to occur on multiple occasions. This study details how genomic plasticity within lineages of recombinogenic bacteria can permit adaptation to clinical interventions over remarkably short time scales.
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Croucher
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.forename: Christophe
authors.initials: C
authors.lastname: Fraser
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
authors.forename: John
authors.initials: J
authors.lastname: Burton
authors.forename: Mark
authors.initials: M
authors.lastname: van der Linden
authors.forename: Lesley
authors.initials: L
authors.lastname: McGee
authors.forename: Anne
authors.initials: A
authors.lastname: von Gottberg
authors.forename: Jae Hoon
authors.initials: JH
authors.lastname: Song
authors.forename: Kwan Soo
authors.initials: KS
authors.lastname: Ko
authors.forename: Bruno
authors.initials: B
authors.lastname: Pichon
authors.forename: Stephen
authors.initials: S
authors.lastname: Baker
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Parry
authors.forename: Lotte M
authors.initials: LM
authors.lastname: Lambertsen
authors.forename: Dea
authors.initials: D
authors.lastname: Shahinas
authors.forename: Dylan R
authors.initials: DR
authors.lastname: Pillai
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Mitchell
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
authors.forename: Alexander
authors.initials: A
authors.lastname: Tomasz
authors.forename: Keith P
authors.initials: KP
authors.lastname: Klugman
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: William P
authors.initials: WP
authors.lastname: Hanage
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
mesh_terms: D000222:Adaptation, Physiological; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D000940:Antigenic Variation; D004251:DNA Transposable Elements; D024901:Drug Resistance, Multiple, Bacterial; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D006801:Humans; D017720:Molecular Epidemiology; D010802:Phylogeny; D058974:Phylogeography; D011008:Pneumococcal Infections / Q000188:drug therapy / Q000382:microbiology*; D022242:Pneumococcal Vaccines / Q000276:immunology; D020641:Polymorphism, Single Nucleotide; D039002:Prophages / Q000235:genetics; D011995:Recombination, Genetic; D012641:Selection, Genetic; D012703:Serotyping; D017108:Streptococcus Phages / Q000235:genetics; D013296:Streptococcus pneumoniae / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000276:immunology
chemical_list: D000900:Anti-Bacterial Agents; D004251:DNA Transposable Elements; D022242:Pneumococcal Vaccines