title: Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone.
abstract: BACKGROUND
  Pneumococcal β-lactam resistance was first detected in Iceland in the late 1980s, and subsequently peaked at almost 25% of clinical isolates in the mid-1990s largely due to the spread of the internationally-disseminated multidrug-resistant PMEN2 (or Spain6B-2) clone of Streptococcus pneumoniae.
  
  
  RESULTS
  Whole genome sequencing of an international collection of 189 isolates estimated that PMEN2 emerged around the late 1960s, developing resistance through multiple homologous recombinations and the acquisition of a Tn5253-type integrative and conjugative element (ICE). Two distinct clades entered Iceland in the 1980s, one of which had acquired a macrolide resistance cassette and was estimated to have risen sharply in its prevalence by coalescent analysis. Transmission within the island appeared to mainly emanate from Reykjavík and the Southern Peninsular, with evolution of the bacteria effectively clonal, mainly due to a prophage disrupting a gene necessary for genetic transformation in many isolates. A subsequent decline in PMEN2's prevalence in Iceland coincided with a nationwide campaign that reduced dispensing of antibiotics to children in an attempt to limit its spread. Specific mutations causing inactivation or loss of ICE-borne resistance genes were identified from the genome sequences of isolates that reverted to drug susceptible phenotypes around this time. Phylogenetic analysis revealed some of these occurred on multiple occasions in parallel, suggesting they may have been at least temporarily advantageous. However, alteration of 'core' sequences associated with resistance was precluded by the absence of any substantial homologous recombination events.
  
  
  CONCLUSIONS
  PMEN2's clonal evolution was successful over the short-term in a limited geographical region, but its inability to alter major antigens or 'core' gene sequences associated with resistance may have prevented persistence over longer timespans.
authors: Nicholas J
authors: NJ
authors: Croucher
authors: William P
authors: WP
authors: Hanage
authors: Simon R
authors: SR
authors: Harris
authors: Lesley
authors: L
authors: McGee
authors: Mark
authors: M
authors: van der Linden
authors: Herminia
authors: H
authors: de Lencastre
authors: Raquel
authors: R
authors: Sá-Leão
authors: Jae-Hoon
authors: JH
authors: Song
authors: Kwan Soo
authors: KS
authors: Ko
authors: Bernard
authors: B
authors: Beall
authors: Keith P
authors: KP
authors: Klugman
authors: Julian
authors: J
authors: Parkhill
authors: Alexander
authors: A
authors: Tomasz
authors: Karl G
authors: KG
authors: Kristinsson
authors: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. sdb@sanger.ac.uk.
authors: Stephen D
authors: SD
authors: Bentley
mesh_terms: D001483:Base Sequence; D002702:Chloramphenicol Resistance / Q000235:genetics; D002999:Clone Cells; D004196:Disease Outbreaks; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D006801:Humans; D007055:Iceland / Q000453:epidemiology; D016013:Likelihood Functions; D008826:Microbial Sensitivity Tests; D010802:Phylogeny; D011995:Recombination, Genetic; D013290:Streptococcal Infections / Q000453:epidemiology / Q000235:genetics / Q000382:microbiology* / Q000635:transmission*; D013296:Streptococcus pneumoniae / Q000235:genetics* / Q000302:isolation & purification; D013997:Time Factors