Science
28 January 2011 vol 331, issue 6016, pages 365-496
http://www.sciencemag.org/current.dtl

Research Articles
Rapid Pneumococcal Evolution in Response to Clinical Interventions

Nicholas J. Croucher, Simon R. Harris, Christophe Fraser, Michael A. Quail, John Burton, Mark van der Linden, Lesley McGee, Anne von Gottberg, Jae Hoon Song, Kwan Soo Ko, Bruno Pichon, Stephen Baker, Christopher M. Parry, Lotte M. Lambertsen, Dea Shahinas, Dylan R. Pillai, Timothy J. Mitchell, Gordon Dougan, Alexander Tomasz, Keith P. Klugman, Julian Parkhill, William P. Hanage, and Stephen D. Bentley
Science 28 January 2011: 430-434.[DO

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 (Spain23F-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.