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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.

Original publication




Journal article


Science (New York, N.Y.)

Publication Date





430 - 434


The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.


Humans, Streptococcus pneumoniae, Prophages, Streptococcus Phages, Pneumococcal Infections, DNA Transposable Elements, Pneumococcal Vaccines, Anti-Bacterial Agents, Serotyping, Adaptation, Physiological, Evolution, Molecular, Phylogeny, Drug Resistance, Multiple, Bacterial, Antigenic Variation, Recombination, Genetic, Polymorphism, Single Nucleotide, Genome, Bacterial, Selection, Genetic, Molecular Epidemiology, Phylogeography