TY - JOUR TI - The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci AU - D'Aeth, Joshua C AU - van der Linden, Mark PG AU - McGee, Lesley AU - de Lencastre, Herminia AU - Turner, Paul AU - Song, Jae-Hoon AU - Lo, Stephanie W AU - Gladstone, Rebecca A AU - Sá-Leão, Raquel AU - Ko, Kwan Soo AU - Hanage, William P AU - Breiman, Robert F AU - Beall, Bernard AU - Bentley, Stephen D AU - Croucher, Nicholas J AU - The GPS Consortium A2 - Rainey, Paul B A2 - Soldati-Favre, Dominique A2 - Falush, Daniel A2 - Kilian, Mogens VL - 10 PY - 2021 DA - 2021/07/14 SP - e67113 C1 - eLife 2021;10:e67113 DO - 10.7554/eLife.67113 UR - https://doi.org/10.7554/eLife.67113 AB - Multidrug-resistant Streptococcus pneumoniae emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition of gene cassettes. Both occurred in the otherwise contrasting histories of the antibiotic-resistant S. pneumoniae lineages PMEN3 and PMEN9. A single PMEN3 clade spread globally, evading vaccine-induced immunity through frequent serotype switching, whereas locally circulating PMEN9 clades independently gained resistance. Both lineages repeatedly integrated Tn916-type and Tn1207.1-type elements, conferring tetracycline and macrolide resistance, respectively, through homologous recombination importing sequences originating in other species. A species-wide dataset found over 100 instances of such interspecific acquisitions of resistance cassettes and flanking homologous arms. Phylodynamic analysis of the most commonly sampled Tn1207.1-type insertion in PMEN9, originating from a commensal and disrupting a competence gene, suggested its expansion across Germany was driven by a high ratio of macrolide-to-β-lactam consumption. Hence, selection from antibiotic consumption was sufficient for these atypically large recombinations to overcome species boundaries across the pneumococcal chromosome. KW - streptococcus pneumoniae KW - AMR KW - recombination KW - genomics KW - epidemiology JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -