{"doi":"10.7554/elife.67113","title":"The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci","abstract":"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 Tn 916 -type and Tn 1207.1 -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 Tn 1207.1 -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.","journal":"eLife","year":2021,"id":162753,"datarank":0.9820182224814087,"base_score":3.828641396489095,"endowment":3.828641396489095,"self_citation_contribution":0.5742962094733643,"citation_network_contribution":0.40772201300804434,"self_endowment_contribution":0.5742962094733643,"citer_contribution":0.40772201300804434,"corpus_percentile":null,"corpus_rank":null,"citation_count":45,"citer_count":17,"citers_with_citation_signal":13,"citers_with_endowment":13,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9316,"is_data_producer":true,"deposit_databanks":{"figshare":["10.6084/m9.figshare.c.5306462.v1"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":681179,"name":"Mark PG van der Linden","orcid":null,"position":1,"is_corresponding":false},{"id":228835,"name":"Lesley McGee","orcid":"0000-0001-8214-921X","position":2,"is_corresponding":false},{"id":681180,"name":"Hermı́nia de Lencastre","orcid":null,"position":3,"is_corresponding":false},{"id":228840,"name":"Paul Turner","orcid":"0000-0002-1013-7815","position":4,"is_corresponding":false},{"id":681181,"name":"Jae-Hoon Song","orcid":null,"position":5,"is_corresponding":false},{"id":228838,"name":"Stephanie W. 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