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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.

Original publication

DOI

10.7554/eLife.67113

Type

Journal article

Journal

Elife

Publication Date

14/07/2021

Volume

10

Keywords

AMR, epidemiology, genetics, genomics, infectious disease, microbiology, recombination, streptococcus pneumoniae, Anti-Bacterial Agents, DNA Transposable Elements, Drug Resistance, Bacterial, Gene Transfer, Horizontal, Genes, Bacterial, Germany, Humans, Macrolides, Phylogeny, Pneumococcal Vaccines, Serogroup, Serotyping, Streptococcus pneumoniae