The impact of fixed recombination events was quantified by applying the ClonalFrame algorithm on the Lp genome alignment (intraspecific alignment; 1,028,806 bp). We detected recombination events on all branches of the clonal genealogy (Fig. 4). ClonalFrame estimated two values, ρ/θ and r/m, where the former measures the frequency of occurrence of recombination relative to mutation and the latter how important the effect of recombination is in genetic diversification relative to mutation. The ρ/θ was 0.124 (95% credibility interval of 0.177–0.133), implying that fixed recombination events have transferred relatively large portions of the genome between strains and/or serogroups. The r/m was 2.174 (95% credibility interval of 2.092–2.241), demonstrating that recombination events have played a larger role in shaping Lp genomes. The importance of recombination in Lp is supported by a study where 69 Lp1 genome sequenced samples isolated over 11 years in Spain showed that 98% of SNP diversity between strains was explained by only 16 recombination events18. The r/m value reported between these strains was 47.93.