Lineage-specific evolution in Listeria monocytogenes detected by analysis of a panel of Swiss isolates from food and human origin

Listeria monocytogenes is the causative agent of Listeriosis, a foodborne infection and characterised by outbreaks with high mortality. In the past years, outbreak analysis has shifted from PFGE to core genome MLST (cgMLST) and a difference of ≤10 cgMLST alleles was identified as the most appropriate cut off. The cgMLST scheme contributes significantly to the analysis of outbreaks but is less suitable to provide insight in the overall population structure. In the present work, we characterize the differences in the evolution of lineage I and II and the impact they have on the identification of outbreak isolates starting from the genome sequences of a panel of 166 Swiss L. monocytogenes clinical and food isolates. We included in the analysis recently published genomes from Germany (414 isolates) and Holland (128 isolates). Using data of pairwise cgMLST and SNP differences of these 708 isolates, we can clearly identify the genetic diversity associated to outbreaks (≤10 differences), sublineages (≤150 differences) and lineages. The sublineages identified by SNP and cgMLST match the clustering of the PopPUNK software. When broken down for lineages, data show clearly that lineage II has a lower mutation rate within sublineages but a higher diversity between sublineages. Admixture analysis confirms that the increased diversity between sublineages in lineage II is due to horizontal gene transfer and recombination. While our data show that genome evolution is lineage-specific in L. monocytogenes, the cut off for the identification of outbreaks remains identical between both lineages.