Zamudio et al Environmental Microbiology 2020 SUPPELMENTARY DATA 10.1111/1462-2920.15111

Zamudio R, RD Haigh, JD Ralph, M De Ste Croix, T Tasara, K Zurfluh, MJ Kwun, AD Millard, SD Bentley, NJ Croucher, R Stephan, MR Oggioni. 2020. Lineage specific evolution and gene flow in Listeria monocytogenes is independent of bacteriophages. Environmental Microbiology. 2020 doi 10.1111/1462-2920.15111 Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracing of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage specific characteristics call for a more detailed understanding of evolution. In our work we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes.