Plasmid Analysis

Plasmid reconstruction from WGS data was performed by PLACNETw method (Vielva et al., 2017). In PLACNETw representation, most plasmids can be recognized by their replication initiation proteins (RIPs) and/or RELaxase proteins (REL), both of them considered as plasmid markers. Incompatibility groups (Inc) and pMLST subtypes were in silico determined with PlasmidFinder and pMLST (Carattoli et al., 2014), respectively, via the CGE online services.³ Besides, reconstructed plasmids were subtyped according to the exact relaxase family subtype by phylogenetic comparison with previously defined relaxases subfamilies (Alvarado et al., 2012). Reconstructed plasmids and references belonging to the same Inc groups were compared by using BRIG (Alikhan et al., 2011) and EasyFig tools (Sullivan et al., 2011). All reference plasmids used in this study were recovered from NCBI database⁴ (Supplementary Table S3).