Fig. 2

Hi-C links between the clusters and plasmid markers, integrons, and ARGs, identified in the WW sample and affiliated with Alpha- Beta-, Gamma-, and Delta-Proteobacteria. Each tip of the phylogenetic tree represents a cluster. For clarity only clusters having a contact with plasmid markers, integrons, or ARGs are shown (results showing all clusters are presented in Figs. S6 and S7). The presence or absence of a link is shown on the heatmap to the right of the tree, and the color shading represents the intensity of the normalized Hi-C link signals. a Aeromonadaceae were identified as a natural reservoir of ARGs. b Clusters affiliated with the genus Acinetobacter showed high Hi-C linkage to ARGs conferring resistance to aminoglycosides, beta-lactams, tetracycline, phenicol, and macrolides. c Most plasmids detected belonged to clusters related to Enterobacteriaceae. d As expected, BHR plasmids were linked to clusters with phylogenetic affiliations broader than the NHR plasmids. e Class 2 and 3 integrons were associated with clusters affiliated with the Neisseriaceae. The arrow indicates a cluster in Comamonadaceae which had a strong link to an IncP-1β plasmid