Additional file 10 of High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria
Creators: name: Che, You
name: Xu, Xiaoqing
name: Yang, Yu
name: Břinda, Karel
name: Hanage, William
name: Yang, Chao
name: Zhang, Tong
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Additional file 10: Supplementary Figure 1. The schematic view of the genetic constitution of all the identified conjugative plasmids using Plascad. Supplementary Figure 2. Differences in plasmid composition among WWTPs-associated MDR isolates. a, Pairwise similarity of plasmid composition (measured by Jaccard index). b, Jaccard index frequency distribution (including all Jaccard similarity: 0-1). c, Zoom view of Jaccard index (Jaccard similarity above 0) frequency distribution. Supplementary Figure 3. Phylogeny of a total of 623 Escherichia flexneri (WWTPs: 37; Public: 586) based on core genome SNPs. Supplementary Figure 4. Distinct plasmid profiles between WWTPs-associated isolates (a: E. flexneri; b: K. pneumoniae) and their closet human/anima-associated relatives in the public database. Supplementary Figure 5, a, Bipartite network of potential horizontal transfer of ARGs among plasmids. Five major plasmid clusters are indicated by white dotted circles with cluster numbers (1-5), which match the five lineages identified in Fig. 5. The most widely transferred ARG cluster (i.e., aph(3’)-I, blaTEM-1, floR, and tetA) is highlighted by vivid cyan dotted circle in the center of the network. b, Global distribution of the ARG clusters. The size of each node indicates the number of plasmids carrying the corresponding ARG clusters, and the colored lines denote the corresponding clusters. Pie charts are plotted showing the summary of all the plasmids involved. Supplementary Figure 6. Potential horizontal transfer of ARG clusters conferring resistance to four antibiotics across diverse chromosome backgrounds (25 in total) and ecological barriers. a, Global spread of the ARG clusters. The size of each node indicates the number of bacterial chromosomes carrying the corresponding ARG clusters, and the colored lines denote the corresponding clusters. b, Maximum likelihood phylogenetic analysis of a total of 25 genomes (WWTPs: 8; Public: 27) carrying the shared ARGs clusters. The colored names denote the corresponding ARG clusters. Supplementary Figure 7. ISs play a critical role in expanding the transfer range of ARGs. Supplementary Figure 8. VFs are closely associated with ISs in plasmids. a, Genetic maps for the co-localized hypervirulence determinants (iuc and iro loci). b, Plasmids with only iuc loci. c, Plasmids with mrk loci. Genes that make up all the VFs are highlighted with red arrows. ISs and ARGs are indicated (IS1, IS2, ISKpn28, IS3, and IS26 are specified and other ISs are colored green). MDR-hypervirulent plasmids are highlighted with dark pink asterisk on the left. Grey shading indicates homology blocks sharing between different plasmids. Supplementary Figure 9. Mosaic plots showing the relationship between toxin-antitoxin systems, ARGs and categories of plasmids by Fisher’s exact test. Supplementary Figure 10. ISs play an important role for plasmid evolution by maintaining the plasticity necessary to balance the cost of plasmid maintenance.