Additional file 1. This DOCX document contains supplementary notes and supplementary figures S1 to S8. Fig. S1. Pan-genome growth curve fitting. Fig. S2. Hypothetical genes involve in multiple antibiotic resistance. Fig. S3. GO enrichment analysis of meropenem resistance associated genes. Fig. S4. GO term similarity score distribution of (A) all gene pairs; (B) cumulative distribution of core-core and accessory-accessory edges. Fig. S5. The distribution of individual networks (including STRING, RefSeq, ESKAPE, and Domain-sharing networks) associated with log-likelihood scores (LLS; with GO term similarity > 0.6). Fig. S6. (A) Edge and (B) node contribution of each network (C) Unique nodes are all accessory genes. Fig. S7. Power-law distribution and component size of all networks. Fig. S8. Genome statistics of the excluded and included genomes.