Additional file 1 of Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

Additional file 1: Table S1. Overview of isolates in our dataset. Table S2. Genome assembly statistics. Table S3. Accessions for Illumina-ONT hybrid assemblies. Table S4. Disruptions in OmpF/OmpK35 porin gene. Table S5. Disruptions in OmpC/OmpK36 porin gene. Table S6. Genomic location of resistance genes. Table S7. List of genes identified as ESBL or AmpC. Table S8. Read-based identification of carbapenemases in resistant isolates for which no resistance mechanism was found in the assemblies. Table S9. Size of species-specific core-genome alignments. Table S10. 44 multi-species geographic signatures found in a single city. Table S11. Functional annotation of genes present in 44 signatures. Table S12. Prevalence of functional categories across the 44 signatures. Table S13. Differences in the core genome between same-species isolates from the same patient. Table S14. Carbapenemase carrying isolates. Table S15. Cluster of related Klebsiella pneumoniae isolates with double-porin mutations. Table S16. Pairs of closely-related CSE and CRE isolates, where the CRE carried a carbapenemase not found in the CSE. Table S17. Identification of circular plasmids (>2 kb). Table S18. MOB-suite plasmid group predictions. Table S19. Isolates which carry a blaKPC-containing signature. Table S20. Genomic background of instances of Sig5.1-CP and Sig5.6-CP.