Table A: isolates description.

The thirteen ST-742 isolates are listed with a summary description of their sequencing and the related genomics data available the NCBI GenBank database. Table B: antibiotic resistance profile. The table contains the MIC values for all strains organized by type of antibiotics. The EUCAST or PK/PD interpretations are given by color (RED = resistant, ORANGE = intermediate, GREEN = sensitive). Table C: location of genomic islands and genetic clusters. Results from the three different software tools to predict the genomic locations of mobile elements and secondary metabolites clusters. Table D: list of isolates from NCBI used for the population structure. The genome sequences of the isolates were downloaded from the RefSeq database (release 98). Table E: features of plasmid pP1Bm2009. List of annotated features of plasmid 1 in patient 1 annotated using hmmer and eggNOG with a summary count of genes per COG categories. Table F: features of plasmid pP2Bm2011a. List of annotated features of plasmid 1 in patient 2 annotated using hmmer and eggNOG with a summary count of genes per COG categories and a comparison of COG categories between pP1Bm2009 and pP2Bm2011a. Table G: master list of large structural variations. List of all structural variations identified using the long reads (Nanopore data). Table H: filtered list of large structural variations. The filtering steps are described in the Materials and Methods section. Table I: master list SNPs. List of all SNPs identified when comparing the 13 isolates against P1Bm2009. Table J: regions of high SNPs density. Detailed start and stop positions of the regions displayed on the Figs 5, 6 and 7. Table K: SNPs isolates patient 2. List of SNPs identified when comparing the P2Bm2011b against P2Bm2011a. Table L: List of loci under selection reported in previous studies. This list contains the loci that were highlighted in previous longitudinal studies of B. multivorans infections of patients with cystic fibrosis. For each study, we mention the locus number (as reported), the NCBI protein accession number, whether or not the locus was present in the ST-742 strains, and whether there was a SNP found in the locus for the longitudinal isolates from patient 1. Table M: COG annotation of the genes in high-density SNP regions. Here we list the proteins found in the regions enriched in SNPs (Tables I and J in S1 Tables), functionally annotated with their COG categories. The graphic at the top compares the specific presence of the COG categories in those high-density SNP regions versus the complete genome. (XLSX)