Table 1: Description of sampling sites and number of positive samples in each site.

Table 2: Number of positive samples and presumptive ESBL-E. coli, calculations of CFUs and final number of confirmed ESBL-E. coli. Table 3: Metadata for all 315 collected samples. Table 4: Metadata for all 564 sequenced ESBL-producing E. coli isolates. Table 5.1: Significance of differences in MLST-STs diversity between sample types. Table 5.2: Significance of differences in MLST-STs diversity between regions (A) and differences of ST composition between regions (B) Table 5.3: Significance of differences in MLST-STs diversity between aquatic environments. Table 5.4: Significance of differences in phylogroups diversity between sample types based on richness (A) and differences of phylogroups composition between sample types (B) Table 5.5: Significance of differences in phylogroups diversity between regions based on richness (A) and Shannon index (B) and differences of phylogroups composition between regions (C) Table 6: Prevalence of phylogroups in all three sample types: sediment, water and WWTP. Table 7: ENA submission data for each isolate. (XLSX)