David M. Gordon

Summary We previously characterized the genetic diversity of Escherichia coli strains isolated from septic tanks in the Canberra region, Australia. In this study, we used repetitive element palindromic (REP) PCR fingerprinting to identify dominant REP‐types belonging to phylogroups A and B1 strains across septic tanks. Subsequently, 76 E . coli strains were selected for whole‐genome sequencing and phenotype microarrays. Comparative genome analysis was performed to compare septic tank E . coli genomes with a collection of 433 E . coli isolates from different hosts and freshwater. Clonal complexes (CCs) 10 ( n = 15) and 399 ( n = 10) along with sequence type (ST) 401 ( n = 9) were the common lineages in septic tanks. CC10 strains have been detected from animal hosts and freshwater, whereas CC399 and ST401 strains appeared to be associated with septic tanks as they were uncommon in isolates from other sources. Comparative genome analysis revealed that CC399 and ST401 were genetically distinct from other isolates and carried an abundance of niche‐specific traits involved in environmental adaptation. These strains also showed distinct metabolic characteristics, such as the ability to utilize pectin, which may provide a fitness advantage under nutrient‐limited conditions. The results of this study characterized the adaptive mechanisms allowing E . coli to persist in wastewater.