FIG 2.

Characteristics of samples where DAEC was most likely the causative agent. (A) Estimated metagenomic abundance of the reference commensal E. coli (strain HS, in light red) and the DAEC isolate (in red) recovered from the sample, along with the ELISA-based detection of rotavirus and bioinformatic detection of Adenovirus_F for each sample analyzed (rows). Samples where high-quality E. coli MAGs were recovered from the corresponding metagenome are denoted by a star. (B) Presence (detection) of four hallmark virulence factors in the metagenome, including the DAEC marker gene (afaB) and three enterotoxins, i.e., the hemolysin subunit B (hlyB), the heat-labile enterotoxin (eltA), and the secreted autotransporter toxin (sat). (C) Estimated E. coli intrapopulation diversity measured by ANIr of reads against the reference commensal strain HS (light orange) and the isolate obtained from the sample (dark brown). To avoid any potential bias by low in situ abundance, only samples where the average sequence depth of the reference genome was ≥1× were evaluated for ANIr. (D) Number of isolates that originated from cases of diarrhea (in red) versus control samples (in green) and were assigned in the same core-genome-based clonal complex as the isolate (epidemiology).