Fig. 4

Strain-level signatures of E. coli EBI matches in the gut. A Cladogram of all E. coli reference genomes for which a related strain was identified in at least one E. coli EBI case or E. coli-colonized control. Color strip denotes STs identified in at least three infants (the remainder are grouped as “other”). The bar chart indicates the frequency at which each reference genome was identified for E. coli EBI cases with a matching strain in their gut (match), those without a matching strain identified (non-match), or E. coli-colonized control infants. B Relative abundance of E. coli phylogroup B2 between groups as in A. C Virulence factor (VF) genes encoded by Enterobacteriaceae associated with E. coli EBI matches compared to E. coli-colonized controls as determined through generalized linear mixed effect models. Points are sized by their BH-adjusted p value (q) and colored by their VF functional category