Fig. 4

Enterobacteriaceae clone residency using the average estimate. All Enterobacteriaceae clones were plotted according to their log 10 transformed residence time in days (a). Clones were grouped according their phylogroup (E. coli) or into an “Other” category if ≤6 representative isolates were observed (Other = B2.1, n = 4; B2.2, n = 4; D, n = 6; E, n = 4; Cryptic Escherichia clade IV, n = 1; C. freundii, n = 1; K. pneumoniae, n = 1). Groups had significantly different residence time (ANOVA, F = 3.729, p = 0.0037) and following correction for multiple comparisons (Holm-Sidak’s test), groups A and B2.3 resided significantly longer than A.1 (p = 0.0338, p = 0.0171, respectively). Red dots identify clones that were present at the outset of the study, throughout the entire study period, or at the end of the study. These clones were presumed to have colonized participants beyond the study period. Contingency table analysis (Chi-square test) was used to test whether significantly more clones were observed beyond the study period in some groups versus others (b) or whether significantly more resident clones were present (c) among the longest lived phylogroups (A, B2.3, and F) compared to other groups. Both comparisons were significant and p-values are shown in each panel