Inferred growth rates of E. coli strains from patients with IBD and healthy subjects. [A] Inferred growth rates [using iRep [genome replication index]] of E. coli strains from patients with a pouch, CD, UC and healthy subjects. *p <0.05; ***p <0.001; Kruskal–Wallis test. [B] Spearman correlation between iRep and the relative abundance of E. coli in the microbiomes from corresponding metagenomic samples. [C] iRep of E. coli strains from subjects who had used antibiotics in the past month [Abx+] compared with subjects who were antibiotic-free for at least 1 month [Abx-]. [D] iRep of E. coli strains from patients with a pouch who were treated with ciprofloxacin, grouped according to the number of resistant mutations in drug target genes [gyrA and parC]. Zero mutations represent ciprofloxacin-sensitive strains. ‘Abx+ during treatment’ and ‘Abx-’ division define samples from patients taken during antibiotic treatment or in the absence of antibiotics for at least 1 month, respectively. In panels A, C, and D, box plot whiskers mark observations within the 1.5 interquartile range of the upper and lower quartiles. IBD, inflammatory bowel disease; UC, ulcerative colitis; CD, Crohn’s disease.