Characterization of the effects of sub-inhibitory antibiotic exposure on phage and colicin induction in a panel of Escherichia coli strains sampled from the adult and infant human gut

The aim of our study was to investigate strain-level variation in prophage induction for a panel of naturally occurring E. coli isolates (n =16) from the healthy adult and infant gut in response to diverse antibiotics representing 12 classes. This group of E. coli included 7 spontaneous phage induction phenotypes. First, we used whole genome sequencing (WGS) and bioinformatic analysis to characterize the number and diversity of phages associated with each isolate. We then assessed in vitro variation in prophage induction in response to different antibiotics by exposing strains to sub-inhibitory concentrations of commonly used antibiotics (of human and veterinary medicine) estimating phages using soft-agar overlay assays. In addition to phage induction, certain antibiotics were identified as potent inducers of colicins, which was verified using additional genetic and phenotypic analysis. Finally, detailed genetic characterization revealed the presence of diverse virulence related traits in these strains isolated from asymptomatic, healthy human hosts.