A genomic island of an extraintestinal pathogenic Escherichia coli Strain enables the metabolism of fructooligosaccharides, which improves intestinal colonization

Abstract

Prebiotics such as fructooligosaccharides (FOS) are increasingly being used in some countries for improving human and animal health and as an alternative to antibiotic growth promoters in animals, with various degrees of success. It has been observed that FOS stimulate the proliferation of probiotic bacteria and, at the same time, decrease the population of bacteria associated with disease. This observation assumes that pathogenic bacteria do not metabolize FOS and, therefore, lose their competitive advantage over beneficial bacteria. Here we present evidence that some pathogenic Escherichia coli strains can metabolize FOS and show that this property helps the bacterium colonize the intestine. These findings highlight the potential risk that a high level of prebiotic usage could lead to the emergence of well-adapted pathogenic strains that metabolize prebiotic substances.

FIG. 1.

Gene organization of the fos locus of E. coli strain BEN2908. The locus comprises fosR (aec47, putative regulator), fosT (aec46, putative sugar transporter), fosGH1 (aec45, putative glycoside hydrolase), fosX (aec44, unknown function), fosGH2 (aec43, putative glycoside hydrolase), fosY (aec42, unknown function), and fosK (aec41, putative fructose kinase).

FIG. 2.

The metabolism of scFOS is mediated by locus 2 of AGI-3. E. coli strains BEN2908 (solid black curve) and BEN2908Δaec46 (dashed gray curve) (A) or MG1655 (dashed gray curve) and MG1655/pGEMT::aec41-47 (solid black curve) (B) were grown in M9 medium containing 0.5% scFOS at 37°C with agitation.

FIG. 3.

Preferential use of the shorter-chain FOS. E. coli strain BEN2908 was grown in M9 medium containing either 5 mM GF2 (green curve), 5 mM GF3 (purple curve), or 5 mM GF4 (red curve) at 37°C with agitation.

FIG. 4.

Competition between E. coli strains BEN2908 and BEN2908ΔfosT to colonize the chicken intestine. Axenic chickens (A), SPF chickens (B), or SPF chickens receiving a dietary supplement of 0.5% scFOS in drinking water (C) were fed with strains BEN2908 and BEN2908ΔfosT together (each at 5 × 10⁶ CFU/chicken). The proportion of each strain in animal feces was monitored over time, and CI were calculated. Horizontal bars indicate the geometric means of CI, and diamonds indicate individual CI. Statistical analyses were conducted using the Mann-Whitney U test, measuring the difference between CI in feces samples and in the inoculum. The calculated P values are presented, with values below 0.05 considered significant.

FIG. 5.

Monitoring of chicken intestine colonization by E. coli strain BEN2908 (filled squares) and its mutant derivative BEN2908ΔfosT (open circles). Axenic chickens (A), SPF chickens (B), or SPF chickens receiving a dietary supplement of 0.5% scFOS in drinking water (C) were fed with strains BEN2908 and BEN2908ΔfosT together (each at 5 × 10⁶ CFU/chicken). The presence of each strain in the feces was monitored over time. Bars represent standard errors of the log₁₀ (mean number of CFU/g of feces) for each set of eight chickens.