DYNAMICS OF ANTIBIOTIC RESISTANCE IN THE HUMAN GUT MICROBIOME REVEALED BY LONGITUDINAL METAGENOMICS OF ANTIBIOTIC-TREATED PATIENTS

Inflammatory bowel diseases (IBD) are complex diseases, derived from the interaction of human genetics, environmental, immunological and microbial factors. The importance of the microbiota in IBD has been suggested by multiple clinical observations and experimental models.
Here we studied patients with complicated ulcerative colitis who underwent complete large bowel resection with the reconstruction of a pouch from the normal small bowel. In many of these patients, de-novo inflammation of the pouch (pouchitis) develops after surgery. Pouchitis has multiple similarities with Crohn`s disease. Antibiotics, mainly fluoroquinolones (FQ), are an effective first line therapy for pouchitis, however, patients may become antibiotic-dependent.
By applying shotgun metagenomics to 230 faecal samples obtained longitudinally from 50 patients with pouchitis we explored the effects of long-term antibiotic treatment on the microbiome dynamics and on the emergence of resistance.
The most common FQ-resistance mechanism we observed was point mutations in chromosomal drug target genes. A high fraction of the microbial community was FQ-resistant and dominated by resistant species from Enterobacterales and Lactobacillales. Furthermore, according to our data chronic antibiotic treatment increases the probability that species will acquire multidrug resistance plasmids. Strain-level analysis revealed that Escherichia coli strains develop resistance independently in different lineages in-patient after several weeks of antibiotic administration and can persist for 3-8 months following treatment discontinuation. The persistence of antibiotic-resistant genotypes was associated with longer treatment periods.
Prolonged antibiotic treatment was successful in elimination of putatively pro-inflammatory species, but only moderately decreased bacterial load, implying that resistant bacteria can reach very high abundance and compensate for the loss of sensitive species in terms of biomass in treated patients.