Tetracyclines serve as broad-spectrum antibiotics to treat bacterial infections. The discovery of new tetracycline resistance genes has led to new questions about the underlying mechanisms of resistance, gene transfer, and their relevance to human health. We tracked changes in the abundance of a 55-kbp conjugative transposon (CTn214) carrying
tetQ,
a tetracycline resistance gene, within a
Bacteroides fragilis
metagenome-assembled genome derived from shotgun sequencing of microbial DNA extracted from the ileal pouch of a patient with ulcerative colitis. The mapping of metagenomic reads to CTn214 revealed the multi-copy nature of a 17,044-nt region containing
tetQ
in samples collected during inflammation and uninflamed visits.
B. fragilis
cultivars isolated from the same patient during periods of inflammation harbored CTn214 integrated into the chromosome or both a circular, multi-copy, extrachromosomal region of the CTn214 containing
tetQ
and the corresponding integrated form. The tetracycline-dependent mechanism for the transmission of CTn214 is nearly identical to a common conjugative transposon found in the genome of
B. fragilis
(CTnDOT), but the autonomously amplified nature of a circular 17,044-nt region of CTn214 that codes for
tetQ
and the integration of the same sequence in the linear chromosome within the same cell is a novel observation. Genome and transcriptome sequencing of
B. fragilis
cultivars grown under different concentrations of tetracycline and ciprofloxacin indicates that
tetQ
in strains containing the circular form remains actively expressed regardless of treatment, while the expression of
tetQ
in strains containing the linear form increases only in the presence of tetracycline.
IMPORTANCE
The exchange of antibiotic production and resistance genes between microorganisms can lead to the emergence of new pathogens. In this study, short-read mapping of metagenomic samples taken over time from the illeal pouch of a patient with ulcerative colitis to a
Bacteroides fragilis
metagenome-assembled genome revealed two distinct genomic arrangements of a novel conjugative transposon, CTn214, that encodes tetracycline resistance. The autonomous amplification of a plasmid-like circular form from CTn214 that includes
tetQ
potentially provides consistent ribosome protection against tetracycline. This mode of antibiotic resistance offers a novel mechanism for understanding the emergence of pathobionts like
B. fragilis
and their persistence for extended periods of time in patients with inflammatory bowel disease.