Description and evolution of a nimB gene-coding, composite mobilizable transposon, MTnBf8, of Bacteroides fragilis

Abstract

Background In Bacteroides strains, metronidazole resistance is encoded mainly by the so-called nim genes, which are usually carried on plasmids; however, chromosomal presence is also known (e.g., nimB). Usually, the nim genes are activated by insertion sequence (IS) elements, conferring resistance. Molecular epidemiological observations predict that this configuration most likely arose before the formation of the best-known carrier mobile genetic elements. Objective To determine the nimB genetic element and study its evolution. Methods To fulfill the goals, the whole-genome sequence of B. fragilis BF8, inverse PCRs, and bioinformatic analyses were used. Results A novel mobilizable transposon, MTnBf8, is described, with an integrated part, TnNimB1, that carries the chromosomal nimB gene. Cassettes similar to TnNimB1 were found in Bacteroides-related species in fecal metagenomes, but these species did not harbor IS1168. In inverse PCR, the excised intermediates of MTnBf8 and TnNimB1 were detected, thereby confirming their mobility. In alignments of nucleotide and protein sequences, the existence of the TnNimBs and at least three groups of integrative elements of Bacteroides could be confirmed, and a scheme for the emergence of different nimB-carrying elements was drawn. Conclusion The data presented here could explain the above-mentioned emergence of MTnBf8/TnNimB1 and the IS-nimB configurations and their expected spread.