Insertion of a novel DNA sequence, 1S1186, upstream of the silent carbapenemase gene cfiA, promotes expression of carbapenem resistance in clinical isolates of Bacteroides fragilis

Abstract

A small number of isolates of Bacteroides fragilis, an anaerobic pathogen of the human intestinal flora, carries a copy (or copies) of the carbapenemresistance gene, cfiA, which may be silent or expressed. We have studied the mechanism of activation of the frequently silent gene in in vitro-selected mutants and in clinical isolates. In both types of strains, activation was observed as the consequence of the insertion, at several possible sites, of a novel 1.3 kb insertion sequence, IS1186, immediately upstream of the carbapenemase gene. IS1186 has two open reading frames, on opposite strands, with coding capacities for a 41.2 kDa (ORF1) and a 22.5kDa (ORF2) protein. The 41.2kDa protein has homology with some proteins predicted from open reading frames of IS elements or DNA direct repeats of aerobic, but not anaerobic, Gram-negative bacteria. Upon insertion, transcription of cfiA was found to be driven from a promoter identified on the right end of IS1186. In one instance, insertion occurred into the putative ribosome-binding site of cfiA, leaving intact the tetranucleotide AGAA which is concluded to be a fully functional ribosome-binding site. Between 3 and 14 copies of IS1186 were detected per genome and the element was found, within the species B. fragilis, almost exclusively in the subgroup carrying the cifA gene.