Two Multidrug-Resistant Clinical Isolates of Bacteroides fragilis Carry a Novel Metronidazole Resistance nim Gene ( nimJ )

Abstract

dTwo multidrug-resistant Bacteroides fragilis clinical isolates contain and express a novel nim gene, nimJ, that is not recognized by the "universal" nim primers and can confer increased resistance to metronidazole when introduced into a susceptible strain on a multicopy plasmid. HMW615, an appendiceal isolate, contains at least two copies of nimJ on its genome, while HMW616, an isolate from a patient with sepsis, contains one genomic copy of nimJ. B. fragilis NimJ is phylogenetically closer to Prevotella baroniae NimI and Clostridium botulinum NimA than to the other known Bacteroides Nim proteins. The predicted protein structure of NimJ, based on fold recognition analysis, is consistent with the crystal structures derived for known Nim proteins, and specific amino acid residues important for substrate binding in the active site are conserved. This study demonstrates that the "universal" nim primers will not detect all nim genes with the ability to confer metronidazole resistance, but nimJ alone cannot account for the very high metronidazole MICs of these resistant clinical isolates.

Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing

“…Mechanisms concerning b-lactam/b-lactamase inhibitor combinations have not been fully elucidated, but appear to be dependant on IS element insertion directly upstream of cepA and concomitant membrane modifications such as porin loss [5]. Carbapenem resistance is caused by expression of a metallo-b-lactamase encoded by the cfiA gene, and metronidazole resistance is associated with the presence of the nitroimidazole resistance genes nimA-H and nimJ [4,6]. While ermB, ermF, and ermG genes that encode a macrolideelincomycinestreptogramin (MLS) mechanism are the main causes of clindamycin resistance, msrSA and mefA-mediated macrolideelincosamid resistance, and lincomycin and erythromycin resistance conferred by a linA type gene (linAn2) have also been demonstrated in Bacteroides spp.…”

The Ellis Island Effect

“…Genomes were compared by the sequence comparison feature of the SEED server 9 . Comparisons of known CTns and the BF-HMW 615 genome sequence were analyzed as described earlier 7 . The Double ACT server (http://www.hpa-bioinfotools.org.uk) was used to generate the comparison file with the BLASTN function and a cutoff of 1000–2000.…”

“…BF-HMW615 is resistant to multiple antibiotics, including metronidazole. Our analysis identified a nimJ gene which conferred increased MICs to metronidazole when introduced into a susceptible strain 7 and nimJ is carried on a novel conjugative transposon. We are now reporting the identification of this novel conjugative transposon, CTnHyb (for “hybrid”), which contains genes from Gram-positive bacteria.…”

Anaerobic Infections

“…The most commonly used molecular techniques are PCR amplifications to identify nim genes or cfiA-type metalloβ-lactamases (see below for explanation). A novel nim gene, nimJ, was recently described by our laboratory; it confers increased metronidazole MICs and is not recognized by the universal nim primers [120]. Detection of nim genes was described in 1996 using the universal primers NIM-3 and NIM-5 [116] followed by restriction analysis to identify the specific nim type [117].…”