Plasmids plP419 and plP421 from Bacteroides: 5-nitroimidazole resistance genes and their upstream insertion sequence elements

Abstract

The genetic organization of two different 5-nitroimidazole (5-Ni) resistance genes was investigated: nimC and nimD from Bacteroides plasmids plP419 and plP421, respectively. The nimC gene (492 bp) and the nimD gene (495 bp) directed the synthesis of polypeptides with deduced molecular masses of 18.37 kDa and 1848 kDa, respectively. The predicted proteins showed 6 7 4 3 % identity and 78-91 O/ O similarity with the products of two other nimA and nimB genes previously described and could be derived from a common ancestral gene. An insertion sequence element (IS1170) was identified upstream of the nimC gene. IS1170 is 1604 bp in length and is flanked by'imperfect inverted repeats (15 bp). IS1770 is similar to the Bacteroides insertion sequence element IS942 with an identity of 70% a t the nucleotide level. The single copy of IS1170 present on plasmid plP419 is integrated 24 bp upstream of the initiation codon of nimC. Similar genetic organization was found on plasmid plP421. One copy of another insertion sequence (151169) was found 4 bp upstream of the first ATG codon of the nimD gene. This element (1325 bp) shows a strong homology a t the nucleotide level (70% identity) with IS1186 and IS1168 found to be associated with the Bacteroides carbapenem resistance gene cfiA, and the 5-Ni'genes nimA and nimB, respectively. There is strong evidence that, as in the case of the &A gene, the transcription of the four nim genes so far studied is directed by outward-oriented promoters, carried on the right ends of the different insertion sequence elements.

Structural Basis of 5-Nitroimidazole Antibiotic Resistance

“…Nim gene-based resistance has so far only been encountered in the Bacteroides (17)(18)(19)(20). Nevertheless, the mobile nature of Nim genes, localized on mobilizable plasmids (17)(18)(19)(20), poses a real threat of 5-Ni drug resistance spreading among bacteria occupying close niches. Bacteroides and Helicobacter are indeed exposed to an increasing selection pressure toward resistance against 5-Ni drugs, and gene transfer from these species is not theoretically impossible.…”

“…pIP417 (NimA), pIP419 (NimC), and pIP421 (NimD) (17)(18)(19)(20). A fifth Nim gene, NimE, was discovered that confers resistance to high MTR concentrations in strains from Bacteroides thetaiotaomicron, B. fragilis, and Bacteroides ovatus (21).…”

Bacteroides: the Good, the Bad, and the Nitty-Gritty

“…This is the case for the IS-borne promoters that can be found upstream of the cfiA or ccrA gene (189), macrolide resistance genes (205), and metronidazole resistance nim genes (259,278).…”

“…The nim gene can be "silent" unless activated by IS elements (111). Four nim genes (nimA to -D) can occur in all Bacteroides species; each of these genes is associated with a distinct mobile genetic element, and each also has a specific activating IS (111,148,211,278). The presence of any one of these genes can be detected by PCR (279).…”

Multidrug-resistant Bacteroides fragilis group on the rise in Europe?

“…The cfiA gene could not be detected on these plasmids by Southern hybridization, so its location was chromosomal, as is usually the case for cfiA genes. The analysis of the metronidazole resistance mechanism was done by PCR sequencing and Southern blotting (Só ki et al, 2006), and revealed a nim plasmid, pIP421 (Trinh et al, 1995), in this strain by examination of molecular size (7.3 kb), nim gene type (nimD), the IS element activating this nimD gene (IS1169), and Southern blotting of its EcoRI and EcoRV restriction fragments. Further molecular analysis detected the ermF, tetQ and tetX variant resistance genes in this strain (Bartha et al, 2011).…”