Genomic context of resistance genes within a French clinical MDR Proteus mirabilis: identification of the novel genomic resistance island GIPmi1.

ABSTRACT

Objectives: To determine the location of the antibiotic resistance genes in the MDR Proteus mirabilis PmPHI clinical isolate. Methods: WGS and de novo assembly were performed. BLAST searches were used to identify relevant contigs. PCR and Sanger sequencing were used to link the fragments of interest and fill the gaps. Results: P. mirabilis PmPHI was resistant to six classes of antibiotics penicillins, aminoglycosides, phenicols, tetracyclines, folate inhibitors and fluoroquinolones. A novel genomic resistance island (GIPmi1) of 55.8 kb was located at the 3' end of trmE. The backbone shared 93% identity with a genomic sequence of Enterobacter cloacae DSM 16690. The MDR region was composed of two class 1 integrons [one Tn402-type (estX-qacE) and one In5-type (aadB-aadA2)], separated by a region containing many parts of transposons. An external circular form of GIPmi1 was detected; however, mobilization by an A/C plasmid failed. In addition, an SXT/R391 integrative and conjugative element (ICEPmiFra1) was inserted into prfC. It carried floR, the sul2-strA-strB cluster and a composite transposon flanked by two copies of a tISPpu12 element that contains a class 1 integron (dfrA32-ereA1-aadA2), Tn4352 (aphA1a) and tetA(C). A class 2 integron (dfrA1-sat2-aadA1) was also identified on Tn7 as well as point mutations in gyrA and parC accounting for quinolone resistance. Conclusions: The finding of the new genomic island GIPmi1 belonging to the same superfamily of genomic islands as SGI1/SGI2/PGI1/AGI1 and of the integrative conjugative element ICEPmiFra1 (SXT/R391 family) suggested that these genetic elements might be key mediators of resistance gene acquisition in P. mirabilis.