Dynamic state of plasmid genomic architectures resulting from XerC/D-mediated site-specific recombination in Acinetobacter baumannii Rep_3 superfamily resistance plasmids carrying blaOXA-58- and TnaphA6-resistance modules

Abstract

The acquisition of blaOXA genes encoding different carbapenem-hydrolyzing class-Dβ-lactamases (CHDL) represents a main determinant of carbapenem resistance inthe nosocomial pathogen Acinetobacter baumannii. The blaOXA-58 gene, in particular,is generally embedded in similar resistance modules (RM) carried by plasmidsunique to the Acinetobacter genus lacking self-transferability. The ample variationsin the immediate genomic contexts in which blaOXA-58-containing RMs are insertedamong these plasmids, and the almost invariable presence at their borders of nonidentical28-bp sequences potentially recognized by the host XerC and XerD tyrosinerecombinases (pXerC/D-like sites), suggested an involvement of these sites in thelateral mobilization of the gene structures they encircle. However, whether and howthese pXerC/D sites participate in this process is only beginning to be understood.Here, we used a series of experimental approaches to analyze the contribution ofpXerC/D-mediated site-specific recombination to the generation of structuraldiversity between resistance plasmids carrying pXerC/D-bounded blaOXA-58- andTnaphA6-containing RM harbored by two phylogenetically- and epidemiologicallycloselyrelated A. baumannii strains of our collection, Ab242 and Ab825, duringadaptation to the hospital environment. Our analysis disclosed the existence ofdifferent bona fide pairs of recombinationally-active pXerC/D sites in these plasmids,some mediating reversible intramolecular inversions and others reversible plasmidfusions/resolutions. All of the identified recombinationally-active pairs shared identicalGGTGTA sequences at the cr spacer separating the XerC- and XerD-binding regions.The fusion of two Ab825 plasmids mediated by a pair of recombinationally-activepXerC/D sites displaying sequence differences at the cr spacer could be inferred onthe basis of sequence comparison analysis, but no evidence of reversibility couldbe obtained in this case. The reversible plasmid genome rearrangements mediatedby recombinationally-active pairs of pXerC/D sites reported here probably representsan ancient mechanism of generating structural diversity in the Acinetobacter plasmidpool. This recursive process could facilitate a rapid adaptation of an eventual bacterialhost to changing environments, and has certainly contributed to the evolution ofAcinetobacter plasmids and the capture and dissemination of blaOXA-58 genes among Acinetobacter and non-Acinetobacter populations co-residing in the hospital niche.