Comparative Genomics of the IncA/C Multidrug Resistance Plasmid Family

Abstract

Multidrug resistance (MDR) plasmids belonging to the IncA/C plasmid family are widely distributed among Salmonella and other enterobacterial isolates from agricultural sources and have, at least once, also been identified in a drug-resistant Yersinia pestis isolate (IP275) from Madagascar. Here, we present the complete plasmid sequences of the IncA/C reference plasmid pRA1 (143,963 bp), isolated in 1971 from the fish pathogen Aeromonas hydrophila, and of the cryptic IncA/C plasmid pRAx (49,763 bp), isolated from Escherichia coli transconjugant D7-3, which was obtained through pRA1 transfer in 1980. Using comparative sequence analysis of pRA1 and pRAx with recent members of the IncA/C plasmid family, we show that both plasmids provide novel insights into the evolution of the IncA/C MDR plasmid family and the minimal machinery necessary for stable IncA/C plasmid maintenance. Our results indicate that recent members of the IncA/C plasmid family evolved from a common ancestor, similar in composition to pRA1, through stepwise integration of horizontally acquired resistance gene arrays into a conserved plasmid backbone. Phylogenetic comparisons predict type IV secretion-like conjugative transfer operons encoded on the shared plasmid backbones to be closely related to a group of integrating conjugative elements, which use conjugative transfer for horizontal propagation but stably integrate into the host chromosome during vegetative growth. A hipAB toxin-antitoxin gene cluster found on pRA1, which in Escherichia coli is involved in the formation of persister cell subpopulations, suggests persistence as an early broad-spectrum antimicrobial resistance mechanism in the evolution of IncA/C resistance plasmids.

Host range diversification within the IncP-1 plasmid group

“…Among the self-transmissible plasmids in the Proteobacteria, the IncP-1 group is unique with respect to both the number of available plasmid sequences deposited in GenBank so far and the high sequence diversity within the group. Such a divergence in the plasmid backbone genes within an Inc group (,80 % amino-acid sequence identity between homologues) has also been reported for the groups IncQ (Loftie-Eaton & Rawlings, 2012), IncP-9 (Sevastsyanovich et al, 2008) and IncX (Johnson et al, 2012), whereas relatively low divergence was observed among the currently available plasmid sequences of groups IncA/C (Fricke et al, 2009), IncI (Takahashi et al, 2011) andIncP-7 (Yano et al, 2010). Reduced similarity was observed, for an as yet unknown reason, specifically in a partitioning gene in IncI and IncP-7 groups despite high similarity in the replication and transfer genes within the Inc groups (Takahashi et al, 2011;Yano et al, 2010).…”

Functional metagenomic characterization of antibiotic resistance genes in agricultural soils from China

“…Some of the ARGs were closely linked with a number of widespread mobile genetic elements (MGEs), including plasmids, transposons and integrons, which were involved in horizontal transfer of ARGs among environmental bacteria (Fluit and Schmitz, 1999;Fricke et al, 2009;Li et al, 2012;. These ARGs could be missed when screening a microbial chromosomal DNA derived metagenomic library.…”

The Importance of Mobile Genetic Elements in the Evolution of Salmonella: Pathogenesis, Antibiotic Resistance and Host Adaptation

“…The genomic comparison of seven IncA/C plasmids showed that these plasmids share a common backbone, including the origin of replication and a conjugative plasmid transfer system (Welch et al, 2007;Fricke et al, 2009). Several loci containing antimicrobial resistance determinants are distributed along the plasmids, and are integrated at few sites within the conserved plasmid backbone; they are generally located as resistance gene arrays, composed of resistance genes and mobile genetic elements such as insertion sequences, transposons or integrons (Fricke et al, 2009). For example, in the IncA/C plasmids of Yersinia pestis and Salmonella Newport, a Tn21 transposon is inserted in a similar location but some nucleotide divergence is evident and its orientation is reversed (Welch et al, 2007;Fricke et al, 2009).…”

“…Recent comparative studies have addressed the evolutionary relationships among the IncA/C plasmids from Salmonella enterica, Escherichia coli, Yersinia pestis, Yersinia ruckeri, Vibrio cholera, Photobacterium damselae and Aeromonas salmonicida (Welch et al, 2007;Kim et al, 2008;McIntosh et al, 2008;Pan et al, 2008;Fricke et al, 2009;Call et al, 2010). The genomic comparison of seven IncA/C plasmids showed that these plasmids share a common backbone, including the origin of replication and a conjugative plasmid transfer system (Welch et al, 2007;Fricke et al, 2009). Several loci containing antimicrobial resistance determinants are distributed along the plasmids, and are integrated at few sites within the conserved plasmid backbone; they are generally located as resistance gene arrays, composed of resistance genes and mobile genetic elements such as insertion sequences, transposons or integrons (Fricke et al, 2009).…”

“…They have attracted the attention of the research community due to their ability to acquire antimicrobial resistance traits and to mobilize across geographical and taxonomical borders (Fricke et al, 2009). Recent comparative studies have addressed the evolutionary relationships among the IncA/C plasmids from Salmonella enterica, Escherichia coli, Yersinia pestis, Yersinia ruckeri, Vibrio cholera, Photobacterium damselae and Aeromonas salmonicida (Welch et al, 2007;Kim et al, 2008;McIntosh et al, 2008;Pan et al, 2008;Fricke et al, 2009;Call et al, 2010). The genomic comparison of seven IncA/C plasmids showed that these plasmids share a common backbone, including the origin of replication and a conjugative plasmid transfer system (Welch et al, 2007;Fricke et al, 2009).…”