Diversity and Homogeneity among Small Plasmids of Aeromonas salmonicida subsp. salmonicida Linked with Geographical Origin

Abstract

Furunculosis, which is caused by Aeromonas salmonicida subsp. salmonicida, is a major salmonid disease in fish farms worldwide. Several plasmids found in this bacterium confer phenotypes such drug resistance and virulence. Small plasmids (pAsa1, pAsa2, pAsa3, and pAsal1) related to ColE1- and ColE2-type replicons are usually present in its normal plasmidome. In the present study, with the objective to investigate if these plasmids display particularities related to the origin of the isolates bearing them, a total of 153 isolates, including 78 new and 75 previously described, were analyzed for the presence of small plasmids by PCR and DNA restriction fragment profiling. A geographical dichotomy between Canadian and European isolates for their propensity to do not have pAsa3 or pAsal1 was found. In addition, the genotyping analysis led to the identification of two European isolates harboring an unusual pAsal1. An investigation by next-generation sequencing (NGS) of these two isolates shed light on two pAsal1 variants (pAsal1C and pAsal1D). As with pAsal1B, another pAsal1 variant previously described, these two new variants bore a second insertion sequence (ISAS5) in addition to the usual ISAS11. The characterization of these variants suggested that they could predominate over the wild-type pAsal1 in stressful conditions such as growth at temperatures of 25°C and above. To obtain a comprehensive portrait of the mutational pressure on small plasmids, 26 isolates whose DNA had been sequenced by NGS were investigated. pAsa3 and pAsal1 were more prone to mutations than pAsa1 and pAsa2, especially in the mobA gene, which encodes a relaxase and a primase. Lastly, the average copy number of each plasmid per cell was assessed using raw sequencing data. A clear trend with respect to the relative proportion per cell of each plasmid was identified. Our large-scale study revealed a geographical dichotomy in small plasmid repertoire in addition to a clear trend for pAsa3 and pAsal1 to be more frequently altered. Moreover, we present the discovery of two new variants of pAsal1: pAsal1C and pAsal1D.

The mosaic architecture ofAeromonas salmonicidasubsp.salmonicidapAsa4 plasmid and its consequences on antibiotic resistance

“…This is an additional example of IS activity responsible for plasmid variations in A. salmonicida subsp. salmonicida (Attéré et al, 2015; Najimi et al, 2009; Trudel et al, 2013; Vincent et al, 2014b). Moreover, pAsa4c bears IS Kpn3 , originally described on the Klebsiella pneumoniae plasmid pRDDHA.…”

“…Contigs from two other A. salmonicida strains, RS 534 (NCBI wgs ) (Vincent et al, 2016b) and JF3517 that had been sequenced previously (Attéré et al, 2015) were mapped against pAsa4, pAsa4b, and pAsa4c using CONTIGuator version 2.7.4 (Galardini et al, 2011). …”

“…salmonicida is under stressful conditions (IS AS1 , IS AS2 and IS AS11 ) (Gustafson, Chu & Trust, 1994; Tanaka et al, 2012). Furthermore, many plasmid variants display transpositions or IS-mediated recombinations when compared to their reference (IS AS 5 in many plasmids, IS Ec 9 in pSN254b) (Attéré et al, 2015; Najimi et al, 2009; Trudel et al, 2013; Vincent et al, 2014b). Given the high number of ISs in the genome of this bacterium (Studer, Frey & Vanden Bergh, 2013; Vincent et al, 2016b), we hypothesize that ISs play a role in plasmid reshaping (Tanaka, Frenette & Charette, 2013).…”

Genome-based insights into the resistome and mobilome of multidrug-resistant Aeromonas sp. ARM81 isolated from wastewater

“…have been fully sequenced and analyzed. These plasmids are of various sizes (between 2524 and 198,307 bp) and some are cryptic (e.g., pAsa1, pAsa2 and pAsa3) (Attere et al 2015), while others harbor virulence and/or antibiotic resistance genes (e.g., pAsa4 and pAsa5) (Vincent et al 2014). Several other studies have investigated the transposable mobilome of Aeromonas spp., which led to the identification of novel transposons and insertion sequences [e.g., (Reith et al 2008; Dobiasova et al 2015)].…”

Detection and quantification of Aeromonas salmonicida in fish tissue by real‐time PCR

“…; Attéré et al . ), quantitative real‐time PCR data were transformed to express the results as genomic copies (genomic units, GU).…”