Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida

Abstract

BackgroundAeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The Aeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the genomes of A. salmonicida subspecies have been reported to date.ResultsWe sequenced the genomes of additional A. salmonicida isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links between A. salmonicida subspecies. Their relative phylogenetic positions were confirmed by a core genome phylogeny based on 1645 gene sequences. The Indian isolates, which formed a sub-group together with A. salmonicida subsp. pectinolytica, were able to grow at either at 18 °C and 37 °C, unlike the A. salmonicida psychrophilic isolates that did not grow at 37 °C. Amino acid frequencies, GC content, tRNA composition, loss and gain of genes during evolution, pseudogenes as well as genes under positive selection and the mobilome were studied to explain this intraspecies dichotomy.ConclusionInsertion sequences appeared to be an important driving force that locked the psychrophilic strains into their particular lifestyle in order to conserve their genomic integrity. This observation, based on comparative genomics, is in agreement with previous results showing that insertion sequence mobility induced by heat in A. salmonicida subspecies causes genomic plasticity, resulting in a deleterious effect on the virulence of the bacterium. We provide a proof-of-concept that selfish DNAs play a major role in the evolution of bacterial species by modeling genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2381-3) contains supplementary material, which is available to authorized users.

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

“…Afterwards, the culture was suspended in TSB, diluted and plated on TSA with either 5 μg/ml tetracycline (pAsa4 and pAsa4b) or 5 μg/ml chloramphenicol (pAsa4 and pAsa4c). Plates were incubated overnight at 37 °C to select against A. salmonicida which is psychrophilic (Vincent et al, 2016b). Large colonies were picked and suspended in TSB with appropriate selection.…”

“…salmonicida , insertion sequences (ISs) are responsible for several genomic modifications (Vincent et al, 2016b). ISs are made of a transposase gene and inverted repeats.…”

“…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). …”

Antibiotic resistance due to an unusual ColE1-type replicon plasmid in Aeromonas salmonicida

“…salmonicida isolates (Table 2). Isolates A449 and RS 534, known to bear a gene of the cat family since they contain the large plasmid pAsa4 (Reith et al, 2008;Vincent et al, 2016), were used for comparative purposes. Additionally, the 2004-05MF26 and 2009-144K3 CHL-resistant isolates, which harbour, respectively, the plasmids pSN254b and pAB5S9b known to bear a floR gene , were also used to have a more complete panel of CHL resistance genes.…”

Leichte Neucodierung von Selenocystein in der Natur

“…pectinolytica 34mel, [18] einem Stamm der γ-proteobakterium-A.-salmonicida -Subspezies, konnte bereits bestätigt werden. Im Unterschied zu anderen Aeromonas -Spezies paaren die pectinolytica -Subspezies und der Stamm Y577 [19] die tRNA Sec ACA mit dem UGU-Cys-Codon in fdhF . Die anaerobe metabolische Markierung von pectinolytica -Zellen mit 75 Se führte, zusätzlich deren In-vivo-FDH-Aktivität (Abbildung 2C), zu radioaktiver FDH H (Abbildung 2D).…”