Plasmid composition in Aeromonas salmonicida subsp. salmonicida 01-B526 unravels unsuspected type three secretion system loss patterns

Abstract

Background Aeromonas salmonicida subsp. salmonicida is a ubiquitous psychrophilic waterborne bacterium and a fish pathogen. The numerous mobile elements, especially insertion sequences (IS), in its genome promote rearrangements that impact its phenotype. One of the main virulence factors of this bacterium, its type three secretion system (TTSS), is affected by these rearrangements. In Aeromonas salmonicida subsp. salmonicida most of the TTSS genes are encoded in a single locus on a large plasmid called pAsa5, and may be lost when the bacterium is cultivated at a higher temperature (25 °C), producing non-virulent mutants. In a previous study, pAsa5-rearranged strains that lacked the TTSS locus on pAsa5 were produced using parental strains, including 01-B526. Some of the generated deletions were explained by homologous recombination between ISs found on pAsa5, whereas the others remained unresolved. To investigate those rearrangements, short- and long-read high-throughput sequencing technologies were used on the A. salmonicida subsp. salmonicida 01-B526 whole genome.ResultsWhole genome sequencing of the 01-B526 strain revealed that its pAsa5 has an additional IS copy, an ISAS5, compared to the reference strain (A449) sequence, which allowed for a previously unknown rearrangement to occur. It also appeared that 01-B526 bears a second large plasmid, named pAsa9, which shares 40 kbp of highly similar sequences with pAsa5. Following these discoveries, previously unexplained deletions were elucidated by genotyping. Furthermore, in one of the derived strains a fusion of pAsa5 and pAsa9, involving the newly discovered ISAS5 copy, was observed.ConclusionThe loss of TTSS and hence virulence is explained by one consistent mechanism: IS-driven homologous recombination. The similarities between pAsa9 and pAsa5 also provide another example of genetic diversity driven by ISs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3921-1) contains supplementary material, which is available to authorized users.

An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity

“…However, in the last years, many studies suggested that a growth temperature greater than 22 • C induces major rearrangements in A. salmonicida, such as the loss of the type three secretion system (T3SS) which is an important virulence factor in the bacteria, resulting in non-virulent strains in fish and model hosts. This is consistent with the fact that this bacterium infects cold-water fish, including salmonids that do not survive in temperatures above 25 • C [27,28].…”

Pathogenic characterization of Aeromonas salmonicida subsp. masoucida turbot isolate from China

“…Therefore, the lost pattern taken place in RZ6S‐1 is similar to the less frequent rearrangement reported by Tanaka et al. (2017).…”

“…The most frequent rearrangement leads to the only loss of T3SS locus. A less frequent rearrangement leads to loss of T3SS locus together with upstream fragment (~40 kbp) (Tanaka et al., 2017). Interestingly, this upstream fragment covers the main components of T4SS gene cluster (TraY‐TraM), and therefore, the less frequent rearrangement leads to the loss of both T3SS and T4SS.…”

Beyond the A‐layer: adsorption of lipopolysaccharides and characterization of bacteriophage‐insensitive mutants of Aeromonas salmonicida subsp. salmonicida

“…A). In order to create mutants showing new phenotypes in regard of bacteriophage’s interaction, M15879‐11 strain was grown at 25°C, a temperature known to promote genomic rearrangements that include the loss of the T3SS locus (Daher et al , ; Tanaka et al , ). We generated the M15879‐11‐R3 (AS‐R3) and M15879‐11‐R5 (AS‐R5) mutant strains, and noticed that those had lost their T3SS, confirming that genomic alterations occurred (Fig.…”

“…salmonicida M15879‐11 was cultured at 25°C twice over 3 days to initiate the homologous recombination of the plasmid pAsa5 (Daher et al , ) under stressful conditions. After a week, isolated colonies were analyzed by PCR to detect clones that lost genes encoding the T3SS (Tanaka et al , ). Two rearranged strains derived from A. salmonicida subsp.…”