Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins

Emond-Rheault, Jean Guillaume; Vincent, Antony T.; Trudel, Mélanie V.; Brochu, Francis; Boyle, Brian; Tanaka, Katherine H.; Attéré, Sabrina A.; Jubinville, Éric; Loch, Thomas P.; Winters, Andrew D.; Faisal, Mohamed; Frenette, Michel; Derôme, Nicolas; Charette, Steve J.

doi:10.1016/j.vetmic.2014.11.014

Cited by 35 publications

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“…Derived strains 01-B516–3, 01-B516–11 and 01-B516–30 were also genotyped for AsaGEI1a (accession number KJ626178) presence and were found positive for that genomic island, whereas 01-B516 carries AsaGEI2a [13]. AsaGEI s (for Aeromonas salmonicida GEnomic Island) are found in some A. salmonicida subsp.…”

Section: Resultsmentioning

confidence: 99%

“…They contain some phage-related genes and many ORFs coding for hypothetical protein. Consequently, their role remains to be determined [13–15]. …”

Section: Resultsmentioning

confidence: 99%

“…Moreover, AsaGEI types are linked with their geographic origin and strains bearing AsaGEI1a are found in North America [13]. Since all 01-B516 ‘derived’ strains genotyped positive for pAsa9 and AsaGEI1a , and that two of them have a ZA-rearranged pAsa5, we concluded these three strains were mislabelled when they were obtained, and are instead 01-B526-derived strains.…”

Section: Resultsmentioning

confidence: 99%

“…A. salmonicida subsp. salmonicida strain genomes have been shown to bear a wide array of mobile elements [4, 12], genomic islands [13–15], and transferable plasmids [2, 3, 5, 16]. The close relationship between the mobile elements from this species and those of Salmonella enterica has raised concerns about its ability to act as a reservoir of antibiotic resistance genes, which could transfer to human pathogens [5, 7].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2017

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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.

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Section: Resultsmentioning

confidence: 99%

“…They contain some phage-related genes and many ORFs coding for hypothetical protein. Consequently, their role remains to be determined [13–15]. …”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2017

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“…salmonicida (79). GIs belong to the flexible genetic pool, as they normally carry genes that are not essential for growth but provide advantages under unfavorable conditions (20).…”

Section: Melanin Biosynthesis One Of the Most Distinctive Phenotypicmentioning

confidence: 99%

Living in an Extremely Polluted Environment: Clues from the Genome of Melanin-Producing Aeromonas salmonicida subsp. pectinolytica 34mel ^T

Paván

Pavan

López

et al. 2015

Appl Environ Microbiol

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d Aeromonas salmonicida subsp. pectinolytica 34mel T can be considered an extremophile due to the characteristics of the heavily polluted river from which it was isolated. While four subspecies of A. salmonicida are known fish pathogens, 34melT belongs to the only subspecies isolated solely from the environment. Genome analysis revealed a high metabolic versatility, the capability to cope with diverse stress agents, and the lack of several virulence factors found in pathogenic Aeromonas. The most relevant phenotypic characteristics of 34mel T are pectin degradation, a distinctive trait of A. salmonicida subsp. pectinolytica, and melanin production. Genes coding for three pectate lyases were detected in a cluster, unique to this microorganism, that contains all genes needed for pectin degradation. Melanin synthesis in 34melT is hypothesized to occur through the homogentisate pathway, as no tyrosinases or laccases were detected and the homogentisate 1,2-dioxygenase gene is inactivated by a transposon insertion, leading to the accumulation of the melanin precursor homogentisate. Comparative genome analysis of other melanogenic Aeromonas strains revealed that this gene was inactivated by transposon insertions or point mutations, indicating that melanin biosynthesis in Aeromonas occurs through the homogentisate pathway. Horizontal gene transfer could have contributed to the adaptation of 34mel T to a highly polluted environment, as 13 genomic islands were identified in its genome, some of them containing genes coding for fitness-related traits. Heavy metal resistance genes were also found, along with others associated with oxidative and nitrosative stresses. These characteristics, together with melanin production and the ability to use different substrates, may explain the ability of this microorganism to live in an extremely polluted environment.A eromonas salmonicida subsp. pectinolytica 34melT is a melanin-producing Aeromonas strain that degrades polypectate, which is an unusual characteristic among Aeromonas species (1). It was isolated from the heavily polluted water of the Riachuelo, the last part of the Matanza River, located in Buenos Aires, Argentina. This river has received the effluents of hundreds of tanneries and other industries, as well as urban sewage and fuels, for more than a century. Among the contaminants found in this environment, which has high organic matter and low dissolved oxygen contents, are hydrocarbons, polychlorinated biphenyls, pesticides, arsenic, and heavy metals, such as chromium, lead, copper, mercury, and nickel (2-4). A molecular analysis of the microbial diversity of river water and sediments from the isolation site showed the presence of bacteria belonging to several taxa. Analysis of 16S rRNA gene sequences revealed the presence of bacteria belonging to the Beta-, Gamma-, and Epsilonproteobacteria in the water, as well as a higher level of diversity in the sediments, in which Alpha-, Beta-, Gamma-, and Deltaproteobacteria, Firmicutes, and Bacteroidetes were detected (5).The ge...

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Isolation of vB_AsaM_LPM4 reveals the dynamics of Prophage 3 in Aeromonas salmonicida subsp. salmonicida

et al. 2023

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Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins

Cited by 35 publications

References 30 publications

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

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

Living in an Extremely Polluted Environment: Clues from the Genome of Melanin-Producing Aeromonas salmonicida subsp. pectinolytica 34mel ^T

Isolation of vB_AsaM_LPM4 reveals the dynamics of Prophage 3 in Aeromonas salmonicida subsp. salmonicida

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Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins

Cited by 35 publications

References 30 publications

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

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

Living in an Extremely Polluted Environment: Clues from the Genome of Melanin-Producing Aeromonas salmonicida subsp. pectinolytica 34mel T

Isolation of vB_AsaM_LPM4 reveals the dynamics of Prophage 3 in Aeromonas salmonicida subsp. salmonicida

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Living in an Extremely Polluted Environment: Clues from the Genome of Melanin-Producing Aeromonas salmonicida subsp. pectinolytica 34mel ^T