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Hossain A, Gnanagobal H, Cao T, Chakraborty S, Chukwu-Osazuwa J, Soto-Dávila M, Vasquez I, Santander J. Role of cold shock proteins B and D in Aeromonas salmonicida subsp. salmonicida physiology and virulence in lumpfish ( Cyclopterus lumpus). Infect Immun 2024; 92:e0001124. [PMID: 38920386 PMCID: PMC11320987 DOI: 10.1128/iai.00011-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
Cold shock proteins (Csp) are pivotal nucleic acid binding proteins known for their crucial roles in the physiology and virulence of various bacterial pathogens affecting plant, insect, and mammalian hosts. However, their significance in bacterial pathogens of teleost fish remains unexplored. Aeromonas salmonicida subsp. salmonicida (hereafter A. salmonicida) is a psychrotrophic pathogen and the causative agent of furunculosis in marine and freshwater fish. Four csp genes (cspB, cspD, cspA, and cspC) have been identified in the genome of A. salmonicida J223 (wild type). Here, we evaluated the role of DNA binding proteins, CspB and CspD, in A. salmonicida physiology and virulence in lumpfish (Cyclopterus lumpus). A. salmonicida ΔcspB, ΔcspD, and the double ΔcspBΔcspD mutants were constructed and characterized. A. salmonicida ΔcspB and ΔcspBΔcspD mutants showed a faster growth at 28°C, and reduced virulence in lumpfish. A. salmonicida ΔcspD showed a slower growth at 28°C, biofilm formation, lower survival in low temperatures and freezing conditions (-20°C, 0°C, and 4°C), deficient in lipopolysaccharide synthesis, and low virulence in lumpfish. Additionally, ΔcspBΔcspD mutants showed less survival in the presence of bile compared to the wild type. Transcriptome analysis revealed that 200, 37, and 921 genes were differentially expressed in ΔcspB, ΔcspD, and ΔcspBΔcspD, respectively. In ΔcspB and ΔcspBΔcspD virulence genes in the chromosome and virulence plasmid were downregulated. Our analysis indicates that CspB and CspD mostly act as a transcriptional activator, influencing cell division (e.g., treB), virulence factors (e.g., aexT), and ultimately virulence.
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Affiliation(s)
- Ahmed Hossain
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Hajarooba Gnanagobal
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Trung Cao
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Setu Chakraborty
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Joy Chukwu-Osazuwa
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Manuel Soto-Dávila
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Ignacio Vasquez
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, Ocean Science Center, St. John's, Newfoundland, Canada
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Cantillo Villa Y, Triga A, Katharios P. Polyinfection in Fish Aeromoniasis: A Study of Co-Isolated Aeromonas Species in Aeromonas veronii Outbreaks. Pathogens 2023; 12:1337. [PMID: 38003801 PMCID: PMC10674900 DOI: 10.3390/pathogens12111337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
We studied the phenotypic and genomic characteristics related to the virulence and antibiotic resistance of two Aeromonas strains, which were co-isolated before an outbreak of Aeromonas veronii among diseased seabass on Agathonisi Island, Greece, in April 2015. The first strain, AG2.13.2, is a potentially pathogenic mesophilic variant of Aeromonas salmonicida, and the second, AG2.13.5, corresponds to an Aeromonas rivipollensis related to A. rivipollensis KN-Mc-11N1 with an ANI value of 97.32%. AG2.13.2 lacks the type III secretion system just like other mesophilic strains of A. salmonicida. This characteristic has been associated with lower virulence. However, the genome of AG2.13.2 contains other important virulence factors such as type II and type VI secretion systems, and toxins such as rtxA, aerolysin aer/act, and different types of hemolysins. The strain also carries several genes associated with antibiotic resistance such as the tetE efflux pump, and exhibits resistance to tetracycline, ampicillin, and oxolinic acid. In an in vivo challenge test with gilthead seabream larvae, the A. veronii bv sobria strain AG5.28.6 exhibited the highest virulence among all tested strains. Conversely, both A. salmonicida and A. rivipollensis showed minimal virulence when administered alone. Interestingly, when A. veronii bv sobria AG5.28.6 was co-administered with A. rivipollensis, the larvae survival probability increased compared to those exposed to A. veronii bv sobria AG5.28.6 alone. This finding indicates an antagonistic interaction between A. veronii bv sobria AG5.28.6 and A. rivipollensis AG2.13.5. The co-administration of A. veronii bv sobria AG5.28.6 with Aeromonas salmonicida did not yield distinct survival probabilities. Our results validate that the primary pathogen responsible for European seabass aeromoniasis is Aeromonas veronii bv sobria.
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Affiliation(s)
- Yanelys Cantillo Villa
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), 71500 Gournes, Greece; (Y.C.V.); (A.T.)
- Department of Biology, University of Crete, 71110 Heraklion, Greece
| | - Adriana Triga
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), 71500 Gournes, Greece; (Y.C.V.); (A.T.)
- Department of Biology, University of Crete, 71110 Heraklion, Greece
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), 71500 Gournes, Greece; (Y.C.V.); (A.T.)
- Aquatic Biologicals, Thalassocosmos, 71500 Gournes, Greece
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3
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Marcoux PÉ, Girard SB, Fournier KC, Tardif CA, Gosselin A, Charette SJ. Interaction of pAsa5 and pAsa8 Plasmids in Aeromonas salmonicida subsp. salmonicida. Microorganisms 2023; 11:2685. [PMID: 38004697 PMCID: PMC10673383 DOI: 10.3390/microorganisms11112685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
The plasmid known as pAsa5 is present in Aeromonas salmonicida subsp. salmonicida, a fish pathogen. The pAsa5 plasmid carries genes that are essential for the bacterium's virulence. Recombination events are known to occur in pAsa5, resulting in the loss of certain segments or the acquisition of additional genetic elements. For example, the transposon carried by the large pAsa8 plasmid was found to be inserted into the pAsa5 plasmid in the SHY16-3432 strain, enabling the addition of antibiotic resistance genes to this plasmid, which does not normally possess any. In this study, we present the isolation of additional strains carrying pAsa8. Further analyses of these strains revealed that a fusion between pAsa5 and the complete version of pAsa8 is possible. The pAsa8 transposon insertion in pAsa5 seen in the SHY16-3432 strain appears to be an aberrant event compared to the fusion of the two full-length plasmids. A 22-nucleotide sequence, present in both plasmids, serves as the site for the fusion of the two plasmids. Moreover, it is possible to introduce pAsa8 through conjugation into naive strains of A. salmonicida subsp. salmonicida and once the plasmid is within a new strain, the fusion with pAsa5 is detectable. This study reveals a previously unexplored aspect of pAsa5 plasmid biology, highlighting an additional risk for the spread of antibiotic resistance genes in A. salmonicida subsp. salmonicida.
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Affiliation(s)
- Pierre-Étienne Marcoux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Sarah B. Girard
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Kim C. Fournier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Catherine A. Tardif
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Ariane Gosselin
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve J. Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC G1V 4G5, Canada
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Kroniger T, Mehanny M, Schlüter R, Trautwein-Schult A, Köllner B, Becher D. Effect of Iron Limitation, Elevated Temperature, and Florfenicol on the Proteome and Vesiculation of the Fish Pathogen Aeromonas salmonicida. Microorganisms 2022; 10:microorganisms10091735. [PMID: 36144337 PMCID: PMC9503180 DOI: 10.3390/microorganisms10091735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
We analyzed the proteomic response of the Gram-negative fish pathogen A. salmonicida to iron limitation, an elevated incubation temperature, and the antibiotic florfenicol. Proteins from different subcellular fractions (cytosol, inner membrane, outer membrane, extracellular and outer membrane vesicles) were enriched and analyzed. We identified several iron-regulated proteins that were not reported in the literature for A. salmonicida before. We could also show that hemolysin, an oxidative-stress-resistance chaperone, a putative hemin receptor, an M36 peptidase, and an uncharacterized protein were significantly higher in abundance not only under iron limitation but also with an elevated incubation temperature. This may indicate that these proteins involved in the infection process of A. salmonicida are induced by both factors. The analysis of the outer membrane vesicles (OMVs) with and without applied stresses revealed significant differences in the proteomes. OMVs were smaller and contained more cytoplasmic proteins after antibiotic treatment. After cultivation with low iron availability, several iron-regulated proteins were found in the OMVs, indicating that A. salmonicida OMVs potentially have a function in iron acquisition, as reported for other bacteria. The presence of iron-regulated transporters further indicates that OMVs obtained from ‘stressed’ bacteria might be suitable vaccine candidates that induce a protective anti-virulence immune response.
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Affiliation(s)
- Tobias Kroniger
- Institute of Microbiology, Department of Microbial Proteomics, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Mina Mehanny
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, 17489 Greifswald, Germany
| | - Anke Trautwein-Schult
- Institute of Microbiology, Department of Microbial Proteomics, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Bernd Köllner
- Institute of Immunology, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Dörte Becher
- Institute of Microbiology, Department of Microbial Proteomics, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
- Correspondence: ; Tel.: +49-3834-420-5903
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5
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To Be or Not to Be Mesophilic, That Is the Question for Aeromonas salmonicida. Microorganisms 2022; 10:microorganisms10020240. [PMID: 35208695 PMCID: PMC8879556 DOI: 10.3390/microorganisms10020240] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 02/05/2023] Open
Abstract
The bacterium Aeromonas salmonicida has long been known to be one of the most feared pathogens in fish farming. However, the more we discover about this bacterial species, the more we question whether it is really exclusively an aquatic pathogen. In recent years, it has become obvious that this bacterial species includes a myriad of strains with various lifestyle and ecological niches, including the well-known strict psychrophiles, the first bacteria known of the species, and the newly described mesophilic strains. The mesophiles are able to grow at low temperatures, but even better at temperatures of approximately 37 °C, which strict psychrophiles cannot do. In this perspective article, we address some aspects surrounding this dual lifestyle in A. salmonicida, including the impact of mobile genetic elements, and how future research around this bacterial species may focus on the psychrophilic/mesophilic dichotomy, which makes A. salmonicida an increasingly interesting and relevant model for the study of speciation.
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6
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Comparative Genomics of Typical and Atypical Aeromonas salmonicida Complete Genomes Revealed New Insights into Pathogenesis Evolution. Microorganisms 2022; 10:microorganisms10010189. [PMID: 35056638 PMCID: PMC8780938 DOI: 10.3390/microorganisms10010189] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Aeromonas salmonicida is a global distributed Gram-negative teleost pathogen, affecting mainly salmonids in fresh and marine environments. A. salmonicida strains are classified as typical or atypical depending on their origin of isolation and phenotype. Five subspecies have been described, where A. salmonicida subsp. salmonicida is the only typical subspecies, and the subsp. achromogenes, masoucida, smithia, and pectinolytica are considered atypical. Genomic differences between A. salmonicida subsp. salmonicida isolates and their relationship with the current classification have not been explored. Here, we sequenced and compared the complete closed genomes of four virulent strains to elucidate their molecular diversity and pathogenic evolution using the more accurate genomic information so far. Phenotypes, biochemical, and enzymatic profiles were determined. PacBio and MiSeq sequencing platforms were utilized for genome sequencing. Comparative genomics showed that atypical strains belong to the subsp. salmonicida, with 99.55% ± 0.25% identity with each other, and are closely related to typical strains. The typical strain A. salmonicida J223 is closely related to typical strains, with 99.17% identity with the A. salmonicida A449. Genomic differences between atypical and typical strains are strictly related to insertion sequences (ISs) activity. The absence and presence of genes encoding for virulence factors, transcriptional regulators, and non-coding RNAs are the most significant differences between typical and atypical strains that affect their phenotypes. Plasmidome plays an important role in A. salmonicida virulence and genome plasticity. Here, we determined that typical strains harbor a larger number of plasmids and virulence-related genes that contribute to its acute virulence. In contrast, atypical strains harbor a single, large plasmid and a smaller number of virulence genes, reflected by their less acute virulence and chronic infection. The relationship between phenotype and A. salmonicida subspecies’ taxonomy is not evident. Comparative genomic analysis based on completed genomes revealed that the subspecies classification is more of a reflection of the ecological niche occupied by bacteria than their divergences at the genomic level except for their accessory genome.
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7
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Mekasha S, Linke D. Secretion Systems in Gram-Negative Bacterial Fish Pathogens. Front Microbiol 2022; 12:782673. [PMID: 34975803 PMCID: PMC8714846 DOI: 10.3389/fmicb.2021.782673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial fish pathogens are one of the key challenges in the aquaculture industry, one of the fast-growing industries worldwide. These pathogens rely on arsenal of virulence factors such as toxins, adhesins, effectors and enzymes to promote colonization and infection. Translocation of virulence factors across the membrane to either the extracellular environment or directly into the host cells is performed by single or multiple dedicated secretion systems. These secretion systems are often key to the infection process. They can range from simple single-protein systems to complex injection needles made from dozens of subunits. Here, we review the different types of secretion systems in Gram-negative bacterial fish pathogens and describe their putative roles in pathogenicity. We find that the available information is fragmented and often descriptive, and hope that our overview will help researchers to more systematically learn from the similarities and differences between the virulence factors and secretion systems of the fish-pathogenic species described here.
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Affiliation(s)
- Sophanit Mekasha
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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8
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Frequency and diversity of small plasmids in mesophilic Aeromonas isolates from fish, water and sediment. Plasmid 2021; 118:102607. [PMID: 34800545 DOI: 10.1016/j.plasmid.2021.102607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/10/2021] [Accepted: 11/14/2021] [Indexed: 11/21/2022]
Abstract
Plasmids are autonomous genetic elements ubiquitously present in bacteria. In addition to containing genetic determinants responsible for their replication and stability, some plasmids may carry genes that help bacteria adapt to different environments, while others without a known function are classified as cryptic. In this work we identified and characterized plasmids from a collection of mesophilic Aeromonas spp. (N = 90) isolated from water, sediments and fish. A total of 15 small plasmids ranging from 2287 to 10,558 bp, with an incidence of 16.7% (15/90) was found. Plasmids were detected in A. hydrophila (6), A. veronii (4), A. taiwanensis (2), A. jandaei (1), A. media (1) and Aeromonas sp. (1). There were no large or megaplasmids in the strains studied in this work. Analysis of coding sequences identified proteins associated to replication, mobilization, antibiotic resistance, virulence and stability. A considerable number of hypothetical proteins with unknown functions were also found. Some strains shared identical plasmid profiles, however, only two of them were clones. Small plasmids could be acting as a gene repositories as suggested by the presence of a gene encoding for a putative zonula occludens toxin (Zot) that causes diarrhea and the qnrB gene involved in quinolone resistance harbored in plasmids pAerXII and pAerXIII respectively.
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9
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Vincent AT, Intertaglia L, Loyer V, Paquet VE, Adouane É, Martin P, Bérard C, Lami R, Charette SJ. AsaGEI2d: a new variant of a genomic island identified in a group of Aeromonas salmonicida subsp. salmonicida isolated from France, which bears the pAsa7 plasmid. FEMS Microbiol Lett 2021; 368:6145018. [PMID: 33605980 DOI: 10.1093/femsle/fnab021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/17/2021] [Indexed: 12/22/2022] Open
Abstract
Genomic islands (Aeromonas salmonicida genomic islands, AsaGEIs) are found worldwide in many isolates of Aeromonas salmonicida subsp. salmonicida, a fish pathogen. To date, five variants of AsaGEI (1a, 1b, 2a, 2b and 2c) have been described. Here, we investigate a sixth AsaGEI, which was identified in France between 2016 and 2019 in 20 A. salmonicida subsp. salmonicida isolates recovered from sick salmon all at the same location. This new AsaGEI shares the same insertion site in the chromosome as the other AsaGEI2s as they all have a homologous integrase gene. This new AsaGEI was thus named AsaGEI2d, and has five unique genes compared to the other AsaGEIs. The isolates carrying AsaGEI2d also bear the plasmid pAsa7, which was initially found in an isolate from Switzerland. This plasmid provides resistance to chloramphenicol thanks to a cat gene. This study reveals more about the diversity of the AsaGEIs.
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Affiliation(s)
- Antony T Vincent
- Département des Sciences Animales, Faculté des Sciences de l'agriculture et de l'alimentation, Université Laval, 2425, rue de l'Agriculture, Quebec City, QC G1V 0A6, Canada
| | - Laurent Intertaglia
- Sorbonne Université, CNRS, Bio2mar, Observatoire Océanologique de Banyuls sur Mer, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - Victor Loyer
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC G1V 0A6, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, 2725 Chemin Sainte-Foy, Quebec City, QC G1V 4G5, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC G1V 0A6, Canada
| | - Valérie E Paquet
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC G1V 0A6, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, 2725 Chemin Sainte-Foy, Quebec City, QC G1V 4G5, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC G1V 0A6, Canada
| | - Émilie Adouane
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, Observatoire Océanologique de Banyuls sur Mer, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - Patrick Martin
- Conservatoire national du Saumon sauvage, Larma, 43 300 Chanteuges, France
| | - Céline Bérard
- Conservatoire national du Saumon sauvage, Larma, 43 300 Chanteuges, France
| | - Raphaël Lami
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, Observatoire Océanologique de Banyuls sur Mer, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC G1V 0A6, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, 2725 Chemin Sainte-Foy, Quebec City, QC G1V 4G5, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC G1V 0A6, Canada
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10
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Marcoux PÉ, Vincent AT, Massicotte MA, Paquet VE, Doucet ÉJ, Hosseini N, Trudel MV, Byatt G, Laurent M, Frenette M, Charette SJ. Systematic Analysis of the Stress-Induced Genomic Instability of Type Three Secretion System in Aeromonas salmonicida subsp. salmonicida. Microorganisms 2020; 9:microorganisms9010085. [PMID: 33396556 PMCID: PMC7823893 DOI: 10.3390/microorganisms9010085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023] Open
Abstract
The type three secretion system (TTSS) locus of Aeromonas salmonicida subsp. salmonicida, located on the plasmid pAsa5, is known to be lost when the bacterium is grown at temperatures of 25 °C. The loss of the locus is due to the recombination of the insertion sequences flanking the TTSS region. However, the mechanism involved in this recombination is still elusive. Here, we analyzed 22 A. salmonicida subsp. salmonicida strains that had already lost their TTSS locus, and we systematically explored another 47 strains for their susceptibility to lose the same locus when grown at 25 °C. It appeared that strains from Europe were more prone to lose their TTSS locus compared to Canadian strains. More specifically, it was not possible to induce TTSS loss in Canadian strains that have AsaGEI2a, a genomic island, and prophage 3, or in Canadian strains without a genomic island. A comparative genomic approach revealed an almost perfect correlation between the presence of a cluster of genes, not yet characterized, and the susceptibility of various groups of strains to lose their locus. This cluster of genes encodes putative proteins with DNA binding capacity and phage proteins. This discovery creates new opportunities in the study of pAsa5 thermosensitivity.
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Affiliation(s)
- Pierre-Étienne Marcoux
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (M.-A.M.); (V.E.P.); (É.J.D.); (N.H.); (M.V.T.); (G.B.); (M.L.)
- Hôpital Laval, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Antony T. Vincent
- Département des Sciences Animales, Faculté des Sciences de L’agriculture et de L’alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Marie-Ange Massicotte
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (M.-A.M.); (V.E.P.); (É.J.D.); (N.H.); (M.V.T.); (G.B.); (M.L.)
- Hôpital Laval, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Valérie E. Paquet
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (M.-A.M.); (V.E.P.); (É.J.D.); (N.H.); (M.V.T.); (G.B.); (M.L.)
- Hôpital Laval, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Émilie J. Doucet
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (M.-A.M.); (V.E.P.); (É.J.D.); (N.H.); (M.V.T.); (G.B.); (M.L.)
- Hôpital Laval, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Nava Hosseini
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (M.-A.M.); (V.E.P.); (É.J.D.); (N.H.); (M.V.T.); (G.B.); (M.L.)
- Hôpital Laval, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Mélanie V. Trudel
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (M.-A.M.); (V.E.P.); (É.J.D.); (N.H.); (M.V.T.); (G.B.); (M.L.)
- Hôpital Laval, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Gabriel Byatt
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (M.-A.M.); (V.E.P.); (É.J.D.); (N.H.); (M.V.T.); (G.B.); (M.L.)
- Hôpital Laval, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Mathilde Laurent
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (M.-A.M.); (V.E.P.); (É.J.D.); (N.H.); (M.V.T.); (G.B.); (M.L.)
- Hôpital Laval, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Michel Frenette
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada;
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de Médecine Dentaire, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve J. Charette
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Pavillon Charles-Eugène-Marchand, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (M.-A.M.); (V.E.P.); (É.J.D.); (N.H.); (M.V.T.); (G.B.); (M.L.)
- Hôpital Laval, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada;
- Correspondence: ; Tel.: +418-656-2131 (ext. 406914)
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Vincent AT, Hosseini N, Charette SJ. The Aeromonas salmonicida plasmidome: a model of modular evolution and genetic diversity. Ann N Y Acad Sci 2020; 1488:16-32. [PMID: 33040386 DOI: 10.1111/nyas.14503] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/30/2020] [Accepted: 09/09/2020] [Indexed: 12/14/2022]
Abstract
High-throughput genomic sequencing has helped to reveal the plasmidome of Aeromonas salmonicida. This literature review provides an overview of A. salmonicida's rich plasmidome by presenting all the plasmids identified so far, addressing their biological importance and the functional links between them. The plasmids of A. salmonicida, especially those bearing antibiotic resistance genes, can provide clues about interactions of this species with other pathogens (animals and humans), as is the case for pRAS3-3432 and Chlamydia suis or pSN254b and Salmonella enterica. In addition to antibiotic resistance, plasmids play an important role in the virulence of A. salmonicida, particularly for the subspecies salmonicida and the plasmid pAsa5, which carries genes for the type-three secretion system, a virulence factor essential for the bacterium. The A. salmonicida plasmidome also has many cryptic plasmids with no known biological function, but which can be used for the acquisition of new genetic elements. Striking examples are pAsa7 and pAsaXII that provide, respectively, resistance to chloramphenicol and formaldehyde and are derivatives of cryptic pAsa2.
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Affiliation(s)
- Antony T Vincent
- Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Quebec, Canada
| | - Nava Hosseini
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Quebec, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (Hôpital Laval), Quebec City, Quebec, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Quebec, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (Hôpital Laval), Quebec City, Quebec, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada
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Vences A, Abushattal S, Matanza XM, Dubert J, Uzun E, Ogut H, Osorio CR. Highly Transferable pAQU-Related Plasmids Encoding Multidrug Resistance Are Widespread in the Human and Fish Pathogen Photobacterium damselae subsp. damselae in Aquaculture Areas in the Black Sea. MICROBIAL ECOLOGY 2020; 80:507-518. [PMID: 32385615 DOI: 10.1007/s00248-020-01519-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
The marine bacterium Photobacterium damselae subsp. damselae is a pathogen that causes disease in diverse marine animals, and is also a serious opportunistic human pathogen that can cause fatal infections. Strains of this pathogen isolated from diseased European sea bass in aquaculture facilities in the Turkish coast of the Black Sea were found to exhibit reduced sensitivity to multiple antimicrobials. Selected representative strains were subjected to complete genome sequencing and plasmid characterization. It was found that multidrug resistant (MDR) isolates harboured large conjugative plasmids sharing part of their sequence backbone with pAQU-group plasmids, hitherto reported exclusively in China and Japan. Four new pAQU-group versions of plasmids were identified in the present study, containing distinct combinations of the resistance determinants tetB, floR, sul2, qnrVC, dfrA and strAB. Conjugative transfer of pPHDD2-OG2, a representative plasmid of 170,998 bp, occurred at high frequencies (2.2 × 10-2 transconjugants per donor cell), to E. coli and to pathogenic P. damselae subsp. damselae and subsp. piscicida strains. Upon transfer, pPHDD2-OG2 conferred reduced susceptibility to a number of antimicrobials to the recipient strains. Comparative genomics analysis of host strains suggested that these MDR plasmids of the pAQU-group were acquired by different genetic lineages of Pdd. This study provides evidence that P. damselae subsp. damselae isolated from diseased fish constitute a reservoir for conjugative MDR pAQU-group plasmids in the Mediterranean basin, and have the potential to spread to diverse bacterial species.
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Affiliation(s)
- Ana Vences
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
| | - Saqr Abushattal
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
| | - Xosé M Matanza
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
| | - Javier Dubert
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
| | - Ecren Uzun
- Surmene Faculty of Marine Sciences, Department of Fisheries Technology Engineering, Karadeniz Technical University, Trabzon, Turkey
| | - Hamdi Ogut
- Faculty of Natural Sciences, Architecture and Engineering, Department of Bioengineering, Bursa Technical University, Bursa, Turkey
| | - Carlos R Osorio
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain.
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Wang P, Li J, He TT, Li N, Mo ZL, Nie P, Xie HX. Pathogenic characterization of Aeromonas salmonicida subsp. masoucida turbot isolate from China. JOURNAL OF FISH DISEASES 2020; 43:1145-1154. [PMID: 32720397 DOI: 10.1111/jfd.13224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Aeromonas salmonicida is a gram-negative bacterium that is the causative agent of furunculosis. An A. salmonicida strain was isolated from diseased turbot (Scophthalmus maximus) with the sign of furunculosis from North China. Based on vapA gene, the strain was further classified as A. salmonicida subsp. masoucida RZ6S-1. Culturing RZ6S-1 strain at high temperature (28°C) obtained the virulence attenuated strain RZ6S. Genome sequence comparison between the two strains revealed the loss of the type IV secretion system (T4SS) and type III secretion system (T3SS) from the native plasmid pAsmB-1 and pAsmC-1 of wild-type strain RZ6S-1, respectively. Further study demonstrated that the wild-type strain RZ6S-1, but not its derivative mutant RZ6S, can stimulate apoptosis. Elevated protein level of cleaved caspase-3 was detected from epithelioma papulosum cyprinid (EPC) cells infected with wild-type strain RZ6S-1 as compared with that infected with RZ6S strain. Meanwhile, the invasion of the mutant strain RZ6S was about 17-fold higher than the wild-type strain RZ6S-1, suggesting that some protein(s) from A. salmonicida subsp. masoucida RZ6S-1 suppress its invasion. The RZ6S mutant strain was attenuated, since its LD50 is over 10,000 times higher compared to the wild-type strain as revealed in the turbot infection model.
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Affiliation(s)
- Ping Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jie Li
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Tian Tian He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Nan Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhao Lan Mo
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Pin Nie
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hai Xia Xie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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14
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Fernández-Bravo A, Figueras MJ. An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity. Microorganisms 2020; 8:microorganisms8010129. [PMID: 31963469 PMCID: PMC7022790 DOI: 10.3390/microorganisms8010129] [Citation(s) in RCA: 266] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
The genus Aeromonas belongs to the Aeromonadaceae family and comprises a group of Gram-negative bacteria widely distributed in aquatic environments, with some species able to cause disease in humans, fish, and other aquatic animals. However, bacteria of this genus are isolated from many other habitats, environments, and food products. The taxonomy of this genus is complex when phenotypic identification methods are used because such methods might not correctly identify all the species. On the other hand, molecular methods have proven very reliable, such as using the sequences of concatenated housekeeping genes like gyrB and rpoD or comparing the genomes with the type strains using a genomic index, such as the average nucleotide identity (ANI) or in silico DNA–DNA hybridization (isDDH). So far, 36 species have been described in the genus Aeromonas of which at least 19 are considered emerging pathogens to humans, causing a broad spectrum of infections. Having said that, when classifying 1852 strains that have been reported in various recent clinical cases, 95.4% were identified as only four species: Aeromonas caviae (37.26%), Aeromonas dhakensis (23.49%), Aeromonas veronii (21.54%), and Aeromonas hydrophila (13.07%). Since aeromonads were first associated with human disease, gastroenteritis, bacteremia, and wound infections have dominated. The literature shows that the pathogenic potential of Aeromonas is considered multifactorial and the presence of several virulence factors allows these bacteria to adhere, invade, and destroy the host cells, overcoming the immune host response. Based on current information about the ecology, epidemiology, and pathogenicity of the genus Aeromonas, we should assume that the infections these bacteria produce will remain a great health problem in the future. The ubiquitous distribution of these bacteria and the increasing elderly population, to whom these bacteria are an opportunistic pathogen, will facilitate this problem. In addition, using data from outbreak studies, it has been recognized that in cases of diarrhea, the infective dose of Aeromonas is relatively low. These poorly known bacteria should therefore be considered similarly as enteropathogens like Salmonella and Campylobacter.
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Abolghait SK, Mohamed MF, Aly SM, Garbaj AM, Moawad AA. Attenuated virulence of pigment-producing mutant of Aeromonas veroniibv. sobriain HeLa cells and Nile tilapia ( Oreochromis niloticus). Int J Vet Sci Med 2019. [DOI: 10.1016/j.ijvsm.2013.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Said K. Abolghait
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Suez Canal University,41522 Ismailia, Egypt
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Tripoli University,13662 Tripoli, Libya
| | - Mohamed F. Mohamed
- Department of Fish Health, World Fish Center, Regional Research Center for Africa and West Asia, Abbassa, Sharkia, Egypt
| | - Salah M. Aly
- Department of Fish Health, World Fish Center, Regional Research Center for Africa and West Asia, Abbassa, Sharkia, Egypt
| | - Aboubaker M. Garbaj
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Tripoli University,13662 Tripoli, Libya
| | - Ashraf A. Moawad
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Tripoli University,13662 Tripoli, Libya
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
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Rupp M, Pilo P, Müller B, Knüsel R, von Siebenthal B, Frey J, Sindilariu PD, Schmidt-Posthaus H. Systemic infection in European perch with thermoadapted virulent Aeromonas salmonicida (Perca fluviatilis). JOURNAL OF FISH DISEASES 2019; 42:685-691. [PMID: 30806486 DOI: 10.1111/jfd.12970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 06/09/2023]
Abstract
In non-salmonid fish, Aeromonas salmonicidacan cause local infections with severe skin ulcerations, known as atypical furunculosis. In this study, we present a systemic infection by a virulent A. salmonicidain European perch (Perca fluviatilis).This infection was diagnosed in a Swiss warm water recirculation aquaculture system. The isolate of A. salmonicida encodes a type three secretion system (TTSS) most likely located on a plasmid similar to pAsa5/pASvirA, which is known to specify one of the main virulence attributes of the species A. salmonicida. However, the genes specifying the TTSS of the perch isolate show a higher temperature tolerance than strains isolated from cold-water fish. The function of the TTSS in virulence was verified in a cytotoxicity test using bluegill fry and epithelioma papulosum cyprinid cells.
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Affiliation(s)
- Melanie Rupp
- Centre for Fish and Wildlife Health, University of Bern, Bern, Switzerland
| | - Paola Pilo
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Barbara Müller
- Centre for Fish and Wildlife Health, University of Bern, Bern, Switzerland
| | | | | | - Joachim Frey
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
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Investigation of the virulence and genomics of Aeromonas salmonicida strains isolated from human patients. INFECTION GENETICS AND EVOLUTION 2019; 68:1-9. [DOI: 10.1016/j.meegid.2018.11.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/22/2018] [Accepted: 11/27/2018] [Indexed: 11/23/2022]
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Rouleau FD, Vincent AT, Charette SJ. Genomic and phenotypic characterization of an atypical Aeromonas salmonicida strain isolated from a lumpfish and producing unusual granular structures. JOURNAL OF FISH DISEASES 2018; 41:673-681. [PMID: 29315617 DOI: 10.1111/jfd.12769] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 06/07/2023]
Abstract
Aeromonas salmonicida strains are roughly classified into two categories, typical and atypical strains. The latter mainly regroup isolates that present unusual phenotypes or hosts, comparatively to the typical strains that belong to the salmonicida subspecies. This study focuses on an uncharacterized atypical strain, M18076-11, isolated from lumpfish (Cyclopterus lumpus) and not part of the four recognized Aeromonas salmonicida subspecies. This isolate presents an unreported phenotype in the A. salmonicida species: the formation of large granular aggregates. Granules are formed of a heterogeneous mix of live and dead cells, with live cells composing the majority of the population. Even if no mechanism was determined to cause cellular aggregation, small globular structures at the cell surface were observed, which might affect granular formation. Pan-genome phylogenetic analysis indicated that this strain groups alongside the masoucida subspecies. However, phenotypic tests showed that these strains have diverging phenotypes, suggesting that M18076-11 might belong to a new subspecies. Also, a pAsal1-like plasmid, which was only reported in strains of the subspecies salmonicida, was discovered in M18076-11. This study sheds light on unsuspected diversity in A. salmonicida subspecies and stresses the need of thorough identification when a new strain is encountered, as unique traits might be discovered.
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Affiliation(s)
- F D Rouleau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, chemin Sainte-Foy, Quebec, Canada
| | - A T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, chemin Sainte-Foy, Quebec, Canada
| | - S J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, chemin Sainte-Foy, Quebec, Canada
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Vincent AT, Rouleau FD, Moineau S, Charette SJ. Study of mesophilic Aeromonas salmonicida A527 strain sheds light on the species' lifestyles and taxonomic dilemma. FEMS Microbiol Lett 2018; 364:4604818. [PMID: 29126137 DOI: 10.1093/femsle/fnx239] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/07/2017] [Indexed: 12/20/2022] Open
Abstract
The Gram-negative bacterium Aeromonas salmonicida contains five subspecies: salmonicida, smithia, achromogenes, masoucida and pectinolytica. Pectinolytica is a mesophilic subspecies with the ability to thrive at a wide range of temperatures, including 37°C, while the four other subspecies are psychrophilic, restricted to lower temperatures. The psychrophilic subspecies are known to infect a wide range of fishes. However, there is no evidence of pathogenicity for the mesophilic subspecies pectinolytica. Study of the differences between the mesophilic and psychrophilic subspecies is hampered by the lack of completely sequenced and closed genomes from the mesophilic subspecies. A previous study reported that insertion sequences, which can induce genomic rearrangements at temperatures around 25°C, could be one of the determinants explaining the differences in lifestyle (mesophilic or psychrophilic) between the subspecies. In this study, the genome of mesophilic strain A527 of A. salmonicida was sequenced, closed and analyzed to investigate the mesophilic-psychrophilic discrepancy. This reference genome supports the hypothesis that insertion sequences are major determinants of the lifestyle differences between the A. salmonicida subspecies. Moreover, the phylogenetic analysis performed to position strain A527 within the taxonomy raises an issue regarding the intraspecies structure of A. salmonicida.
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Affiliation(s)
- Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada, G1V 0A6.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada, G1V 0A6.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, Canada, G1V 4G5
| | - François D Rouleau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada, G1V 0A6.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada, G1V 0A6.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, Canada, G1V 4G5
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada, G1V 0A6.,Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, Canada, G1V 0A6.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Quebec City, QC, Canada, G1V 0A6
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada, G1V 0A6.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, Canada, G1V 0A6.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, Canada, G1V 4G5
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Bartkova S, Leekitcharoenphon P, Aarestrup FM, Dalsgaard I. Epidemiology of Danish Aeromonas salmonicida subsp. salmonicida in Fish Farms Using Whole Genome Sequencing. Front Microbiol 2017; 8:2411. [PMID: 29259599 PMCID: PMC5723325 DOI: 10.3389/fmicb.2017.02411] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/21/2017] [Indexed: 12/12/2022] Open
Abstract
Furunculosis, a serious infection caused by the bacterium Aeromonas salmonicida subsp. salmonicida is common in sea-reared rainbow trout production in Denmark. Developing an effective control strategy requires knowledge of the epidemiology, as well as the genomic and virulent variability of the Danish A. salmonicida subsp. salmonicida isolates. To obtain this, the genomes of 101 A. salmonicida subsp. salmonicida, including 99 Danish isolates, one Scottish strain and the type strain NCIMB 1102, were sequenced using the Illumina HiSeq platform. Isolates were de novo assembled, examined for presence of plasmids, virulence and iron acquisition proteins, genomic islands, and antibiotic resistance genes. Single Nucleotide Polymorphisms were aligned and subjected to Bayesian temporal phylogenetic and maximum likelihood tree reconstruction using the published genome of A. salmonicida subsp. salmonicida A449 as reference. Bayesian temporal phylogenetic reconstruction suggests that four major introductions of A. salmonicida subsp. salmonicida into Denmark have occurred. The introductions correlate with the freshwater and subsequent seawater expansion of rainbow trout production. Initial transmission of the bacterium could have been from seawater to freshwater or vice versa, and most minor clades include a mixture of strains from different fresh- and seawater farms. Genomic variation of A. salmonicida subsp. salmonicida mostly appeared to be associated with their plasmids and plasmid encoded virulence factors. Nine A. salmonicida subsp. salmonicida isolates harbored worldwide known antibiotic resistance genes against several antibiotics and there is an indication that 33% of the isolates contained the genomic island AsaGEI1b. These findings not only support the usefulness of whole genome sequencing for genetic studies of homogeneous bacteria in general, but provide novel information about the Danish A. salmonicida subsp. salmonicida population, with implications for vaccine development in efforts to better protect Danish rainbow trout in the future.
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Affiliation(s)
- Simona Bartkova
- Section for Bacteriology and Pathology, National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Inger Dalsgaard
- Section for Bacteriology and Pathology, National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
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Tanaka KH, Vincent AT, Emond-Rheault JG, Adamczuk M, Frenette M, Charette SJ. Plasmid composition in Aeromonas salmonicida subsp. salmonicida 01-B526 unravels unsuspected type three secretion system loss patterns. BMC Genomics 2017; 18:528. [PMID: 28701230 PMCID: PMC5508783 DOI: 10.1186/s12864-017-3921-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 07/04/2017] [Indexed: 01/21/2024] Open
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. Results Whole 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. Conclusion The 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 material The 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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Affiliation(s)
- Katherine H Tanaka
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, avenue de la Médecine, Quebec, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045, avenue de la Médecine, Quebec, G1V 0A6, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, 2725, chemin Sainte-Foy, Quebec, G1V 4G5, Canada
| | - Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, avenue de la Médecine, Quebec, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045, avenue de la Médecine, Quebec, G1V 0A6, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, 2725, chemin Sainte-Foy, Quebec, G1V 4G5, Canada
| | - Jean-Guillaume Emond-Rheault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, avenue de la Médecine, Quebec, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045, avenue de la Médecine, Quebec, G1V 0A6, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, 2725, chemin Sainte-Foy, Quebec, G1V 4G5, Canada
| | - Marcin Adamczuk
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilii Miecznikowa 1, 02-096, Warsaw, Poland
| | - Michel Frenette
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045, avenue de la Médecine, Quebec, G1V 0A6, Canada.,Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, 2420, rue de la Terrasse, Quebec, G1V 0A6, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030, avenue de la Médecine, Quebec, G1V 0A6, Canada. .,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045, avenue de la Médecine, Quebec, G1V 0A6, Canada. .,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, 2725, chemin Sainte-Foy, Quebec, G1V 4G5, Canada.
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Vandecraen J, Chandler M, Aertsen A, Van Houdt R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol 2017; 43:709-730. [PMID: 28407717 DOI: 10.1080/1040841x.2017.1303661] [Citation(s) in RCA: 232] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transposable elements (TE), small mobile genetic elements unable to exist independently of the host genome, were initially believed to be exclusively deleterious genomic parasites. However, it is now clear that they play an important role as bacterial mutagenic agents, enabling the host to adapt to new environmental challenges and to colonize new niches. This review focuses on the impact of insertion sequences (IS), arguably the smallest TE, on bacterial genome plasticity and concomitant adaptability of phenotypic traits, including resistance to antibacterial agents, virulence, pathogenicity and catabolism. The direct consequence of IS transposition is the insertion of one DNA sequence into another. This event can result in gene inactivation as well as in modulation of neighbouring gene expression. The latter is usually mediated by de-repression or by the introduction of a complete or partial promoter located within the element. Furthermore, transcription and transposition of IS are affected by host factors and in some cases by environmental signals offering the host an adaptive strategy and promoting genetic variability to withstand the environmental challenges.
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Affiliation(s)
- Joachim Vandecraen
- a Microbiology Unit, Interdisciplinary Biosciences , Belgian Nuclear Research Centre (SCK•CEN) , Mol , Belgium.,b Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre , Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering , KU Leuven , Leuven , Belgium
| | - Michael Chandler
- c Laboratoire de Microbiologie et Génétique Moléculaires, Centre national de la recherche scientifique , Toulouse , France
| | - Abram Aertsen
- b Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre , Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering , KU Leuven , Leuven , Belgium
| | - Rob Van Houdt
- a Microbiology Unit, Interdisciplinary Biosciences , Belgian Nuclear Research Centre (SCK•CEN) , Mol , Belgium
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Bartkova S, Kokotovic B, Skall HF, Lorenzen N, Dalsgaard I. Detection and quantification of Aeromonas salmonicida in fish tissue by real-time PCR. JOURNAL OF FISH DISEASES 2017; 40:231-242. [PMID: 27193829 DOI: 10.1111/jfd.12505] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 06/05/2023]
Abstract
Furunculosis, a septicaemic infection caused by the bacterium Aeromonas salmonicida subsp. salmonicida, currently causes problems in Danish seawater rainbow trout production. Detection has mainly been achieved by bacterial culture, but more rapid and sensitive methods are needed. A previously developed real-time PCR assay targeting the plasmid encoded aopP gene of A. salmonicida was, in parallel with culturing, used for the examination of five organs of 40 fish from Danish freshwater and seawater farms. Real-time PCR showed overall a higher frequency of positives than culturing (65% of positive fish by real-time PCR compared to 30% by a culture approach). Also, no real-time PCR-negative samples were found positive by culturing. A. salmonicida was detected by real-time PCR, though not by culturing, in freshwater fish showing no signs of furunculosis, indicating possible presence of carrier fish. In seawater fish examined after an outbreak and antibiotics treatment, real-time PCR showed the presence of the bacterium in all examined organs (1-482 genomic units mg-1 ). With a limit of detection of 40 target copies (1-2 genomic units) per reaction, a high reproducibility and an excellent efficiency, the present real-time PCR assay provides a sensitive tool for the detection of A. salmonicida.
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Affiliation(s)
- S Bartkova
- National Veterinary Institute, Section for Bacteriology and Pathology, Technical University of Denmark, Frederiksberg C, Denmark
| | - B Kokotovic
- National Veterinary Institute, Section for Bacteriology and Pathology, Technical University of Denmark, Frederiksberg C, Denmark
| | - H F Skall
- Department of Animal Science, Aarhus University, Aarhus N, Denmark
| | - N Lorenzen
- Department of Animal Science, Aarhus University, Aarhus N, Denmark
| | - I Dalsgaard
- National Veterinary Institute, Section for Bacteriology and Pathology, Technical University of Denmark, Frederiksberg C, Denmark
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Tanaka KH, Vincent AT, Trudel MV, Paquet VE, Frenette M, Charette SJ. The mosaic architecture of Aeromonas salmonicida subsp. salmonicida pAsa4 plasmid and its consequences on antibiotic resistance. PeerJ 2016; 4:e2595. [PMID: 27812409 PMCID: PMC5088629 DOI: 10.7717/peerj.2595] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 09/21/2016] [Indexed: 01/10/2023] Open
Abstract
Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis in salmonids, is an issue especially because many isolates of this bacterium display antibiotic resistances, which limit treatments against the disease. Recent results suggested the possible existence of alternative forms of pAsa4, a large plasmid found in A. salmonicida subsp. salmonicida and bearing multiple antibiotic resistance genes. The present study reveals the existence of two newly detected pAsa4 variants, pAsa4b and pAsa4c. We present the extensive characterization of the genomic architecture, the mobile genetic elements and the antimicrobial resistance genes of these plasmids in addition to the reference pAsa4 from the strain A449. The analysis showed differences between the three architectures with consequences on the content of resistance genes. The genomic plasticity of the three pAsa4 variants could be partially explained by the action of mobile genetic elements like insertion sequences. Eight additional isolates from Canada and Europe that bore similar antibiotic resistance patterns as pAsa4-bearing strains were genotyped and specific pAsa4 variants could be attributed to phenotypic profiles. pAsa4 and pAsa4c were found in Europe, while pAsa4b was found in Canada. In accordance with their content in conjugative transfer genes, only pAsa4b and pAsa4c can be transferred by conjugation in Escherichia coli. The plasticity of pAsa4 variants related to the acquisition of antibiotic resistance indicates that these plasmids may pose a threat in terms of the dissemination of antimicrobial-resistant A. salmonicida subsp. salmonicida bacteria.
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Affiliation(s)
- Katherine H Tanaka
- Institut de biologie intégrative et des systèmes, Québec, Canada; Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada; Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada
| | - Antony T Vincent
- Institut de biologie intégrative et des systèmes, Québec, Canada; Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada; Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada
| | - Mélanie V Trudel
- Institut de biologie intégrative et des systèmes, Québec, Canada; Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada; Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada
| | - Valérie E Paquet
- Institut de biologie intégrative et des systèmes, Québec, Canada; Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada; Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada
| | - Michel Frenette
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada; Groupe de recherche en écologie buccale (GREB), Université Laval, Québec, Canada
| | - Steve J Charette
- Institut de biologie intégrative et des systèmes, Québec, Canada; Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada; Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada
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Long M, Nielsen TK, Leisner JJ, Hansen LH, Shen ZX, Zhang QQ, Li A. Aeromonas salmonicidasubsp.salmonicidastrains isolated from Chinese freshwater fish contain a novel genomic island and possible regional-specific mobile genetic elements profiles. FEMS Microbiol Lett 2016; 363:fnw190. [DOI: 10.1093/femsle/fnw190] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 01/15/2023] Open
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26
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Design of an Immersion Vaccine Against Aeromonad Septicemia in Perch (Perca fluviatilis L.). Methods Mol Biol 2016. [PMID: 27076300 DOI: 10.1007/978-1-4939-3389-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The production of an immersion vaccine and the vaccination procedure to immunize fry of perch (Perca fluviatilis L.) against pathogenic Aeromonas sobria that harbor a type III secretion system is described. The vaccine, based on chemically inactivated A. sobria, enables rapid vaccination of a large number of fish by immersion of fry in an aqueous vaccine suspension during 5 min, giving them high protection during fattening under open water conditions in a freshwater lake for at least 4 months.
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Vincent AT, Trudel MV, Freschi L, Nagar V, Gagné-Thivierge C, Levesque RC, Charette SJ. Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida. BMC Genomics 2016; 17:44. [PMID: 26753691 PMCID: PMC4709979 DOI: 10.1186/s12864-016-2381-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/06/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Aeromonads 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. RESULTS We 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. CONCLUSION Insertion 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.
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Affiliation(s)
- Antony T Vincent
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, G1V 4G5, QC, Canada.
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
| | - Mélanie V Trudel
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, G1V 4G5, QC, Canada.
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
| | - Luca Freschi
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
- Département de microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Quebec City, QC, Canada.
| | - Vandan Nagar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.
| | - Cynthia Gagné-Thivierge
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, G1V 4G5, QC, Canada.
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
- Département de microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Quebec City, QC, Canada.
| | - Steve J Charette
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, G1V 4G5, QC, Canada.
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
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Attéré SA, Vincent AT, Trudel MV, Chanut R, Charette SJ. Diversity and Homogeneity among Small Plasmids of Aeromonas salmonicida subsp. salmonicida Linked with Geographical Origin. Front Microbiol 2015; 6:1274. [PMID: 26635745 PMCID: PMC4655240 DOI: 10.3389/fmicb.2015.01274] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 10/31/2015] [Indexed: 01/31/2023] Open
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.
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Affiliation(s)
- Sabrina A Attéré
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec City, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
| | - Antony T Vincent
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec City, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
| | - Mélanie V Trudel
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec City, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
| | - Romain Chanut
- Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
| | - Steve J Charette
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec City, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
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Emond-Rheault JG, Vincent AT, Trudel MV, Frey J, Frenette M, Charette SJ. AsaGEI2b: a new variant of a genomic island identified in theAeromonas salmonicidasubsp.salmonicidaJF3224 strain isolated from a wild fish in Switzerland. FEMS Microbiol Lett 2015; 362:fnv093. [DOI: 10.1093/femsle/fnv093] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2015] [Indexed: 12/24/2022] Open
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Vincent AT, Tanaka KH, Trudel MV, Frenette M, Derome N, Charette SJ. Draft genome sequences of two Aeromonas salmonicida subsp. salmonicida isolates harboring plasmids conferring antibiotic resistance. FEMS Microbiol Lett 2015; 362:fnv002. [DOI: 10.1093/femsle/fnv002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Tanaka KH, Frenette M, Charette SJ. IS-mediated loss of virulence by Aeromonas salmonicida: A tangible piece of an evolutionary puzzle. Mob Genet Elements 2014; 3:e23498. [PMID: 23734295 PMCID: PMC3661141 DOI: 10.4161/mge.23498] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/04/2013] [Accepted: 01/04/2013] [Indexed: 11/22/2022] Open
Abstract
Insertion sequences (IS) are abundant in the bacterial fish pathogen Aeromonas salmonicida genome. IS are involved in rearrangement events that lead to the loss of virulence. In previous work, we studied a plasmid rearrangement that causes the deletion of the type three secretion system in A. salmonicida, resulting in a loss of virulence. We showed that the rearrangement is caused by the recombination of two IS (ISAS11) on an unstable plasmid (pAsa5). However, many rearrangements cannot be explained by our experimental approach and are thought to be the result of more complex or incomplete rearrangement events, as suggested by other plasmid loss profiles observed in various A. salmonicida strains. In this commentary, we examine the genetic instability of A. salmonicida indicating that its genome is rapidly evolving.
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Affiliation(s)
- Katherine H Tanaka
- Institut de biologie intégrative et des système; Pavillon Charles-Eugène-Marchand; Université Laval; Quebec City, QC Canada ; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec; Hôpital Laval; Quebec City, QC Canada
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Detection of variants of the pRAS3, pAB5S9, and pSN254 plasmids in Aeromonas salmonicida subsp. salmonicida: multidrug resistance, interspecies exchanges, and plasmid reshaping. Antimicrob Agents Chemother 2014; 58:7367-74. [PMID: 25267667 DOI: 10.1128/aac.03730-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The ubiquitous water-borne Gram-negative bacterium Aeromonas salmonicida subsp. salmonicida is the causative agent of furunculosis, a worldwide disease in fish farms. Plasmids carrying antibiotic resistance genes have already been described for this bacterium. The aim of the present study was to identify and characterize additional multidrug resistance plasmids in A. salmonicida subsp. salmonicida. We sequenced the plasmids present in two multiple antibiotic-resistant isolates using high-throughput technologies. We also investigated 19 other isolates with various multidrug resistance profiles by genotyping PCR and assessed their resistance to tetracycline. We identified variants of the pAB5S9 and pSN254 plasmids that carry several antibiotic resistance genes and that have been previously reported in bacteria other than A. salmonicida subsp. salmonicida, which suggests a high level of interspecies exchange. Genotyping analyses and the antibiotic resistance profiles of the 19 other isolates support the idea that multiple versions of pAB5S9 and pSN254 exist in A. salmonicida subsp. salmonicida. We also identified variants of the pRAS3 plasmid. The present study revealed that A. salmonicida subsp. salmonicida harbors a wide variety of plasmids, which suggests that this ubiquitous bacterium may contribute to the spread of antibiotic resistance genes in the environment.
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Abstract
Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point mutations. In a long-term evolution experiment, twelve Escherichia coli populations have been propagated in a glucose-limited environment for over 25 years. We used whole-genome mapping (optical mapping) combined with genome sequencing and PCR analysis to identify the large-scale chromosomal rearrangements in clones from each population after 40,000 generations. A total of 110 rearrangement events were detected, including 82 deletions, 19 inversions, and 9 duplications, with lineages having between 5 and 20 events. In three populations, successive rearrangements impacted particular regions. In five populations, rearrangements affected over a third of the chromosome. Most rearrangements involved recombination between insertion sequence (IS) elements, illustrating their importance in mediating genome plasticity. Two lines of evidence suggest that at least some of these rearrangements conferred higher fitness. First, parallel changes were observed across the independent populations, with ~65% of the rearrangements affecting the same loci in at least two populations. For example, the ribose-utilization operon and the manB-cpsG region were deleted in 12 and 10 populations, respectively, suggesting positive selection, and this inference was previously confirmed for the former case. Second, optical maps from clones sampled over time from one population showed that most rearrangements occurred early in the experiment, when fitness was increasing most rapidly. However, some rearrangements likely occur at high frequency and may have simply hitchhiked to fixation. In any case, large-scale rearrangements clearly influenced genomic evolution in these populations. Bacterial chromosomes are dynamic structures shaped by long histories of evolution. Among genomic changes, large-scale DNA rearrangements can have important effects on the presence, order, and expression of genes. Whole-genome sequencing that relies on short DNA reads cannot identify all large-scale rearrangements. Therefore, deciphering changes in the overall organization of genomes requires alternative methods, such as optical mapping. We analyzed the longest-running microbial evolution experiment (more than 25 years of evolution in the laboratory) by optical mapping, genome sequencing, and PCR analyses. We found multiple large genome rearrangements in all 12 independently evolving populations. In most cases, it is unclear whether these changes were beneficial themselves or, alternatively, hitchhiked to fixation with other beneficial mutations. In any case, many genome rearrangements accumulated over decades of evolution, providing these populations with genetic plasticity reminiscent of that observed in some pathogenic bacteria.
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Vanden Bergh P, Frey J. Aeromonas salmonicida subsp. salmonicida in the light of its type-three secretion system. Microb Biotechnol 2013; 7:381-400. [PMID: 24119189 PMCID: PMC4229320 DOI: 10.1111/1751-7915.12091] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 11/30/2022] Open
Abstract
Aeromonas salmonicida subsp. salmonicida is an important pathogen in salmonid aquaculture and is responsible for the typical furunculosis. The type-three secretion system (T3SS) is a major virulence system. In this work, we review structure and function of this highly sophisticated nanosyringe in A. salmonicida. Based on the literature as well as personal experimental observations, we document the genetic (re)organization, expression regulation, anatomy, putative functional origin and roles in the infectious process of this T3SS. We propose a model of pathogenesis where A. salmonicida induces a temporary immunosuppression state in fish in order to acquire free access to host tissues. Finally, we highlight putative important therapeutic and vaccine strategies to prevent furunculosis of salmonid fish.
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Affiliation(s)
- Philippe Vanden Bergh
- Institute of Veterinary Bacteriology, University of Bern, Länggassstrasse 122, Bern, Switzerland
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The Aeromonas salmonicida subsp. salmonicida exoproteome: determination of the complete repertoire of Type-Three Secretion System effectors and identification of other virulence factors. Proteome Sci 2013; 11:42. [PMID: 24073886 PMCID: PMC3852671 DOI: 10.1186/1477-5956-11-42] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/23/2013] [Indexed: 01/24/2023] Open
Abstract
Background Aeromonas salmonicida subsp. salmonicida, the etiologic agent of furunculosis, is a major pathogen of fisheries worldwide. Several virulence factors have been described, but the type-three secretion system (T3SS) is recognized as having a major effect on virulence by injecting effectors directly into fish cells. In this study we used high-throughput proteomics to display the differences between in vitro secretome of A. salmonicida wild-type (wt, hypervirulent, JF2267) and T3SS-deficient (isogenic ΔascV, extremely low-virulent, JF2747) strains in exponential and stationary phases of growth. Results Results confirmed the secretion of effectors AopH, AexT, AopP and AopO via T3SS, and for the first time demonstrated the impact of T3SS in secretion of Ati2, AopN and ExsE that are known as effectors in other pathogens. Translocators, needle subunits, Ati1, and AscX were also secreted in supernatants (SNs) dependent on T3SS. AopH, Ati2, AexT, AopB and AopD were in the top seven most abundant excreted proteins. EF-G, EF-Tu, DnaK, HtpG, PNPase, PepN and MdeA were moderately secreted in wt SNs and predicted to be putative T3 effectors by bioinformatics. Pta and ASA_P5G088 were increased in wt SNs and T3-associated in other bacteria. Ten conserved cytoplasmic proteins were more abundant in wt SNs than in the ΔascV mutant, but without any clear association to a secretion system. T1-secreted proteins were predominantly found in wt SNs: OmpAI, OmpK40, DegQ, insulinase ASA_0716, hypothetical ASA_0852 and ASA_3619. Presence of T3SS components in pellets was clearly decreased by ascV deletion, while no impact was observed on T1- and T2SS. Our results demonstrated that the ΔascV mutant strain excreted well-described (VapA, AerA, AerB, GCAT, Pla1, PlaC, TagA, Ahe2, GbpA and enolase) and yet uncharacterized potential toxins, adhesins and enzymes as much as or even more than the wt strain. Other putative important virulence factors were not detected. Conclusions We demonstrated the whole in vitro secretome and T3SS repertoire of hypervirulent A. salmonicida. Several toxins, adhesins and enzymes that are not part of the T3SS secretome were secreted to a higher extent in the extremely low-virulent ΔascV mutant. All together, our results show the high importance of an intact T3SS to initiate the furunculosis and offer new information about the pathogenesis.
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Dallaire-Dufresne S, Tanaka KH, Trudel MV, Lafaille A, Charette SJ. Virulence, genomic features, and plasticity of Aeromonas salmonicida subsp. salmonicida, the causative agent of fish furunculosis. Vet Microbiol 2013; 169:1-7. [PMID: 23890675 DOI: 10.1016/j.vetmic.2013.06.025] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/13/2013] [Accepted: 06/22/2013] [Indexed: 11/24/2022]
Abstract
The bacterium Aeromonas salmonicida subsp. salmonicida is the causative agent of furunculosis, a systemic disease of fish in the salmonid family. Furunculosis is a ubiquitous disease that affects aquaculture operations worldwide and is characterized by high mortality and morbidity. A better understanding of the bacterium is required to find a cure. Thereby, this review centers on A. salmonicida subsp. salmonicida, its major virulence factors, and its genome. The classification and characteristics of A. salmonicida subsp. salmonicida, the virulence factors, such as the A-layer, extracellular molecules, and type three secretion system as well as the characteristics and plasticity of its genome are described.
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Affiliation(s)
- Stéphanie Dallaire-Dufresne
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada G1V 4G5
| | - Katherine H Tanaka
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada G1V 4G5
| | - Mélanie V Trudel
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada G1V 4G5
| | - Andrée Lafaille
- Faculté de Médecine Vétérinaire, Université de Montréal, 3200 rue Sicotte, St-Hyacinthe, QC, Canada J2S 7C6
| | - Steve J Charette
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada G1V 4G5; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6.
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Trudel MV, Tanaka KH, Filion G, Daher RK, Frenette M, Charette SJ. Insertion sequence AS5 (IS AS5 ) is involved in the genomic plasticity of Aeromonas salmonicida.. Mob Genet Elements 2013; 3:e25640. [PMID: 23956951 PMCID: PMC3742599 DOI: 10.4161/mge.25640] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/02/2013] [Accepted: 07/05/2013] [Indexed: 12/16/2022] Open
Abstract
The genome of the fish pathogen Aeromonas salmonicida subsp salmonicida harbors a large number of insertion sequences (ISs), many of which are located on plasmids. In the present study, we analyzed the small plasmid profile of A. salmonicida strains to identify evidences of plasmid alterations. Ten out of 78 strains analyzed displayed an unconventional plasmid profile. However the HER1104 strain was unique, having a positive PCR signal for pAsal1 plasmid despite not carrying this plasmid. Instead, HER1104 was bearing a plasmid at higher molecular weight than pAsal1. We characterized this new larger plasmid, which we called pAsal1B since it is a derivative of pAsal1 containing one more complete IS (ISAS5) than the parental plasmid. An additional 96 bp relic of ISAS5 was also present in pAsal1B. These results propose that ISAS5 is another active mobile genetic element in A. salmonicida subsp salmonicida and provided further proof of the genomic plasticity of this bacterium.
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Affiliation(s)
- Mélanie V Trudel
- Institut de Biologie Intégrative et des Systèmes (IBIS); Pavillon Charles-Eugène-Marchand; Université Laval; Quebec City, QC Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec; Quebec City, QC Canada
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Characterization of Aeromonas hydrophila wound pathotypes by comparative genomic and functional analyses of virulence genes. mBio 2013; 4:e00064-13. [PMID: 23611906 PMCID: PMC3638308 DOI: 10.1128/mbio.00064-13] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aeromonas hydrophila has increasingly been implicated as a virulent and antibiotic-resistant etiologic agent in various human diseases. In a previously published case report, we described a subject with a polymicrobial wound infection that included a persistent and aggressive strain of A. hydrophila (E1), as well as a more antibiotic-resistant strain of A. hydrophila (E2). To better understand the differences between pathogenic and environmental strains of A. hydrophila, we conducted comparative genomic and functional analyses of virulence-associated genes of these two wound isolates (E1 and E2), the environmental type strain A. hydrophila ATCC 7966T, and four other isolates belonging to A. aquariorum, A. veronii, A. salmonicida, and A. caviae. Full-genome sequencing of strains E1 and E2 revealed extensive differences between the two and strain ATCC 7966T. The more persistent wound infection strain, E1, harbored coding sequences for a cytotoxic enterotoxin (Act), a type 3 secretion system (T3SS), flagella, hemolysins, and a homolog of exotoxin A found in Pseudomonas aeruginosa. Corresponding phenotypic analyses with A. hydrophila ATCC 7966T and SSU as reference strains demonstrated the functionality of these virulence genes, with strain E1 displaying enhanced swimming and swarming motility, lateral flagella on electron microscopy, the presence of T3SS effector AexU, and enhanced lethality in a mouse model of Aeromonas infection. By combining sequence-based analysis and functional assays, we characterized an A. hydrophila pathotype, exemplified by strain E1, that exhibited increased virulence in a mouse model of infection, likely because of encapsulation, enhanced motility, toxin secretion, and cellular toxicity. Aeromonas hydrophila is a common aquatic bacterium that has increasingly been implicated in serious human infections. While many determinants of virulence have been identified in Aeromonas, rapid identification of pathogenic versus nonpathogenic strains remains a challenge for this genus, as it is for other opportunistic pathogens. This paper demonstrates, by using whole-genome sequencing of clinical Aeromonas strains, followed by corresponding virulence assays, that comparative genomics can be used to identify a virulent subtype of A. hydrophila that is aggressive during human infection and more lethal in a mouse model of infection. This aggressive pathotype contained genes for toxin production, toxin secretion, and bacterial motility that likely enabled its pathogenicity. Our results highlight the potential of whole-genome sequencing to transform microbial diagnostics; with further advances in rapid sequencing and annotation, genomic analysis will be able to provide timely information on the identities and virulence potential of clinically isolated microorganisms.
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Beaz-Hidalgo R, Figueras MJ. Aeromonas spp. whole genomes and virulence factors implicated in fish disease. JOURNAL OF FISH DISEASES 2013; 36:371-388. [PMID: 23305319 DOI: 10.1111/jfd.12025] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 09/20/2012] [Accepted: 09/23/2012] [Indexed: 05/27/2023]
Abstract
It is widely recognized that Aeromonas infections produce septicaemia, and ulcerative and haemorrhagic diseases in fish, causing significant mortality in both wild and farmed freshwater and marine fish species that damage the economics of the aquaculture sector. The descriptions of the complete genomes of Aeromonas species have allowed the identification of an important number of virulence genes that affect the pathogenic potential of these bacteria. This review will focus on the most relevant information derived from the available Aeromonas genomes in relation to virulence and on the diverse virulence factors that actively participate in host adherence, colonization and infection, including structural components, extracellular factors, secretion systems, iron acquisition and quorum sensing mechanisms.
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Affiliation(s)
- R Beaz-Hidalgo
- Unitat de Microbiologia, Departament de Ciènces Médiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
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Abolghait SK. Suicide plasmid-dependent IS1-element untargeted integration into Aeromonas veronii bv. sobria generates brown pigment-producing and spontaneous pelleting mutant. Curr Microbiol 2013; 67:91-9. [PMID: 23436029 DOI: 10.1007/s00284-013-0335-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 02/04/2013] [Indexed: 11/30/2022]
Abstract
Foodborne Gram-negative pathogens belonging to the genus Aeromonas are variable in harboring insertion sequence (IS) elements that play an important role in the generation of dysfunctional relatives of known genes. Using suicide plasmids carrying an IS1-element, untargeted integration is a common problem during experimental trials to generate specific mutations by homologous recombination. In this work, different strains of Aeromonas veronii bv. sobria (AeG1 and ATCC 9071T), A. hydrophila ATCC 19570, and A. sobria ATCC 43979T are examined for acquisition of IS1-element from pYAK1 suicide plasmid. It was found that untargeted integration of IS1-element is encountered only in ATCC 9071T strain. Such untargeted integration generates a novel brown pigment-producing and spontaneous pelleting (BP(+)SP(+)) mutant. Furthermore, BP(+)SP(+) mutant strain secretes significantly higher quantity of PilF homologous protein than the wild-type strain and displays an enhanced protein tyrosine phosphorylation activity. Thus, current work shows that Aeromonas spp. strains are variable in their susceptibility for suicide plasmid-dependent IS1-element untargeted integration as well as the susceptible strain is changed to mimic pigment-producing and spontaneous pelleting strains that are naturally occurring among heterogeneous group of foodborne aeromonads.
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Affiliation(s)
- Said Kamal Abolghait
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Suez Canal University, 41522, Ismailia, Egypt.
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Studer N, Frey J, Vanden Bergh P. Clustering subspecies of Aeromonas salmonicida using IS630 typing. BMC Microbiol 2013; 13:36. [PMID: 23406017 PMCID: PMC3608246 DOI: 10.1186/1471-2180-13-36] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 02/05/2013] [Indexed: 11/17/2022] Open
Abstract
Background The insertion element IS630 found in Aeromonas salmonicida belongs to the IS630-Tc1-mariner superfamily of transposons. It is present in multiple copies and represents approximately half of the IS present in the genome of A. salmonicida subsp. salmonicida A449. Results By using High Copy Number IS630 Restriction Fragment Length Polymorphism (HCN-IS630-RFLP), strains of various subspecies of Aeromonas salmonicida showed conserved or clustering patterns, thus allowing their differentiation from each other. Fingerprints of A. salmonicida subsp. salmonicida showed the highest homogeneity while ‘atypical’ A. salmonicida strains were more heterogeneous. IS630 typing also differentiated A. salmonicida from other Aeromonas species. The copy number of IS630 in Aeromonas salmonicida ranges from 8 to 35 and is much lower in other Aeromonas species. Conclusions HCN-IS630-RFLP is a powerful tool for subtyping of A. salmonicida. The high stability of IS630 insertions in A. salmonicida subsp. salmonicida indicates that it might have played a role in pathoadaptation of A. salmonicida which has reached an optimal configuration in the highly virulent and specific fish pathogen A. salmonicida subsp. salmonicida.
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Affiliation(s)
- Nicole Studer
- Institute of Veterinary Bacteriology, University of Bern, Länggassstrasse 122, Bern, Switzerland
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