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Ucieklak K, Wojtys-Tekiel S, Leroy G, Le Devendec L, Baron S, Kaszowska M. New Structure of Aeromonas salmonicida O-Polysaccharide Isolated from Ill Farmed Fish. Microorganisms 2024; 12:1575. [PMID: 39203417 PMCID: PMC11355949 DOI: 10.3390/microorganisms12081575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/08/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024] Open
Abstract
The diversity of O-polysaccharides (O-antigens) among 28 Aeromonas salmonicida strains isolated from ill fish has been determined by using high-resolution magic angle spinning (HR MAS) NMR spectroscopy. The new O-polysaccharide has been identified in two isolates. This new structure was investigated by 1H and 13C NMR spectroscopy and matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The following structure of the linear hexasaccharide repeating unit of A. salmonicida O-antigen has been established: →3)-α-L-Rhap-(1→3)-α-D-ManpNAc-(1→2)-β-D-Glcp-(1→3)-α-L-Rhap2OAc4OAc-(1→3)-β-D-ManpNAc-(1→3)-α-D-Glcp-(1→. This new A. salmonicida O-polysaccharide was detected among two isolates collected from trout and turbot fish in 2010 and 2011, respectively. Further investigations should be conducted to evaluate the distribution of this new O-polysaccharide among a larger collection of isolates, depending on their geographic origin, the species of fish, and the health status of the fish.
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Affiliation(s)
- Karolina Ucieklak
- Laboratory of Microbial Immunochemistry and Vaccines, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (K.U.); (S.W.-T.)
| | - Sylwia Wojtys-Tekiel
- Laboratory of Microbial Immunochemistry and Vaccines, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (K.U.); (S.W.-T.)
| | - Garance Leroy
- Laboratory of Marine Biotechnology and Chemistry, University of Western Brittany, EMR CNRS 6076, IUEM, 29000 Quimper, France
| | - Laëtitia Le Devendec
- Mycoplasmology-Bacteriology and Antimicrobial Resistance Unit Ploufragan Plouzane-Niort Laboratory (ANSES), 22440 Ploufragan, France; (L.L.D.)
| | - Sandrine Baron
- Mycoplasmology-Bacteriology and Antimicrobial Resistance Unit Ploufragan Plouzane-Niort Laboratory (ANSES), 22440 Ploufragan, France; (L.L.D.)
| | - Marta Kaszowska
- Laboratory of Microbial Immunochemistry and Vaccines, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (K.U.); (S.W.-T.)
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Hosseini N, Chehreghani M, Moineau S, Charette SJ. Centroid of the bacterial growth curves: a metric to assess phage efficiency. Commun Biol 2024; 7:673. [PMID: 38822127 PMCID: PMC11143336 DOI: 10.1038/s42003-024-06379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 05/23/2024] [Indexed: 06/02/2024] Open
Abstract
Phage replication can be studied using various approaches, including measuring the optical density (OD) of a bacterial culture in a liquid medium in the presence of phages. A few quantitative methods are available to measure and compare the efficiency of phages by using a single index based on the analysis of OD curves. However, these methods are not always applicable to non-canonical OD curves. Using the concept of center of area (centroid), we developed a metric called Centroid Index (CI), sensitive to the trend of the growth curves (OD distribution) including bacterial regrowth, which is not considered by the methods already available. We also provide a user-friendly software to facilitate the calculation of CI. This method offers an alternative and more precise way to determine phage efficiency by considering the OD variations over time, which may help in the selection of phages for biocontrol applications.
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Affiliation(s)
- Nava Hosseini
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.
| | - Mahdi Chehreghani
- Department of Mechanical Engineering, McGill University, Montreal, QC, H3A 0C3, Canada
| | - Sylvain Moineau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada
- 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
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.
- 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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Dehdashti S, Mohseni P, Ghanbarpour R, Aslani S, Moradiyan MS, Kalantar-Neyestanaki D. The emergence of carbapenem-resistance and New Delhi metallo-β-lactamase-1 ( blaNDM-1) among Salmonella spp. in Kerman, Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2024; 16:29-38. [PMID: 38682060 PMCID: PMC11055441 DOI: 10.18502/ijm.v16i1.14868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Background and Objectives Salmonella species (spp) are the most prevalent zoonotic pathogens that cause outbreaks of gastroenteritis worldwide. Therefore evaluation of the profile of antibiotic resistance, virulence factors, and plasmid replicon types in these bacteria is necessary to control and prevent the spread of potentially pathogenic and drug-resistant strains. Materials and Methods This study was performed on 39 Salmonella spp. The antibacterial susceptibility of isolates to various antibiotic agents was determined using disk diffusion test. β-lactamases (bla) including ESBLs, AmpC, MBLs, and virulence genes were detected by PCR methods. Plasmid incompatibility groups among the isolates were identified using PCR-based replicon typing (PBRT). Results The most prevalent virulent gene was phoP/Q (84.6%). slyA, sopB, and stn were identified in 79.4% (n=31), 69.2% (n=27), and 2.5% (n=1) of the isolates, respectively. The antibiotic susceptibility testing showed that 30.7% of the isolates were ESBL-producing. blaTEM (41%; n=16) was the most frequent β-lactamase gene among the isolates followed by blaNDM-1 (15.4%; n=6), blaDHA (7.7%; n=3), and blaCTX-M (1.5%; n=1). Six different plasmid replicon types, including IncP (n=9; 23%), IncFIC (n=3; 7.70%), IncY (n=3; 7.70%), IncI1-Iγ (n=2; 5.12%), IncFIIAs (n=1; 2.56%), and IncN (n=1; 2.56%) were observed among the isolates. Conclusion Our study showed the emergence of carbapenem-resistant and blaNDM-1 among Salmonella spp. for the first time in Kerman, Iran. Since Salmonella spp. plays an important role in the transmission of resistance genes in livestock and humans in the food chains, so more stringent control policies are recommended to prevent the circulation of drug-resistant and potentially pathogenic strains from animals to humans.
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Affiliation(s)
- Sanaz Dehdashti
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Parvin Mohseni
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Reza Ghanbarpour
- Molecular Microbiology Research Group, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Sajad Aslani
- Department of Pharmaceutics, Faculty of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Davood Kalantar-Neyestanaki
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Department of Medical Microbiology (Bacteriology and Virology), Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
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Ahiable MG, Matsunaga K, Hokin M, Iida K, Befu F, Oshima SI. In Vitro Efficacy of Isobutyl Cyanoacrylate Nanoparticles against Fish Bacterial Pathogens and Selection Preference by Rainbow Trout ( Oncorhynchus mykiss). Microorganisms 2023; 11:2877. [PMID: 38138020 PMCID: PMC10745873 DOI: 10.3390/microorganisms11122877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 12/24/2023] Open
Abstract
The upsurge in havoc being wreaked by antibiotic-resistant bacteria has led to an urgent need for efficacious alternatives to antibiotics. This study assessed the antibacterial efficacy of two isobutyl cyanoacrylate nanoparticles (iBCA-NPs), D6O and NP30, against major bacterial pathogens of fish. In vivo tests on rainbow trout were preceded by in vitro tests of minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). NP30 exhibited higher efficacy than D60, but both iBCA-NPs demonstrated dose-dependent and species-specific in vitro antibacterial properties against the bacterial isolates. Generally, Gram-negative bacteria were more resistant to the iBCA-NPs. Streptococcus iniae, Tenacibaculum maritimum, and Photobacterium damselae were particularly sensitive to both iBCA-NPs. Administered to rainbow trout at 3571.4 mg (iBCA-NP)/kg feed, the iBCA-NPs produced a relative gain rate and survival rates comparable to the control (p > 0.05). The condition factor and the hepatosomatic and viscerosomatic indices of fish were indifferentiable (p > 0.05) between the iBCA-NP groups and the control. The iBCA-NPs caused no alteration in stress, oxidative stress (superoxide dismutase, SOD), plasma complement titer, or lysozyme activity. This study presents the first report of antibacterial activity of iBCA-NPs against Gram-negative bacteria. The results of this study suggest that D60 and NP30 may contribute to reducing the amounts of antibiotics and chemotherapeutic agents used in aquaculture.
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Affiliation(s)
- Mawuko G. Ahiable
- Laboratory of Cell Structure and Function, Division of Marine Bioresource Science, Graduate School of Kuroshio Science, Kochi University, Nankoku Kochi 783-8502, Japan; (M.G.A.); (K.M.); (M.H.)
| | - Kouki Matsunaga
- Laboratory of Cell Structure and Function, Division of Marine Bioresource Science, Graduate School of Kuroshio Science, Kochi University, Nankoku Kochi 783-8502, Japan; (M.G.A.); (K.M.); (M.H.)
| | - Mao Hokin
- Laboratory of Cell Structure and Function, Division of Marine Bioresource Science, Graduate School of Kuroshio Science, Kochi University, Nankoku Kochi 783-8502, Japan; (M.G.A.); (K.M.); (M.H.)
| | - Kazuhiro Iida
- Chikami Miltec Inc., 1-6-3 Ohtesuji, Kochi City 780-0842, Japan; (K.I.); (F.B.)
| | - Fumiaki Befu
- Chikami Miltec Inc., 1-6-3 Ohtesuji, Kochi City 780-0842, Japan; (K.I.); (F.B.)
| | - Syun-Ichirou Oshima
- Laboratory of Cell Structure and Function, Division of Marine Bioresource Science, Graduate School of Kuroshio Science, Kochi University, Nankoku Kochi 783-8502, Japan; (M.G.A.); (K.M.); (M.H.)
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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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6
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Hosseini N, Paquet VE, Marcoux PÉ, Alain CA, Paquet MF, Moineau S, Charette SJ. MQM1, a bacteriophage infecting strains of Aeromonas salmonicida subspecies salmonicida carrying Prophage 3. Virus Res 2023; 334:199165. [PMID: 37385348 PMCID: PMC10410586 DOI: 10.1016/j.virusres.2023.199165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/30/2023] [Accepted: 06/27/2023] [Indexed: 07/01/2023]
Abstract
Aeromonas salmonicida subsp. salmonicida is a Gam-negative bacterium responsible for furunculosis in fish. Because this aquatic bacterial pathogen has a rich reservoir of antibiotic-resistant genes, it is essential to investigate antibacterial alternatives, including the use of phages. Yet, we have previously demonstrated the inefficiency of a phage cocktail designed against A. salmonicida subsp. salmonicida strains due to a phage resistance phenotype associated to a prophage, namely Prophage 3. To bypass this resistance, one of the solutions is to isolate novel phages capable of infecting Prophage 3-bearing strains. Here we report on the isolation and characterization of the new virulent phage vB_AsaP_MQM1 (or MQM1), which is highly specific to A. salmonicida subsp. salmonicida strains. Phage MQM1 inhibited the growth of 01-B516, a strain carrying Prophage 3, including when combined to the previous phage cocktail. MQM1 infected 26 out of the 30 (87%) Prophage 3-bearing strains tested. Its linear dsDNA genome contains 63,343 bp, with a GC content of 50.2%. MQM1 genome can encode 88 proteins and 8 tRNAs, while no integrase or transposase-encoding genes were found. This podophage has an icosahedral capsid and a non-contractile short tail. We suggest that MQM1 may be a good addition to future phage cocktails against furunculosis to resolve the Prophage 3-resistance issue.
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Affiliation(s)
- Nava Hosseini
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, 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 (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; 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
| | - Pierre-Étienne Marcoux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Charles-Antoine Alain
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Maude F Paquet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Sylvain Moineau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; 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.; Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC, G1V 0A6, Canada.; 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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7
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Host Dependent-Transposon for a Plasmid Found in Aeromonas salmonicida subsp. salmonicida That Bears a catB3 Gene for Chloramphenicol Resistance. Antibiotics (Basel) 2023; 12:antibiotics12020257. [PMID: 36830168 PMCID: PMC9952659 DOI: 10.3390/antibiotics12020257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Plasmids that carry antibiotic resistance genes occur frequently in Aeromonas salmonicida subsp. salmonicida, an aquatic pathogen with severe consequences in salmonid farming. Here, we describe a 67 kb plasmid found in the A. salmonicida subsp. salmonicida Strain SHY15-2939 from Quebec, Canada. This new plasmid, named pAsa-2939 and identified by high throughput sequencing, displays features never found before in this bacterial species. It contains a transposon related to the Tn21 family, but with an unusual organization. This transposon bears a catB3 gene (chloramphenicol resistance) that has not been detected yet in A. salmonicida subsp. salmonicida. The plasmid is transferable by conjugation into Aeromonas hydrophila, but not into Escherichia coli. Based on PCR analysis and genomic sequencing (Illumina and PacBio), we determined that the transposon is unstable in A. salmonicida subsp. salmonicida Strain SHY15-2939, but it is stable in A. hydrophila trans-conjugants, which explains the chloramphenicol resistance variability observed in SHY15-2939. These results suggest that this bacterium is likely not the most appropriate host for this plasmid. The presence of pAsa-2939 in A. salmonicida subsp. salmonicida also strengthens the reservoir role of this bacterium for antibiotic resistance genes, even those that resist antibiotics not used in aquaculture in Québec, such as chloramphenicol.
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8
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Leduc GR, Paquet VE, Piché LC, Vincent AT, Charette SJ. Isolation of vB_AsaM_LPM4 reveals the dynamics of Prophage 3 in Aeromonas salmonicida subsp. salmonicida. Arch Virol 2023; 168:72. [PMID: 36670249 DOI: 10.1007/s00705-022-05623-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 10/24/2022] [Indexed: 01/21/2023]
Abstract
Aeromonas salmonicida subsp. salmonicida causes furunculosis, a major infection that affects fish farms worldwide. We isolated phage vB_AsaM_LPM4 (LPM4) from a diseased fish. Based on its DNA sequence, LPM4 is identical to the uncharacterized Prophage 3, a prophage present mostly in North American A. salmonicida subsp. salmonicida isolates that bear the genomic island AsaGEI2a. Prophage 3 and AsaGEI2a are inserted side by side in the bacterial chromosome. The LPM4/Prophage 3 sequence is similar to that of other prophages found in various members of the genus Aeromonas. LPM4 specifically infects A. salmonicida subsp. salmonicida strains that do not already bear Prophage 3. The presence of an A-layer on the surface of the bacteria is not necessary for the adsorption of phage LPM4 but seems to facilitate its infection process. We also successfully produced lysogenic strains that bear Prophage 3 using sensitive strains with different genetic backgrounds, suggesting that there is no interdependency between LPM4 and AsaGEIs. PCR analysis of the excision dynamics of Prophage 3 and AsaGEIs revealed that these genetic elements can spontaneously excise themselves from the bacterial chromosome independently of one another. Through the isolation and characterization of LPM4, this study reveals new facets of Prophage 3 and AsaGEIs.
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Affiliation(s)
- Gabrielle R Leduc
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada.,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
| | - Valérie E Paquet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada.,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
| | - Laurie C Piché
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada.,Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada.,Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada. .,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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9
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Hofer RN, Lin A, House BC, Purvis CN, Harris BJ, Symes SJK, Giles DK. Exogenous polyunsaturated fatty acids (PUFAs) influence permeability, antimicrobial peptide resistance, biofilm formation and membrane phospholipid structure in an A-layer and non-A-layer strain of Aeromonas salmonicida. JOURNAL OF FISH DISEASES 2023; 46:31-45. [PMID: 36088584 DOI: 10.1111/jfd.13715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Aeromonas salmonicida is a Gram-negative bacterium that can infect a wide host range of fish populations, including salmonids and non-salmonids as well as freshwater and marine life. Some strains of A. salmonicida cause the disease furunculosis, which can cause lethargy, intestinal inflammation, ulcers, haemorrhaging and death. The infection is spread through fish-to-fish contact, and the presence of infection can have devastating effects on cultivated fish populations. The purpose of this study was to explore the ability of non-A-layer and A-layer A. salmonicida strains to incorporate polyunsaturated fatty acids (PUFAs) into their lipid profile and test the phenotypic effects thereof. Lipids were extracted from PUFA-exposed cultures and analysed for lipid modification by thin-layer chromatography and ultraperformance liquid chromatography-mass spectrometry, showing A. salmonicida, regardless of A-layer, capable of incorporating all seven of the PUFAs studied. Phenotypic effects were determined through the use of assays that tested for biofilm formation, membrane permeability and cyclic peptide susceptibility. Temperature-dependent effects on biofilm formation were observed, and PUFA exposure showed significant (p < .001) increases in membrane permeability as tested by the uptake of the hydrophobic compounds crystal violet and ethidium bromide. Additionally, some PUFAs elicited modest protection and vulnerability against the membrane-targeting cyclic peptides polymyxin B (PMB) and colistin. The diverse, strain-specific responses to exogenous PUFAs may allude to evolved adaptive strategies that enhance survival, persistence and virulence of non-pathogenic and pathogenic members of bacteria that oscillate between environmental and fish host niches.
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Affiliation(s)
- Rachel N Hofer
- Department of Chemistry and Physics, The University of Tennessee at Chattanooga, Chattanooga, Tennessee, USA
| | - Allen Lin
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, Tennessee, USA
| | - Benjamin C House
- Department of Chemistry and Physics, The University of Tennessee at Chattanooga, Chattanooga, Tennessee, USA
| | - Christopher N Purvis
- Department of Chemical Engineering, The University of Tennessee at Chattanooga, Chattanooga, Tennessee, USA
| | - Bradley J Harris
- Department of Chemical Engineering, The University of Tennessee at Chattanooga, Chattanooga, Tennessee, USA
| | - Steven J K Symes
- Department of Chemistry and Physics, The University of Tennessee at Chattanooga, Chattanooga, Tennessee, USA
| | - David K Giles
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, Tennessee, USA
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10
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Ai J, Li Y, Lv Y, Zhong X, Li J, Yang A. Study on microbes and antibiotic resistance genes in karst primitive mountain marshes - A case study of Niangniang Mountain in Guizhou, China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 247:114210. [PMID: 36306620 DOI: 10.1016/j.ecoenv.2022.114210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/25/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Previous research on antibiotic resistance genes and microorganisms centered on those in urban sewage treatment plants, breeding farms, hospitals and others with serious antibiotic pollution. However, at present, there are evident proofs that antibiotic resistance genes (ARGs) indeed exist in a primitive environment hardly without any human's footprints. Accordingly, an original karst mountain swamp ecosystem in Niangniang Mountain, Guizhou, China, including herbaceous swamp, shrub swamp, sphagnum bog and forest swamp, was selected to analyze the physical and chemical parameters of sediments. Moreover, microbial compositions, functions, as well as their connections with ARGs were assayed and analyzed using metagenomic technology. The results showed that there was no significant difference in the dominant microorganisms and ARGs in the four marshes, in which the dominant bacteria phyla were Proteobacteria (37.82 %), Acidobacteriota (22.17 %) and Actinobacteriota (20.64 %); the dominant archaea Euryarchaeota. (1.00 %); and the dominant eukaryotes Ascomycota (0.07 %), with metabolism as their major functions. Based on the ARDB database, the number of ARGs annotated reached 209 including 30 subtypes, and the dominant ARGs were all Bacitracin resistance genes (bacA, 84.77 %). In terms of the diversity of microorganisms and ARGs, the herbaceous swamp ranked the top, and the shrub swamp were at the bottom. Correlation analysis between microorganisms and resistance genes showed that, apart from aac2ic, macB, smeE, tetQ, and tetL, other ARGs were positively correlated with microorganisms. Among them, baca coexisted with microorganisms. Pearson correlation analysis results showed that contrary to ARGs, microorganisms were more affected by environmental factors.
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Affiliation(s)
- Jia Ai
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Qiannan Ecological Environment Monitoring Center, Duyun 558000, China
| | - Yancheng Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, China.
| | - Yang Lv
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China
| | - Xiong Zhong
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, China
| | - Aijiang Yang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, China
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11
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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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Susceptibility to Bismuth(III) of Aquaculture Bacterial Pathogens: Effectiveness of Bismuth-Deferiprone Therapy against Vibrio anguillarum Infection in Fish. Microorganisms 2021; 9:microorganisms9112399. [PMID: 34835524 PMCID: PMC8622636 DOI: 10.3390/microorganisms9112399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 11/17/2022] Open
Abstract
Bismuth is a heavy metal with antibacterial properties that has a long history of medicinal use. The results reported here suggest that bismuth(III) (chelated with deferiprone) could be used in aquaculture systems to treat bacterial disease outbreaks, greatly reducing antibiotic use. We tested bismuth susceptibility in a collection of aquaculture bacterial pathogens. In the presence of bismuth concentrations ranging from 1.3 to 13 µM, most bacteria started showing a drastic decrease in their growth ability, although with high inter- and intraspecific variability. The minimal inhibitory concentrations of bismuth ranged from 13 to more than 780 µM, depending on bacterial species and strain. The results of in vivo assays suggest that low concentrations of bismuth could be especially effective to treat vibriosis caused by Vibrio anguillarum, since bismuth greatly reduced mortality in experimentally infected fish without any observable side effects. A bismuth therapy, alone or combined with other antimicrobials, could contribute to reduce the use of antibiotics in aquaculture.
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Hosseini N, Paquet VE, Chehreghani M, Moineau S, Charette SJ. Phage Cocktail Development against Aeromonas salmonicida subsp. salmonicida Strains Is Compromised by a Prophage. Viruses 2021; 13:2241. [PMID: 34835047 PMCID: PMC8621227 DOI: 10.3390/v13112241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/22/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
Aquaculture is a rapidly growing food production sector. Fish farmers are experiencing increasing problems with antibiotic resistance when fighting against pathogenic bacteria such as Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis. Phage therapy may provide an alternative, but effective use must be determined. Here, we studied the inhibition of A. salmonicida subsp. salmonicida strains by five phages (HER98 [44RR2.8t.2], HER110 [65.2], SW69-9, L9-6 and Riv-10) used individually or as combinations of two to five phages. A particular combination of four phages (HER98 [44RR2.8t.2], SW69-9, Riv-10, and HER110 [65.2]) was found to be the most effective when used at an initial multiplicity of infection (MOI) of 1 against the A. salmonicida subsp. salmonicida strain 01-B526. The same phage cocktail is effective against other strains except those bearing a prophage (named Prophage 3), which is present in 2/3 of the strains from the province of Quebec. To confirm the impact of this prophage, we tested the effectiveness of the same cocktail on strains that were either cured or lysogenized with Prophage 3. While the parental strains were sensitive to the phage cocktail, the lysogenized ones were much less sensitive. These data indicate that the prophage content of A. salmonicida subsp. salmonicida can affect the efficacy of a cocktail of virulent phages for phage therapy purposes.
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Affiliation(s)
- Nava Hosseini
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada; (N.H.); (V.E.P.); (S.M.)
- 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
| | - Valérie E. Paquet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada; (N.H.); (V.E.P.); (S.M.)
- 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
| | - Mahdi Chehreghani
- Department of Mechanical Engineering, McGill University, Montreal, QC H3A 0C3, Canada;
| | - Sylvain Moineau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada; (N.H.); (V.E.P.); (S.M.)
- 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
- Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve J. Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada; (N.H.); (V.E.P.); (S.M.)
- 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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14
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Cheng X, Lu Y, Song Y, Zhang R, ShangGuan X, Xu H, Liu C, Liu H. Analysis of Antibiotic Resistance Genes, Environmental Factors, and Microbial Community From Aquaculture Farms in Five Provinces, China. Front Microbiol 2021; 12:679805. [PMID: 34248893 PMCID: PMC8264556 DOI: 10.3389/fmicb.2021.679805] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/19/2021] [Indexed: 11/18/2022] Open
Abstract
The excessive use of antibiotics speeds up the dissemination and aggregation of antibiotic resistance genes (ARGs) in the environment. The ARGs have been regarded as a contaminant of serious environmental threats on a global scale. The constant increase in aquaculture production has led to extensive use of antibiotics as a means to prevent and treat bacterial infections; there is a universal concern about the environmental risk of ARGs in the aquaculture environment. In this study, a survey was conducted to evaluate the abundance and distributions of 10 ARGs, bacterial community, and environmental factors in sediment samples from aquatic farms distributed in Anhui (AP1, AP2, and AP3), Fujian (FP1, FP2, and FP3), Guangxi (GP1, GP2, and GP3), Hainan (HP1, HP2, and HP3), and Shaanxi (SP1, SP2, and SP3) Province in China. The results showed that the relative abundance of total ARGs was higher in AP1, AP2, AP3, FP3, GP3, HP1, HP2, and HP3 than that in FP1, FP2, GP1, GP2, SP1, SP2, and SP3. The sul1 and tetW genes of all sediment samples had the highest abundance. The class 1 integron (intl1) was detected in all samples, and the result of Pearson correlation analysis showed that the intl1 has a positive correlation with the sul1, sul2, sul3, blaOXA, qnrS, tetM, tetQ, and tetW genes. Correlation analysis of the bacterial community diversity and environmental factors showed that the Ca2+ concentration has a negative correlation with richness and diversity of the bacterial community in these samples. Of the identified bacterial community, Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidota were the predominant phyla in these samples. Redundancy analysis showed that environmental factors (TN, TP, Cl–, and Ca2+) have a positive correlation with the bacterial community (AP1, GP1, GP2, GP3, SP1, SP2, and SP3), and the abundance of ARGs (sul1, tetW, qnrS, and intl1) has a positive correlation with the bacterial community (AP2, AP3, HP1, HP2, and HP3). Based on the network analysis, the ARGs (sul1, sul2, blaCMY, blaOXA, qnrS, tetW, tetQ, tetM, and intl1) were found to co-occur with bacterial taxa from the phyla Chloroflexi, Euryarchaeota, Firmicutes, Halobacterota, and Proteobacteria. In conclusion, this study provides an important reference for understanding the environmental risk associated with aquaculture activities in China.
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Affiliation(s)
- Xu Cheng
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Yitong Lu
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Yanzhen Song
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Ruifang Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xinyan ShangGuan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Hongzhou Xu
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chengrong Liu
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Haixia Liu
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
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15
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Draft Genome Sequence of an Aeromonas salmonicida subsp. salmonicida Strain from the Canadian Pacific Coast Bearing a Variant of pRAS1. Microbiol Resour Announc 2021; 10:10/18/e00291-21. [PMID: 33958402 PMCID: PMC8103872 DOI: 10.1128/mra.00291-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The genome sequencing of Aeromonas salmonicida subspecies salmonicida strain 2004-072 revealed a plasmid bearing a region carrying antibiotic resistance genes very similar to the one found in the plasmid pRAS1, an IncU family plasmid. This new plasmid was named pRAS1b. The genome sequencing of Aeromonas salmonicida subspecies salmonicida strain 2004-072 revealed a plasmid bearing a region carrying antibiotic resistance genes very similar to the one found in the plasmid pRAS1, an IncU family plasmid. This new plasmid was named pRAS1b.
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16
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Characterization of bacteriophage T7-Ah reveals its lytic activity against a subset of both mesophilic and psychrophilic Aeromonas salmonicida strains. Arch Virol 2021; 166:521-533. [PMID: 33394168 DOI: 10.1007/s00705-020-04923-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022]
Abstract
Aeromonas salmonicida strains cause problematic bacterial infections in the aquaculture industry worldwide. The genus Aeromonas includes both mesophilic and psychrophilic species. Bacteriophages that infect Aeromonas spp. strains are usually specific for mesophilic or psychrophilic species; only a few bacteriophages can infect both types of strains. In this study, we characterized the podophage T7-Ah, which was initially found to infect the Aeromonas salmonicida HER1209 strain. The burst size of T7-Ah against its original host is 72 new virions per infected cell, and its burst time is 30 minutes. It has been found that this phage can lyse both mesophilic and psychrophilic A. salmonicida strains, as well as one strain of Escherichia coli. Its genome comprises 40,153 bp of DNA and does not contain any recognizable toxin or antibiotic resistance genes. The adsorption rate of the phage on highly sensitive bacterial strains was variable and could not be related to the presence or absence of a functional A-layer on the surface of the bacterial strains. The lipopolysaccharide migration patterns of both resistant and sensitive bacterial strains were also studied and compared to investigate the nature of the potential receptor of this phage on the bacterial surface. This study sheds light on the surprising diversity of lifestyles of the bacterial strains sensitive to phage T7-Ah and opens the door to the potential use of this phage against A. salmonicida infections in aquaculture.
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Cooper AL, Carter C, McLeod H, Wright M, Sritharan P, Tamber S, Wong A, Carrillo CD, Blais BW. Detection of carbapenem-resistance genes in bacteria isolated from wastewater in Ontario. Facets (Ott) 2021. [DOI: 10.1139/facets-2020-0101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacterial carbapenem resistance is a major public health concern since these antimicrobials are often the last resort to treat serious human infections. To evaluate methodologies for detection of carbapenem resistance, carbapenem-tolerant bacteria were isolated from wastewater treatment plants in Toronto, Ottawa, and Arnprior, Ontario. A total of 135 carbapenem-tolerant bacteria were recovered. Polymerase chain reaction (PCR) indicated the presence of carbapenem hydrolysing enzymes KPC ( n = 10), GES ( n = 5), VIM ( n = 7), and IMP ( n = 1), and β-lactamases TEM ( n = 7), PER ( n = 1), and OXA-variants ( n = 16). A subset of 46 isolates were sequenced and analysed using ResFinder and CARD-RGI. Both programs detected carbapenem resistance genes in 35 sequenced isolates and antimicrobial resistance genes (ARGs) conferring resistance to multiple class of other antibiotics. Where β-lactamase resistance genes were not initially identified, lowering the thresholds for ARG detection enabled identification of closely related β-lactamases. However, no known carbapenem resistance genes were found in seven sequenced Pseudomonas spp. isolates. Also of note was a multi-drug-resistant Klebsiella pneumoniae isolate from Ottawa, which harboured resistance to seven antimicrobial classes including β-lactams. These results highlight the diversity of genes encoding carbapenem resistance in Ontario and the utility of whole genome sequencing over PCR for ARG detection where resistance may result from an assortment of genes.
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Affiliation(s)
- Ashley L. Cooper
- Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1A 0Y9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Cassandra Carter
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Hana McLeod
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Marie Wright
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Prithika Sritharan
- Applied Science and Environmental Technology, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Sandeep Tamber
- Microbiology Research Division, Bureau of Microbial Hazards, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Catherine D. Carrillo
- Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1A 0Y9, Canada
| | - Burton W. Blais
- Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1A 0Y9, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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18
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Yang Y, Chen Y, Cai Y, Xing S, Mi J, Liao X. The relationship between culturable doxycycline-resistant bacterial communities and antibiotic resistance gene hosts in pig farm wastewater treatment plants. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 206:111164. [PMID: 32858327 DOI: 10.1016/j.ecoenv.2020.111164] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
Pig farm wastewater treatment plants (WWTPs) are an important repository for resistant bacterial communities (RBCs) and antibiotic resistance genes (ARGs). However, the relationship between RBCs and ARG hosts has not been well characterized. In this study, water samples from influent and effluent from five pig farm WWTPs were collected. Gradient concentrations of doxycycline (DOX) were used to screen the culturable RBCs. The abundance of 21 subtypes of ARGs and the bacterial community were investigated. This study detected a large number of culturable DOX-RBCs and ARGs in the influent and effluent of pig farm WWTPs. The abundances of ARGs and RBCs in all effluent samples was significantly lower than that in the influent samples (P < 0.05), which indicated that the WWTPs can effectively remove most ARGs and RBCs in pig farm wastewater. The main potential culturable RBCs in pig farm wastewater were the dominant bacteria Proteobacteria, Actinobacteria, Pseudomonas, and Rheinheimera. However, most of the ARGs were mainly present in Bacteroidetes, Actinobacteria, Corynebacteriaceae, Macellibacteroides, Acinetobacter, and Enterobacteriaceae, which are considered potential ARG hosts. The results presented here showed that there were obvious differences between the species of culturable DOX-RBCs and ARG hosts in the pig farm WWTPs, which may be due to various environmental factors. This highlights the urgent need for further research on the relationship between RBCs and ARG hosts.
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Affiliation(s)
- Yiwen Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agriculture University, Guangzhou, 510642, China
| | - Yingxi Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agriculture University, Guangzhou, 510642, China
| | - Yingfeng Cai
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agriculture University, Guangzhou, 510642, China
| | - Sicheng Xing
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agriculture University, Guangzhou, 510642, China
| | - Jiandui Mi
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agriculture University, Guangzhou, 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agriculture University, Guangzhou, 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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19
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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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20
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Yang Y, Wu R, Hu J, Xing S, Huang C, Mi J, Liao X. Dominant denitrifying bacteria are important hosts of antibiotic resistance genes in pig farm anoxic-oxic wastewater treatment processes. ENVIRONMENT INTERNATIONAL 2020; 143:105897. [PMID: 32615347 DOI: 10.1016/j.envint.2020.105897] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
The anoxic-oxic (A/O) wastewater treatment process that is widely used in pig farms in China is an important repository for antibiotic resistance genes (ARGs). However, the distribution of ARGs and their hosts in the A/O process has not been well characterized. In this study, the wastewaters in the anoxic and oxic tanks for A/O processes were collected from 38 pig farms. The concentrations of 20 subtypes of ARGs, 5 denitrification-related genes, 2 integrons, and bacterial community composition were investigated. Bacterial genome binning was performed using metagenome sequencing. In this study, 20 subtypes of ARGs and integrons were detected in all sampling sites. A total of 16 of the 20 subtypes of ARGs were detected with the highest abundance in anoxic tanks, and sul1 was detected with a maximum average abundance of 19.21 ± 0.24 log10 (copies/mL). Cooccurrence patterns were observed for some genes in the pig farm A/O process, such as sul1 and intl1, sul1 and tetG, and tetO and tetW. There was a significant cooccurrence pattern between the dominant denitrifying bacteria and some ARGs (blaTEM, ermB, tetC, tetH and tetQ), so the dominant denitrifying bacteria were considered to be potential ARG hosts. In addition, 170 highly abundant bacterial genome bins were assembled and further confirmed that the denitrifying bacteria Brachymonas, Candidatus Competibacter, Thiobacillus and Steroidobacter were the important ARG hosts in the pig farm A/O process, providing a useful reference for the surveillance and risk management of ARGs in pig farm wastewater.
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Affiliation(s)
- Yiwen Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Ruiting Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jiaxin Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Sicheng Xing
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Chunbo Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jiandui Mi
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agriculture University, Guangzhou 510642, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agriculture University, Guangzhou 510642, China.
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21
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Derome N, Filteau M. A continuously changing selective context on microbial communities associated with fish, from egg to fork. Evol Appl 2020; 13:1298-1319. [PMID: 32684960 PMCID: PMC7359827 DOI: 10.1111/eva.13027] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
Fast increase of fish aquaculture production to meet consumer demands is accompanied by important ecological concerns such as disease outbreaks. Meanwhile, food waste is an important concern with fish products since they are highly perishable. Recent aquaculture and fish product microbiology, and more recently, microbiota research, paved the way to a highly integrated approach to understand complex relationships between host fish, product and their associated microbial communities at health/disease and preservation/spoilage frontiers. Microbial manipulation strategies are increasingly validated as promising tools either to replace or to complement traditional veterinary and preservation methods. In this review, we consider evolutionary forces driving fish microbiota assembly, in particular the changes in the selective context along the production chain. We summarize the current knowledge concerning factors governing assembly and dynamics of fish hosts and food microbial communities. Then, we discuss the current microbial community manipulation strategies from an evolutionary standpoint to provide a perspective on the potential for risks, conflict and opportunities. Finally, we conclude that to harness evolutionary forces in the development of sustainable microbiota manipulation applications in the fish industry, an integrated knowledge of the controlling abiotic and especially biotic factors is required.
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Affiliation(s)
- Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de BiologieUniversité LavalQuébecQCCanada
| | - Marie Filteau
- Département de BiologieUniversité LavalQuébecQCCanada
- Département des Sciences des alimentsInstitut sur la nutrition et les aliments fonctionnels (INAF)Université LavalQuébecQCCanada
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22
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A Mesophilic Aeromonas salmonicida Strain Isolated from an Unsuspected Host, the Migratory Bird Pied Avocet. Microorganisms 2019; 7:microorganisms7120592. [PMID: 31757113 PMCID: PMC6955901 DOI: 10.3390/microorganisms7120592] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/18/2022] Open
Abstract
Aeromonas salmonicida is a Gram-negative bacterium, known as a fish pathogen since its discovery. Although the species was initially considered psychrophilic, a mesophilic subspecies (pectinolytica) and many other mesophilic strains still not attributed to subspecies have been described in the last two decades. These mesophilic strains were sampled from various sources, including humans, and some of them are known to be pathogenic. In this study, we describe a strain, JF2480, which was isolated from the spleen, and also found the kidney and liver of a dead pied avocet (Recurvirostra avosetta), a type of migratory bird inhabiting aquatic environments. A core genome phylogenomic analysis suggests that JF2480 is taxonomically distant from other known A. salmonicida subspecies. The genome sequence confirms that the strain possesses key virulence genes that are present in the typical A. salmonicida psychrophilic subspecies, with the exception of the genes encoding the type three secretion system (T3SS). Bacterial virulence assays conducted on the surrogate host Dictyostelium discoideum amoeba confirmed that the strain is virulent despite the lack of T3SS. Bacterial growth curves showed that strain JF2480 grow well at 40 °C, the body temperature of the pied avocet, and even faster at 41 °C, compared to other mesophilic strains. Discovery of this strain further demonstrates the extent of the phylogenomic tree of this species. This study also suggests that A. salmonicida can infect a wider array of hosts than previously suspected and that we need to rethink the way we perceive A. salmonicida's natural environment.
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23
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Massicotte MA, Vincent AT, Schneider A, Paquet VE, Frenette M, Charette SJ. One Aeromonas salmonicida subsp. salmonicida isolate with a pAsa5 variant bearing antibiotic resistance and a pRAS3 variant making a link with a swine pathogen. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:313-320. [PMID: 31299566 DOI: 10.1016/j.scitotenv.2019.06.456] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
The Gram-negative bacterium Aeromonas salmonicida subsp. salmonicida is an aquatic pathogen which causes furunculosis to salmonids, especially in fish farms. The emergence of strains of this bacterium exhibiting antibiotic resistance is increasing, limiting the effectiveness of antibiotherapy as a treatment against this worldwide disease. In the present study, we discovered an isolate of A. salmonicida subsp. salmonicida that harbors two novel plasmids variants carrying antibiotic resistance genes. The use of long-read sequencing (PacBio) allowed us to fully characterize those variants, named pAsa5-3432 and pRAS3-3432, which both differ from their classic counterpart through their content in mobile genetic elements. The plasmid pAsa5-3432 carries a new multidrug region composed of multiple mobile genetic elements, including a Class 1 integron similar to an integrated element of Salmonella enterica. With this new region, probably acquired through plasmid recombination, pAsa5-3432 is the first reported plasmid of this bacterium that bears both an essential virulence factor (the type three secretion system) and multiple antibiotic resistance genes. As for pRAS3-3432, compared to the classic pRAS3, it carries a new mobile element that has only been identified in Chlamydia suis. Hence, with the identification of those two novel plasmids harboring mobile genetic elements that are normally encountered in other bacterial species, the present study puts emphasis on the important impact of mobile genetic elements in the genomic plasticity of A. salmonicida subsp. salmonicida and suggests that this aquatic bacterium could be an important reservoir of antibiotic resistance genes that can be exchanged with other bacteria, including human and animal pathogens.
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Affiliation(s)
- Marie-Ange Massicotte
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City G1V 0A6, Quebec, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Hôpital Laval, Quebec City, Quebec G1V 4G5, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada
| | - Antony T Vincent
- INRS-Institut Armand-Frappier, Bacterial Symbionts Evolution, Laval City H7V 1B7, QC, Canada
| | - Anna Schneider
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City G1V 0A6, Quebec, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada
| | - Valérie E Paquet
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City G1V 0A6, Quebec, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Hôpital Laval, Quebec City, Quebec G1V 4G5, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada
| | - Michel Frenette
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada; Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire; Université Laval; Quebec City G1V 0A6, Quebec, Canada
| | - Steve J Charette
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City G1V 0A6, Quebec, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Hôpital Laval, Quebec City, Quebec G1V 4G5, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval; Quebec City G1V 0A6, Quebec, Canada.
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24
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Stimulated Growth and Innate Immunity in Brook Charr ( Salvelinus fontinalis) Treated with a General Probiotic (Bactocell ®) and Two Endogenous Probiotics That Inhibit Aeromonas salmonicida In Vitro. Microorganisms 2019; 7:microorganisms7070193. [PMID: 31284626 PMCID: PMC6681104 DOI: 10.3390/microorganisms7070193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 11/17/2022] Open
Abstract
Aeromonas salmonicida subsp. salmonicida is a Gram-negative bacterium causing furunculosis, an opportunistic infection of farmed salmonid fish. Current treatment methods against furunculosis rely heavily on antibiotherapy. However, strains of this opportunistic fish pathogen were found to possess genes that confer resistance to major antibiotics including those used to cure furunculosis. Therefore, dispensing bacterial symbionts as probiotics to susceptible hosts appears to be a promising alternative. Here, we present the genomic characterization and in vivo safety assessment of two brook charr (Salvelinus fontinalis) bacterial symbionts that inhibited A. salmonicida subsp. salmonicida growth in vitro (Pseudomonas fluorescens ML11A and Aeromonas sobria TM18) as well as a commercialized probiotic, Pediococcus acidilactici MA18/5M (Bactocell®). The genomic sequences of ML11A and TM18 obtained by whole-genome shotgun sequencing lack key virulence factor genes found in related pathogenic strains. Their genomic sequences are also devoid of genes involved in the inactivation (or target modification of) several key antimicrobial compounds used in salmonid aquaculture. Finally, when administered daily to live brook charr fingerlings, ML11A, TM18 and Bactocell® helped improve several physiological condition metrics such as mean body weight, Fulton's condition factor and blood plasma lysozyme activity (an indicator for innate immune activity).
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25
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Paquet VE, Vincent AT, Moineau S, Charette SJ. Beyond the A-layer: adsorption of lipopolysaccharides and characterization of bacteriophage-insensitive mutants of Aeromonas salmonicida subsp. salmonicida. Mol Microbiol 2019; 112:667-677. [PMID: 31115938 DOI: 10.1111/mmi.14308] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2019] [Indexed: 12/28/2022]
Abstract
Aeromonas salmonicida subsp. salmonicida is a fish pathogen that causes furunculosis. Antibiotherapy used to treat furunculosis in fish has led to resistance. Virulent phages are increasingly seen as alternatives or complementary treatments against furunculosis in aquaculture environments. For phage therapy to be successful, it is essential to study the natural mechanisms of phage resistance in A. salmonicida subsp. salmonicida. Here, we generated bacteriophage-insensitive mutants (BIMs) of A. salmonicida subsp. salmonicida, using a myophage with broad host range and characterized them. Phage plaques were different depending on whether the A-layer surface array protein was expressed or not. The genome analysis of the BIMs helped to identify mutations in genes involved in the biogenesis of lipopolysaccharides (LPS) and on an uncharacterized gene (ASA_1998). The characterization of the LPS profile and gene complementation assays identified LPS as a phage receptor and confirmed the involvement of the uncharacterized protein ASA_1998 in phage infection. In addition, we confirmed that the presence of an A-layer at the bacterial surface could act as protection against phages. This study brings new elements into our understanding of the phage adsorption to A. salmonicida subsp. salmonicida cells.
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Affiliation(s)
- Valérie E Paquet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.,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
| | | | - Sylvain Moineau
- 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.,Félix d'Hérelle Reference Center for Bacterial Viruses, 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.,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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26
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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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27
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Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
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28
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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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29
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Abstract
ABSTRACT
Major concerns surround the use of antimicrobial agents in farm-raised fish, including the potential impacts these uses may have on the development of antimicrobial-resistant pathogens in fish and the aquatic environment. Currently, some antimicrobial agents commonly used in aquaculture are only partially effective against select fish pathogens due to the emergence of resistant bacteria. Although reports of ineffectiveness in aquaculture due to resistant pathogens are scarce in the literature, some have reported mass mortalities in
Penaeus monodon
larvae caused by
Vibrio harveyi
resistant to trimethoprim-sulfamethoxazole, chloramphenicol, erythromycin, and streptomycin. Genetic determinants of antimicrobial resistance have been described in aquaculture environments and are commonly found on mobile genetic elements which are recognized as the primary source of antimicrobial resistance for important fish pathogens. Indeed, resistance genes have been found on transferable plasmids and integrons in pathogenic bacterial species in the genera
Aeromonas
,
Yersinia
,
Photobacterium
,
Edwardsiella
, and
Vibrio
. Class 1 integrons and IncA/C plasmids have been widely identified in important fish pathogens (
Aeromonas
spp.,
Yersinia
spp.,
Photobacterium
spp.,
Edwardsiella
spp., and
Vibrio
spp.) and are thought to play a major role in the transmission of antimicrobial resistance determinants in the aquatic environment. The identification of plasmids in terrestrial pathogens (
Salmonella enterica
serotypes,
Escherichia coli
, and others) which have considerable homology to plasmid backbone DNA from aquatic pathogens suggests that the plasmid profiles of fish pathogens are extremely plastic and mobile and constitute a considerable reservoir for antimicrobial resistance genes for pathogens in diverse environments.
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30
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Attéré SA, Vincent AT, Paccaud M, Frenette M, Charette SJ. The Role for the Small Cryptic Plasmids As Moldable Vectors for Genetic Innovation in Aeromonas salmonicida subsp. salmonicida. Front Genet 2017; 8:211. [PMID: 29326751 PMCID: PMC5736529 DOI: 10.3389/fgene.2017.00211] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/28/2017] [Indexed: 11/17/2022] Open
Abstract
In Aeromonas salmonicida subsp. salmonicida, a bacterium that causes fish disease, there are two types of small plasmids (<15 kbp): plasmids without known function, called cryptic plasmids, and plasmids that bear beneficial genes for the bacterium. Four among them are frequently detected in strains of A. salmonicida subsp. salmonicida: pAsa1, pAsa2, pAsa3, and pAsal1. The latter harbors a gene which codes for an effector of the type three secretion system, while the three others are cryptic. It is currently unclear why these cryptic plasmids are so highly conserved throughout strains of A. salmonicida subsp. salmonicida. In this study, three small plasmids, named pAsa10, pAsaXI and pAsaXII, are described. Linked to tetracycline resistance, a partial Tn1721 occupies half of pAsa10. A whole Tn1721 is also present in pAsa8, another plasmid previously described in A. salmonicida subsp. salmonicida. The backbone of pAsa10 has no relation with other plasmids described in this bacterium. However, the pAsaXI and pAsaXII plasmids are derivatives of cryptic plasmids pAsa3 and pAsa2, respectively. pAsaXI is identical to pAsa3, but bears a transposon with a gene that encodes for a putative virulence factor. pAsaXII, also found in Aeromonas bivalvium, has a 95% nucleotide identity with the backbone of pAsa2. Like pAsa7, another pAsa2-like plasmid recently described, orf2 and orf3 are missing and are replaced in pAsaXII by genes that encode a formaldehyde detoxification system. These new observations suggest that transposons and particularly Tn1721 are frequent and diversified in A. salmonicida subsp. salmonicida. Moreover, the discovery of pAsaXI and pAsaXII expands the group of small plasmids that are derived from cryptic plasmids and have a function. Although their precise roles remain to be determined, the present study shows that cryptic plasmids could serve as moldable vectors to acquire mobile elements such as transposons. Consequently, they could act as key agents of the diversification of virulence and adaptive traits of Aeromonas salmonicida subsp. salmonicida.
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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
| | - Mégane Paccaud
- 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
| | - Michel Frenette
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada.,Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, 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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Gauthier J, Vincent AT, Charette SJ, Derome N. Strong Genomic and Phenotypic Heterogeneity in the Aeromonas sobria Species Complex. Front Microbiol 2017; 8:2434. [PMID: 29276504 PMCID: PMC5727048 DOI: 10.3389/fmicb.2017.02434] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/23/2017] [Indexed: 12/18/2022] Open
Abstract
Aeromonas sobria is a mesophilic motile aeromonad currently depicted as an opportunistic pathogen, despite increasing evidence of mutualistic interactions in salmonid fish. However, the determinants of its host-microbe associations, either mutualistic or pathogenic, remain less understood than for other aeromonad species. On one side, there is an over-representation of pathogenic interactions in the A. sobria literature, of which only three articles to date report mutualistic interactions; on the other side, genomic characterization of this species is still fairly incomplete as only two draft genomes were published prior to the present work. Consequently, no study specifically investigated the biodiversity of A. sobria. In fact, the investigation of A. sobria as a species complex may have been clouded by: (i) confusion with A. veronii biovar sobria because of their similar biochemical profiles, and (ii) the intrinsic low resolution of previous studies based on 16S rRNA gene sequences and multilocus sequence typing. So far, the only high-resolution, phylogenomic studies of the genus Aeromonas included one A. sobria strain (CECT 4245 / Popoff 208), making it impossible to robustly conclude on the phylogenetic intra-species diversity and the positioning among other Aeromonas species. To further understand the biodiversity and the spectrum of host-microbe interactions in A. sobria as well as its potential genomic diversity, we assessed the genomic and phenotypic heterogeneity among five A. sobria strains: two clinical isolates recovered from infected fish (JF2635 and CECT 4245), one from an infected amphibian (08005) and two recently isolated brook charr probionts (TM12 and TM18) which inhibit in vitro growth of A. salmonicida subsp. salmonicida (a salmonid fish pathogen). A phylogenomic assessment including 2,154 softcore genes corresponding to 946,687 variable sites from 33 Aeromonas genomes confirms the status of A. sobria as a distinct species divided in two subclades, with 100% bootstrap support. The phylogenomic split of A. sobria in two subclades is corroborated by a deep dichotomy between all five A. sobria strains in terms of inhibitory effect against A. salmonicida subsp. salmonicida, gene contents and codon usage. Finally, the antagonistic effect of A. sobria strains TM12 and TM18 suggests novel control methods against A. salmonicida subsp. salmonicida.
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Affiliation(s)
- Jeff Gauthier
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, Canada
| | - Antony T Vincent
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, Canada
| | - Steve J Charette
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, Canada
| | - Nicolas Derome
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, Canada
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The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems. Genes (Basel) 2017; 8:genes8110337. [PMID: 29165361 PMCID: PMC5704250 DOI: 10.3390/genes8110337] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. Recent findings indicated that the main actors of conjugative transfer are not the well-known conjugative or mobilizable plasmids but are the integrated elements. This paper reviews current knowledge on “integrative and mobilizable elements” (IMEs) that have recently been shown to be highly diverse and highly widespread but are still rarely described. IMEs encode their own excision and integration and use the conjugation machinery of unrelated co-resident conjugative element for their own transfer. Recent studies revealed a much more complex and much more diverse lifecycle than initially thought. Besides their main transmission as integrated elements, IMEs probably use plasmid-like strategies to ensure their maintenance after excision. Their interaction with conjugative elements reveals not only harmless hitchhikers but also hunters that use conjugative elements as target for their integration or harmful parasites that subvert the conjugative apparatus of incoming elements to invade cells that harbor them. IMEs carry genes conferring various functions, such as resistance to antibiotics, that can enhance the fitness of their hosts and that contribute to their maintenance in bacterial populations. Taken as a whole, IMEs are probably major contributors to bacterial evolution.
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Vincent AT, Charette SJ. Phylogenetic analysis of the fish pathogen Aeromonas salmonicida underlines the dichotomy between European and Canadian strains for the salmonicida subspecies. JOURNAL OF FISH DISEASES 2017; 40:1241-1247. [PMID: 28105757 DOI: 10.1111/jfd.12595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/06/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Affiliation(s)
- A T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC, Canada
| | - S J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC, Canada
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Wang W, Peng Z, Baloch Z, Hu Y, Xu J, Zhang W, Fanning S, Li F. Genomic characterization of an extensively-drug resistance Salmonella enterica serotype Indiana strain harboring bla NDM-1 gene isolated from a chicken carcass in China. Microbiol Res 2017; 204:48-54. [PMID: 28870291 DOI: 10.1016/j.micres.2017.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 06/13/2017] [Accepted: 07/15/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVES The objective of this study was to genetically characterize the antimicrobial resistance mechanisms of Salmonella enterica serotype Indiana C629 isolated from a chicken carcass in China in 2014. METHODS Antimicrobial susceptibility against a panel of 23 antimicrobial agents was carried out on Salmonella enterica serotype Indiana C629 and assessed according to CLSI standards. Whole-genome sequencing of this isolate was conducted to obtain the complete genome of S. Indiana. RESULTS Salmonella Indiana C629 expressed an XDR phenotype being resistant to more than 20 antimicrobial agents, including imipenem and meropenem. From the analysis of the resistance mechanisms, two mutations were identified in subunit A of DNA gyrase within the quinolone resistance determining region, in addition to the acquisition of mobile efflux pumps encoding oqxA/B/R. Additionally, four beta-lactamases resistance genes (blaCTX-M-65, blaTEM-1, blaOXA-1, and blaNDM-1), five aminoglycosides resistance genes (aac(3)-IV, aac(6')-Ib-cr, aadA2, aadA5, and aph(4)-Ia), two phenicol resistance genes (catB3 and floR), and five trimethoprim/sulfamethoxazole resistance genes (sul1/2/3 and dfrA12/17) were also identified. A total of 191 virulence genes were identified. Among them, 57 belonged to type-three secretion system (T3SS) encoding genes, 55 belonged to fimbrial adherence encoding genes, and 39 belonged to flagella-encoding genes CONCLUSIONS: This study demonstrated that multi-resistance mechanisms consistent with an XDR-phenotype, along with various virulence encoding genes of a S. Indiana strain in China These findings highlight the importance of cooperation among different sectors in order to monitor the spread of resistant pathogens among food animal, foods of animal origin and human beings that might further take measures to protect consumers' health.
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Affiliation(s)
- Wei Wang
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, PR China
| | - Zixin Peng
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, PR China
| | - Zulqarnain Baloch
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China.
| | - Yujie Hu
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, PR China
| | - Jin Xu
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, PR China
| | - Wenhui Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
| | - Séamus Fanning
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, PR China; UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, UK
| | - Fengqin Li
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, PR China.
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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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Wang W, Baloch Z, Peng Z, Hu Y, Xu J, Fanning S, Li F. Genomic characterization of a large plasmid containing a bla NDM-1 gene carried on Salmonella enterica serovar Indiana C629 isolate from China. BMC Infect Dis 2017; 17:479. [PMID: 28687066 PMCID: PMC5501952 DOI: 10.1186/s12879-017-2515-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 06/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The bla NDM-1 gene in Salmonella species is mostly reported in clinical cases, but is rarely isolated from red and white meat in China. METHODS A Salmonella Indiana (S. Indiana) isolate was cultured from a chicken carcass procured from a slaughterhouse in China. Antimicrobial susceptibility was tested against a panel of agents. Whole-genome sequencing of the isolate was carried out and data was analyzed. RESULTS A large plasmid, denoted as plasmid pC629 (210,106 bp), containing a composite cassette, consisting of IS26-bla NDM-1-ble MBL -△trpF-tat-cutA-ISCR1-sul1-qacE△1-aadA2-dfrA12-intI1-IS26 was identified. The latter locus was physically linked with bla OXA-1, bla CTX-M-65, bla TEM-1-encoding genes. A mercury resistance operon merACDEPTR was also identified; it was flanked on the proximal side, among IS26 element and the distally located on the bla NDM-1 gene. Plasmid pC629 also contained 21 other antimicrobial resistance-encoding genes, such as aac(6')-Ib-cr, aac(3)-VI, aadA5, aph(4)-Ia, arr-3, blmS, brp, catB3, dfrA17, floR, fosA, mph(A), mphR, mrx, nimC/nimA, oqxA, oqxB, oqxR, rmtB, sul1, sul2. Two virulence genes were also identified on plasmid pC629. CONCLUSION To the best of our knowledge, this is the first report of bla NDM-1 gene being identified from a plasmid in a S. Indiana isolate cultured from chicken carcass in China.
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Affiliation(s)
- Wei Wang
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for food safety Risk Assessment, Beijing, People's Republic of China
| | - Zulqarnain Baloch
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Zixin Peng
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for food safety Risk Assessment, Beijing, People's Republic of China
| | - Yujie Hu
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for food safety Risk Assessment, Beijing, People's Republic of China
| | - Jin Xu
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for food safety Risk Assessment, Beijing, People's Republic of China
| | - Séamus Fanning
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for food safety Risk Assessment, Beijing, People's Republic of China. .,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield D04 N2E5, Dublin, Ireland. .,Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland.
| | - Fengqin Li
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for food safety Risk Assessment, Beijing, People's Republic of China. .,Microbiology Laboratory, China National Centre for Food Safety Risk Assessment, No.7 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, People's Republic of China.
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Draft Genome Sequence of Pseudomonas fluorescens ML11A, an Endogenous Strain from Brook Charr with Antagonistic Properties against Aeromonas salmonicida subsp. salmonicida. GENOME ANNOUNCEMENTS 2017; 5:5/9/e01716-16. [PMID: 28254983 PMCID: PMC5334590 DOI: 10.1128/genomea.01716-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Pseudomonas fluorescens ML11A, isolated from brook charr, showed a strong in vitro inhibitory effect against Aeromonas salmonicida subsp. salmonicida, a bacterial fish pathogen. Its genome harbors gene clusters for siderophore and bacteriocin biosynthesis and shares 99% whole-genome identity with P. fluorescens A506, a biological control strain used in agriculture.
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