APPLICATION OF COMPARATIVE GENOME IN AQUACULTURE DISEASES DIAGNOSIS
Keywords:
antibiotic resistance, epidemiology, aquaculture diseases, genome, phylogenomics
Abstract
The sustainability of aquaculture industry is critical both for global food security and economic welfare. However, the massive wealth of pathogenic bacteria poses a key challenge to the development of a sustainable bio-control method. Recent advances in genome sequencing study combined with pan-genome analysis can be an efficacious management applied to numerous aquatic pathogens. Thus, routine comparative genome analyses of aquatic pathogens will deduce the phylogenomic diversity and possible evolutionary trends
of aquatic bacterial pathogen strains, elucidate the mechanisms of pathogenesis, as well as estimate patterns of pathogen transmission across epidemiological scales. This study also reviews comparative pan-genome analysis with a particular focus on controlling aquatic diseases, especially for: (i) re-identifying the previously misidentified strain with high accuracy and discovering novel isolates that may be associated with high rate
of fish mortalities, (ii) developing routine pan-PCR based on highly informative identified genetic targets that are capable of distinguishing all the clinical isolates, and finally (iii) studying the multivalent vaccine following reverse vaccinology towards the prevention of numerous aquatic animal diseases.
Downloads
Download data is not yet available.
References
[1] Austin B, Austin DA. Bacterial fish
pathogens - disease of farmed and wild fish.
5th ed. Dordrecht: Springer; 2012.
[2] Henrik Hasman, Dhany Saputra, Thomas
Sicheritz-Ponten, Ole Lund, Christina Aaby
Svendsen, Niels Frimodt-Moller, et al.
Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. Journal
of Clincal Microbiology. 2014; 52(8):3136. DOI: 10.1128/JCM.01369-14.
[3] Sion C. Bayliss, David W. Verner-Jeffreys,
Kerry L. Bartie, David M. Aanensen,
Samuel K. Sheppard, Alexandra Adams,
Edward J. Feil. The promise of whole
genome pathogen sequencing for the molecular epidemiology of emerging aquaculture
pathogens. Front Microbiol. 2017; 8:121.
DOI: 10.3389/fmicb.2017.00121.
[4] Pridgeon Julia W, Phillip H Klesius. Major
bacterial diseases in aquaculture and their
vaccine development. CAB Reviews Perspectives in Agriculture Veterinary Science
Nutrition and Natural Resources. 2012.
DOI: 10.1079/PAVSNNR20127048.
[5] Carding S, Verbeke K, Vipond DT, Corfe
BM, Owen LJ. Dysbiosis of the gut microbiota in disease. Microbial Ecology in
Health and Disease. 2015; 26:26191. DOI:
10.3402/mehd.v26.26191.
[6] Defoirdt T, Sorgeloos P, Bossier P. Alternatives to antibiotics for the control
of bacterial disease in aquaculture. Curr
Opin Microbiol. 2011; 14(3):251–8. DOI:
10.1016/j.mib.2011.03.004.
[7] Reith ME, Singh RK, Curtis B, Boyd JM,
Bouevitch A, Kimball J, et al. The genome
of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of
a fish pathogen. BMC Genomics. 2008;
9:427. DOI: 10.1186/1471-2164-9-427.
[8] Wang Q, Yang M, Xiao J, Wu H, Wang
X, Lv Y, et al. Genome sequence of
the versatile fish pathogen Edwardsiella
tarda provides insights into its adaptation to broad host ranges and intracellular
niches. PLoS One. 2009; 4(10):e7646. DOI: 10.1371/journal.pone.0007646.
[9] Naka H, Dias GM, Thompson CC, Dubay C,
Thompson FL, Crosa JH. Complete genome
sequence of the marine fish pathogen Vibrio
anguillarum harboring the pJM1 virulence
plasmid and genomic comparison with other
virulent strains of V. anguillarum and V.
ordalii. Infect Immun. 2011; 79(7):2889–900. DOI: 10.1128/IAI.05138-11.
[10] Chaudhry V, Prabhu BP. Genomic investigation reveals evolution and lifestyle adaptation of endophytic Staphylococcus epidermidis. Scientific Reports. 2016; 6: 19263.
DOI:10.1038/srep19263.
[11] Colston SM, Fullmer MS, Beka L, Lamy B,
Gogarten JP, Graf J. Bioinformatic genome
comparisons for taxonomic and phylogenetic assignments using Aeromonas as a
test case. mBio. 2014; 5(6):e02136. DOI: 10.1128/mBio.02136-14.
[12] Antony T Vincent, Mélanie V Trudel,
Luca Freschi, Vandan Nagar, Cynthia
Gagné-Thivierge, Roger C Levesque, et
al. Increasing genomic diversity and evidence of constrained lifestyle evolution
due to insertion sequences in Aeromonas
salmonicida. BMC Genomics. 2016; 17:44. DOI:10.1186/s12864-016-2381-3.
[13] Holm KO, Bækkedal C, Soderberg JJ, Hau- ¨
gen P. Complete Genome Sequences of
Seven Vibrio anguillarum Strains as Derived from PacBio Sequencing. Genome
Biology and Evolution. 2018; 10(4):1127–
1131. DOI:10.1093/gbe/evy074.
[14] Frans I, Michiels CW, Bossier P, Willems
KA, Lievens B, Rediers H. Vibrio anguillarum as a fish pathogen: virulence factors,
diagnosis and prevention. Journal of Fish Diseases. 2011; 34(9):643–61.
[15] Rowe-Magnus DA, Guerout AM, Biskri
L, Bouige P, Mazel D. Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res. 2003;13(3):428–442. DOI:10.1101/gr.617103.
[16] Roh HJ, Kim BS, Kim A, Kim NE, Lee Y,
Chun WK, et al. Whole-genome analysis of
multi-drug-resistant Aeromonas veronii isolated from diseased discus (Symphysodon
discus) imported to Korea. Journal of
Fish Diseases. 2019; 42(1):147–153. DOI: 10.1111/jfd.12908.
[17] Ingeborg Frans, Kristof Dierckens, Sam
Crauwels, Ado Van Assche, Jorgen Leisner, Marianne H. Larsen, et al. Does
virulence assessment of Vibrio anguillarum using sea bass (Dicentrarchus labrax)
larvae correspond with genotypic and
phenotypic characterization?. PLoS One.
2013; 8(8):e70477. DOI: 10.1371/journal.pone.0070477
[18] Busschaert P, Frans I, Crauwels S, Zhu B, Willems K, Bossier P, et al. Comparative genome sequencing to assess the genetic diversity and virulence attributes of
15 Vibrio anguillarum isolates. Journal of
Fish Diseases. 2015; 38(9):795–807. DOI: 10.1111/jfd.12290.
[19] Domenico Maione,Immaculada Margarit,
Cira D. Rinaudo, Vega Masignani, Marirosa
Mora, Maria Scarselli, et al. Identification of a universal Group B streptococcus vaccine by multiple genome
screen. Science. 2005; 309(5731):148–150. DOI:10.1126/science.1109869.
[20] Sun Y, Liu C, Sun L. Construction and
analysis of the immune effect of an Edwardsiella tarda DNA vaccine encoding
a D15-like surface antigen. Fish Shellfish Immunol. 2011; 30(1):273–9. DOI:
10.1016/j.fsi.2010.10.020
[21] Sun Y, Liu CS, Sun L. Identification
of an Edwardsiella tarda surface antigen
and analysis of its immunoprotective potential as a purified recombinant subunit
vaccine and a surface-anchored subunit
vaccine expressed by a fish commensal
strain. Vaccine. 2010; 28(40):6603–8. DOI: 10.1016/j.vaccine.2010.07.050.
[22] Khushiramani RM, Maiti B, Shekar M,
Girisha SK, Akash N, Deepanjali A, et
al. Recombinant Aeromonas hydrophila
outer membrane protein 48 (Omp48) induces a protective immune response against
Aeromonas hydrophila and Edwardsiella
tarda. Res Microbiol. 2012; 163(4):286–91. DOI: 10.1016/j.resmic.2012.03.001.
[23] Maiti B, Shetty M, Shekar M, Karunasagar
I, Karunasagar I. Evaluation of two outer
membrane proteins, Aha1 and OmpW of
Aeromonas hydrophila as vaccine candidate for common carp. Vet Immunol Immunopathol. 2012;149(3-4):298–301. DOI:
10.1016/j.vetimm.2012.07.013.
[24] Luo Z, Fu J, Li N, Liu Z, Qin T,
Zhang X, et al. Immunogenic proteins and
their vaccine development potential evaluation in outer membrane proteins (OMPs)
of Flavobacterium columnare. Aquaculture and Fisheries. 2016; 1:1–8. DOI:
10.1016/j.aaf.2016.10.002
[25] Luo Z, Liu Z, Fu J, Zhang Q, Huang B, Nie
P, Immunogenicity and protective role of
antigenic regions from five outer membrane
proteins of Flavobacterium columnare in
grass carp Ctenopharyngodon idella. Chin
J Oceanol Limnol. 2016; 34(6):1247–57.
DOI: 10.1007/s00343-016-5096-z
[26] Mao Z, Ye J, Li M, Xu H, Chen J. Vaccination efficiency of surface antigens and killed
whole cell of Pseudomonas putida in large
yellow croaker (Pseudosciaena crocea). Fish
Shellfish Immunol. 2013; 35(2):375–81.
DOI: 10.1016/j.fsi.2013.04.030.
[27] Castro N, Toranzo AE, Núnez S, Mag- ˜arinos B. Development of an effective Ed- ˜
wardsiella tarda vaccine for cultured turbot (Scophthalmus maximus). Fish Shellfish Immunol. 2008; 25(3):208–212. DOI:
10.1016/j.fsi.2008.05.008.
[28] Kawai K, Liu Y, Ohnishi K, Oshima S. A
conserved 37 kDa outer membrane protein
of Edwardsiella tarda is an effective vaccine
candidate. Vaccine. 2004; 22(25-26):3411–8. DOI: 10.1016/j.vaccine.2004.02.026.
[29] Seong Bin Park, Ho Bin Jang, Seong Won Nho, In Seok Cha, Jun-ichi Hikima, Maki
Ohtani, et al. Outer membrane vesicles
as a candidate vaccine against edwardsiellosis. PLoS One. 2011; 6(3):e17629. DOI:
10.1371/journal.pone.0017629.
[30] LingBing Zeng, Dongliang Wang, NiYa Hu, Qing Zhu, Kaishen Chen, Ke Dong,
et al. A Novel Pan-Genome Reverse
Vaccinology Approach Employing a
Negative-Selection Strategy for Screening
Surface-Exposed Antigens against
leptospirosis. Front Microbiol. 2017; 8:396. DOI: 10.3389/fmicb.2017.00396.
[31] Buján N, Mohammed H, Balboa S, Romalde JL, Toranzo AE, Arias CR, et al. Genetic studies to re-affiliate Edwardsiella
tarda fish isolates to Edwardsiella piscicida
and Edwardsiella anguillarum species. Syst
Appl Microbiol. 2018; 41(1):30–37. DOI:
10.1016/j.syapm.2017.09.004.
[32] Fogelson SB, Petty BD, Reichley SR,
Ware C, Bowser PR, Crim MJ, et al.
Histologic and molecular characterization
of Edwardsiella piscicida infection in
largemouth bass (Micropterus salmoides).
Journal of Veterinary Diagnostic
Investigation. 2016; 28(3):338–44. DOI: 10.1177/1040638716637639.
[33] Joy Y. Yang, Shelise Brooks, Jennifer
A. Meyer, Robert R. Blakesley, Adrian
M. Zelazny, Julia A. Segre, et al. PanPCR, a computational method for designing
bacterium-typing assays based on wholegenome sequence data. Journal of Clinical
Microbiology. 2013; 51(3):752–758. DOI: 10.1128/JCM.02671-12.
pathogens - disease of farmed and wild fish.
5th ed. Dordrecht: Springer; 2012.
[2] Henrik Hasman, Dhany Saputra, Thomas
Sicheritz-Ponten, Ole Lund, Christina Aaby
Svendsen, Niels Frimodt-Moller, et al.
Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. Journal
of Clincal Microbiology. 2014; 52(8):3136. DOI: 10.1128/JCM.01369-14.
[3] Sion C. Bayliss, David W. Verner-Jeffreys,
Kerry L. Bartie, David M. Aanensen,
Samuel K. Sheppard, Alexandra Adams,
Edward J. Feil. The promise of whole
genome pathogen sequencing for the molecular epidemiology of emerging aquaculture
pathogens. Front Microbiol. 2017; 8:121.
DOI: 10.3389/fmicb.2017.00121.
[4] Pridgeon Julia W, Phillip H Klesius. Major
bacterial diseases in aquaculture and their
vaccine development. CAB Reviews Perspectives in Agriculture Veterinary Science
Nutrition and Natural Resources. 2012.
DOI: 10.1079/PAVSNNR20127048.
[5] Carding S, Verbeke K, Vipond DT, Corfe
BM, Owen LJ. Dysbiosis of the gut microbiota in disease. Microbial Ecology in
Health and Disease. 2015; 26:26191. DOI:
10.3402/mehd.v26.26191.
[6] Defoirdt T, Sorgeloos P, Bossier P. Alternatives to antibiotics for the control
of bacterial disease in aquaculture. Curr
Opin Microbiol. 2011; 14(3):251–8. DOI:
10.1016/j.mib.2011.03.004.
[7] Reith ME, Singh RK, Curtis B, Boyd JM,
Bouevitch A, Kimball J, et al. The genome
of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of
a fish pathogen. BMC Genomics. 2008;
9:427. DOI: 10.1186/1471-2164-9-427.
[8] Wang Q, Yang M, Xiao J, Wu H, Wang
X, Lv Y, et al. Genome sequence of
the versatile fish pathogen Edwardsiella
tarda provides insights into its adaptation to broad host ranges and intracellular
niches. PLoS One. 2009; 4(10):e7646. DOI: 10.1371/journal.pone.0007646.
[9] Naka H, Dias GM, Thompson CC, Dubay C,
Thompson FL, Crosa JH. Complete genome
sequence of the marine fish pathogen Vibrio
anguillarum harboring the pJM1 virulence
plasmid and genomic comparison with other
virulent strains of V. anguillarum and V.
ordalii. Infect Immun. 2011; 79(7):2889–900. DOI: 10.1128/IAI.05138-11.
[10] Chaudhry V, Prabhu BP. Genomic investigation reveals evolution and lifestyle adaptation of endophytic Staphylococcus epidermidis. Scientific Reports. 2016; 6: 19263.
DOI:10.1038/srep19263.
[11] Colston SM, Fullmer MS, Beka L, Lamy B,
Gogarten JP, Graf J. Bioinformatic genome
comparisons for taxonomic and phylogenetic assignments using Aeromonas as a
test case. mBio. 2014; 5(6):e02136. DOI: 10.1128/mBio.02136-14.
[12] Antony T Vincent, Mélanie V Trudel,
Luca Freschi, Vandan Nagar, Cynthia
Gagné-Thivierge, Roger C Levesque, et
al. Increasing genomic diversity and evidence of constrained lifestyle evolution
due to insertion sequences in Aeromonas
salmonicida. BMC Genomics. 2016; 17:44. DOI:10.1186/s12864-016-2381-3.
[13] Holm KO, Bækkedal C, Soderberg JJ, Hau- ¨
gen P. Complete Genome Sequences of
Seven Vibrio anguillarum Strains as Derived from PacBio Sequencing. Genome
Biology and Evolution. 2018; 10(4):1127–
1131. DOI:10.1093/gbe/evy074.
[14] Frans I, Michiels CW, Bossier P, Willems
KA, Lievens B, Rediers H. Vibrio anguillarum as a fish pathogen: virulence factors,
diagnosis and prevention. Journal of Fish Diseases. 2011; 34(9):643–61.
[15] Rowe-Magnus DA, Guerout AM, Biskri
L, Bouige P, Mazel D. Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res. 2003;13(3):428–442. DOI:10.1101/gr.617103.
[16] Roh HJ, Kim BS, Kim A, Kim NE, Lee Y,
Chun WK, et al. Whole-genome analysis of
multi-drug-resistant Aeromonas veronii isolated from diseased discus (Symphysodon
discus) imported to Korea. Journal of
Fish Diseases. 2019; 42(1):147–153. DOI: 10.1111/jfd.12908.
[17] Ingeborg Frans, Kristof Dierckens, Sam
Crauwels, Ado Van Assche, Jorgen Leisner, Marianne H. Larsen, et al. Does
virulence assessment of Vibrio anguillarum using sea bass (Dicentrarchus labrax)
larvae correspond with genotypic and
phenotypic characterization?. PLoS One.
2013; 8(8):e70477. DOI: 10.1371/journal.pone.0070477
[18] Busschaert P, Frans I, Crauwels S, Zhu B, Willems K, Bossier P, et al. Comparative genome sequencing to assess the genetic diversity and virulence attributes of
15 Vibrio anguillarum isolates. Journal of
Fish Diseases. 2015; 38(9):795–807. DOI: 10.1111/jfd.12290.
[19] Domenico Maione,Immaculada Margarit,
Cira D. Rinaudo, Vega Masignani, Marirosa
Mora, Maria Scarselli, et al. Identification of a universal Group B streptococcus vaccine by multiple genome
screen. Science. 2005; 309(5731):148–150. DOI:10.1126/science.1109869.
[20] Sun Y, Liu C, Sun L. Construction and
analysis of the immune effect of an Edwardsiella tarda DNA vaccine encoding
a D15-like surface antigen. Fish Shellfish Immunol. 2011; 30(1):273–9. DOI:
10.1016/j.fsi.2010.10.020
[21] Sun Y, Liu CS, Sun L. Identification
of an Edwardsiella tarda surface antigen
and analysis of its immunoprotective potential as a purified recombinant subunit
vaccine and a surface-anchored subunit
vaccine expressed by a fish commensal
strain. Vaccine. 2010; 28(40):6603–8. DOI: 10.1016/j.vaccine.2010.07.050.
[22] Khushiramani RM, Maiti B, Shekar M,
Girisha SK, Akash N, Deepanjali A, et
al. Recombinant Aeromonas hydrophila
outer membrane protein 48 (Omp48) induces a protective immune response against
Aeromonas hydrophila and Edwardsiella
tarda. Res Microbiol. 2012; 163(4):286–91. DOI: 10.1016/j.resmic.2012.03.001.
[23] Maiti B, Shetty M, Shekar M, Karunasagar
I, Karunasagar I. Evaluation of two outer
membrane proteins, Aha1 and OmpW of
Aeromonas hydrophila as vaccine candidate for common carp. Vet Immunol Immunopathol. 2012;149(3-4):298–301. DOI:
10.1016/j.vetimm.2012.07.013.
[24] Luo Z, Fu J, Li N, Liu Z, Qin T,
Zhang X, et al. Immunogenic proteins and
their vaccine development potential evaluation in outer membrane proteins (OMPs)
of Flavobacterium columnare. Aquaculture and Fisheries. 2016; 1:1–8. DOI:
10.1016/j.aaf.2016.10.002
[25] Luo Z, Liu Z, Fu J, Zhang Q, Huang B, Nie
P, Immunogenicity and protective role of
antigenic regions from five outer membrane
proteins of Flavobacterium columnare in
grass carp Ctenopharyngodon idella. Chin
J Oceanol Limnol. 2016; 34(6):1247–57.
DOI: 10.1007/s00343-016-5096-z
[26] Mao Z, Ye J, Li M, Xu H, Chen J. Vaccination efficiency of surface antigens and killed
whole cell of Pseudomonas putida in large
yellow croaker (Pseudosciaena crocea). Fish
Shellfish Immunol. 2013; 35(2):375–81.
DOI: 10.1016/j.fsi.2013.04.030.
[27] Castro N, Toranzo AE, Núnez S, Mag- ˜arinos B. Development of an effective Ed- ˜
wardsiella tarda vaccine for cultured turbot (Scophthalmus maximus). Fish Shellfish Immunol. 2008; 25(3):208–212. DOI:
10.1016/j.fsi.2008.05.008.
[28] Kawai K, Liu Y, Ohnishi K, Oshima S. A
conserved 37 kDa outer membrane protein
of Edwardsiella tarda is an effective vaccine
candidate. Vaccine. 2004; 22(25-26):3411–8. DOI: 10.1016/j.vaccine.2004.02.026.
[29] Seong Bin Park, Ho Bin Jang, Seong Won Nho, In Seok Cha, Jun-ichi Hikima, Maki
Ohtani, et al. Outer membrane vesicles
as a candidate vaccine against edwardsiellosis. PLoS One. 2011; 6(3):e17629. DOI:
10.1371/journal.pone.0017629.
[30] LingBing Zeng, Dongliang Wang, NiYa Hu, Qing Zhu, Kaishen Chen, Ke Dong,
et al. A Novel Pan-Genome Reverse
Vaccinology Approach Employing a
Negative-Selection Strategy for Screening
Surface-Exposed Antigens against
leptospirosis. Front Microbiol. 2017; 8:396. DOI: 10.3389/fmicb.2017.00396.
[31] Buján N, Mohammed H, Balboa S, Romalde JL, Toranzo AE, Arias CR, et al. Genetic studies to re-affiliate Edwardsiella
tarda fish isolates to Edwardsiella piscicida
and Edwardsiella anguillarum species. Syst
Appl Microbiol. 2018; 41(1):30–37. DOI:
10.1016/j.syapm.2017.09.004.
[32] Fogelson SB, Petty BD, Reichley SR,
Ware C, Bowser PR, Crim MJ, et al.
Histologic and molecular characterization
of Edwardsiella piscicida infection in
largemouth bass (Micropterus salmoides).
Journal of Veterinary Diagnostic
Investigation. 2016; 28(3):338–44. DOI: 10.1177/1040638716637639.
[33] Joy Y. Yang, Shelise Brooks, Jennifer
A. Meyer, Robert R. Blakesley, Adrian
M. Zelazny, Julia A. Segre, et al. PanPCR, a computational method for designing
bacterium-typing assays based on wholegenome sequence data. Journal of Clinical
Microbiology. 2013; 51(3):752–758. DOI: 10.1128/JCM.02671-12.
Published
30-December-2020
How to Cite
1.
Nguyen L. APPLICATION OF COMPARATIVE GENOME IN AQUACULTURE DISEASES DIAGNOSIS. journal [Internet]. 30Dec.2020 [cited 22Dec.2024];10(40):172-9. Available from: https://journal.tvu.edu.vn/tvujs_old/index.php/journal/article/view/629
Issue
Section
Articles
