Antonie van Leeuwenhoek

, Volume 109, Issue 7, pp 945–956 | Cite as

Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila

  • Sandeep Ghatak
  • Jochen Blom
  • Samir Das
  • Rajkumari Sanjukta
  • Kekungu Puro
  • Michael Mawlong
  • Ingudam Shakuntala
  • Arnab Sen
  • Alexander Goesmann
  • Ashok Kumar
  • S. V. Ngachan
Original Paper


Aeromonas species are important pathogens of fishes and aquatic animals capable of infecting humans and other animals via food. Due to the paucity of pan-genomic studies on aeromonads, the present study was undertaken to analyse the pan-genome of three clinically important Aeromonas species (A. hydrophila, A. veronii, A. caviae). Results of pan-genome analysis revealed an open pan-genome for all three species with pan-genome sizes of 9181, 7214 and 6884 genes for A. hydrophila, A. veronii and A. caviae, respectively. Core-genome: pan-genome ratio (RCP) indicated greater genomic diversity for A. hydrophila and interestingly RCP emerged as an effective indicator to gauge genomic diversity which could possibly be extended to other organisms too. Phylogenomic network analysis highlighted the influence of homologous recombination and lateral gene transfer in the evolution of Aeromonas spp. Prediction of virulence factors indicated no significant difference among the three species though analysis of pathogenic potential and acquired antimicrobial resistance genes revealed greater hazards from A. hydrophila. In conclusion, the present study highlighted the usefulness of whole genome analyses to infer evolutionary cues for Aeromonas species which indicated considerable phylogenomic diversity for A. hydrophila and hitherto unknown genomic evidence for pathogenic potential of A. hydrophila compared to A. veronii and A. caviae.


Aeromonas Antimicrobial resistance Pan-genome Phylogeny Recombination Virulence 



Authors are thankful to Director, ICAR Research Complex for NEH Region for providing necessary facilities, to Administrator, Nazareth Hospital, Shillong for her support. First author is also thankful to Ms. Dyuti Purkait and Dr. D. Chakraborty for help with data analysis.

Compliance with ethical standards

Conflict of interest

No conflict of interest declared.

Supplementary material

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  1. Alhazmi MI (2015) Isolation of Aeromonas spp. from food products: emerging aeromonas infections and their significance in public health. J AOAC Int 98:927–929. doi: 10.5740/jaoacint.14-257 CrossRefPubMedGoogle Scholar
  2. Alikhan N-F, Petty NK, Ben Zakour NL, Beatson SA (2011) BLAST ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12:402. doi: 10.1186/1471-2164-12-402 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410. doi: 10.1016/S0022-2836(05)80360-2 CrossRefPubMedGoogle Scholar
  4. Beaz-Hidalgo R, Figueras MJ (2013) Aeromonas spp. whole genomes and virulence factors implicated in fish disease. J Fish Dis 36:371–388. doi: 10.1111/jfd.12025 CrossRefPubMedGoogle Scholar
  5. Beaz-Hidalgo R, Agüeria D, Latif-Eugenín F et al (2015a) Molecular characterization of Shewanella and Aeromonas isolates associated with spoilage of common carp (Cyprinus carpio). FEMS Microbiol Lett 362:1–8. doi: 10.1093/femsle/fnu029 CrossRefPubMedGoogle Scholar
  6. Beaz-Hidalgo R, Hossain MJ, Liles MR, Figueras M-J (2015b) Strategies to avoid wrongly labelled genomes using as example the detected wrong taxonomic affiliation for Aeromonas genomes in the GenBank database. PLoS ONE 10:e0115813. doi: 10.1371/journal.pone.0115813 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Blom J, Albaum SP, Doppmeier D et al (2009) EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinform 10:154. doi: 10.1186/1471-2105-10-154 CrossRefGoogle Scholar
  8. Chen P-L, Wu C-J, Tsai P-J et al (2014) Virulence diversity among bacteremic Aeromonas isolates: ex vivo, animal, and clinical evidences. PLoS ONE 9:e111213. doi: 10.1371/journal.pone.0111213 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Colston SM, Fullmer MS, Beka L et al (2014) Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. MBio 5:1–13. doi: 10.1128/mBio.02136-14.Editor CrossRefGoogle Scholar
  10. Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O (2013) Pathogenfinder—distinguishing friend from foe using bacterial whole genome sequence data. PLoS ONE 8:e77302. doi: 10.1371/journal.pone.0077302 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Dias C, Mota V, Murcia AM (2012) Antimicrobial resistance patterns of Aeromonas spp. isolated from ornamental fish. J Aquac Res Dev. doi: 10.4172/2155-9546.1000131 Google Scholar
  12. Elhariry HM (2011) Biofilm formation by Aeromonas hydrophila on green-leafy vegetables: cabbage and lettuce. Foodborne Pathog Dis 8:125–131CrossRefPubMedGoogle Scholar
  13. Evangelopoulou G, Filioussis G, Kritas S et al (2015) Isolation and antimicrobial testing of Aeromonas spp., Citrobacter spp., Cronobacter spp., Enterobacter spp., Escherichia spp., Klebsiella spp., and Trabulsiella spp. from the gallbladder of pigs. Pol J Microbiol Pol Tow Microbiol Pol Soc Microbiol 64:185–188Google Scholar
  14. Figueira V, Vaz-Moreira I, Silva M, Manaia CM (2011) Diversity and antibiotic resistance of Aeromonas spp. in drinking and waste water treatment plants. Water Res 45:5599–5611. doi: 10.1016/j.watres.2011.08.021 CrossRefPubMedGoogle Scholar
  15. Figueras MJ, Beaz-hidalgo R, Hossain MJ, Liles R (2014) Taxonomic affiliation of new genomes should be verified using average nucleotide identity and multilocus phylogenetic analysis. Genome Announc 2:e00927-14. doi: 10.1128/genomeA.00927-14 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Ghatak S, Agarwal RK, Bhilegaonkar KN (2009) Epidemiology of multi-drug resistant Aeromonas spp. J Vet Public Heal 7:1–11Google Scholar
  17. Ghatak S, Agarwal RK, Bhilegaonkar KN, Gill JPS (2012) Molecular detection of food-borne Aeromonas species. Indian J Anim Sci 82:785–793Google Scholar
  18. Ghenghesh KS, Ahmed SF, El-Khalek RA et al (2008) Aeromonas-associated infections in developing countries. J Infect Dev Ctries 2:081–098. doi: 10.3855/jidc.277 CrossRefGoogle Scholar
  19. Ghenghesh KS, Ahmed SF, Cappuccinelli P, Klena JD (2014) Genospecies and virulence factors of Aeromonas species in different sources in a North African country. Libyan J Med 9:25497PubMedGoogle Scholar
  20. Goni-Urriza M (2000) Antimicrobial resistance of mesophilic Aeromonas spp. isolated from two European rivers. J Antimicrob Chemother 46:297–301. doi: 10.1093/jac/46.2.297 CrossRefPubMedGoogle Scholar
  21. Gowda TKGM, Reddy VRAP, Devleesschauwer B et al (2015) Isolation and seroprevalence of Aeromonas spp. among common food animals slaughtered in Nagpur, central India. Foodborne Pathog Dis 12:626–630. doi: 10.1089/fpd.2014.1922 CrossRefPubMedGoogle Scholar
  22. Gray SJ (1984) Aeromonas hydrophila in livestock: incidence, biochemical characteristics and antibiotic susceptibility. J Hyg (Lond) 92:365–375CrossRefGoogle Scholar
  23. Grim CJ, Kozlova EV, Ponnusamy D et al (2014) Functional genomic characterization of virulence factors from necrotizing fasciitis-causing strains of Aeromonas hydrophila. Appl Environ Microbiol 80:4162–4183. doi: 10.1128/AEM.00486-14 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Hathcock TL, Schumacher J, Wright JC, Stringfellow J (1999) The prevalence of Aeromonas species in feces of horses with diarrhea. J Vet Intern Med 13:357–360CrossRefPubMedGoogle Scholar
  25. Hayek N (2013) Lateral transfer and GC content of bacterial resistant genes. Fr Microbiol 4:41. doi: 10.3389/fmicb.2013.00041 Google Scholar
  26. Hoel S, Mehli L, Bruheim T et al (2015) Assessment of microbiological quality of retail fresh sushi from selected sources in Norway. J Food Prot 78:977–982. doi: 10.4315/0362-028X.JFP-14-480 CrossRefPubMedGoogle Scholar
  27. Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267. doi: 10.1093/molbev/msj030 CrossRefPubMedGoogle Scholar
  28. Hyatt D, Chen G-L, Locascio PF et al (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119. doi: 10.1186/1471-2105-11-119 CrossRefGoogle Scholar
  29. Igbinosa IH, Okoh AI (2012) Antibiotic susceptibility profile of Aeromonas species isolated from wastewater treatment plant. Sci World J 2012:764563. doi: 10.1100/2012/764563 Google Scholar
  30. Igbinosa IH, Igumbor EU, Aghdasi F et al (2012) Emerging Aeromonas species infections and their significance in public health. Sci World J 2012:625023. doi: 10.1100/2012/625023 Google Scholar
  31. Isonhood JH, Drake M (2002) Aeromonas species in foods. J Food Prot 65:575–582PubMedGoogle Scholar
  32. Janda JM, Abbott SL (1998) Evolving concepts regarding the genus Aeromonas: an expanding panorama of species, disease presentations, and unanswered questions. Clin Infect Dis 27:332–344. doi: 10.1086/514652 CrossRefPubMedGoogle Scholar
  33. Janda JM, Abbott SL (2010) The genus Aeromonas: taxonomy, pathogenicity, and infection. Clin Microbiol Rev 23:35–73. doi: 10.1128/CMR.00039-09 CrossRefPubMedPubMedCentralGoogle Scholar
  34. Körkoca H, Alan Y, Bozari S et al (2014) Detection of putative virulence genes in Aeromonas isolates from humans and animals. J Infect Dev Ctries 8:1398–1406CrossRefPubMedGoogle Scholar
  35. Krzymińska S, Mokracka J, Koczura R et al (2012) Aeromonas spp.-mediated cell-contact cytotoxicity is associated with the presence of type III secretion system. Antonie Van Leeuwenhoek 101:243–251. doi: 10.1007/s10482-011-9627-5 CrossRefPubMedGoogle Scholar
  36. Linke B, Giegerich R, Goesmann A (2011) Conveyor: a workflow engine for bioinformatic analyses. Bioinformatics 27:903–911. doi: 10.1093/bioinformatics/btr040 CrossRefPubMedGoogle Scholar
  37. Lorén JG, Farfán M, Fusté MC (2014) Molecular phylogenetics and temporal diversification in the genus Aeromonas based on the sequences of five housekeeping genes. PLoS ONE 9:e88805. doi: 10.1371/journal.pone.0088805 CrossRefPubMedPubMedCentralGoogle Scholar
  38. Manna SK, Maurye P, Dutta C, Samanta G (2013) Occurrence and virulence characteristics of Aeromonas species in meat, milk and fish in India. J Food Saf 33:461–469. doi: 10.1111/jfs.12077 CrossRefGoogle Scholar
  39. Martino ME, Fasolato L, Montemurro F et al (2011) Determination of microbial diversity of Aeromonas strains on the basis of multilocus sequence typing, phenotype, and presence of putative virulence genes. Appl Environ Microbiol 77:4986–5000. doi: 10.1128/AEM.00708-11 CrossRefPubMedPubMedCentralGoogle Scholar
  40. Medini D, Donati C, Tettelin H et al (2005) The microbial pan-genome. Curr Opin Genet Dev 15:589–594. doi: 10.1016/j.gde.2005.09.006 CrossRefPubMedGoogle Scholar
  41. Meyer F (2003) GenDB—an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31:2187–2195. doi: 10.1093/nar/gkg312 CrossRefPubMedPubMedCentralGoogle Scholar
  42. Pablos M, Huys G, Cnockaert M et al (2011) Identification and epidemiological relationships of Aeromonas isolates from patients with diarrhea, drinking water and foods. Int J Food Microbiol 147:203–210. doi: 10.1016/j.ijfoodmicro.2011.04.006 CrossRefPubMedGoogle Scholar
  43. Pang M, Jiang J, Xie X et al (2015) Novel insights into the pathogenicity of epidemic Aeromonas hydrophila ST251 clones from comparative genomics. Sci Rep 5:09833. doi: 10.1038/srep09833 CrossRefGoogle Scholar
  44. Pérez-Valdespino A, Fernández-Rendón E, Curiel-Quesada E (2009) Detection and characterization of class 1 integrons in Aeromonas spp. isolated from human diarrheic stool in Mexico. J Basic Microbiol 49:572–578. doi: 10.1002/jobm.200900095 CrossRefPubMedGoogle Scholar
  45. Pinto AD, Terio V, Pinto PD, Tantillo G (2012) Detection of potentially pathogenic Aeromonas isolates from ready-to-eat seafood products by PCR analysis. Int J Food Sci Technol 47:269–273. doi: 10.1111/j.1365-2621.2011.02835.x CrossRefGoogle Scholar
  46. Pridgeon JW, Mu X, Klesius PH (2013) Biochemical and molecular characterization of the novobiocin and rifampicin resistant Aeromonas hydrophila vaccine strain AL09-71 N + R compared to its virulent parent strain AL09-71. Vet Microbiol 165:349–357. doi: 10.1016/j.vetmic.2013.03.018 CrossRefPubMedGoogle Scholar
  47. Seshadri R, Joseph SW, Chopra AK et al (2006) Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades. J Bacteriol 188:8272–8282. doi: 10.1128/JB.00621-06 CrossRefPubMedPubMedCentralGoogle Scholar
  48. Shakir Z, Khan S, Sung K et al (2012) Molecular characterization of fluoroquinolone-resistant Aeromonas spp. isolated from imported shrimp. Appl Environ Microbiol 78:8137–8141. doi: 10.1128/AEM.02081-12 CrossRefPubMedPubMedCentralGoogle Scholar
  49. Sierra JC, Suarez G, Sha J et al (2010) Unraveling the mechanism of action of a new type III secretion system effector AexU from Aeromonas hydrophila. Microb Pathog 49:122–134. doi: 10.1016/j.micpath.2010.05.011 CrossRefPubMedPubMedCentralGoogle Scholar
  50. Silver AC, Williams D, Faucher J et al (2011) Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data. PLoS ONE. doi: 10.1371/journal.pone.0016751 Google Scholar
  51. Soares SC, Silva A, Trost E et al (2013) The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains. PLoS ONE 8:e53818. doi: 10.1371/journal.pone.0053818 CrossRefPubMedPubMedCentralGoogle Scholar
  52. Sreedharan K, Philip R, Singh ISB (2012) Virulence potential and antibiotic susceptibility pattern of motile aeromonads associated with freshwater ornamental fish culture systems: a possible threat to public health. Braz J Microbiol 43:754–765. doi: 10.1590/S1517-83822012000200040 CrossRefPubMedPubMedCentralGoogle Scholar
  53. Stratev D, Odeyemi OA (2015) Antimicrobial resistance of Aeromonas hydrophila isolated from different food sources: a mini-review. J Infect Public Health. doi: 10.1016/j.jiph.2015.10.006 PubMedGoogle Scholar
  54. Tettelin H, Riley D, Cattuto C, Medini D (2008) Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol 11:472–477. doi: 10.1016/j.mib.2008.09.006 CrossRefPubMedGoogle Scholar
  55. Tuševljak N, Rajić A, Waddell L et al (2012) Prevalence of zoonotic bacteria in wild and farmed aquatic species and seafood: a scoping study, systematic review, and meta-analysis of published research. Foodborne Pathog Dis 9:487–497. doi: 10.1089/fpd.2011.1063 CrossRefPubMedGoogle Scholar
  56. Underwood AP, Mulder A, Gharbia S, Green J (2005) Virulence Searcher: a tool for searching raw genome sequences from bacterial genomes for putative virulence factors. Clin Microbiol Infect 11:770–772. doi: 10.1111/j.1469-0691.2005.01210.x CrossRefPubMedGoogle Scholar
  57. Vivas J, Carracedo B, Riaño J et al (2004) Behavior of an Aeromonas hydrophila aroA live vaccine in water microcosms. Appl Environ Microbiol 70:2702–2708CrossRefPubMedPubMedCentralGoogle Scholar
  58. Yano Y, Hamano K, Tsutsui I et al (2015) Occurrence, molecular characterization, and antimicrobial susceptibility of Aeromonas spp. in marine species of shrimps cultured at inland low salinity ponds. Food Microbiol 47:21–27. doi: 10.1016/ CrossRefPubMedGoogle Scholar
  59. Zankari E, Hasman H, Cosentino S et al (2012) Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640–2644. doi: 10.1093/jac/dks261 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Sandeep Ghatak
    • 1
  • Jochen Blom
    • 2
  • Samir Das
    • 1
  • Rajkumari Sanjukta
    • 1
  • Kekungu Puro
    • 1
  • Michael Mawlong
    • 3
  • Ingudam Shakuntala
    • 1
  • Arnab Sen
    • 1
  • Alexander Goesmann
    • 2
  • Ashok Kumar
    • 4
  • S. V. Ngachan
    • 5
  1. 1.Division of Animal HealthICAR Research Complex for NEH RegionUmiamIndia
  2. 2.Bioinformatics and Systems BiologyJustus-Liebig-University GiessenGiessenGermany
  3. 3.Nazareth HospitalLaitumukhrah, ShillongIndia
  4. 4.Division of Veterinary Public HealthIndian Veterinary Research InstituteIzatnagarIndia
  5. 5.ICAR Research Complex for NEH RegionUmiamIndia

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