Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using aeromonas as a test case

mBio

Volumn 5, Issue 6, 2014, Pages

  Colston, Sophie M ^a   Fullmer, Matthew S ^a   Beka, Lidia ^a   Lamy, Brigitte ^b,c   Peter Gogarten, J ^a   Graf, Joerg ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

^b UNIV MONTPELLIER   (France)

^c MONTPELLIER UNIVERSITY HOSPITAL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; RIBOSOME PROTEIN; BACTERIAL DNA;

AEROMONAS; ARTICLE; AVERAGE NUCLEOTIDE IDENTITY; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BIOINFORMATICS; CLADISTICS; CONTROLLED STUDY; DNA DNA HYBRIDIZATION; EXPANDED CORE GENE; GENETIC DISTANCE; GENETIC PARAMETERS; GENOME ANALYSIS; HOUSEKEEPING GENE; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PHYLOGENY; SEQUENCE HOMOLOGY; TAXONOMY; BACTERIAL GENOME; BIOLOGY; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; PROCEDURES;

AEROMONAS; BACTERIA (MICROORGANISMS); PROKARYOTA;

AEROMONAS; COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; GENOME, BACTERIAL; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84920901632     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.02136-14     Document Type: Article

References (85)

1. Didelot X, Bowden R, Wilson DJ, Peto TE, Crook DW. 2012. Transforming clinical microbiology with bacterial genome sequencing. Nat. Rev. Genet. 13:601–612. http://dx.doi.org/10.1038/nrm3437.
2. Pallen MJ, Loman NJ, Penn CW. 2010. High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. Curr. Opin. Microbiol. 13:625-631. http://dx.doi.org/10.1016/j.mib.2010.08.003.
3. Ribeca P, Valiente G. 2011. Computational challenges of sequence classification in microbiomic data. Brief. Bioinform. 12:614–625. http://dx.doi.org/10.1093/bib/bbr019.
4. Chen L, Xiong Z, Sun L, Yang J, Jin Q. 2012. VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res. 40:D641–D645. http://dx.doi.org/10.1093/nar/gkr989.
5. Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, Fitzgerald M, Godfrey P, Haas BJ, Murphy CI, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, Desmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Møller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP. 2012. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc. Natl. Acad. Sci. U. S. A. 109:3065–3070. http://dx.doi.org/10.1073/pnas.1121491109.
6. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ. 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere.” Proc. Natl. Acad. Sci. U. S. A. 103: 12115–12120. http://dx.doi.org/10.1073/pnas.0605127103.
7. Bomar L, Maltz M, Colston S, Graf J. 2011. Directed culturing of microorganisms using metatranscriptomics. mBio 2(2):e00012-11. http://dx.doi.org/10.1128/mBio.00012-11.
8. Schnoes AM, Brown SD, Dodevski I, Babbitt PC. 2009. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLOS Comput. Biol. 5:e1000605. http://dx.doi.org/10.1371/journal.pcbi.10000605.
9. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. http://dx.doi.org/10.1186/1471-2105-14-60.
10. Chun J, Rainey FA. 2014. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int. J. Syst. Evol. Microbiol. 64: 316–324. http://dx.doi.org/10.1099/ijs.0.054171-0.
11. Brenner DJ, Staley JT, Krieg NR. 2005. Classification of procaryotic organisms and the concept of bacterial speciation, p 27316–32. In Brenner DJ, Staley JT, Krieg NR, Garrity GM (ed), Bergey’s manual of systematic bacteriology, vol 2. The proteobacteria. Springer Verlag, New York, NY.
12. Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR, Clark WA. 1992. International code of nomenclature of Bacteria: bacteriological code, 1990 revision. ASM Press, Washington, DC.
13. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P, Maiden MC, Nesme X, Rosselló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB. 2002. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52:1043–1047. http://dx.doi.org/10.1099/ijs.0.02360-0.
14. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P, Thompson FL, Swings J. 2005. Opinion: re-evaluating prokaryotic species. Nat. Rev. Microbiol. 3:733–739. http://dx.doi.org/10.1038/nrmicro1236.
15. Chan JZ, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ. 2012. Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol. 12:302. http://dx.doi.org/10.1186/1471-2180-12-302.
16. Konstantinidis KT, Tiedje JM. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. U. S. A. 102: 2567–2572. http://dx.doi.org/10.1073/pnas.0409727102.
17. Clarke SC, Diggle MA, Edwards GF. 2002. Multilocus sequence typing and porA gene sequencing differentiates strains of Neisseria meningitidis during case clusters. Br. J. Biomed. Sci. 59:160–162.
18. Kämpfer P, Glaeser SP. 2012. Prokaryotic taxonomy in the sequencing era—the polyphasic approach revisited. Environ. Microbiol. 14:291–317. http://dx.doi.org/10.1111/j.1462-2920.2011.02615.x.
19. Lapierre P, Lasek-Nesselquist E, Gogarten JP. 2014. The impact of HGT on phylogenomic reconstruction methods. Brief. Bioinform. 15:79–90. http://dx.doi.org/10.1093/bib.bbs050.
20. Chain PSG, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A, Consortium GSCHMPJ, Detter JC. 2009. Genomics. Genome project standards in a new era of sequencing. Science (New York, NY) 326:236–237. http://dx.doi.org/10.1126/science.1180614.
21. Auch AF, von Jan M, Klenk HP, Göker M. 2010. Digital DNA-DNA hybridization for microbial species delineation by means of genome-togenome sequence comparison. Stand. Genomic Sci. 2:117–134. http://dx.doi.org/10.4056/sigs.531120.
22. Konstantinidis KT, Ramette A, Tiedje JM. 2006. Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Appl. Environ. Microbiol. 72:7286-7293. http://dx.doi.org/10.1128/AEM.01398-06.
23. Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U. S. A. 106: 19126–19131. http://dx.doi.org/10.1073/pnas.0906412106.
24. Scortichini M, Marcelletti S, Ferrante P, Firrao G. 2013. A genomic redefinition of Pseudomonas avellanae species. PLoS One 8:e75794. http://dx.doi.org/10.1371/journal.pone.0075794.
25. Tarazona E, Lucena T, Arahal DR, Macián MC, Ruvira MA, Pujalte MJ. 2014. Multilocus sequence analysis of putative Vibrio mediterranei strains and description of Vibrio thalassae sp. nov. Syst. Appl. Microbiol. 37: 320–328. http://dx.doi.org/10.1016/j.syapm.2014.05.005.
26. Janda JM, Abbott SL. 2010. The genus Aeromonas: taxonomy, pathogenicity, and infection. Clin. Microbiol. Rev. 23:35–73. http://dx.doi.org/10.1128/CMR.00039-09.
27. Cheesman SE, Neal JT, Mittge E, Seredick BM, Guillemin K. 2011. Epithelial cell proliferation in the developing zebrafish intestine is regulated by the Wnt pathway and microbial signaling via Myd88. Proc. Natl. Acad. Sci. U. S. A. 108:4570-4577. http://dx.doi.org/10.1073/pnas.1000072107.
28. Martin-Carnahan A, Joseph SW. 2005. Genus I. Aeromonas Stanier 1943: 213AL, p 5574570–578. In Brenner DJ, Krieg NR, Staley JT, Garrity GM (ed), Bergey’s manual of systematic bacteriology, vol 2, 2nd ed. Springer Verlag, New York, NY.
29. Huys G, Cnockaert M, Swings J. 2005. Aeromonas culicicola Pidiyar et al. 2002 is a later subjective synonym of Aeromonas veronii Hickman-Brenner et al. 1987. Syst. Appl. Microbiol. 28:604–609. http://dx.doi.org/10.1016/j.syapm.2005.03.012.
30. Huys G, Kämpfer P, Swings J. 2001. New DNA-DNA hybridization and phenotypic data on the species Aeromonas ichthiosmia and Aeromonas allosaccharophila: A. ichthiosmia Schubert et al. 1990 is a later synonym of A. veronii Hickman-Brenner et al. 1987. Syst. Appl. Microbiol. 24: 177–182. http://dx.doi.org/10.1078/0723-2020-00038.
31. Collins MD, Martinez-Murcia AJ, Cai J. 1993. Aeromonas enteropelogenes and Aeromonas ichthiosmia are identical to Aeromonas trota and Aeromonas veronii, respectively, as revealed by small-subunit rRNA sequence analysis. Int. J. Syst. Bacteriol. 43:855-856. http://dx.doi.org/10.1099/00207713-43-4-855.
32. Huys G, Denys R, Swings J. 2002. DNA-DNA reassociation and phenotypic data indicate synonymy between Aeromonas enteropelogenes Schubert et al. 1990 and Aeromonas trota Carnahan et al. 1991. Int. J. Syst. Evol. Microbiol. 52:1969–1972. http://dx.doi.org/10.1099/ijs.0.01996-0.
33. Roger F, Marchandin H, Jumas-Bilak E, Kodjo A, colBVH study group, Lamy B. 2012. Multilocus genetics to reconstruct aeromonad evolution. BMC Microbiol. 12:62. http://dx.doi.org/10.1186/1471-2180-12-62.
34. Martinez-Murcia AJ, Monera A, Saavedra MJ, Oncina R, Lopez-Alvarez M, Lara E, Figueras MJ. 2011. Multilocus phylogenetic analysis of the genus Aeromonas. Syst. Appl. Microbiol. 34:189–199. http://dx.doi.org/10.1016/j.syapm.2010.11.014.
35. Miñana-Galbis D, Farfán M, Albarral V, Sanglas A, Lorén JG, Fusté MC. 2013. Reclassification of Aeromonas hydrophila subspecies anaerogenes. Syst. Appl. Microbiol. 36:306-308. http://dx.doi.org/10.1016/j.syapm.2013.04.006.
36. Huys G, Kämpfer P, Albert MJ, Kühn I, Denys R, Swings J. 2002. Aeromonas hydrophila subsp. dhakensis subsp. nov., isolated from children with diarrhoea in Bangladesh, and extended description of Aeromonas hydrophila subsp. hydrophila (Chester 1901) Stanier 1943 (approved lists 1980). Int. J. Syst. Evol. Microbiol. 52:705–712. http://dx.doi.org/10.1099/ijs.0.01844-0.
37. Figueras MJ, Beaz-Hidalgo R, Senderovich Y, Laviad S, Halpern M. 2011. Re-identification of Aeromonas isolates from chironomid egg masses as the potential pathogenic bacteria Aeromonas aquariorum. Environ. Microbiol. Rep. 3:239-244. http://dx.doi.org/10.1111/j.1758-2229.2010.00216.x.
38. Beaz-Hidalgo R, Martínez-Murcia A, Figueras MJ. 2014. Corrigendum to “Reclassification of Aeromonas hydrophila subsp. dhakensis Huys et al. 2002 and Aeromonas aquariorum Martínez-Murcia et al. 2008 as Aeromonas dhakensis sp. nov. comb nov. and emendation of the species Aeromonas hydrophila.” [Syst. Appl. Microbiol. 36:171–176, 2013.] Syst. Appl. Microbiol. 37:543. http://dx.doi.org/10.1016/j.syapm.2012.12.007.
39. Martino ME, Fasolato L, Montemurro F, Rosteghin M, Manfrin A, Patarnello T, Novelli E, Cardazzo B. 2011. Definition of microbial diversity in Aeromonas strains based on multilocus sequence typing, phenotype and presence of putative genes of virulence. Appl. Environ. Microbiol. 77:4986–5000. http://dx.doi.org/10.1128/AEM.00708-11.
40. Loren JG, Farfan M, Fuste MC. 2014. Molecular phylogenetics and temporal diversification in the genus Aeromonas based on the sequences of five housekeeping genes. PLoS One 9:e88805. http://dx.doi.org/10.1371/journal.pone.0088805.
41. Silver AC, Williams D, Faucher J, Horneman AJ, Gogarten JP, Graf J. 2011. Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data. PLoS One 6:e16751. http://dx.doi.org/10.1371/journal.pone.0016751.
42. Morandi A, Zhaxybayeva O, Gogarten JP, Graf J. 2005. Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strains. J. Bacteriol. 187:6561-6564. http://dx.doi.org/10.1128/JB.187.18.6561-6564.2005.
43. Roger F, Lamy B, Jumas-Bilak E, Kodjo A, colBVH Study Group, Marchandin H. 2012. Ribosomal multi-operon diversity: an original perspective on the genus Aeromonas. PLoS One 7:e46268. http://dx.doi.org/10.1371/journal.pone.0046268.
44. Beaz-Hidalgo R, Martinez-Murcia A, Figueras MJ. 2013. Reclassification of Aeromonas hydrophila subsp. dhakensis Huys et al. 2002 and Aeromonas aquariorum Martinez-Murcia et al. 2008 as Aeromonas dhakensis sp. nov. comb. nov. and emendation of the species Aeromonas hydrophila. Syst. Appl. Microbiol. 36:171–176. http://dx.doi.org/10.1016/j.syapm.2012.12.007.
45. Grim CJ, Kozlova EV, Ponnusamy D, Fitts EC, Sha J, Kirtley ML, van Lier CJ, Tiner BL, Erova TE, Joseph SJ, Read TD, Shak JR, Joseph SW, Singletary E, Felland T, Baze WB, Horneman AJ, Chopra AK. 2014. Functional genomic characterization of virulence factors from necrotizing fasciitis-causing strains of Aeromonas hydrophila. Appl. Environ. Microbiol. 80:4162–4183. http://dx.doi.org/10.1128/AEM.00486-14.
46. Carnahan AM, Behram S, Joseph SW. 1991. Aerokey II: a flexible key for identifying clinical Aeromonas species. J. Clin. Microbiol. 29:2843–2849.
47. Beaz-Hidalgo R, Alperi A, Buján N, Romalde JL, Figueras MJ. 2010. Comparison of phenotypical and genetic identification of Aeromonas strains isolated from diseased fish. Syst. Appl. Microbiol. 33:149–153. http://dx.doi.org/10.1016/j.syapm.2010.02.002.
48. Martínez-Murcia A, Monera A, Alperi A, Figueras MJ, Saavedra MJ. 2009. Phylogenetic evidence suggests that strains of Aeromonas hydrophila subsp. dhakensis belong to the species Aeromonas aquariorum sp. nov. Curr. Microbiol. 58:76-80. http://dx.doi.org/10.1007/s00284-008-9278-6.
49. Giltner CL, Bobenchik AM, Uslan DZ, Deville JG, Humphries RM. 2013. Ciprofloxacin-resistant Aeromonas hydrophila cellulitis following leech therapy. J. Clin. Microbiol. 51:1324-1326. http://dx.doi.org/10.1128/JCM.03217-12.
50. Martínez-Murcia A, Beaz-Hidalgo R, Svec P, Saavedra MJ, Figueras MJ, Sedlacek I. 2013. Aeromonas cavernicola sp. nov., isolated from fresh water of a brook in a cavern. Curr. Microbiol. 66:197–204. http://dx.doi.org/10.1007/s00284-012-0253-x.
51. Beiko RG, Harlow TJ, Ragan MA. 2005. Highways of gene sharing in prokaryotes. Proc. Natl. Acad. Sci. U. S. A. 102:14332–14337. http://dx.doi.org/10.1073/pnas.0504068102.
52. Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51:492–508. http://dx.doi.org/10.1080/10635150290069913.
53. Andam CP, David W, Gogarten JP. 2010. Biased gene transfer mimics patterns created through shared ancestry. Proc. Natl. Acad. Sci. U. S. A. 107:10679–10684. http://dx.doi.org/10.1073/pnas.1001418107.
54. Pace NR, Sapp J, Goldenfeld N. 2012. Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life. Proc. Natl. Acad. Sci. 109:1011–1018. http://dx.doi.org/10.1073/pnas.1109716109.
55. Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP, Gogarten JP. 2011. A rooted net of life. Biol. Direct 6:45. http://dx.doi.org/10.1186/1745-6150-6-45.
56. Bansal MS, Alm EJ, Kellis M. 2013. Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss. J. Comput. Biol. 20:738–754.
57. García JA, Larsen JL, Dalsgaard I, Pedersen K. 2000. Pulsed-field gel electrophoresis analyis of Aeromonas salmonicida ssp. salmonicida. FEMS Microbiol. Lett. 190:163–166. http://dx.doi.org/10.1111/j.1574-6968.2000.tb09280.x.
58. Thompson CC, Vicente ACP, Souza RC, Vasconcelos ATR, Vesth T, Alves N, Ussery DW, Iida T, Thompson FL. 2009. Genomic taxonomy of vibrios. BMC Evol. Biol. 9:258. http://dx.doi.org/10.1186/1471-2148-9-258.
59. Chen PL, Wu CJ, Chen CS, Tsai PJ, Tang HJ, Ko WC. 2014. A comparative study of clinical Aeromonas dhakensis and Aeromonas hydrophila isolates in southern Taiwan: A. dhakensis is more predominant and virulent. Clin. Microbiol. Infect. 20:O428–O434. http://dx.doi.org/10.1111/1469-0691.12456.
60. Sambrook J, Russell DW. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor, New York, NY.
61. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42: D206–D214. http://dx.doi.org/10.1093/nar/gkt1226.
62. Bomar L, Stephens WZ, Nelson MC, Velle K, Guillemin K, Graf J. 2013. Draft genome sequence of Aeromonas veronii Hm21, a symbiotic isolate from the medicinal leech digestive tract. Genome Announc. 1(5):e00800-13. http://dx.doi.org/10.1128/genomeA.00800-13.
63. Gouy M, Guindon S, Gascuel O. 2010. SeaView, version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27:221–224. http://dx.doi.org/10.1093/molbev/msp259.
64. Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. http://dx.doi.org/10.1186/1471-2105-5-113.
65. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML. Syst. Biol. 59:307–321. http://dx.doi.org/10.1093/sysbio/syq010.
66. Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Paley S, Popescu L, Pujar A, Shearer AG, Zhang P, Karp PD. 2010. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 38:D473–D479. http://dx.doi.org/10.1093/nar/gkp875.
67. van Dongen S, Abreu-Goodger C. 2012. Using MCL to extract clusters from networks. Methods Mol. Biol. 804:281–295. http://dx.doi.org/10.1007/978-1-61779-361-5_15.
68. Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30: 1575–1584. http://dx.doi.org/10.1093/nar/30.7.1575.
69. Price MN, Dehal PS, Arkin AP. 2010. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490. http://dx.doi.org/10.1371/journal.pone.0009490.
70. Swofford DL. 2002. PAUP*: phylogenetic analysis using parsimony (and other methods), 4th ed. Sinauer Associates, Sunderland, MA.
71. Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European Molecular Biology open software suite. Trends Genet. 16:276–277. http://dx.doi.org/10.1016/S0168-9525(00)02024-2.
72. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690. http://dx.doi.org/10.1093/bioinformatics/btl446.
73. Shimodaira H, Hasegawa M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247. http://dx.doi.org/10.1093/bioinformatics/17.12.1246.
74. Seshadri R, Joseph SW, Chopra AK, Sha J, Shaw J, Graf J, Haft D, Wu M, Ren Q, Rosovitz MJ, Madupu R, Tallon L, Kim M, Jin S, Vuong H, Stine OC, Ali A, Horneman AJ, Heidelberg JF. 2006. Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades. J. Bacteriol. 188: 8272–8282. http://dx.doi.org/10.1128/JN.00621-06.
75. Spataro N, Farfán M, Albarral V, Sanglas A, Lorén JG, Fusté MC, Bosch E. 2013. Draft genome sequence of Aeromonas molluscorum strain 848TT, isolated from bivalve molluscs. Genome Announc. 1(3):e00382-13. http://dx.doi.org/10.1128/genomeA.00382-13.
76. Beatson SA, das Graças de Luna M, Bachmann NL, Alikhan NF, Hanks KR, Sullivan MJ, Wee BA, Freitas-Almeida AC, Dos Santos PA, de Melo JT, Squire DJ, Cunningham AF, Fitzgerald JR, Henderson IR. 2011. Genome sequence of the emerging pathogen Aeromonas caviae. J. Bacteriol. 193:1286–1287. http://dx.doi.org/10.1128/JB.01337-10.
77. Wu CJ, Wang HC, Chen CS, Shu HY, Kao AW, Chen PL, Ko WC. 2012. Genome sequence of a novel human pathogen, Aeromonas aquariorum. J. Bacteriol. 194:4114–4115. http://dx.doi.org/10.1128/JB.00621-12.
78. Chan KG, Puthucheary SD, Chan XY, Yin WF, Wong CS, Too WS, Chua KH. 2011. Quorum sensing in Aeromonas species isolated from patients in Malaysia. Curr. Microbiol. 62:167–172. http://dx.doi.org/10.1007/s00284-010-9689-z.
79. Tekedar HC, Waldbeiser GC, Karsi A, Liles MR, Griffin MJ, Vamenta S, Sonstegard T, Hossain M, Schroeder SG, Khoo L, Lawrence ML. 2013. Complete genome sequence of a channel catfish epidemic isolate, Aeromonas hydrophila strain ML09-119. Genome Announc. 1(5):e00755-13. http://dx.doi.org/10.1128/genomeA.00755-13.
80. Han JE, Kim JH, Choresca C, Shin SP, Jun JW, Park SC. 2013. Draft genome sequence of a clinical isolate, Aeromonas hydrophila SNUFPC-A8, from a moribund cherry salmon (Oncorhynchus masou masou). Genome Announc. 1(1):e00133-12. http://dx.doi.org/10.1128/genomeA.00133-12.
81. Chai B, Wang H, Chen X. 2012. Draft genome sequence of highmelanin-yielding Aeromonas media strain WS. J. Bacteriol. 194: 6693–6694. http://dx.doi.org/10.1128/JB.01807-12.
82. Han JE, Kim JH, Shin SP, Jun JW, Chai JY, Park SC. 2013. Draft genome sequence of Aeromonas salmonicida subsp. achromogenes AS03, an atypical strain isolated from crucian carp (Carassius carassius) in the Republic of Korea. Genome Announc. 1:e00791-13. http://dx.doi.org/10.1128/genomeA.00791-132229.
83. Reith ME, Singh RK, Curtis B, Boyd JM, Bouevitch A, Kimball J, Munholland J, Murphy C, Sarty D, Williams J, Nash JH, Johnson SC, Brown LL. 2008. The genome of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of a fish pathogen. BMC Genomics 9:427. http://dx.doi.org/10.1186/1471-2164-9-427.
84. Charette SJ, Brochu F, Boyle B, Filion G, Tanak7a KH, Derome N. 2012. Draft genome sequence of the virulent strain 01-B526 of the fish pathogen Aeromonas salmonicida. J. Bacteriol. 194:722–723. http://dx.doi.org/10.1128/JB.06276-11.
85. Li Y, Liu Y, Zhou Z, Huang H, Ren Y, Zhang Y, Li G, Zhou Z, Wang L. 2011. Complete genome sequence of Aeromonas veronii strain B565. J. Bacteriol. 193:3389–3390. http://dx.doi.org/10.1128/JB.00347-11.