Phylogenetic analysis and the evolution of the 18S rRNA gene typing system of Acanthamoeba

Journal of Eukaryotic Microbiology

Volumn 62, Issue 1, 2015, Pages 69-84

  Fuerst, Paul A ^a   Booton, Gregory C ^a   Crary, Monica ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

sequence types, T2 T6, T20; Species names

Indexed keywords

CLASSIFICATION; CYST; DATABASE; DEVELOPMENTAL BIOLOGY; GENE EXPRESSION; MOLECULAR ANALYSIS; MORPHOLOGY; PHYLOGENETICS; PROTOZOAN; RECONSTRUCTION; RNA; SPECIES DIVERSITY;

ACANTHAMOEBA; ACANTHAMOEBIDAE;

PROTOZOAL DNA; RNA 18S;

ACANTHAMOEBA; CLASSIFICATION; DNA SEQUENCE; GENETIC DATABASE; GENETIC VARIATION; GENETICS; MOLECULAR EVOLUTION; NOMENCLATURE; PHYLOGENY; RIBOTYPING; RNA GENE; STANDARDS; UTILIZATION;

ACANTHAMOEBA; DATABASES, GENETIC; DNA, PROTOZOAN; EVOLUTION, MOLECULAR; GENES, RRNA; GENETIC VARIATION; PHYLOGENY; RIBOTYPING; RNA, RIBOSOMAL, 18S; SEQUENCE ANALYSIS, DNA; TERMINOLOGY AS TOPIC;

EID: 84921830535     PISSN: 10665234     EISSN: 15507408     Source Type: Journal    
DOI: 10.1111/jeu.12186     Document Type: Review

References (79)

1. Abe, N., &, Kimata, I,. 2010. Genotyping of Acanthamoeba isolates from corneal scrapings and contact lens cases of Acanthamoeba Keratitis patients in Osaka, Japan. Jpn J. Infect. Dis., 63 (4), 299-301.
2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., &, Lipman, D. J., 1990. Basic local alignment search tool. J. Mol. Biol., 215: 403-410.
3. Alves, J. M. P., Gusmão, C. X., Teixeira, M. M. G., Freitas, D., Foronda, A. S., &, Affonso, H. T., 2000. Random amplified polymorphic DNA profiles as a tool for the characterization of Brazilian keratitis isolates of the genus Acanthamoeba. Braz. J. Med. Biol. Res., 33: 19-26.
4. Bandelt, H. J., Quintana-Murci, L., Salas, A., &, Macaulay, V., 2002. The fingerprint of phantom mutations in mitochondrial DNA data. Am. J. Hum. Genet., 71: 1150-1160.
5. Barton, N. H., Briggs, D. E. G., Eisen, J. A., Goldstein, D. B., &, Patel, N. H., 2007. Evolution. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
6. Beier, C. L., Horn, M., Michel, R., Schweikert, M., Gortz, H. D., &, Wagner, M., 2002. The Genus Caedibacter Comprises Endosymbionts of Paramecium spp. Related to the Rickettsiales (Alphaproteobacteria) and to Francisella tularensis. (Gammaproteobacteria). Appl. Environ. Microbiol., 68: 6043-6050.
7. Bogler, S. A., Zarley, C. D., Burianek, L. L., Fuerst, P. A., &, Byers, T. J., 1983. Interstrain mitochondrial-DNA polymorphism detected in Acanthamoeba by restriction endonuclease analysis. Mol. Biochem. Parasitol., 8: 145-163.
8. Booton, G. C., Kelly, D. J., Chu, Y.-W., Seal, D., Houang, E., Lam, D., Byers, T. J., &, Fuerst, P. A., 2002. 18S rDNA sequence typing and tracking of Acanthamoeba sp. from Corneal scrapes, contact lenses, lens cases and home water supplies of Acanthamoeba keratitis patients in Hong Kong. J. Clin. Microbiol., 40: 1621-1625.
9. Booton, G. C., Lares-Villa, F., Kelly, D. J., Fuerst, P. A., &, Byers, T. J.,. 2003. Multiple alleles of Acanthamoeba nuclear small subunit ribosomal RNA genes: further evidence of possible genetic exchange between closely related strains. Xth International Meeting on the Biology and Pathogenicity of Free-Living Amoebae Proceedings, ITSON-DIEP, Cd., p. 83-91. Obregon, Mexico.
10. Booton, G. C., Visvesvara, G. S., Byers, T. J., Kelly, D. J., &, Fuerst, P. A., 2005. Differential distribution of Acanthamoeba spp. genotypes in Acanthamoeba keratitis (AK) and non-keratitis infections: implications for potential pathogenicity. J. Clin. Microbiol., 43: 1689-1693.
11. Byers, T. J., Bogler, S. A., &, Burianek, L. L., 1983. Analysis of mitochondrial-DNA variation as an approach to systematic relationships in the genus Acanthamoeba. J. Protozool., 30: 198-203.
12. Castellani, A., 1930a. An amoeba found in cultures of a yeast: preliminary note. J. Trop. Med. Hyg., 1930 (33): 160.
13. Castellani, A., 1930b. An amoeba growing in cultures of a yeast: second note. J. Trop. Med. Hyg., 33: 188.
14. Castellani, A., 1930c. An amoeba growing in cultures of a yeast: third note. J. Trop. Med. Hyg., 33: 221.
15. Castellani, A., 1930d. An amoeba growing in cultures of a yeast: fourth note. J. Trop. Med. Hyg., 33: 237.
16. Clayton, R. A., Sutton, G., Hinkle, P. S., Bult, C., &, Fields, C., 1995. Intraspecific variation of small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int. J. Syst. Bacteriol., 45: 595-599.
17. Comandon, J., &, de Fonbrune, P., 1937. Observation in vivo de la caryocinese d'une amibe: Acanthamoeba (enregistrement cinematographique). C. R. Soc. Biol. Paris, 124: 1299.
18. Corsaro, D., &, Venditti, D., 2010. Phylogenetic evidence for a new genotype of Acanthamoeba (Amoebozoa, Acanthamoebida). Parasitol. Res., 107: 233-238.
19. Crary, M. J,. 2012. Genetic variability and its relationship to Acanthamoeba pathogenesis. Ph.D. thesis. The Ohio State University, Columbus, OH. 152 p.
20. Daggett, P. M., Sawyer, T. K., &, Nerad, T. A., 1982. Distribution and possible interrelationships of pathogenic and non-pathogenic Acanthamoeba from aquatic environments. Microb. Ecol., 8: 371-386.
21. Daggett, P. M., Lipscomb, D., Sawyer, T. K., &, Nerad, T. A., 1985. A molecular approach to the phylogeny of Acanthamoeba. Biosystems, 18: 399-405.
22. De Jonckheere, J. F., 1983. Isoenzyme and total protein-analysis by agarose isoelectric-focusing, and taxonomy of the genus Acanthamoeba. J. Protozool., 30: 701-706.
23. Douglas, M., 1930. Notes on the classification of the amoeba found by Castellani in cultures of yeast-like fungus. J. Trop. Med. Hyg., 33: 258-259.
24. Eickbush, T. H., &, Eickbush, D. G., 2007. Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics, 175: 477-485.
25. Felsenstein, J., 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol., 17: 368-376.
26. Fuerst, P. A,. 2014. Insights from the DNA databases: approaches to the phylogenetic structure of Acanthamoeba. Exp. Parasitol. 145: S39-S45.
27. Fuerst, P. A., &, Booton, G. C., 2007. The phylogenetic structure of Acanthamoeba as seen through the window of the small subunit ribosomal RNA gene: genotypes and "species" do not reflect the same image. Jpn J. Protozool, 40: 168.
28. Gast, R. J., 2001. Development of an Acanthamoeba-specific reverse dot-blot and the discovery of a new ribotype. J. Eukaryot. Microbiol., 48: 609-615.
29. Gast, R. J., Fuerst, P. A., &, Byers, T. J., 1994. Discovery of group I introns in the nuclear small subunit ribosomal RNA genes of Acanthamoeba. Nucleic Acid Res, 22: 592-596.
30. Gast, R. J., Ledee, D. R., Fuerst, P. A., &, Byers, T. J., 1996. Subgenus systematics of Acanthamoeba: four nuclear 18S rDNA sequence types. J. Eukaryot. Microbiol., 43 (6): 498-504.
31. Gunderson, J. H., &, Sogin, M. L., 1986. Length variation in eukaryotic rRNAs: small subunit rRNAs from the protists Acanthamoeba castellanii and Euglena gracilis. Gene, 44: 63-70.
32. Harris, D. J., 2003. Can you bank on GenBank? Trends Ecol. Evol., 18: 317-319.
33. Hewett, M. K., Robinson, B. S., Monis, P. T., &, Saint, C. P., 2003. Identification of a new Acanthamoeba 18S rRNA gene sequence type, corresponding to the species Acanthamoeba jacobsi Sawyer, Nerad and Visvesvara, 1992 (Lobosea: Acanthamoebidae). Acta Protozool., 42: 325-329.
34. Hewitt, R., 1937. The natural habitat and distribution of Hartmannella castellanii (Douglas), a reported contaminant of bacterial cultures. J. Parasitol., 23: 491-495.
35. Hill, F., Gemünd, C., Benes, V., Ansorge, W., &, Gibson, J., 2000. An estimate of large-scale sequencing accuracy. EMBO Rep., 1: 29-31.
36. Hillis, D. M., &, Dixon, M. T., 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. Q. Rev. Biol., 66: 411-453.
37. Horn, M., Fritsche, T. R., Gautom, R. K., Schleifer, K. H., &, Wagner, M., 1999. Novel bacterial endosymbionts of Acanthamoeba spp. Related to the Paramecium caudatum Symbiont Caedibacter caryophilus. Environ. Microbiol., 1: 357-367.
38. Huelsenbeck, J. P., &, Ronquist, F., 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17: 754-755.
39. Karlin, S., Bergman, A., &, Gentles, A. J., 2001. Annotation of the Drosophila genome. Nature, 411: 259-260.
40. Kohsler, M., Leitner, B., Blaschitz, M., Michel, R., Aspock, H., &, Walochnik, J., 2006. ITS1 sequence variabilities correlate with 18S rDNA sequence types in the genus Acanthamoeba (Protozoa: Amoebozoa). Parasitol. Res., 98: 86-93.
41. Kudryavtsev, A., Wylezich, C., Schlegel, M., Walochnik, J., &, Michel, R., 2009. Ultrastructure, SSU rRNA gene sequences and phylogenetic relationships of Flamella Schaeffer, 1926 (Amoebozoa), with description of three new species. Protist, 160: 21-40.
42. Lahr, D. J. G., Grant, J. R., &, Katz, L. A., 2013. Multigene phylogenetic reconstruction of the Tubulinea (Amoebozoa) corroborates four of the six major lineages, while additionally revealing that shell composition does not predict phylogeny in the Arcellinida. Protist, 164: 323-339.
43. Lanocha, N., Kosik-Bogacka, D., Maciejewska, A., Sawczuk, M., &, Wilk, A., 2009. The Occurrence Acanthamoeba (free living amoeba) in environmental and respiratory samples in Poland. Acta Protozool., 48: 271-279.
44. Ledee, D. R., Booton, G. C., Awwad, M. H., Sharma, S., Aggarwal, R. K., Niszl, I. A., Markus, M. B., Fuerst, P. A., &, Byers, T. J., 2003. Advantages of using mitochondrial 16S rDNA sequences to classify clinical isolates of Acanthamoeba. Invest. Ophthalmol. Vis. Sci., 44: 1142-1149.
45. Ledee, D. R., Iovieno, A., Miller, D., Mandal, N., Diaz, M., Fell, J., Fini, M. E., &, Alfonso, E. C., 2009. Molecular identification of T4 and T5 genotypes in isolates from acanthamoeba keratitis patients. J. Clin. Microbiol., 47: 1458-1462.
46. 2 affects soil microbial diversity associated with trembling aspen. Environ. Microbiol., 10: 926-941.
47. Ma, P., Visvesvara, G. S., Martinez, A. J., Theodore, F. H., Daggett, P.-M., &, Sawyer, T. K., 1990. Naegleria and Acanthamoeba infections. Rev. Infect. Dis., 12: 490-513.
48. Ma, P., Willaert, E., Juechter, K. B., &, Stevens, A. R., 1981. A case of keratitis due to Acanthamoeba in New York, New York, and features of 10 cases. J. Infect. Dis., 143: 662-667.
49. Magnet, A., Fenoy, S., Galvan, A. L., Izquierdo, F., Rueda, C., Fernandez Vadillo, C., &, del Aguila, C,. 2013. A year long study of the presence of free living amoeba in Spain. Water Res. 47: 6966-6972.
50. Magnet, A., Henriques-Gil, N., Galvan-Diaz, A. L., Izquiedo, F., Fenoy, S., &, del Aguila, C., 2014. Novel Acanthamoeba 18S rRNA gene sequence type from an environmental isolate. Parasitol. Res., 113: 2845-2850.
51. Neff, R. J., 1957. Purification, axenic cultivation, and description of a soil amoeba, Acanthamoeba sp. J. Protozool., 4: 176-182.
52. Noor, M. A. F., &, Larkin, J. C., 2000. A re-evaluation of 12S ribosomal RNA variability in Drosophila pseudoobscura. Mol. Biol. Evol., 17: 938-941.
53. Nuprasert, W., Putaporntip, C., Pariyakanok, L., &, Jongwutiwes, S., 2010. Identification of a novel T17 genotype of Acanthamoeba from environmental isolates and T10 genotype causing keratitis in Thailand. J. Clin. Microbiol., 48: 4636-4640.
54. Page, F. C., 1967a. Taxonomic criteria for limax amoebae, with descriptions of 3 new species of Hartmannella and 3 of Vahlkampfia. J. Protozool., 14: 499-521.
55. Page, F. C., 1967b. Re-definition of the genus Acanthamoeba with descriptions of three species. J. Protozool., 14: 709-724.
56. Puschkarew, B. M., 1913. Über die Verbreitung der Süsswasserprotozoen durch die Luft. Arch. Protistenk., 23: 323-362.
57. Pussard, M., 1966. Le genre Acanthamoeba Volkonsky, 1931 (Hartmannellidae-Amoebida). Protistologica, 2: 71-94.
58. Pussard, M., &, Pons, R., 1977. Morphologie de la paroi kystique et taxonomie du genre Acanthamoeba (Protozoa, Amoebida). Protistologica, 13: 557-598.
59. Qvarnstrom, Y., Nerad, T. A., &, Visvesvara, G. S., 2013. Characterization of a new pathogenic Acanthamoeba Species, A. byersi n. sp., isolated from a human with fatal amoebic encephalitis. J. Eukaryot. Microbiol., 60: 626-633.
60. Ray, D. L., &, Hayes, R. E., 1954. Hartmannella astronyxis: a new species of free-living amoeba. Cytology and life cycle. J. Morphol., 95: 159-188.
61. Reich, K., 1933. Studien über die Bodenprotozoen Palästinas. Arch. Protistenk., 79: 76-98.
62. Risler, A., Coupat-Goutaland, B., &, Pelandakis, M., 2013. Genotyping and phylogenetic analysis of Acanthamoeba isolates associated with keratitis. Parasitol. Res., 112: 3807-3816.
63. Rogerson, A., &, Patterson, D. J., 2002. The Naked Ramicristate Amoebae (Gymnamoebae). In:, Lee, J. J., Leedale, G. F., &, Bradbury, P., (ed.), An Illustrated Guide to the Protozoa, 2nd ed. Society of Protozoologists, Lawrence, KS. p. 1023-1053.
64. Saitou, N., &, Nei, M., 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4: 406-425.
65. Sawyer, T. K., &, Griffin, J. L., 1975. A proposed new family, Acanthamoebidae n. fam. (order Amoebida), for certain cyst-forming filose amoebae. Trans. Am. Microsc. Soc., 94: 93-98.
66. Schroeder, J. M., Booton, G. C., Hay, J., Niszl, I. A., Seal, D. V., Markus, M. B., Fuerst, P. A., &, Byers, T. J., 2001. Use of subgenic 18S ribosomal DNA PCR and sequencing for genus and genotype identification of acanthamoebae from humans with keratitis and from sewage sludge. J. Clin. Microbiol., 39: 1903-1911.
67. Singh, B. N., 1952. Nuclear division in nine species of small free-living amoebae and its bearing on the classification of the order Amoebida. Philos. Trans. Roy. Soc. London B, 236: 405-461.
68. Singh, B. N., &, Das, S. R., 1970. Studies on pathogenic and non-pathogenic small free-living amoebae and the bearing of nuclear division on the classification of the order Amoebida. Philos. Trans. Roy. Soc. London B, 259: 435-476.
69. Smirnov, A. V., Chao, E., Nassonova, E. S., &, Cavalier-Smith, T., 2011. A revised classification of naked lobose amoebae (Amoebozoa: Lobosa). Protist, 162: 545-570.
70. Stothard, D. R., Schroeder-Diedrich, J. M., Awwad, M. H., Gast, R. J., Ledee, D. R., Rodriguez- Zaragoza, S., Dean, C. L., Fuerst, P. A., &, Byers, T. J,. 1998. The evolutionary history of the genus Acanthamoeba and the identification of eight new 18S rRNA gene sequence types. J. Eukaryot. Microbiol. 45: 45-54.
71. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., &, Kumar, S., 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony method. Mol. Biol. Evol., 28: 2731-2739.
72. Visvesvara, G. S., 1991. Classification of Acanthamoeba. Rev. Infect. Dis., 13 (Suppl. 5): S369-S372.
73. Visvesvara, G. S., Booton, G. C., Kelley, D. J., Fuerst, P., Sriram, R., Finkelstein, A., &, Garner, M. M., 2007. In vitro culture, serologic and molecular analysis of Acanthamoeba isolated from the liver of a keel-billed toucan (Ramphastos sulfuratus). Vet. Parasitol., 143: 74-78.
74. Visvesvara, G. S., Martinez, A. J., Schuster, F. L., Leitch, G. J., Wallace, S. V., Sawyers, T. K., &, Anderson, M., 1990. Leptomyxid amoeba, a new agent of amebic meningoencephalitis in humans and animals. J. Clin. Microbiol., 28: 2750-2756.
75. Visvesvara, G. S., Schuster, F. L., &, Martinez, A. J,. 1993. Balamuthia mandrillaris, N. G., N. Sp., agent of amebic meningoencephalitis in humans and other animals. J. Eukaryot. Microbiol. 40: 504-514.
76. Volkonsky, M., 1931. Hartmannella castellanii Douglas et classification des Hartmannelles. Arch. Zool. Exp. Gen., 72: 317-339.
77. Weekers, P. H. H., Gast, R. J., Fuerst, P. A., &, Byers, T. J., 1994. Sequence variations in small-subunit ribosomal RNAs of Hartmannella vermiformis and their phylogenetic implications. Mol. Biol. Evol., 11: 684-690.
78. Walochnik, J., Haller-Schöber, E.-M., Kolli, H., Picher, O., Obwaller, A., &, Aspöck, H., 2000. Discrimination between clinically relevant and nonrelevant Acanthamoeba strains isolated from contact lens-wearing keratitis patients in Austria. J. Clin. Microbiol., 38: 3932-3936.
79. Zhao, G., Sun, S. Y., Zhao, J., &, Xie, L. X., 2010. Genotyping of Acanthamoeba isolates and clinical characteristics of patients with Acanthamoeba keratitis in China. J. Med. Microbiol., 59: 462-466.