Numerical phenetic classification of clinically significant aerobic sporoactinomycetes and related organisms

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 84, Issue 1, 2003, Pages 39-68

  Trujillo, Martha E ^a   Goodfellow, Michael ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Clinically significant sporoactinomycetes; Computer assisted identification; Numerical classification

Indexed keywords

CLASSIFICATION; FUNGUS; IDENTIFICATION METHOD; MICROORGANISM;

ACTINOBACTERIA; ACTINOMADURA; AEROBIC BACTERIUM; ALGORITHM; ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATE; CLASSIFICATION; CONTROLLED STUDY; DATA ANALYSIS; DIAGNOSTIC TEST; ENZYME ASSAY; GENUS; INFRASPECIFIC RANK; MATHEMATICAL ANALYSIS; MYCETOMA; NOCARDIOPSIS; NONHUMAN; PRINCIPAL COORDINATE ANALYSIS; PRIORITY JOURNAL; STREPTOMYCES; STREPTOMYCES ALBUS; TAXONOMY; THERMOBIFIDA; THERMOMONOSPORA;

ACTINOMYCETALES; ACTINOMYCETALES INFECTIONS; CLUSTER ANALYSIS; DATA INTERPRETATION, STATISTICAL; HUMANS; PHENOTYPE; PHYLOGENY;

ACTINOBACTERIA (CLASS); ACTINOCORALLIA; ACTINOMADURA; ACTINOMADURA LATINA; ACTINOMADURA MADURAE; ACTINOMADURA PELLETIERI; BACTERIA (MICROORGANISMS); FUNGI; NOCARDIOPSIS; STREPTOMYCES; STREPTOMYCES ALBUS; STREPTOMYCES ANULATUS; STREPTOMYCES SOMALIENSIS; STREPTOMYCINEAE; THERMOBIFIDA; THERMOMONOSPORA; UNCULTURED ACTINOMYCETE;

EID: 0038455642     PISSN: 00036072     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1024401004258     Document Type: Article

References (72)

1. Alderson G. 1985. The application and relevance of non-hierarchic methods in bacterial taxonomy. In: Goodfellow M., Jones D. and Priest F.G. (eds), Computer-Assisted Bacterial Systematics. Academic Press, London, pp. 227-273.
2. Alderson G. and Goodfellow M. 1979. Classification and identification of actinomycetes causing mycetoma. Post. Hig. I Med. Dósw 44: 109-124.
3. Alderson G., Athalye M. and White R.P. 1984. Numerical methods in the taxonomy of sporoactinomycetes. In: Ortiz-Ortiz L., Bojalil L.F. and Yakoleff V. (eds), Biological, Biochemical and Biomedical Aspects of Actinomycetes. Academic Press, London, pp. 597-615.
4. Atalan E., Manfio G.P., Ward A.C., Kroppenstedt R.M. and Goodfellow M. 2000. Biosystematic studies on novel streptomycetes from soil. Antonie van Leeuwenhoek 77: 337-353.
5. Athalye M., Lacey J. and Goodfellow M. 1981. Selective isolation and enumeration of actinomycetes using rifampicin. J. appl. Bact 51: 289-297.
6. Athalye M., Goodfellow M., Lacey J. and White R.P. 1985. Numerical classification of Actinomadura and Nocardiopsis. Int. J. Syst. Bacteriol. 35: 86-98.
7. Baril L., Boiron P., Manceron V., Ely S.O.O., Jamet P., Favre E. et al. 1999. Refractory craniofacial actinomycetoma due to Streptomyces somaliensis that required salvage therapy with amikacin and imipenem. Clin. Infect. Dis. 29: 460-461.
8. Berd D. 1973. Laboratory identification of clinically important aerobic actinomycetes. Appl. Microbiol. 25: 665-681.
9. Develoux M., Dieng M.T. and Ndiaye B. 1999. Mycetoma. J. Mycol. Med. 9: 179-209.
10. Elzein S., Quintana E.T., Hamid M.E., Maldonado L.A., Ahmed A.O., Kim B. et al. 2001. Characterisation of streptomycetes that cause mycetoma Abstracts of the 12th International Symposium on the Biology of Actinomycetes. The University of British Columbia, Vancouver, Canada, pp. 103.
11. Evtushenko L.I., Taran V.V., Akimov V.N., Kroppenstedt R.M., Tiedje J.M. and Stackebrandt E. 2000. Nocardiopsis tropica sp. nov., nom. rev. and Nocardiopsis dassonvillei subsp albirubida subsp. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 50: 73-81.
12. Fischer A., Kroppenstedt R.M. and Stackebrandt E. 1983. Molecular-genetic and chemotaxonomic studies on Actinomadura and Nocardiopsis. J. Gen. Microbiol. 129: 3433-3446.
13. Goodfellow M. 1996. Actinomycetes: Actinomyces, Actinomadura, Nocardia, Streptomyces and related taxa. In: Collee J.G., Fraser A.G., Marmion B.P. and Simmons A. (eds), Mackie and McCartney Practical Medical Microbiology. Churchill Livingstone, Edinburgh, pp. 343-359.
14. Goodfellow M. 1998. Nocardia and related genera. In: Balows A. and Duerden B.I. (eds), Topley Wilson's Microbiology and Microbial Infections. Systematic Bacteriology Vol. 2. 9th edn. Arnold, London, pp. 463-489.
15. Goodfellow M. and Pirouz T. 1982. Numerical classification of sporoactinomycetes containing meso-diaminopimelic acid in the cell wall. J. Gen. Microbiol. 128: 503-527.
16. Goodfellow M., Alderson G. and Lacey J. 1979. Numerical taxonomy of Actinomadura and related actinomycetes. J. Gen. Microbiol. 112: 95-111.
17. Goodfellow M., Weaver C.R. and Minnikin D.E. 1982. Numerical classification of rhodococci, corynebacteria and related organisms. J. Gen. Microbiol. 128: 731-745.
18. Goodfellow M., Embley T.M. and Austin B. 1985. Numerical taxonomy and emended description of Renibacterium salmoninarum. J. Gen. Microbiol. 131: 2739-2752.
19. Goodfellow M., Lonsdale C., James A.L. and MacNamara O.C. 1987. Rapid biochemical tests for the characterisation of streptomycetes. FEMS Microbiol. Lett. 43: 39-44.
20. Goodfellow M., Stanton L.J., Simpson K.E. and Minnikin D.E. 1990. Numerical and chemical classification of Actinoplanes and some related actinomycetes. J. Gen. Microbiol. 136: 19-36.
21. Goodfellow M., Trujillo M.E. and Alderson G. 1995. Approaches towards the identification of sporoactinomycetes that cause mycetoma. Biotechnologia 7-8: 271-286.
22. Gordon R.E. 1976. A taxonomist's obligation. In: Goodfellow M., Brownell G.H. and Serrano J.A. (eds), The Biology of the Nocardiae. Academic Press, London, pp. 66-73.
23. Grund E. and Kroppenstedt R.M. 1990. Chemotaxonomy and numerical taxonomy of the genus Nocardiopsis Meyer 1976. Int. J. Syst. Bacteriol. 40: 5-11.
24. Hamid M.E., Chun J., Magee J.G., Minnikin D.E. and Goodfellow M. 1994. Rapid characterization and identification of mycobacteria using fluorogenic enzyme tests. Zbl. Bakt. 280: 433-438.
25. Jones K.L. 1949. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J. Bacteriol. 57: 141-146.
26. Kim B., Sabin N., Minnikin D.E., Zakrzewska-Czerwinska J., Mordarski M. and Goodfellow M. 1999. Classification of thermophilic streptomycetes including the description of Streptomyces thermoalcalitolerans sp. nov. Int. J. Syst. Bacteriol. 49: 7-17.
27. Kroppenstedt R.M. 1992. The genus Nocardiopsis. In: Balows A., Trüper H.G., Dworkin W., Harder W. and Schleifer K.H. (eds), The Prokaryotes. 2nd edn. Springer Verlag, New York, pp. 1139-1156.
28. Kroppenstedt R.M., Stackebrandt E. and Goodfellow M. 1990. Taxonomic revision of the actinomycete genera Actinomadura and Micromonospora. Syst. Appl. Microbiol. 13: 148-160.
29. Labeda D.P. 2001. Crossiella gen. nov., a new genus related to Streptoalloteicus. Int. J. Syst. Evol. Microbiol. 51: 1575-1579.
30. Langham C.D., Williams S.T., Sneath P.H.A. and Mortimer A.M. 1989. New probability matrices for identification of Streptomyces. J. Gen. Microbiol. 135: 121-133.
31. Lu Z., Wang L., Zhang Y., Shi Y., Liu Z., Quintana E.T. et al. 2003. Two new species of Actinomadura:Actinomadura catellatospora sp. nov. andActinomadura glaucoflava. Int. J. Syst. Microbiol. (in press).
32. Manfio G.P., Zakrzewska-Czerwinska J., Atalan E. and Goodfellow M. 1995. Towards minimal standards for the description of-Streptomyces species. Biotechnologia 7-8: 242-253.
33. McCarthy A.J. and Cross T. 1984. A taxonomic study of Thermomonospora and other monosporic actinomycetes. J. Gen Microbiol. 130: 5-15.
34. McNeil M.M., Brown J.M., Jarvis W.R. and Ajello O.L. 1990. Comparisons of species distribution and antimicrobial susceptibility of aerobic actinomycetes from clinical specimens. Rev. Infect. Dis. 12: 778-783.
35. McNeil M.M. and Brown J.M. 1994. The medically important aerobic actinomycetes epidemiology and microbiology. Clin. Microbiol. Rev. 7: 357-417.
36. McNeil M.M., Brown J.M., Scalise G. and Piersimoni C. 1992. Nonmycetomic Actinomadura madurae infection in a patient with AIDS. J. Clin. Microbiol. 30: 1008-1010.
37. Meyer J. 1976. Nocardiopsis; a new genus of the order Actinomycetales. Int. J. Syst. Bacteriol. 26: 487-493.
38. AL. In: Williams S.T., Sharpe M.E. and Holt J.G. (eds), Bergey's Manual of Systematic Bacteriology Vol. 4. Williams Wilkins, Baltimore, pp. 2511-2526.
39. Mishra S.K., Gordon R.E. and Barnett D.A. 1980. Identification of nocardiae and streptomycetes of medical importance. J. Clin. Microbiol. 728-736.
40. Ndiaye B., Develoux M., Dieng M.T., Kane A., Ndir O. and Raphenon G. 2000. Actual presentation of mycetoma situation in Senegal. J. Mycol. Med. 10: 140-144.
41. Ochi K.S., Miyadoh S. and Tamura T. 1991. Polyacrylamide gel electrophoresis analysis of ribosomal protein At-L30 as a novel approach to actinomycete taxonomy: application to the genera Actinomadura and Microtetraspora. Int. J. Syst. Bacteriol. 41: 234-239.
42. O'Donnell A.G., Falconer C., Goodfellow M., Ward A.C. and Williams E. 1993. Biosystematics and diversity amongst novel carboxydotrophic actinomycetes. Antonie van Leeuwenhoek 64: 325-340.
43. Poschner J., Kroppenstedt R.M., Fischer A. and Stackebrandt E. 1985. DNA:DNA reassociation and chemosystematic studies on Actinomadura, Microbispora, Microtetraspora, Micropolyspora and Nocardiopsis. System. Appl. Microbiol. 6: 264-270.
44. Rainey F.A., Ward-Rainey N., Kroppenstedt R.M. and Stackebrandt E. 1996. The genus Nocardiopsis represents a phylogenetically coherent and a distinct actinomycete lineage: Proposal of Nocardiopsaceae fam nov. Int. J. Syst. Bacteriol. 46: 1088-1092.
45. Schaal K.P. 1985. Laboratory diagnosis of actinomycete diseases. In: Goodfellow M. and Minnikin D.E. (eds), Chemical Methods in Bacterial Systematics. Academic Press, London, pp. 359-381.
46. Schaal K.P. and Beaman B.L. 1984. Clinically significant actinomycetes. In: Goodfellow M., Mordarski M. and Williams S.T. (eds), The Biology of the Actinomycetes. Academic Press, London, pp. 389-424.
47. Schaal K.P. and Lee H.-J. 1992. Actinomycete infections in humans - a review. Gene 115: 201-211.
48. Sindhuphak W.E., MacDonald E. and Head E. 1985. Actinomycetoma caused by Nocardiopsis dassonvillei. Arch. Dermatol. 121: 1332-1334.
49. Silvestri L.G., Turri M., Hill L.R. and Gilardi D. 1962. A quantitative approach to systematics of actinomycetes based on overall similarity. In: Ainsworth G.C. and Sneath P.H.A. (eds), Microbial Classification. Cambridge University Press, Cambridge, pp. 333-360.
50. Sneath P.H.A. 1957. Some thoughts on bacterial classification. J. Gen. Microbiol. 17: 184-200.
51. Sneath P.H.A. 1978. Classification of micro-organisms. In: Norris J.R. and Richmond M.H. (eds), Essays in Microbiology. John Wiley Sons, Chichester, pp. 1-31.
52. Sneath P.H.A. 1979a. BASIC program for identification of an unknown with presence-absence data against an identification matrix of percent positive characters. Comp. Geosci. 5: 195-213.
53. Sneath P.H.A. 1979b. BASIC program for character separation indices from an identification matrix of percent positive characters. Comp. Geosci. 5: 349-357.
54. Sneath P.H.A. 1980a. BASIC program for the most diagnostic properties of groups from an identification matrix of percent positive characters. Comp. Geosci. 6: 21-26.
55. Sneath P.H.A. 1980b. BASIC program for determining the best identification scores possible for the most typical example when compared with an identification matrix of percent positive characters. Comp. Geosci. 6: 27-34.
56. Sneath P.H.A. 1980c. BASIC program for determining overlap between groups in an identification matrix of percent positive characters. Comp. Geosci. 6: 267-278.
57. Sneath P.H.A. and Johnson R. 1972. The influence on numerical taxonomic similarities of errors in microbiological tests. J. Gen. Microbiol. 72: 377-392.
58. Sneath P.H.A. and Sokal R.R. 1973. Numerical Taxonomy. The Principles and Practice of Numerical Classification. W.H. Freeman, Baltimore.
59. Society for Actinomycetes Japan 2001. Identification Manual of Actinomycetes. Business Centre for Academic Societies, Tokyo, Japan.
60. Sokal R.R. and Michener C.D. 1958. A statistical method for evaluating systematic relationships. Kans. Univ. Sci. Bull. 38: 1409-1438.
61. Sokal R.R. and Rohlf F.J. 1962. The comparison of dendrograms by objective methods. Taxon XI 33-40.
62. Stackebrandt E., Rainey F.A. and Ward-Rainey N.-L. 1997. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int. J. Syst. Bacteriol. 47: 479-491.
63. Staneck J.L. and Roberts G.D. 1974. Simplified approach to identification of aerobic actinomycetes by thin layer chromatography. Appl. Microbiol. 28: 226-231.
64. Trujillo M.E. and Goodfellow M. 1997. Polyphasic taxonomic study of clinically significant actinomadurae including the description of Actinomadura latina sp. nov. Zbl. Bakt. 285: 212-233.
65. Whitham T.S., Athalye M., Minnikin D.E. and Goodfellow M. 1993. Numerical and chemical classification of Streptosporangium and some related taxa. Antonie van Leeuwenhoek 64: 387-429.
66. Wilkinson B.J. and Jones D. 1977. A numerical taxonomic survey of Listeria and related bacteria. J. Gen. Microbiol. 77: 317-330.
67. Williams S.T., Goodfellow M., Wellington E.M.H., Vickers J.C., Alderson G., Sneath P.H.A. et al. 1983. A probability matrix for identification of some streptomycetes. J. Gen. Microbiol 129: 1815-1830.
68. AL. In: Williams S.T., Sharpe M.E. and Holt J.G. (eds), Bergey's Manual of Systematic Bacteriology Vol. 4. Williams and Wilkins, Baltimore, pp. 2452-2492.
69. Wishart D. 1978. Clustan User Manual, Version IC, Release 2. 3rd edn. Edinburgh University Program Library Unit, Edinburgh.
70. Wust J., Lanzendorfer H., von Graevenitz A., Gloer H.J. and Schmid B. 1990. Peritonitis caused by Actinomadura madurae in a patent on CAPD. Eur. J. Clin. Microbiol. Infect. Dis. 9: 700-701.
71. Zhang Z., Wang Y. and Ruan J. 1998. Reclassification of Thermomonospora and Microtetraspora. Int. J. Syst. Bacteriol. 48: 411-422.
72. Zhang Z., Kudo T., Nakayima Y. and Wang Y. 2001. Clarification of the relationship between the members of the familyThermomonosporaceae on the basis of 16S rDNA, 16S-23S rRNA internal transcribed spacer and 23S rDNA sequences and chemotaxonomic analyses. Int. J. Syst. Evol. Microbiol. 51: 373-383.