Использование нового метода ПЦР-фингерпринтинга для дифференциации микроорганизмов на низших таксономических уровнях

Список литературы

1. Биргер М.О. Справочник по микробиологическим и вирусологическим методам исследования // М.: Медицина. 1982. С. 126−162.
2. Булыгина Е.С. Систематика Грамотрицательных метилотрофных бактерий на основе анализа нуклеотидных последовательностей 5S рибосомных РНК // Кандидатская дисс. 1991.
3. Гальченко В.Ф., Абрамочкина Ф. Н., Безрукова JI.B., Соколова Е. Н., Иванов М. В. Видовой состав аэробной метанотрофной микрофлоры черного моря // Микробиология. 1988. Т. 57. С. 305−310.
4. Головлев E. JI Метастабильность фенотипа у бактерий // Микробиология. 1998. Т. 59. № 2. С. 149−155.
5. Головлев E.JI. О старых проблемах новой систематики бактерий // Микробиология. 1998. Т. 67. № 2. С. 281−286.
6. Дорошенко Е.В., Лойко Н. Г., Ильинская О. Н., Колпаков А. И., Горнова И. Б., Климанова Е. В., Эль-Регистан Г.И. Характеристика диссоциантов Bacillus cereus // Микробиология. 2001. Т. 70. № 6. С. 811−819.
7. Дубинина И.Г., Щербо С. Н., Макаров В. Б. Метод полимеразной цепной реакции в лабораторной практике // Клиническая лабораторная диагностика. 1997. № 7. С. 4−6.
8. Игнатов А.Н., Кугинуки Я., Хида К. Возбудитель бактериозов капустных Xanthomonas campestris. О создании устойчивых к ксантомонадам растений семейства Brassiceae II Сельскохозяйственная биология. 2002. Т. 5. С. 75−84.
9. Игнатов А.Н., Поляков K.JL, Самохвалов А. Н. Количественный анализ серологических признаков Xanthomonas campestris И Сельскохозяйственная биология. 1998. № 1. С. 106−115.
10. Милько Е. С. Егоров Н.С. Гетерогенность популяции бактерий и процесс диссоциации // М.: Изд-во МГУ. 1991. С. 143.
11. Прозоров, А А Рекомбинантные перестройки генома бактерий и адаптация к среде обитания // Микробиология. 2001. Т. 70. № 5. С. 581−594.
12. Турова Т.П. Филогения прокариот на основании анализа аминокислотных и нуклеотидных последовательностей // Успехи микробиологии. 1983. Т. 18. С. 92−112.
13. Турова Т.П. Использование гибридизационного анализа нуклеиновых кислот для идентификации бактерий//Успехи микробиологии. 1992. Т. 25. С. 185−211.
14. Цыганкова С.В., Булыгина Е. С., Кузнецов Б. Б., Хабибулин С. С., Дорошенко Е. В., Эль-Регистан Г.И. Получение внутрипопуляционных диссоциантов некоторых бацилл и применение метода DIR-ПЦР для их идентификации // Микробиология. 2004. Т. 73. № 3. С. 398−405.
15. Чемерис А.В., Ахунов Э. Д., Вахитов В. А. Секвенирование ДНК / Под ред. В. А. Вахитова. М.: Наука. 1999. С. 199−204.
16. Шлегель Г. Общая микробиология / Под ред. Е. Н. Кондратьевой. М.: Мир. 1987.
17. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z. f Miller W. and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs // Nucleic Acids Res. 1997. V. 25. P. 3389−3402.
18. Alvarez A.M., Benedict A.A., Mizumoto C.Y., Hunter J.E., Gabriel D.W. Serological, pathological and genetic diversity among strains of Xanthomonas campestris infecting crucifers // Phytopathology. 1994. V. 84. P. 1449−1357.
19. Amann R.I., Ludwig W., Schleifer K-H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation // Microbiol. Rev. 1995. V. 59. P. 143−169.
20. Aroson A.I., Beckman W., Dunn P. Bacillus thuringiensis and related insect pathogens // Microbiol. Rev. 1986. V. 50. P. 1−24.
21. Ash C., Farrow A.E., Dorsch M., Stackebrandt E., Collins M. Comparative analysis of Bacillus anthracis, Bacillus cereus and related species on the basis of reverse transcriptase sequencing of 16s rRNA//Int. J. Syst. Bacteriol. 1991. V. 41. P. 343−346.
22. Ash C., Farrow J.A.E., Wallbanks S., Collins M.D. Phylogenetic heterogenety of the genus Bacillus revealed by comparative analysis of small-subunits-ribosomal RNA sequences // Lett. Appl. Microbiol. 1991. V. 13. P. 202−206.
23. Barry Т., Colleran G., Glennon M., Dunican L.K., Gannon F. The 16S/23S ribosomal spacer region as a target for DNA probes to identify eubacteria//PCR methods Appl. 1991. V. 5. P. 51−56.
24. Benson D.R., Xanna D. Frankia diversity in an alder stands as estimated by sodium dodecyl sulfate polyacrylamide gel electrophoresis of whole-cell proteins // Can. J. Bot. 1983. V. 61. P. 2919−2923.
25. Bergey’s. Manual of determinative bacteriology // Eds.: Holt J.G. et al., Williams and Wilkins, Baltimore. 1984.
26. Birch A., Hausler A., Ruttener C., Hutter R. Chromosomal deletions and Rearrangement in Streptomyces glaucescens И J. Bacteriol. 1991. P. 3531−3538.
27. Birnboim H.C., Doly J. A raoid alkaline extraction procedure for screening recombinant plasmid DNA // Nucl. Acids. Res. 1979. V. 7. P. 1513−1523.
28. Bradbury J.F. Xanthomonas Dawson 1939 // In Bergeys manual of systematic bacteriology. Eds.: N.R. Krig and J.G. Holt, Williams and Wilkins Co., Baltimore. 1984. V. 1. P. 199−210.
29. Bravo A. Phylogenetic relationships of Bacillus thuringiensis б-endotoxin family proteins and their functional domains // J. Bacteriol. 1997. V. 179. P. 2793−2801.
30. Bravo A., Jansens S., Peferoen M. Immunocytochemical localization of Bacillus thuringiensis insecticidal crystal proteins in intoxicated insects // J. Invertebr. Pathol. 1992. V. 60. P. 237−246.
31. Brousseau R., Saint-Onge A., Prefontaine G., Masson L., Cabana J. Arbitrary primer polymerase chain reaction, a powerful method to identity Bacillus thuringiensis serovars and strains //Appl. Envir. Microbiol. 1993. V. 59. P. 114−119.
32. Buss H.J., Denner E.B.W., Lubitz W. Classification and identification Bacteria: current approacher to an old problem. Overview of the methods used in bacterial systematics // J. Biotecnology. 1996. V. 47 P. 3−38.
33. Caetano-Anolles G., Bassam B.G., Gresshoff P.M. DNA amplification fingerprinting using very short arbitrary oligonucleotide primers // Bio/Texnology 1991. V. 9. P. 553−557.
34. Carozzi N.B., Kramer V.C., Warm G.W., Evola S., Kozill M. Prediction of insecticidal activity of Bacillus thuringiensis strains by polymerase chain reaction product profiles // Appl. Envir. Microbiol. 1991. V. 57. P. 3057−3061.
35. Ceron J., Covarrubias L., Quintero R., Ortiz A., Ortiz M., Aranda E., Lina L., Bravo A. PCR analysis of the Cryl insecticidal crystal family genes from Bacillus thuringiensis II Appl. Envir. Microbiol. 1994. V. 60. P. 353−356.
36. Ceron J., Ortiz A., Quintero R., Guereca L., Bravo A. Specific PCR primers directed to identify Ciyl and Crylll genes within a Bacillus thuringiensis strain collection // Appl. Envir. Microbiol. 1995. V. 61. P. 3826−3831.
37. Chaley M.B., Korotkov E.V., Skryabin K.G. The method revealing latent periodicity of the nucleotide sequences modified for a case of small samples // DNA Res. 1999. V. 6. P.153−163.
38. Charteris W. Taguchi systems of experimental design and data analysis A quality engineering technology for the food industry // J. Soc. Dairy. Technol. 1992. V. 45. P. 33−49.
39. Collins M.D., Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications // Microbiol. Rev. 1981. V. 45. P.316−354.
40. Coloe P.G., Slattery J.F., Cavanaugh P., Vaughan J. The cellular fatty acid composition of Campylobacter species isolated from cases of enteritis in man and animals // J. Hyg. 1986. V. 96. P. 225−229.
41. Conzalez J.M., Brown Jr. B.J., Carlton B.C. Transfer of Bacillus thuringiensis plasmids coding for 5-endotoxin among strains of Bacillus thuringiensis and Bacillus cereus И Proc. Natl. Acad. USA. 1982. V. 79. P. 6951−6955.
42. Devereux R., Kane M.D., Winfrey J., Stahl D.A. Genus- and group-specific hybridization probes for determinative and environmental studies of sulfate-reducing bacteria // System. Appl. Microbiol. 1992. V. 15. P.601−609.
43. Dubiley S., Kirillov E., Mirzabekov A. Polymorphism analysis and gene detection by minisequencing on an array of gel-immobilized primers // Nucleic Acids Res. 1999. V. 27. P. 19.
44. Dye D.W. and Lelliott R.A. Genus II. Xanthomonas И In: Bergey’s manual of determinative bacteriology, 8th ed. Eds.: R.E. Bushanan and N.E. Gibbons, Williams and Wilkins, Baltimore. 1974. P. 243−249.
45. Edmilson R., Goncalves E.R., Rosato Y.B. Phylogenetic analysis of Xanthomonas species based upon 16S-23S rDNA intergenic spacer sequences // IJSEM. 2002. V. 52. P. 355−361.
46. Eisenach K.D., Sifford M.D., Cave M.D., Bates J.H., Crawford J.T. Detection of
47. Mycobacterium tuberculosis in sputum samples using a polymerase chain reaction // Am. Rev. Respir. Dis. 1991. V.144. P. 1160−1163.
48. Farrelly V., Rainey F.A., Stackrbrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of baterial spacies // Appl. Environ. Microbiol. 1995. V. 61. P.2798−2801.
49. Feitelson J.S. The Bacillus thuringiensis family tree // In: Advanced engineered pesticides. Ed.: L. Kim, Marcel Dekker, Inc., New York, N.Y. 1993. P. 63−72.
50. Fleming J., Sanserverino J., Sayler G.S. Quantitative relationship between naphthalene catabolic frequency and exspression in predicting PAN degradation in soils at town gas manufacturing sites // Environ. Sci. Technol. 1993. V. 27. P. 1068−1074.
51. Flor H. Current status of the gene-for-gene concept // Annu. Rev. Phytopathol. 1971. V. 9. P. 275−296.
52. Frachon E., Hamon S., Nicolas L., de Baijac H. Cellular fatty acid analysis as a potential tool for predicting mosquitocidal activity of Bacillus sphaericus strains // Appl. Envir. Microbiol. 1991. V. 57. P. 3394−3398.
53. George M.L.C., Bustamam M., Cruz W.T., Leach J.E., Nelson R.J. Movement of Xanthomonas oryzae pv. oryzae in southeast Asia detected using PCR-based DNA fingerprinting // Phytopathology. 1997. V.87. P. 302−309.
54. Gibson J.R., Slater E., Xery J., Tompkins D.S., Owen R.J. Use of an amplified-fragment length polymorphism technique to fingerprint and differentiate isolates of Helicobacter pylori II J. Clin. Microbiol. 1998. V. 36. P. 2580−2585.
55. Gonzalez R. and Hanna B.A. Evaluation of Gen-Probe DNA hybridization systems for the identification of Mycobacterium tuberculosis and Mycobacterium avium-intracellulare // Diagn. Microbiol. Infect. Dis. 1987. V.8. P. 69−77.
56. Gurtler V., Mayall B.C. Genetic transfer and genome evolution in MRSA // Microbiology. 2001. V. 147. P. 3195−3197.
57. Gurtler V., Wilson V.A., Mayall B.C. Classification of medically important Clostridia using restiction endonuclease site differences of PCR-amplified 16S rRNA // J. Gen. Microbiol. 1991. V. 137. P. 2673−2679.
58. Guschin D.Y., Mobarry В., Prudnikov D., Stahl D.A., Ritmann B.E. and Mirzabekov A.D. Oligonucleotide microchips as genosensors for determinative and environmental stadies in microbiology//Appl. Environ. Microbiol. 1997. V. 65. P. 2397−2402.
59. Hammens W.P., Vogel R.F. The genus Lactobacillus. II In: The genera of lactic acid bacteria. The lactic acid bacteria. Eds.: B.J.B. Wood and W.H. Holzapfel, Blackie Academie and Professional, Glasgow, Scotland. 1995. V. 2. P. 19−54.
60. Hauben L., Vauterin L., Swings J., Moore E.R.S. Comparison of 16S ribosomal DNA sequences of all Xanthomonas species // Int. J. Syst. Bacteriology. 1997. V. 47. P. 328−335.
61. Heimpel A.M., Angus T.A. The taxonomy of insect pathogens related to Bacillus cereus Frankland and Frankland // Canadian J. Microbiol. 1958. V. 4 P. 531−541.
62. Herdman M. J., Waterbury J.B. Deoxyribonucleic acid base composition of Cyanobacteria // J. Gen. Microbiol. 1979. V. 111. P.63−85.
63. Hofte H., Whiteley H.R. Insecticidal crystal proteins of Bacillus thuringiensi // Microbiol. Rev. 1989. V. 53. P.242−255.
64. Honeycutt R., Sobral B.W., McClelland M. Polymerase chain reaction (PCR) detection and quantification using a short PCR product and a synthetic internal positive control // Anal. Biochem. 1997. V. 248. P.303−306.
65. Honeycutt R.J., Sobral B.W., McClelland M. tRNA intergenic spacers reveal polymorphisms diagnostic for Xanthomonas albilineans // Microbiology. 1995. V. 141. P. 3229−3239.
66. Hulton C.S.J., Higgins C.F., Sharp P.M. ERIC sequences: a novel family of repetitive elements in the genomes of Escerichia coli, Salmonella typhimurium, and other enterobacteria I I Mol. Microbiol. 1991. V. 5. P. 825−834.
67. Hung C.H., Yang C.F., Yang C.Y., Tseng Y.H. Involvement of tonB-exbBDlD2 operon in infection of Xanthomonas campestris phage phi L7 I I Biochem. Biophys. Res. Commun. 2003. V. 21. P. 878−884.
68. Ignatov A.N., Kuginuki Y., Hida K. Pathotypes of Xanthomonas campestris pv. campestris in Japan // Acta Phytopathologica et Entomologica Hungarica. 1999. V. 34. P. 177−181.
69. Ishiwata S. On a find of severe flacherie (sotto disease) // Dainihon Sanshi Kaiho. 1901. V. 114. P. 1−5.
70. Jaccard P. Novelles recgerches sur la distribution florale // Bull. Soc. Vaud. Sci. Nat. 1908. V. 44. P. 223−270.
71. Jang P., Vauterin L., Vancanneyt M., Swings J., Kersters K. Application of fatty acid methyl easters for the taxonomic analysis of the genus Xanthomonas И Syst. Appl. Microbiol. 1993. V. 16. P. 47−71.
72. Jassen P., Maquelin K., Coopman R., Tjerberg I., Bonvet P., Kerstens K., Dijkshoorn L. Discrimination of Acinetobacter genomic species by AFLP fingerprinting // Int. Syst. Bacteriol. 1997. V. 47. P. 1179−1187.
73. Jensen M.A., Webster J.A., Straus N. Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms // Appl. Environ. Microbiol. 1993. V. 59. P. 945−952.
74. Johnson E.A. Bacillus cereus food poisoning // In: Food science and technology: a series of monographs. Foodborn diseases. Ed.: D.O. Diver, Academic press, Troy, MO, USA. 1990. P. 127 136.
75. Joung K.-B., Cote J.-C. A phylogenetic analysis of Bacillus thuringiensis serovars by RFLP-based rybotyping // J. Appl. Microbiol. 2001. V. 91. P. 279−289.
76. Joung K.-B., Cote J.-C. Phylogenetic analysis of Bacillus thuringiensis serovars based on 16S rRNA gene restriction fragment length polymorphisms // J. Appl. Microbiol. 2001. V. 90. P. 115 122.
77. Juarez-Perez V.M., Ferrandis M.D., Frutos K. PCR-based approach for detection of novel Bacillus thuringiensis cry genes //Appl. Envir. Microbiol. 1997. V. 63. P. 2997−3002.
78. Kaltenboeck В., Kousoulas K.G., Storz J. Structures of and allelic diversity and relationships among the major outer membrane protein (ompA) genes of the four chlamydial species // J. Bacteriol. 1993. V. 175. P. 487−502.
79. Kamoun S., Kadmar H.V., Tola E., Kado C.I. Incompatible interaction between crucifers and Xanthomonas campestris involves a vasicular hypersensitive response: role of the hrpX locus // Molecular plant-microbe interactions. 1992. V.5. P. 22−33.
80. Kendall M.G. Rank Correlation Methods, 3nd ed. // Charles Griffin, London. 1970.
81. Kim H-S. Comparative study of the frequency, flagellar serotype, crystal shape, toxicity, and cry gene contents of Bacillus thuringiensis from three environments // Curr. Microbiol. 2000. V. 41. P. 250−256.
82. Kim J., Nietfeld J., Benson A.K. Octamer-based genome scanning distinguishes a unique subpopulation of E. coli 0157: H7 strains in cattle // PNAS. 1999. V. 96. P. 13 288−13 293.
83. Knowles B.H. Mechanism of action of Bacillus thuringiensis insecticidal 5-endotoxins // Adv. Insect. Physiol. 1994.V. 24. P.275−308.
84. Kostman J.R., Edlind T.D., LiPuma J.J., Stull T.L. Molecular epidemiology of Pseudomonas cepacia determined by polymerase chain reaction ribotyping // J. Clin. Microbiol. 1992. V. 30. P. 2084−2087.
85. Kronstad J.W., Whiteley H.R. Three classes of homologous Bacillus thuringiensis crystal-protein genes // Gene. 1986. V. 43. P. 29−40.
86. Kryweinczyk J. Antigenic composition of delta-endotoxin as an aid in identification of Bacillus thuringiensis varieties // Technical report IP-X-12. Canadian Forestry Service, Ottawa, Ontario, Canada. 1977.
87. Kuo W.S., Chak K.F. Identification of novel cry-type genes from Bacillus thuringiensis strains on the basis of restriction fragment length polymorfism of the PCR-amplified DNA // Appl. Envir. Microbiol. 1996. V. 62. P. 1369−1377.
88. Lane D.J. 16S/23S rRNA sequencing // In: Nucleic Acid Techniques in Bacterial systematics. Eds.: E. Stackebrandt and M. Goodfellow, John Wiley and Sons, Chichester. 1991.
89. Lawrence D., Heltefuss S., Seifer H.S.H. DifFeretiation of Bacillus anthracis from Bacillus cereus by gas chromatographic whole-cell fatty acid analysis // J. Clin. Microbiol. 1991. V. 29. P. 1508−1512.
90. Lawrence J.G., Ochman H., Hartl D.L. Molecular and evolutionary relationships among enteric bacteria//J. Gen. Microbiol. 1991. V. 137. P. 1911−1921.
91. Lecadet M.-M., Frachon E., Cosmao Dumanior V. et.al. Updating the H-antigen classification of Bacillus thuringiensis II J. Appl. Microbiol. 1999. V. 86. P. 660−672.
92. Less M.A., Newnan D.M.and Garland S.M. Comparison of a DNA probe assay with culture for the detection of Chlamydia thrachomatis // J. Med. Microbiol. 1991. V. 35. P. 159−161.
93. Leyns F., De Cleene M., Swings J.-G., De Ley J. The host range of the Xanthomonas II Bot. Rev. 1984. V. 50. P. 308−356.
94. Liang Y., Patel S.S., Dean D.H. Irreversible binding kinetics of Bacillus thuringiensis Cry IA 5-endotoxins to gypsy moth brush border membanes vesicles is directly correlated to toxicity // J. Biol. Chem. 1995. V. 270. P. 24 719−24 724.
95. Liesack W., Weyland H., Stackrbrandt E. Potential risk of gene amplifycation by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria // Microb. Ecol. 1991. V. 21. P. 191−198.
96. Link W., Dixens C., Singh M., Schwall M., Melchinger A.E. Genetic diversity in European and Mediterranean faba bean germ plasm revealed by RAPD markers // Theor. Appl. Genet. 1995. V. 90. P. 27−32.
97. Louws F.G., Rademaker J.L.W., de Bruijn F.G. The three Ds of PCR-based genomic analysis of phytobacteria: diversity, detection and disease diagnosis // Ann. Rev. Phytopathol. 1999. V. 37. P. 81−125.
98. Mahillon J., Chandler M. Insertion sequences // Microbiol. Mol. Biol. Rev. 1998. V. 62. P. 725−774.
99. Mantel N. The detection of disease clustering and a generalized regression approach // Cancer Res. 1967. V. 27. P. 209−220.
100. Manz W., Amann R., Ludwig W., Wagner M., Schleifer K.-H. Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions // System. Appl. Microbiol. 1992. V. 14. P. 593−600.
101. Marchesi J.R., Sato Т., Weightman A.J., Martin T.A., Fry J.C., Hiom S.J., Wade W.G. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA//Appl. Environ. Microbiol. 1998. V. 64. P. 795−799.
102. Matheson V.G., Munakata-Marr J., Hopkins G.D., McCarty P.L., Tiedje J.M., Forney L.J. A novel means to develop strain-specific DNA probes for detecting bacteria in the environment // Apll. Environ. Microbiol. 1997. V. 63. P. 2863−2869.
103. Mayer L.W. Use of plasmid profiles in epidemiologic surveillance of diseases outbreaks and in tracing the transmission of antibiotic resistance // Clin. Microbiol. Rev. 1988. V. 1. P. 228−243.
104. Mazurek G.H., Reddy V., Marston B.J., Haas W.H., Crawford J.T. DNA fingerprinting by infrequent-restriction-site amplification // J. Clin. Microbiol. 1996. V. 34, P. 2386−2390.
105. Milch H. Advance in bacterial typing methods // Acta. Microbiol. Immunol. Hung. 1998. V. 45. P. 401−408.
106. Mobarry B.K., Wagner M., Urbain V., Rittmann B.E., Stahl D.A. Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria // Appl. Environ. Microbiol. 1996. V. 62. P.2156−2162.
107. Murray B.E., Singh K.V., Heath J.D., Sharma B.R., Weinstock G.M. Comparison of genomic DNAs of different enterococcus isolates using restriction endonucleases with infrequent recognition sites //J. Clinic. Microbiol. 1990. V.28. P. 2059−2063.
108. Myers L.E., Silva S.V.P.S., Procuniar J.D., Little P.B. Genomic fingerprinting of Haemophilus somnus isolates using a random amplified polymorphic DNA assay // J. Clin. Microbiol. 1993. V. 31. P. 512−517.
109. Nachtigall M. Characterization of Xanthomonas campestris pv. campestris isolates by immunological and molecular biological methods // In: Federal Centre for Breeding Research on Cultivated plants. Annual Report. 1998.
110. Nastasi A., Mammina C., Villafrate M.R. rDNA fingerprinting as tool in epidemiological analysis of Salmonella typhi infections // Epidemiol. Infect. 1991. V. 107. P. 565−576.
111. Nei M., Li W.H. Mathematical model for studying genetic variation in terms of restriction endonucleases // Proc. Natl. Acad. Sci. USA 1979. V. 76. P. 5269−5273.
112. Ohba M., Aizawa K. Frequency of cry ' spore forming Bacillus cereus possessing flagellar antigens of Bacillus thuringiensis // J. of Basic Microbiol. 1986. V. 26 P. 185−188.
113. Olsen J.E., Aabo S., Hill W., Notermans S., Wernars K., Granum P.E., Popovic Т., Rasmussen H.N., Olsvik O. Probes and polymerase chain reaction for detection of food-borne bacterial pathogens // Int. J. Food Microbiol. 1995. V. 28. P. 1−78.
114. Pace N.R., Stahl D.A., Lane D.J. and Olsen G.J. The analysis of natural microbial populations by ribosomal RNA sequences // In: Advances in microbial ecology. Ed.: K.C. Marshall, Plenun press, New York, N.Y. 1986, P. 1−55.
115. Paul J. H., Cesaares L., Thurmond J. Amplification of the rbcL gene from dissolved and particulate DNA from aquatic environments // Appl. Environ. Microbiol. 1990. V. 56. P. 19 631 966.
116. Pearson K. On the coefficient of racial likeness // Biometrika. 1962. V. 18. P. 105−117.
117. Peinado M.A., Malkhosyan S., Velazquez A., Perucho M. Isolation and characterization of allelic losses and gains in colorectal tumors by arbitrarily primed polymerase chain reaction // Proc. Natl. Acad. Sci. USA. 1992. V. 89. P. 10 065−10 069.
118. Pichard S.L., Campbell L., Paul J. H. Diversity of the ribulose bisphosphate carboxylase/Oxygenase form 1 gene (rbcL) in natural phytoplankton communities // Appl. Environ. Microbiol. 1997. V. 63. P. 3600−3606.
119. Poh C.L., Yeo C.C., Tay L. Genome fingerprinting by pulsed-field gel electrophoresis and ribotyping to differentiate Pseudomonas aeruginosa serotype 011 strains // Eur. J. Clinic. Microbiol. Infect. Dis. 1992. V. 11. P. 817−822.
120. Poulsen L.K., Ballard G., Stahl D.A. Use of rRNK fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms // Appl. Microbiol. 1993. V. 59. P.1354−1360.
121. Reysenbach A-L., Giver L.J., Wickham G.S., Pace N.R. Differential amplification of rRNA genes by polymerase chain reaction//Appl. Environ. Microbiol. 1992. V. 58. P. 3417−3418.
122. Rossier O., Van de Ackerveken G., Bonas U. HrpB2 and HrpF from Xanthomonas are type Ш-secreted proteins and essential for pathogenicity and recognition by the host plant // Mol. Microbiol. 2000. V. 38. P. 828−838.
123. Salzberg S.L., Salzberg A.J., Kerlavage A.R., Tomb J.F. Skewed oligomers and origins of replication // Gene. 1998. V. 217. P. 57−67.
124. Sambrook J., Fritsch E.F., Manniatis. Molecular cloning: a laboratory manual, 2nd ed. / Ed.: C. Nolan, Cold Spring Harbor Laboratory press, Cold Spring Harbor, N.Y. 1989.
125. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors // Proc. Natl. Acad. Sci. USA. 1977. V. 84. P. 5463−5467.
126. Sayada C., Denamur E., Orfila J., Catalan F., Elion J. Rapid genotyping of the Chlamydia trachomatis major outer membrane protein by the polymerase chain reaction // FEMS Microbiol. Lett. 1991. V. 83, P. 73−78.
127. Shaad N.W., Vidaver A.K., Lacy G.H., Rudolph K., Jones J.B. Evaluation of proposed amended names of several Pseudomonads and Xanthomonads and recommendations // Phytopathology. 2000. V. 90. P. 208−213.
128. Schleifer K.H., Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications // Bacteriol. Rev. 1972. V. 36. P. 407−477.
129. Schlichting С., Branger С., Fournier J.-M. Typing of Staphylococcus aureus by pulsed-field gel electrophoresis, zymotyping, capsular typing and phage typing: resolution of clonal relationships //J. Clinic. Microbiol. 1993. V. 31. P. 227−232.
130. Smith R.A., Couche G.A. The phylloplane as a soyrse of Bacillus thuringiensis variants // Appl. Envir. Microbiol. 1991. V. 57. P. 311−315.
131. Stern M.J., Ames G.F.L., Smith N.H., Robinson E.C., Higgins C.F. Repetative extragenic palindromic sequences: a major component of the bacterial genome // Cell. 1984. V. 37. P. 10 151 026.
132. Taguchi G., Wu Y. Introduction to off-line quality control // Japan Quality Control * Organisation. Nagoya, Japan. 1980.
133. Tajima F., Nei M. Estimation of evolutionary distance between nucleotide sequences // Mol. Biol. EvoL 1984. V. 1. P. 269−285.
134. Tram C., Simonet M., Nicolas M.-H., Offredo C., Grimont F., Lefevre M., Ageron E., Debure A., Grimont P.A.D. Molecular typing of nosocomial isolates of Legionella pneumophila serogroup 3 //J. Clinic. Microbiol. 1990. V. 28. P. 242−245.
135. Tsang A.Y., Denner J.C., Brennen P.J., McClatchey J.K. Clinical and epidemiological importance of typing Mycobacterium avium complex isolates // J. Clinic. Microbiol. 1992. V. 30. P. 479−484.
136. Turnbull P.C.B., Huston R.A., Ward M.J., Jones M.N., Quinn C.P., Finnie N.J., Duggleby C.J., Kramer J.M., Melling J. Bacillus anthracis but not always anthrax // J. Appl. Bacteriol. 1992. V. 72. P. 21−28.
137. Ueda Т., Suga Y, Yashiro N., Matsuguchi T. Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of niffl gene sequences // J. Bacterid. 1995. V. 177. P. 1414−1417.
138. Van de Peer, Y., De Wachter R. TRECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows Environment Comput // Appl. Biosci. 1994. V. 10. P. 569−570.
139. Vauterin L., Hoste В., Kersters K., Swings J. Rectification of Xanthomonas II Int. J. Syst. Bacteriology. 1995. V. 45. P. 472−489.
140. Vauterin L., Swings J., Kersters K. Grouping of Xanthomonas campestris pathovars by SDS-PAGE of proteins//J. Gen. Microbiol. 1991. V. 137. P. 1677−1687.
141. Versalotic J., Koeuth Т., Lupski J.R. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes // Nucleic Acids Res. 1991. V. 19. P. 68 236 831.
142. Vines A., Reeves M.W., Hunter S., Swaminathan B. Restriction fragment length polymorphism in four virulence-associated genes of Listeria monocytogenes II Res. Microbiol.1992. V. 143. P. 281−294.
143. Vos P., Hogers R., Bleeker M., Reijans M., van de Lee Т., Homes M., Frijters A., Pot J., Peleman J., Muiper M., Zabeau M. AFLP: a new concept for DNA fingerprinting // Nucleic Acids Res. 1995. V. 21. P. 4407−4414.
144. Ward D.M., Bateson M.M., Weller R. and Ruff-Roberts A.L. Ribosomal RNA analysis of microorganisms as they occur in nature // In: Advances in microbial ecology. Ed.: K.C. Marshall, Plenun press, New York, N.Y. 1992. P.219−286.
145. Way J.S., Josephson K.L., Pillai S.D., Abbaszadegan M., Gebra C.P., Pepper I.L. Specific detection of Salmonella spp. by multiplex polymerase chain reaction // Appl. Environ. Mocrobiol.1993. V. 59. P. 1473−1479.
146. Welsh J., McClelland M. Fingerprinting genomes using PCR with arbitrary primers // Nucleic Acids Res. 1990. V. 18. P. 7213−7218.
147. Wiedmann M., Barany F., Batt C.A. Detection of Listeria monocytogenes with a nonisotopic polymerase chain reaction-coupled ligase chain reaction assay // Appl. Environ. Mocrobiol. 1993. V. 59. P. 2743−2745.
148. Williams J. G-K., Kubelik A.R., Livak K.J., Rafalski J.A., Tingey S.V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers // Nucleic Acids Res. 1990. V. 18. P. 6531−6535.
149. Woese C.R. Bacterial evolution // Microbiol. Rev. 1987. V. 51. P. 221 -271.
150. Yakubu D.E., Abadi F.J., Pennington Т.Н. Molecular typing methods for Neisseria meningitides H J. Med. Microbiol. 1999. V. 48. P. 1055−1064.
151. Yang P., De Vos P., Kersters K., Swings J. Polyamine patterns as chemotaxonomic markers for the genus Xanthomonas // Int. J. Syst. Bacteriol. 1993. V. 43. P. 709−714.
152. Zahner V., Momen H., Salles C.A., Rablnovitch I. A comparative study of enzyme variation in Bacillus cereus and Bacillus thuringiensis И J. Appl. Bacteriol. 1989. V. 67. P. 275−282.
153. Zehr J.P., Mellon M., Braun S., Litaker W., Steppe Т., Paerl H.W. Diversity of heterotrophic nitrogen fixation genes in a marine cyanobacterial mat // Appl. Environ. Microbiol. 1995. V. 61. P. 2527−2532.
154. Zeigler D.R. Gene sequences useful for predicting relatedness of whole genomes in bacteria // USEM. 2003. V. 53. P. 1893−1900.