Methods for typing std pathogens (N. Gonorrhoeae, C. Trachomatis, T. Pallidum)

Abstract

Phenotypic methods were initially used for bacterial typing yet they have a number of drawbacks limiting their use. Methods of molecular and genetic typing have become wide-spread today. Among these methods, bacterial typing based on multilocus sequence
typing (Multilocus Sequence Typing - MLST) has been developing at the fastest rate. However, schemes of molecular
and genetic typing of STD pathogens as compared to other bacteria are insufficiently developed, which considerably complicates
the planning of measures aimed at the reduction of their spread.

References

  1. Bandea C. I., Kubota K., Brown T. M. et al. Typing of Chlamydia trachomatis strains from urine samples by amplification and sequencing the major outer membrane protein gene (omp1). Sex Transm Infect 2001; 77: 419-422.
  2. Bensch S., Akesson M. Ten years of AFLP in ecology and evolution: why so few animals- Mol Ecol 2005; 14: 2899-2914.
  3. Bouvet P. J., Grimont P. A. Identification and biotyping of clinical isolates of Acinetobacter. Ann Inst Pasteur Microbiol 1987; 138: 569-578.
  4. Brisse S., Fussing V., Ridwan B. et al. Automated ribotyping of vancomycinresistant Enterococcus faecium isolates. J Clin Microbiol 2002; 40: 1977-1984.
  5. Brisse S., Verduin C. M., Milatovic D. et al. Distinguishing species of the Burkholderia cepacia complex and Burkholderia gladioli by automated ribotyping. J Clin Microbiol 2000; 38: 1876-1884.
  6. Butt N. J., Lambden P. R., Heckels J. E. The nucleotide sequence of the por gene from Neisseria gonorrhoeae strain P9 encoding outer membrane protein PIB. Nucleic Acids Res 1990; 18: 4258.
  7. Camarena J. J., Nogueira J. M., Dasi M. A., et al. DNA amplification fingerprinting for subtyping Neisseria gonorrhoeae strains. Sex Transm Dis 1995; 22: 128-136.
  8. Cannon J. G., Buchanan T. M., Sparling P. F. Confirmation of association of protein I serotype of Neisseria gonorrhoeae with ability to cause disseminated infection. Infect Immun. 1983; 40: 816-819.
  9. Centurion-Lara A., Castro C., Castillo R. et al. The flanking region sequences of the 15-kDa lipoprotein gene differentiate pathogenic treponemes. J Infect Dis 1998; 177: 1036-1040.
  10. Centurion-Lara A., Molini B. J., Godornes C. et al. Molecular differentiation of Treponema pallidum subspecies. J Clin Microbiol 2006; 44: 3377-3380.
  11. Chang C. H., Chang Y. C., Underwood A. et al. VNTRDB: a bacterial variable number tandem repeat locus database. Nucleic Acids Res 2007; 35: D416-D421.
  12. Cooke S. J., de la Paz H., La Poh C. et al. Variation within serovars of Neisseria gonorrhoeae detected by structural analysis of outermembrane protein PIB and by pulsed-field gel electrophoresis. Microbiology 1997; 143 ( Pt 4): 1415-1422.
  13. De la Fuente L., Vazquez J.A. Multilocus enzyme analysis of African type penicillinase-producing Neisseria gonorrhoeae (PPNG) strains isolated in Spain. Sex Transm Dis 1991; 18: 150-152.
  14. Derrick J. P., Urwin R., Suker J. et al. Structural and evolutionary inference from molecular variation in Neisseria porins. Infect Immun 1999; 67: 2406-2413.
  15. Dworzanski J. P., Deshpande S. V., Chen R. et al. Mass spectrometrybased proteomics combined with bioinformatic tools for bacterial classification 1. J Proteome Res 2006; 5: 76-87.
  16. Dworzanski J. P., Snyder A. P. Classification and identification of bacteria using mass spectrometry-based proteomics 2. Expert Rev Proteomics 2005; 2: 863-878.
  17. Facklam R., Beall B., Efstratiou A. et al. emm typing and validation of provisional M types for group A streptococci 71. Emerg Infect Dis 1999; 5: 247-253.
  18. Feavers I. M., Gray S. J., Urwin R. et al. Multilocus sequence typing and antigen gene sequencing in the investigation of a meningococcal disease outbreak. J Clin Microbiol 1999; 37: 3883-3887.
  19. Fraser C. M., Norris S. J., Weinstock G. M. et al. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 1998; 281: 375-388.
  20. Frenay H. M., Bunschoten A. E., Schouls L. M. et al. Molecular typing of methicillin resistant Staphylococcus aureus on the basis of protein A gene polymorphisms. Eur J Clin Microbiol Infect Dis 1996; 15: 768-770.
  21. Frothingham R., Meeker-O'Connell W. A. Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 1998; 144 ( Pt 5): 1189-1196.
  22. Gaston M. A., Hunter P. R. Efficient selection of tests for bacteriological typing schemes. J Clin Pathol 1989; 42: 763-766.
  23. Geornaras I., Kunene N. F., von Holy A., Hastings J. W. Amplified fragment length polymorphism fingerprinting of Pseudomonas strains from a poultry processing plant. Appl Environ.Microbiol 1999; 65: 3828-3833.
  24. Gevers D., Huys G., Swings J. Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol Lett 2001; 205: 31-36.
  25. Goering R. V. Molecular epidemiology of nosocomial infection: analysis of chromosomal restriction fragment patterns by pulsedfield gel electrophoresis 27. Infect Control Hosp Epidemiol 1993; 14: 595-600.
  26. Goering R. V., Tenover F. C. Epidemiological interpretation of chromosomal macro-restriction fragment patterns analyzed by pulsedfield gel electrophoresis 17. J Clin Microbiol 1997; 35: 2432-2433.
  27. Gotschlich E. C., Seiff M. E., Blake M. S.,. Koomey M. Porin protein of Neisseria gonorrhoeae: cloning and gene structure. Proc Natl
  28. Acad Sci U.S.A 1987; 84: 8135-8139.
  29. Healy M., Huong J., Bittner T. et al. Microbial DNA typing by automated repetitive-sequence-based PCR 45. J Clin Microbiol 2005; 43: 199-207.
  30. Hobbs M. M., Alcorn T. M., Davis R. H. et al. Molecular typing of Neisseria gonorrhoeae causing repeated infections: evolution of porin during passage within a community. J Infect Dis 1999; 179: 371-381.
  31. Hunter P. R., Gaston M. A. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J Clin Microbiol 1988; 26: 2465-2466.
  32. Jackson K. A., Edwards-Jones V., Sutton C. W. et al. Optimisation of intact cell MALDI method for fingerprinting of methicillin-resistant Staphylococcus aureus 13. J Microbiol Methods 2005; 62: 273-284.
  33. Jalal H., Stephen H., Alexander S. et al. Development of real-time PCR assays for genotyping of Chlamydia trachomatis. J Clin Microbiol 2007; 45: 2649-2653.
  34. Jonsdottir K., Kristjansson M., Hjaltalin O. J. et al. The molecular epidemiology of genital Chlamydia trachomatis in the greater Reykjavik area, Iceland. Sex Transm Dis 2003; 30: 249-256.
  35. Jurstrand M., Falk L., Fredlund H. et al. Characterization of Chlamydia trachomatis omp1 genotypes among sexually transmitted disease patients in Sweden. J Clin Microbiol 2001; 39: 3915-3919.
  36. Klint M., Fuxelius H. H., Goldkuhl R. R. et al. High-resolution genotyping of Chlamydia trachomatis strains by multilocus sequence analysis. J Clin Microbiol 2007; 45: 1410-1414.
  37. Klint M., Lofdahl M., Ek C. et al. Lymphogranuloma venereum prevalence in Sweden among men who have sex with men and characterization of Chlamydia trachomatis ompA genotypes. J Clin Microbiol 2006; 44: 4066-4071.
  38. LaFond R. E., Molini B. J., Van Voorhis W. C. et al. Antigenic variation of TprK V regions abrogates specific antibody binding in syphilis. Infect Immun. 2006; 74: 6244-6251.
  39. Lau Q. C., Chow V. T., Poh C. L. Differentiation of Neisseria gonorrhoeae strains by polymerase chain reaction and restriction fragment length polymorphism of outer membrane protein IB genes. Genitourin. Med 1995; 71: 363-366.
  40. Li H., Dillon J. A. Utility of ribotyping, restriction endonuclease analysis and pulsed-field gel electrophoresis to discriminate between isolates of Neisseria gonorrhoeae of serovar IA-2 which require arginine, hypoxanthine or uracil for growth. J Med Microbiol 1995; 43: 208-215.
  41. Lin J. J., Kuo J., Ma J. A PCR-based DNA fingerprinting technique: AFLP for molecular typing of bacteria. Nucleic Acids Res 1996; 24: 3649-3650.
  42. Lindberg R., Fredlund H., Nicholas R. et al. Neisseria gonorrhoeae isolates with reduced susceptibility to cefixime and ceftriaxone: association with genetic polymorphisms in penA, mtrR, porB1b, and ponA. Antimicrob Agents Chemother 2007; 51(6): 2117-22.
  43. Lindstedt B.A. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 2005; 26: 2567-2582.
  44. Lundback D., Fredlund H., Berglund T. et al. Molecular epidemiology of Neisseria gonorrhoeae- identification of the first presumed Swedish transmission chain of an azithromycin-resistant strain. APMIS, 2006; 114: 67-71.
  45. Lysen M., Osterlund A., Rubin C. J. et al. Characterization of ompA genotypes by sequence analysis of DNA from all detected cases of Chlamydia trachomatis infections during 1 year of contact tracing in a Swedish County. J Clin Microbiol 2004; 42: 1641-1647.
  46. Maiden M. C. Multilocus sequence typing of bacteria. Annu Rev Microbiol 2006; 60: 561-588.
  47. Maiden M. C., Bygraves J. A., Feil E. et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 1998; 95: 3140-3145.
  48. Martin I. M., Ison C. A., Aanensen D. M. et al. Rapid sequencebased identification of gonococcal transmission clusters in a large metropolitan area. J Infect Dis 2004; 189: 1497-1505.
  49. Maslow J., M. E. Mulligan. Epidemiologic typing systems. Infect Control Hosp Epidemiol 1996; 17: 595-604.
  50. Mayer L. W. Use of plasmid profiles in epidemiologic surveillance of disease outbreaks and in tracing the transmission of antibiotic resistance. Clin Microbiol Rev 1988; 1: 228-243.
  51. Molano M., Meijer C. J., Morre S. A. et al. Combination of PCR targeting the VD2 of omp1 and reverse line blot analysis for typing of urogenital Chlamydia trachomatis serovars in cervical scrape specimens. J Clin Microbiol 2004; 42: 2935-2939.
  52. Moodley P., Martin I. M., Pillay K. et al. Molecular epidemiology of recently emergent ciprofloxacin-resistant Neisseria gonorrhoeae in South Africa. Sex Transm Dis 2006; 33: 357-360.
  53. Ng L. K., Dillon J. R. Typing by serovar, antibiogram, plasmid content, riboprobing, and isoenzyme typing to determine whether Neisseria gonorrhoeae isolates requiring proline, citrulline, and uracil for growth are clonal. J Clin Microbiol 1993; 31: 1555-1561.
  54. O'Rourke M., Ison C. A., Renton A. M. et al. Opa-typing: a highresolution tool for studying the epidemiology of gonorrhoea. Mol Microbiol 1995; 17: 865-875.
  55. Owen R. J., Sutherland K., Fitzgerald C. et al. Molecular subtyping scheme for serotypes HS1 and HS4 of Campylobacter jejuni. J Clin Microbiol 1995; 33: 872-877.
  56. Palmer H. M., Arnold C. Genotyping Neisseria gonorrhoeae using fluorescent amplified fragment length polymorphism analysis. J Clin Microbiol 2001; 39: 2325-2329.
  57. Palmer H. M., Young H. Dramatic increase in a single genotype of TRNG ciprofloxacin-resistant Neisseria gonorrhoeae isolates in men who have sex with men. Int J STD AIDS 2006; 17: 254-256.
  58. Palmer H. M., Young H., Martin I. M. et al. The epidemiology of ciprofloxacin resistant isolates of Neisseria gonorrhoeae in Scotland 2002: a comparison of phenotypic and genotypic analysis. Sex Transm Infect 2005; 81: 403-407.
  59. Perez-Losada M., Viscidi R. P., Demma J. C. et al. Population genetics of Neisseria gonorrhoeae in a high-prevalence community using a hypervariable outer membrane porB and 13 slowly evolving housekeeping genes. Mol Biol Evol 2005; 22: 1887-1902.
  60. Pillay A., Liu H., Chen C. Y. et al. Molecular subtyping of Treponema pallidum subspecies pallidum. Sex Transm Dis 1998; 25: 408-414.
  61. Pillay A., Liu H., Ebrahim S. et al. Molecular typing of Treponema pallidum in South Africa: cross-sectional studies. J Clin Microbiol 2002; 40: 256-258.
  62. Poh C. L., Lau Q. C. Subtyping of Neisseria gonorrhoeae auxotypeserovar groups by pulsed-field gel electrophoresis. J Med Microbiol 1993; 38: 366-370.
  63. Poh C. L., Lau Q. C., Chow V. T. Differentiation of Neisseria gonorrhoeae IB-3 and IB-7 serovars by direct sequencing of protein IB gene and pulsed-field gel electrophoresis. J Med Microbiol 1995; 43: 201-207.
  64. Poh C. L., Ocampo J. C., Loh G. K. Genetic relationships among Neisseria gonorrhoeae serovars analysed by multilocus enzyme electrophoresis. Epidemiol Infect 1992; 108: 31-38.
  65. Poh C. L., Ramachandran V., Tapsall J. W. Genetic diversity of Neisseria gonorrhoeae IB-2 and IB-6 isolates revealed by whole-cell repetitive element sequence-based PCR. J Clin Microbiol 1996; 34: 292-295.
  66. Pourcel C., Vidgop Y., Ramisse F. et al. Characterization of a tandem repeat polymorphism in Legionella pneumophila and its use for genotyping. J Clin Microbiol 2003; 41: 1819-1826.
  67. Purcell B. K., Chamberlain N. R., Goldberg M. S. et al. Molecular cloning and characterization of the 15-kilodalton major immunogen of Treponema pallidum. Infect Immun 1989; 57: 3708-3714.
  68. Sandstrom E., Danielsson D. Serology of Neisseria gonorrhoeae. Classification by co-agglutination. Acta Pathol Microbiol Scand 1980; 88: 27-38.
  69. Sandstrom E. G., Knapp J. S., Buchanan T. B. Serology of Neisseria gonorrhoeae: W-antigen serogrouping by coagglutination and protein I serotyping by enzyme-linked immunosorbent assay both detect protein I antigens. Infect Immun 1982; 35: 229-239.
  70. Sandstrom E. G., Knapp J. S., Reller L. B. et al. Serogrouping of Neisseria gonorrhoeae: correlation of serogroup with disseminated gonococcal infection. Sex Transm Dis 1984; 11: 77-80.
  71. Selander R. K., Caugant D. A., Ochman H. et al. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics 96. Appl Environ.Microbiol 1986; 51: 873-884.
  72. Shopsin B., Gomez M., Montgomery S. O. et al. Evaluation of protein A gene polymorphic region DNA sequencing for typing of Staphylococcus aureus strains. J Clin Microbiol 1999; 37: 3556.
  73. Snyder L. A., Davies J. K., Saunders N. J. Microarray genomotyping of key experimental strains of Neisseria gonorrhoeae reveals gene complement diversity and five new neisserial genes associated with Minimal Mobile Elements. BMC Genomics 2004; 5: 23.
  74. Soriano V. E., Tellez G., Hargis B. M. et al. Typing of Haemophilus paragallinarum strains by using enterobacterial repetitive intergenic consensus-based polymerase chain reaction. Avian Dis 2004; 48: 890-895.
  75. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis 79. J Mol Biol 1975; 98: 503-517.
  76. Spaargaren J., Stoof J., Fennema H. et al. Amplified fragment length polymorphism fingerprinting for identification of a core group of Neisseria gonorrhoeae transmitters in the population attending a clinic for treatment of sexually transmitted diseases in Amsterdam, The Netherlands. J Clin Microbiol 2001; 39: 2335-2337.
  77. Stanley J., Linton D., Desai M. et al. Molecular subtyping of prevalent M serotypes of Streptococcus pyogenes causing invasive disease. J Clin Microbiol 1995; 33: 2850-2855.
  78. Stothard D. R. Use of a reverse dot blot procedure to identify the presence of multiple serovars in Chlamydia trachomatis urogenital infection. J Clin Microbiol 2001; 39: 2655-2659.
  79. Stothard D. R., Boguslawski G., Jones R. B. Phylogenetic analysis of the Chlamydia trachomatis major outer membrane protein and examination of potential pathogenic determinants. Infect Immun. 1998; 66: 3618-3625.
  80. Sutton M. Y., Liu H., Steiner B. et al. Molecular subtyping of Treponema pallidum in an Arizona County with increasing syphilis morbidity: use of specimens from ulcers and blood. J Infect Dis 2001; 183: 1601-1606.
  81. Teanpaisan R., Douglas C. W. Molecular fingerprinting of Porphyromonas gingivalis by PCR of repetitive extragenic palindromic (REP) sequences and comparison with other fingerprinting methods. J Med Microbiol 1999; 48: 741-749.
  82. Thompson D. K., Deal C. D., Ison C. A. et al. A typing system for neisseria gonorrhoeae based on biotinylated oligonucleotide probes to PIB gene variable regions. J Infect Dis 2000; 181: 1652-1660.
  83. Turner K. M., Hanage W. P., Fraser C. et al. Assessing the reliability of eBURST using simulated populations with known ancestry 31. BMC Microbiol 2007; 7: 30.
  84. U'Ren J. M., Schupp J. M., Pearson T. et al. Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping. BMC Microbiol 2007; 7: 23.
  85. Unemo M., Norlen O., Fredlund H. The porA pseudogene of Neisseria gonorrhoeae--low level of genetic polymorphism and a few, mainly identical, inactivating mutations. APMIS, 2005; 113: 410-419.
  86. Unemo M., Palmer H. M., Blackmore T. et al. Global transmission of prolyliminopeptidase-negative Neisseria gonorrhoeae strains: implications for changes in diagnostic strategies. Sex Transm Infect 2007; 83: 47-51.
  87. Unemo M., Sjostrand A., Akhras M. et al. Molecular characterization of Neisseria gonorrhoeae identifies transmission and resistance of one ciprofloxacin-resistant strain 8. APMIS 2007; 115: 231-241.
  88. Unemo M., Vorobieva V., Firsova N. et al. Neisseria gonorrhoeae population in Arkhangelsk, Russia: phenotypic and genotypic heterogeneity. Clin Microbiol Infect 2007; 13: 873-878. 88. van Belkum A., Tassios P. T., Dijkshoorn L. et al. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin Microbiol Infect (13 Suppl) 2007; 3: 1-46.
  89. Viscidi R. P., Demma J. C., Gu J. et al. Comparison of sequencing of the por gene and typing of the opa gene for discrimination of Neisseria gonorrhoeae strains from sexual contacts. J Clin Microbiol 2000; 38: 4430-4438.
  90. Viscidi R. P., Demma J. C. Genetic Diversity of Neisseria gonorrhoeae Housekeeping Genes. J.Clin.Microbiol. 2003; 41: 197-204.
  91. Webster C. A., Towner K. J. Use of RAPD-ALF analysis for investigating the frequency of bacterial cross-transmission in an adult intensive care unit. J Hosp Infect 2000; 44: 254-260.
  92. Xia M., Whittington W. L., Holmes K. K. et al. Pulsed-field gel electrophoresis for genomic analysis of Neisseria gonorrhoeae. J Infect Dis 1995; 171: 455-458.
  93. Xiong L., Kong F., Zhou H.et al. Use of PCR and reverse line blot hybridization assay for rapid simultaneous detection and serovar identification of Chlamydia trachomatis. J Clin Microbiol 2006; 44: 1413-1418.
  94. Zheng H. P., Jiang L. F., Fang D. Y. et al. Application of an oligonucleotide array assay for rapid detecting and genotyping of Chlamydia trachomatis from urogenital specimens. Diagn Microbiol Infect Dis 2007; 57: 1-6.
  95. Pedersen L. N., Podenphant L., Moller J. K. Highly discriminative genotyping of Chlamydia trachomatis using omp1 and a set of variable number tandem repeats. Clin Microbiol Infect 2008; 14: 644-652.

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Copyright (c) 2010 SIDORENKO S.V., SOLOMKA V.S., KOZhUShNAYa O.S., FRIGO N.V., Sidorenko S.V., Solomka V.S., Kozhushnaya O.S., Frigo N.V.

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