Abstract
This chapter describes the mechanism of typing procedures of human pathogens and gives some examples to substantiate the added value of typing and clustering analysis in epidemiology. Three steps need to be discerned in the process toward molecular clustering analysis. First, the pathogen must be recognized and identified (the diagnostic step). Second, the typing of the pathogen genome is performed and third, the clustering of the specific type with other known or newly identified types is needed for added epidemiological information.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Arnold C. (2007) Molecular evolution of Mycobacterium tuberculosis. Clin Microbiol Infect 13: 120–128
Bauer J, Andersen AB, Kremer K, and Miorner H (1999) Usefulness of spoligotyping To discriminate IS6110 low-copy-number Mycobacterium tuberculosis complex strains cultured in Denmark. J Clin Microbiol 37: 2602–2606
Behr MA, and Mostowy S (2007) Molecular tools for typing and branding the tubercle bacillus. Curr Mol Med 7: 309–317
Blanc DS. (2004) The use of molecular typing for epidemiological surveillance and investigation of endemic nosocomial infections. Infect Genet Evol 4: 193–197
Day S, Ward H, Ghani A, Bell G, Goan U, Parker M et al. (1998) Sexual histories, partnerships and networks associated with the transmission of gonorrhoea. Int J STD AIDS 9: 666–671
Deplano A, Schuermans A, Van Eldere J, Witte W, Meugnier H, Etienne J et al. (2000) Multicenter evaluation of epidemiological typing of methicillin-resistant Staphylococcus aureus strains by repetitive-element PCR analysis. The European Study Group on Epidemiological Markers of the ESCMID. J Clin Microbiol 38: 3527–3533
Dunbar SA (2006) Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection. Clin Chim Acta 363: 71–82
Francois P, Huyghe A, Charbonnier Y, Bento M, Herzig S, Topolski I et al. (2005) Use of an automated multiple-locus, variable-number tandem repeat-based method for rapid and high-throughput genotyping of Staphylococcus aureus isolates. J Clin Microbiol 43: 3346–3355
Garaizar J, Rementeria A, and Porwollik S (2006) DNA microarray technology: a new tool for the epidemiological typing of bacterial pathogens? FEMS Immunol Med Microbiol 47: 178–189
Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, Mumford JA, and Holmes EC (2004) Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303: 327–332
Hamill M, Benn P, Carder C, Copas A, Ward H, Ison C, and French P (2007) The clinical manifestations of anorectal infection with lymphogranuloma venereum (LGV) versus non-LGV strains of Chlamydia trachomatis: a case-control study in homosexual men. Int J STD AIDS 18: 472–475
Harmsen D, Claus H, Witte W, Rothganger J, Claus H, Turnwald D, and Vogel U (2003) Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting by using novel software for spa repeat determination and database management. J Clin Microbiol 41: 5442–5448
Huijsdens XW, van Dijke BJ, Spalburg E, van Santen-Verheuvel MG, Heck ME, Pluister GN et al. (2006) Community-acquired MRSA and pig-farming. Ann Clin Microbiol Antimicrob 5: 26
Jonas D, Meyer HG, Matthes P, Hartung D, Jahn B, Daschner FD, and Jansen B (2000) Comparative evaluation of three different genotyping methods for investigation of nosocomial outbreaks of Legionnaires' disease in hospitals. J Clin Microbiol 38: 2284–2291
Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S et al. (1997) Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 35: 907–914
Klint M, Fuxelius HH, Goldkuhl RR, Skarin H, Rutemark C, Andersson SG et al. (2007) High-resolution genotyping of Chlamydia trachomatis strains by multilocus sequence analysis. J Clin Microbiol 45: 1410–1414
Klovdahl AS, Graviss EA, Yaganehdoost A, Ross MW, Wanger A, Adams GJ, and Musser JM (2001) Networks and tuberculosis: an undetected community outbreak involving public places. Soc Sci Med 52: 681–694
Koek AG, Bovee LP, van den Hoek JA, Bos AJ, and Bruisten SM (2006) Additional value of typing Noroviruses in gastroenteritis outbreaks in Amsterdam, The Netherlands. J Clin Virol 35: 167–172
Koeleman JG, Stoof J, Biesmans DJ, Savelkoul PH, and Vandenbroucke-Grauls CM (1998) Comparison of amplified ribosomal DNA restriction analysis, random amplified polymorphic DNA analysis, and amplified fragment length polymorphism fingerprinting for identification of Acinetobacter genomic species and typing of Acinetobacter baumannii. J Clin Microbiol 36: 2522–2529
Kolader ME, Dukers NH, van der Bij AK, Dierdorp M, Fennema JS, Coutinho RA, and Bruisten SM (2006) Molecular epidemiology of Neisseria gonorrhoeae in Amsterdam, The Netherlands, shows distinct heterosexual and homosexual networks. J Clin Microbiol 44: 2689–2697
Kremer K, Arnold C, Cataldi A, Gutierrez MC, Haas WH, Panaiotov S et al. (2005) Discriminatory power and reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains. J Clin Microbiol 43: 5628–5638
Lewis F, Hughes GJ, Rambaut A, Pozniak A, and Leigh Brown AJ (2008) Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med 5: e50
Lindstedt BA (2005) Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 26: 2567–2582
Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R et al. (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95: 3140–3145
Noller AC, McEllistrem MC, Shutt KA, and Harrison LH. (2006) Locus-specific mutational events in a multilocus variable-number tandem repeat analysis of Escherichia coli O157:H7. J Clin Microbiol 44: 374–377
Pilcher CD, Wong JK, and Pillai SK (2008) Inferring HIV transmission dynamics from phylogenetic sequence relationships. PLoS Med 5: e69
Reisig F, Kremer K, Amthor B, van Soolingen D, and Haas WH. (2005) Fast ligation-mediated PCR, a fast and reliable method for IS6110-based typing of Mycobacterium tuberculosis complex. J Clin Microbiol 43: 5622–5627
Schouls LM, van der Heide HG, Vauterin L, Vauterin P, and Mooi FR (2004) Multiple-locus variable-number tandem repeat analysis of Dutch Bordetella pertussis strains reveals rapid genetic changes with clonal expansion during the late 1990 s. J Bacteriol 186: 5496–5505
Schouls LM, van der Ende A, Damen M., and van de Pol I (2006) Multiple-locus variable-number tandem repeat analysis of Neisseria meningitidis yields groupings similar to those obtained by multilocus sequence typing. J Clin Microbiol 44: 1509–1518
Singh A, Goering RV, Simjee S, Foley SL, and Zervos MJ (2006) Application of molecular techniques to the study of hospital infection. Clin Microbiol Rev 19: 512–530
Snell RG, and Wilkins RJ (1986) Separation of chromosomal DNA molecules from C. albicans by pulsed field gel electrophoresis. Nucleic Acids Res 14: 4401–4406
Snipes KP, Hirsh DC, Kasten RW, Hansen LM, Hird DW, Carpenter TE, and McCapes RH (1989) Use of an rRNA probe and restriction endonuclease analysis to fingerprint Pasteurella multocida isolated from turkeys and wildlife. J Clin Microbiol 27: 1847–1853
Spaargaren J, Schachter J, Moncada J, de Vries HJ, Fennema HS, Pena AS et al. (2005) Slow epidemic of lymphogranuloma venereum L2b strain. Emerg Infect Dis 11: 1787–1788
Stene-Johansen K, Tjon G, Schreier E, Bremer V, Bruisten S, Ngui SL et al. (2007) Molecular epidemiological studies show that hepatitis A virus is endemic among active homosexual men in Europe. J Med Virol 79: 356–365
Syvanen AC (2005) Toward genome-wide SNP genotyping. Nat Genet 37 Suppl: S5–S10
Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE, Persing DH., and Swaminathan B (1995) Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol 33: 2233–2239
Tjon G, Xiridou M, Coutinho R, and Bruisten S (2007) Different transmission patterns of hepatitis A virus for two main risk groups as evidenced by molecular cluster analysis. J Med Virol 79: 488–494
van Belkum A, Duim B, Regelink A, Moller L, Quint W, and van Alphen L. (1994) Genomic DNA fingerprinting of clinical Haemophilus influenzae isolates by polymerase chain reaction amplification: comparison with major outer-membrane protein and restriction fragment length polymorphism analysis. J Med Microbiol 41: 63–68
van Belkum A, Kluytmans J, van Leeuwen W, Bax R, Quint W, Peters E et al. (1995) Multicenter evaluation of arbitrarily primed PCR for typing of Staphylococcus aureus strains. J Clin Microbiol 33: 1537–1547
van Belkum A, Scherer S, van Alphen L, and Verbrugh H (1998) Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 62: 275–293
van Belkum A, Tassios PT, Dijkshoorn L, Haeggman S, Cookson B, Fry NK et al. (2007) Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin Microbiol Infect 13 Suppl 3: 1–46
van den Braak N, Simons G, Gorkink R, Reijans M, Eadie K, Kremers K et al. (2004) A new high-throughput AFLP approach for identification of new genetic polymorphism in the genome of the clonal microorganism Mycobacterium tuberculosis. J Microbiol Methods 56: 49–62
van der Zanden AG, Kremer K, Schouls LM, Caimi K, Cataldi A, Hulleman A et al. (2002) Improvement of differentiation and interpretability of spoligotyping for Mycobacterium tuberculosis complex isolates by introduction of new spacer oligonucleotides. J Clin Microbiol 40: 4628–4639
van der Zee A, Verbakel H, van Zon JC, Frenay I, van Belkum A, Peeters M et al. (1999) Molecular genotyping of Staphylococcus aureus strains: comparison of repetitive element sequence-based PCR with various typing methods and isolation of a novel epidemicity marker. J Clin Microbiol 37: 342–349
van Deutekom H, Supply P, de Haas PE, Willery E, Hoijng SP, Locht C et al. (2005) Molecular typing of Mycobacterium tuberculosis by mycobacterial interspersed repetitive unit-variable-number tandem repeat analysis, a more accurate method for identifying epidemiological links between patients with tuberculosis. J Clin Microbiol 43: 4473–4479
van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B et al. (1993) Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 31: 406–409
Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407–4414
Voss A, Loeffen F, Bakker J, Klaassen C, and Wulf M (2005) Methicillin-resistant Staphylococcus aureus in pig farming. Emerg Infect Dis 11: 1965–1966
Ward H, Ison CA, Day SE, Martin I, Ghani AC, Garnett GP et al. (2000) A prospective social and molecular investigation of gonococcal transmission. Lancet 356: 1812–1817
Williams JG, Kubelik AR, Livak KJ, Rafalski JA, and Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18: 6531–6535
Zhang Y, Lu L, Ba L, Liu L, Yang L, Jia M et al. (2006) Dominance of HIV-1 subtype CRF01_AE in sexually acquired cases leads to a new epidemic in Yunnan province of China. PLoS Med 3: e443
Acknowledgment
The authors wish to thank Prof. Dr. R.A. Coutinho for his valuable comments to improve the readability for non-laboratory trained persons.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Bruisten, S.M., Schouls, L. (2009). Molecular Typing and Clustering Analysis as a Tool for Epidemiology of Infectious Diseases. In: Krämer, A., Kretzschmar, M., Krickeberg, K. (eds) Modern Infectious Disease Epidemiology. Statistics for Biology and Health. Springer, New York, NY. https://doi.org/10.1007/978-0-387-93835-6_7
Download citation
DOI: https://doi.org/10.1007/978-0-387-93835-6_7
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-0-387-93834-9
Online ISBN: 978-0-387-93835-6
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)