Abstract
As the use of nucleotide sequence-based typing has become more widespread in the investigation of microbial epidemiology, there has been a natural requirement for curated Internet-based databases that can act as central authorities for nomenclature and type definitions. These facilitate the sharing and comparison of data between laboratories without the need for reference samples. Here, the use of the most common multilocus sequence typing (MLST) and antigen sequence databases are described. In particular, for MLST, the steps required for allele sequence and profile identification are explained along with a detailed overview of searching and matching isolate records. BLAST searching of antigen sequence databases is also described.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Swaminathan, B., Barrett, T. J., Hunter, S. B., and Tauxe, R. V. (2001). PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg. Infect. Dis. 7, 382–389.
Maiden, M. C. J., Bygraves, J. A., Feil, E., Morelli, G., Russell, J. E., 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. U S A 95, 3140–3145.
Maiden, M. C. (2006). Multilocus sequence typing of bacteria. Annu. Rev. Microbiol. 60, 561–588.
Jolley, K. A., Chan, M. S., and Maiden, M. C. (2004). mlstdbNet—distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics 5, 86.
Aanensen, D. M., and Spratt, B. G. (2005). The multilocus sequence typing network: mlst.net. Nucleic Acids Res. 33, W728–W733.
Urwin, R., Russell, J. E., Thompson, E. A., Holmes, E. C., Feavers, I. M., and Maiden, M. C. (2004). Distribution of surface protein variants among hyperinvasive meningococci: implications for vaccine design. Infect. Immun. 72, 5955–5962.
Russell, J. E., Jolley, K. A., Feavers, I. M., Maiden, M. C., and Suker, J. S. (2004). PorA variable regions of Neisseria meningitidis. Emerg. Infect. Dis. 10, 674–678.
Thompson, E. A. L., Feavers, I. M., and Maiden, M. C. J. (2003). Antigenic diversity of meningococcal enterobactin receptor FetA, a vaccine component. Microbiology 149, 1849–1858.
Dingle, K. E., Colles, F. M., Ure, R., Wagenaar, J., Duim, B., Bolton, F. J., et al (2002). Molecular characterisation of Campylobacter jejuni clones: a rational basis for epidemiological investigations. Emerg. Infect. Dis. 8, 949–955.
Kelly, C., Bugg, M., Robinson, C., Mitchell, Z., Davis-Poynter, N., Newton, J. R., et al (2006). Sequence variation of the SeM gene of Streptococcus equi allows discrimination of the source of strangles outbreaks. J. Clin. Microbiol. 44, 480–486.
Baldo, L., Dunning Hotopp, J. C., Jolley, K. A., Bordenstein, S. R., Biber, S. A., Choudhury, R. R., et al (2006). Multilocus sequence typing system for the endosymbiont Wolbachia pipientis. Appl. Environ. Microbiol. 72, 7098–7110.
Jolley, K. A., and Maiden, M. C. (2006). AgdbNet—antigen sequence database software for bacterial typing. BMC Bioinformatics 7, 314.
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., et al (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Jolley, K.A. (2009). Internet-Based Sequence-Typing Databases for Bacterial Molecular Epidemiology. In: Caugant, D. (eds) Molecular Epidemiology of Microorganisms. Methods in Molecular Biology™, vol 551. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-999-4_21
Download citation
DOI: https://doi.org/10.1007/978-1-60327-999-4_21
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60327-998-7
Online ISBN: 978-1-60327-999-4
eBook Packages: Springer Protocols