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Chapter 42 : Online Identification of Species by DNA Sequence Analysis: the Macrophage Infectivity Potentiator Gene as an Example

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Online Identification of Species by DNA Sequence Analysis: the Macrophage Infectivity Potentiator Gene as an Example, Page 1 of 2

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Abstract:

This chapter investigates the feasibility of providing a dedicated database allowing the online identification of putative spp. following standard PCR amplification and sequencing using a previously published identification scheme for . A standard PCR and sequencing protocol based on a previously published sequence-based identification scheme was used to generate a DNA sequence from the macrophage infectivity potentiator gene (mip). Identification of user-generated sequences was performed using tools showing: (i) an alignment of all the sequences from the reference alignment, top five database matches, and the user sequence; (ii) a neighbor-joining tree of the alignment, including the reference species, five closest matches from the database, and the user sequence; and (iii) an alignment of the eight sequences from the combined alignment that are most similar to the user sequence together with percentage similarity scores. It is anticipated that additional genes, including those coding for 16S rRNA, RpoB, and RnpB, will be added to the current identification system to aid in the characterization and identification of known and potential novel members of this genus.

Citation: K. Fry N, Afshar B, Bellamy W, P. Underwood A, M. Ratcliff R, G. Harrison T. 2006. Online Identification of Species by DNA Sequence Analysis: the Macrophage Infectivity Potentiator Gene as an Example, p 156-158. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch42

Key Concept Ranking

Sequence Analysis
0.52583796
Legionella
0.47319737
Sequence Alignment
0.4294512
0.52583796
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References

/content/book/10.1128/9781555815660.ch42
1. Harrison, T. G. 2005. Legionella, p. 17611785. In S. P. Borriello,, P. R. Murray, and G. Funke (ed.). Topley & Wilson’s Microbiology & Microbial Infections, Vol. 2. Bacteriology, 10th ed. Hodder Arnold, London.
2. Ratcliff, R. M.,, J. A. Lanser,, P. A. Manning, and, M. W. Heuzenroeder. 1998. Sequence-based classification scheme for the genus Legionella targeting the mip gene. J. Clin. Microbiol. 36:15601567.

Tables

Generic image for table
TABLE 1

Results of the first EWGLI species proficiency panel (2003 to 2004) from 10 centers

Citation: K. Fry N, Afshar B, Bellamy W, P. Underwood A, M. Ratcliff R, G. Harrison T. 2006. Online Identification of Species by DNA Sequence Analysis: the Macrophage Infectivity Potentiator Gene as an Example, p 156-158. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch42
Generic image for table
TABLE 2

Results of the second EWGLI species proficiency panel (2004 to 2005) from 13 centers

Citation: K. Fry N, Afshar B, Bellamy W, P. Underwood A, M. Ratcliff R, G. Harrison T. 2006. Online Identification of Species by DNA Sequence Analysis: the Macrophage Infectivity Potentiator Gene as an Example, p 156-158. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch42

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