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Chapter 44 : Sequence-Based Genotyping Scheme for

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Sequence-Based Genotyping Scheme for , Page 1 of 2

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Abstract:

Sequence-based genotyping schemes have become widespread as sequencing costs reduce and suitable sequence databases are created. The genus is an ideal choice: the number of species is large and the strains are relatively inert when utilizing traditional biochemical tests. The effects of redundancy within the genetic code result in much less constrained, and hence more informative, genetic variation, especially at the third codon position. However, the homology at primer target sites is correspondingly reduced, making primer design more difficult, and often primers targeting protein-encoding genes must incorporate multiple bases at one or several sites to achieve complete consensus. In conclusion, the genotyping scheme targeting the gene is currently the most tested and discriminatory of all published schemes for identifying strains, short of performing whole chromosome DNA hybridization studies. As additional gene targets are reported for , multilocus sequence typing will become possible, which in turn will ensure that not only will homologous recombination events be detected, but the resolution of significant strain relationships at a subspecies level will be possible.

Citation: Ratcliff R, Lanser J, Heuzenroeder M, Manning P. 2002. Sequence-Based Genotyping Scheme for , p 237-242. In Marre R, Abu Kwaik Y, Bartlett C, Cianciotto N, Fields B, Frosch M, Hacker J, Lück P (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555817985.ch44

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Multilocus Sequence Typing
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Pulsed-Field Gel Electrophoresis
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Figures

Image of FIGURE 1a
FIGURE 1a

UPGMA phylogenetic dendrogram of sequence similarities found among type and wild-type strains of The vertical bar joining two isolates or clusters indicates level of similarity. Reproduced with modifications from ( ) with kind permission of the publishers. #, Isolates (or cluster) which represent potentially novel species.

Citation: Ratcliff R, Lanser J, Heuzenroeder M, Manning P. 2002. Sequence-Based Genotyping Scheme for , p 237-242. In Marre R, Abu Kwaik Y, Bartlett C, Cianciotto N, Fields B, Frosch M, Hacker J, Lück P (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555817985.ch44
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Image of FIGURE 1b
FIGURE 1b

UPGMA phylogenetic dendrogram of sequence similarities found among type and wild-type strains of The vertical bar joining two isolates or clusters indicates level of similarity. Reproduced with modifications from ( ) with kind permission of the publishers. #, Isolates (or cluster) which represent potentially novel species.

Citation: Ratcliff R, Lanser J, Heuzenroeder M, Manning P. 2002. Sequence-Based Genotyping Scheme for , p 237-242. In Marre R, Abu Kwaik Y, Bartlett C, Cianciotto N, Fields B, Frosch M, Hacker J, Lück P (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555817985.ch44
Permissions and Reprints Request Permissions
Download as Powerpoint

References

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