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Chapter 44 : Sequence-Based Genotyping Scheme for Legionella
Sequence-based genotyping schemes have become widespread as sequencing costs reduce and suitable sequence databases are created. The genus Legionella 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 mip gene is currently the most tested and discriminatory of all published schemes for identifying Legionella strains, short of performing whole chromosome DNA hybridization studies. As additional gene targets are reported for Legionella, 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.