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expect for one unit, which differs by a single point mutation and changes the
amino acid ( see Fig. 4 ). Therefore, while spa types 1 and 7 are not identical,
they are closely related and most likely arose directly from one another although
the directionality of ancestry cannot be determined by spa type comparison
only. Furthermore, a number of studies have grouped together strains with
similar repeat motifs into the same spa lineages or spa clonal complexes,
supporting the use of this method to examine macrovariation (10,21,33,39) .
Although S. aureus as a whole does not undergo extensive recombination, the
occurrence of such events within the protein A gene can misalign spa types
relative to PFGE or MLST results; similarly, recombination events can also
alter MLST analysis (32,33) .
There are currently three similar software programs (eGenomics, Ridom, and
Bionumerics) that are able to identify and name repeats, recognize repeat motifs
or order, and assign a spa type from a raw sequence file of the polymorphic
X region. The two most widely used applications, Ridom and eGenomics, use
Fig. 4. eGenomics (http://epigene.egenomics.com) spa -typing tool screenshots
showing aligned repeat sequences for the closely related spa types 1 and 7. The C
A point mutation is highlighted, corresponding to the non-synonymous amino acid
replacement Asn (AAC)
Lys (AAA) and underscoring the need for quality assurance
in DNA sequencing data.
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