Some species within a host group and across host groups could not be differentiated by CE-SSCP. These species tend to be closely related and differ by as few as five nucleotides, such as C. muris and C. andersoni. As the 18S rRNA gene is highly conserved, a locus that has greater variation such as actin (Sulaiman et al., 2000) may enable the differentiation of all species and strains. Although some species had multiple peaks, consistent separation and analysis using genemapper software provides a less subjective scoring method than the visual assessment of gel electrophoresis. In contrast to

the numbers of peaks detected in by CE, multiple bands, which range from find more three to eight, are detected when using conventional gel electrophoresis (Gasser et al., 2004; Jex et al., 2007a). Applications

of SSCP for Cryptosporidium differentiation using 18S rRNA gene have not attempted to identify what the multiple bands represent, but it is likely that they are the sense and antisense strands of the type A and type B copies of the 18S rRNA gene. In CE-SSCP, only one strand is analyzed when a single fluorescent primer is used for amplifications, as performed in this study. Performing CE-SSCP with a second labeled primer would allow both sense and antisense strands to be analyzed concurrently. Previous applications using CE have reported a run-to-run variation that has been controlled for using reference isolates (Gillings et al., 2008; Waldron et al., 2009). In this study, the absolute mobility unit for learn more each species differed from 2 to ifoxetine 10 U between CE-SCCP runs, but relative mobility was consistent for all isolates within a run. The observed shifts in mobility are likely to arise from instrument factors such as variation

in polymer preparation, the concentration of sample that is loaded, slight temperature fluctuations and capillary maintenance. These variables can be controlled for using a size marker and a set of reference samples with a range of mobilities that can then be used to correct the mobilities of test samples for each run. In recent years, molecular studies of Cryptosporidium have resulted in the identification of more than 40 cryptic species/genotypes (Xiao et al., 1999a, b, 2003; Ryan et al., 2003a–c; Power et al., 2004; Zhou et al., 2004; Hill et al., 2008). Establishment of a mobility reference bank using repeated testing of described species will enable CE-SSCP prescreening and selection of variants for subsequent sequencing. At our facility, prescreening using CE-SSCP represents a threefold cost saving per sample compared with DNA sequencing. Its application to epidemiological studies will decrease the sample processing times and minimize sequencing costs. At present, genetic analyzers are expensive and the sample run time is limited by the number of samples that can be processed (commonly 16 per run).