Although more time consuming, the manual method tested appears to outperform automated extraction method in trypanosome detection and cost-effectiveness. Other research has shown the Maxwell® 16 automated system to be an effective DNA extraction method for situations of sampling from an environment that is rich in target DNA (Foley et al., 2011 and Davis et al., 2012). In the case of pathological studies where the majority of DNA present is non-target (e.g. host) DNA, manual extraction methods were found to be more successful (Durnez et al., 2009 and Affolabi et al., 2012). Perhaps, as appears to be the case with our samples, successful automated protocols are targeting shorter DNA segments.