Currently, evaluation of
drug efficacy for
Chagas disease remains a controversial issue with no consensus. In this work, we evaluated the parasitological efficacy of
Nifurtimox treatment in 21 women with chronic
Chagas disease from an area of endemicity in Chile who were treated according to current protocols. Under pre- and posttherapy conditions, blood (B) samples and xenodiagnosis (XD) samples from these patients were subjected to analysis by real-time PCR targeting the nuclear
satellite DNA of Trypanosoma cruzi (Sat
DNA PCR-B, Sat
DNA PCR-XD) and by PCR targeting the minicircle of
kinetoplast DNA of T. cruzi (
kDNA PCR-B,
kDNA PCR-XD) and by T. cruzi genotyping using hybridization minicircle tests in blood and fecal samples of Triatoma infestans feed by XD. In pretherapy,
kDNA PCR-B and
kDNA PCR-XD detected T. cruzi in 12 (57%) and 18 (86%) cases, respectively, whereas Sat
DNA quantitative PCR-B (qPCR-B) and Sat
DNA qPCR-XD were positive in 18 cases (86%) each. Regarding T. cruzi genotype analysis, it was possible to observe in pretherapy the combination of TcI, TcII, and TcV lineages, including mixtures of T. cruzi strains in most of the cases. At 13 months posttherapy, T. cruzi
DNA was detectable in 6 cases (29.6%) and 4 cases (19.1%) by means of Sat
DNA PCR-XD and
kDNA PCR-XD, respectively, indicating treatment failure with recovery of live parasites refractory to
chemotherapy. In 3 cases, it was possible to identify persistence of the baseline genotypes. The remaining 15 baseline PCR-positive cases gave negative results by all molecular and parasitological methods at 13 months posttreatment, suggesting parasite response. Within this follow-up period,
kDNA PCR-XD and Sat
DNA qPCR-XD proved to be more sensitive tools for the parasitological evaluation of the efficacy of
Nifurtimox treatment than the corresponding PCR methods performed directly from blood samples.