The aim of this study was to characterise Discrete Typing Units (DTUs) of 28 isolates of Trypanosoma cruzi from humans (15), triatomines (9), and opossums (4) in the state of Paraná, southern Brazil. For this purpose, we analysed the size polymorphism at the 3' end of the 24Sα ribosomal RNA gene (rRNA) and the restriction fragment length polymorphism (RFLP) of the partial 5' sequence of the mitochondrial Cytochrome Oxidase subunit II gene (COII). Band patterns of the isolates were compared with reference samples of T. cruzi I (Silvio X10 and Col 17G2), T. cruzi II (Esmeraldo and JG), T. cruzi III (222 and 231), T. cruzi IV (CAN III), T. cruzi V (SO3 cl5), and T. cruzi VI (CL Brener). Our results confirmed that rRNA analysis is of limited use for assessing T. cruzi DTUs. COII RFLP analysis was suitable for screening, but for one isolate it was necessary to determine the COII partial sequence to identify the DTU. Only one of the isolates from humans belonged to T. cruzi I; 13 isolates belonged to T. cruzi II and one to T. cruzi III. The four isolates from opossums and five isolates from triatomines were identified as T. cruzi I. Four isolates from triatomines showed patterns of both T. cruzi I and II, indicating mixed infections. This study contributes to the characterisation of the dynamics of T. cruzi populations in southern Brazil.
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