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Background  Chagas disease is a systemic pathology caused by  Trypanosoma cruzi . This parasite reveals remarkable genetic variability, evinced in six Discrete Typing Units (DTUs) named from  T. cruzi  I to  T. cruzi  VI (TcI to TcVI). Recently newly identified genotypes have emerged such as TcBat in Brazil, Colombia and Panama associated to anthropogenic bats. The genotype with the broadest geographical distribution is TcI, which has recently been associated to severe cardiomyopathies in Argentina and Colombia. Therefore, new studies unraveling the genetic structure and natural history of this DTU must be pursued.    Results  We conducted a spatial and temporal analysis on 50 biological clones of  T. cruzi  I (TcI) isolated from humans with different clinical phenotypes, triatomine bugs and mammal reservoirs across three endemic regions for Chagas disease in Colombia. These clones were submitted to a nuclear Multilocus Sequence Typing (nMLST) analysis in order to elucidate its genetic diversity and clustering. After analyzing 13 nuclear housekeeping genes and obtaining a 5821 bp length alignment, we detected two robust genotypes within TcI henceforth named TcI DOM  (associated to human infections) and a second cluster associated to peridomestic and sylvatic populations. Additionaly, we detected putative events of recombination and an intriguing lack of linkage disequilibrium.    Conclusions  These findings reinforce the emergence of an enigmatic domestic  T. cruzi  genotype (TcI DOM ), and demonstrates the high frequency of recombination at nuclear level across natural populations of  T. cruzi . Therefore, the need to pursue studies focused on the diferential virulence profiles of TcI strains. The biological and epidemiological implications of these findings are herein discussed.

Genetic structure of Trypanosoma cruziin Colombia revealed by a High-throughput Nuclear Multilocus Sequence Typing (nMLST) approach