Assessing Trypanosoma cruzi Parasite Diversity through Comparative Genomics: Implications for Disease Epidemiology and Diagnostics

Abstract

Chagas disease is an important vector-borne neglected tropical disease that causes great health and economic losses. The etiological agent, Trypanosoma cruzi, is a protozoan parasite endemic to the Americas, comprised by important diversity, which has been suggested to contribute to poor serological diagnostic performance. Current nomenclature describes seven discrete typing units (DTUs), or lineages. We performed the first large scale analysis of T. cruzi diversity among 52 previously published genomes from strains covering multiple countries and parasite DTUs and assessed how different markers summarize this genetic diversity. We also examined how seven antigens currently used in commercial serologic tests are conserved across this diversity of strains. DTU structuration was confirmed at the whole-genome level, with evidence of sub-DTU diversity, associated in part to geographic structuring. We observed very comparable phylogenetic tree topographies for most of the 32 markers investigated, with clear clustering of sequences by DTU, and a few of these markers suggested some degree of intra-lineage diversity. At least three of the currently used antigens represent poorly conserved sequences, with sequences used in tests quite divergent from sequences in many strains. Most markers are well suited for estimating parasite diversity to DTU level, and a few are particularly well-suited to assess intra-DTU diversity. Analysis of antigen sequences across all strains indicates that antigenic diversity is a likely explanation for limited diagnostic performance in Central and North America.

Molecular ecology of Triatoma dimidiata in southern Belize reveals risk for human infection and the local differentiation of Trypanosoma cruzi parasites

“…This differs from a previous study in which North and Central American TcI parasites clustered together (Dorn et al, 2017). This discrepancy is likely due to the use in the present study of the mini-exon marker rather than the 18S, which provides increased resolution of within-DTU genetic diversity of T. cruzi (Majeau et al, 2019(Majeau et al, , 2021. While a subdivision of TcIV between North and South American clades had been proposed (Yeo et al, 2011), the present study results suggest further geographic substructuring of TcIV between Central and North America.…”

“…The diversity of T. cruzi parasite strains in T. dimidiata was assessed by the mini-exon marker, which provides extensive information on genetic diversity both among and within parasite DTUs (Majeau et al, 2019(Majeau et al, , 2021. Infection with T. cruzi was detected in 24 of 39 bugs (62%), corresponding to 19 of 30 (63%) for ITS-2 haplogroup 2, three of five (60%) for haplogroup 3, one of three (33%) for hybrids (haplogroups 2/3), and one of one (100%) for haplogroup 1A.…”

“…A study of T. dimidiata vectors, including two from Toledo, detected TcI and TcIV parasites, and phylogenetic analysis grouped Central and North American TcI parasites in a single cluster (Dorn et al, 2017). However, a significant geographic structuration of parasite strains within DTUs is emerging (Llewellyn et al, 2009;Majeau et al, 2021), pointing to the likely local differentiation of parasite strains, which may be reflected in differences in transmission cycles or pathogenesis.…”

Diversity and interactions among triatomine bugs, their blood feeding sources, gut microbiota and Trypanosoma cruzi in the Sierra Nevada de Santa Marta in Colombia

“…4 ). Such clusters of sequences were likely paralogous sequences derived from a single parasite strain/clone, given the multicopy nature of the mini-exon marker, and illustrated well the Russian-doll pattern previously described 22 , 33 , 34 . A few bugs presented sequences from more than one cluster, suggesting potential infection with more than one strain of T. cruzi .…”

“…The close relatedness of the T. cruzi strains, which clustered in a large TcIb monophyletic group, further support the conclusion that there are no separate transmission cycles according to domestic or sylvatic habitats, nor according to triatomine species. Interestingly, on a continental scale, we detected a significant genetic structuring of TcI parasites, as proposed before 22 , 43 , and the subgroups proposed before again formed clear clusters, except possibly TcId 27 , 28 , 44 . Also, the frequency of the respective TcI subgroups seems to vary according to the geographic region, with TcIa predominant in North America, and TcId and TcIe predominant in South America.…”