Trypanosoma brucei cattle infections contain cryptic transmission-adapted bloodstream forms at low parasitaemia

Tsetse-transmitted Trypanosoma parasites infect a wide host range and cause Human African Trypanosomiasis and Animal African Trypanosomosis in sub-Saharan Africa. The primary hosts of Trypanosoma brucei in tsetse fly endemic regions are non-human mammals, including agriculturally important cattle. In rodent infection models, T. brucei transitions from proliferative slender to tsetse-transmissible stumpy forms at high parasitaemia in a density-dependent quorum sensing-type process. However, chronic bovine infections are characterised by markedly lower blood parasitaemia levels; in most cases substantially below the density assumed to trigger slender-to-stumpy differentiation. This challenges the current (rodent-based) assumptions and quantitative parameter estimations around the generation of stumpy forms in the mammalian bloodstream by quorum sensing. By combining scRNA-seq and microscopy in the first molecular characterisation of T. brucei forms in cattle blood, we observed mixed populations of parasites with slender and stumpy-like transcriptomes. The appearance of stumpy-like forms coincided with fewer proliferating parasites and parasites exhibited a shortened flagellum indicative of differentiation, despite the absence of an extreme stumpy morphology or developmental marker protein expression. Comparisons with slender and stumpy form transcriptomes from murine infection and in vitro culture demonstrated conserved transcriptomic signatures for both slender and stumpy-like forms in bovines, as well as host specific differences. These similarities and differences are key to understanding parasite development and transmission in its natural host.