Bats host a wide range of blood parasites, including several bat-associated lineages of the genus Trypanosoma. Phylogenetic evidence indicates that bats have played an important role in the evolutionary history of the Trypanosoma cruzi clade, and several members of that broader group, including Trypanosoma livingstonei, are thought to have African bat origins. Despite high bat species richness in Nigeria and widespread cave roosting, the diversity, host associations, and ecological drivers of bat trypanosomes remain undercharacterized in southern West Africa. This study aimed to screen cave-dwelling bats from peri-domestic roosts in Enugu State, southeastern Nigeria, for trypanosome DNA, to document host associations, and to place detected sequences in a phylogenetic context within African bat-associated trypanosomes.
Sampling was conducted in nine caves and one residential building used as bat roosts across eight communities in Enugu State, situated on the Udi-Nsukka Plateau. The caves and roosts sampled were located 0.4–2 km from human residences. In total, 57 bats representing 10 species were captured from these peri-domestic roosts. The regional geology—extensive sandstone formations and fractured landscapes—creates numerous caves that support multispecies bat assemblages, which provide an ecological setting conducive to studying host–parasite interactions in stable roost environments.
Blood and ectoparasite samples from captured bats were screened by PCR for trypanosome DNA. Detected trypanosome sequences were subjected to phylogenetic analyses to determine their placement relative to reference sequences from African bat-associated trypanosomes. Species delimitation analyses were used to assess molecular lineages within the recovered sequences. The nucleotide sequence alignment used for phylogenetic analysis and files associated with the species delimitation (PTP) analysis are publicly available on the Open Science Framework (DOI: 10.17605/OSF.IO/3794C). Sequences generated in this study were deposited in GenBank under accession numbers PV790209–PV790224.
Trypanosome DNA was detected in 22 of 57 bats, representing a prevalence of 38.6% across the sampled assemblage. Positive detections occurred in six species from four families, with species-level counts reported as follows: Rousettus aegyptiacus (1 of 2 individuals), Hipposideros abae (11 of 23), Hipposideros jonesi (1 of 1), Hipposideros ruber (5 of 11), Rhinolophus landeri (2 of 10), and Mops condylurus (2 of 6). Ectoparasites were also collected and assessed as potential components of the bat-associated parasite system, though the primary findings reported focus on trypanosome DNA detected in bat blood samples.
All Nigerian trypanosome sequences clustered within the Trypanosoma livingstonei species group in phylogenetic analyses. This group comprises early-diverging lineages within the Trypanosoma cruzi clade, linking the detected parasites to previously described African bat-associated lineages. The sequences from Nigeria did not form a single homogeneous clade: species delimitation analysis recovered the Nigerian sequences together with other T. livingstonei or T. cf. livingstonei reference sequences across several putative molecular lineages. This pattern indicates phylogenetic structuring within the T. livingstonei species group and suggests the presence of multiple molecular lineages rather than a single, uniform lineage across the study sites.
The exclusive detection of parasites from the T. livingstonei species group across multiple bat species in these cave systems suggests relatively low trypanosome taxonomic diversity within the sampled assemblage, at least at the species-group level. However, the observed phylogenetic structuring implies cryptic molecular diversity within that group. Cave roosts—characterized by stable microclimates, high host densities, and repeated interspecific contact—may facilitate interspecific parasite exposure and contribute to the distribution of closely related trypanosome lineages among several bat hosts. The evolutionary placement of T. livingstonei within the T. cruzi clade underlines the importance of continued surveillance and molecular characterization of bat trypanosomes to better understand host associations and evolutionary relationships relevant to other mammalian trypanosomes.
Molecular screening of peri-domestic cave-roosting bats in southeastern Nigeria revealed a substantial prevalence (38.6%) of trypanosome infections, all attributable to the Trypanosoma livingstonei species group. While the study indicates limited apparent species diversity in this system, it identifies phylogenetic structuring within the group and multiple putative molecular lineages. The authors recommend broader geographic sampling, the inclusion of multilocus genetic data, and ecological measurements to clarify the drivers of trypanosome diversity and to resolve host–parasite relationships within cave-dwelling bat communities.
All data underlying the findings are available without restriction. Supporting files and the R script used to generate figures are hosted on the Open Science Framework (DOI: 10.17605/OSF.IO/3794C). Sequences from this study are in GenBank (PV790209–PV790224). Funding for the project was provided by the Rufford Foundation, Bat Conservation International, the German Research Foundation support for one author, and additional fellowships and grants; funders did not influence study design or reporting. The manuscript reports that the authors declared no competing interests. Specific ethical approvals or permit details were not reported in the provided source text.