Impact of Anthropogenic Disturbance on Native and Invasive Trypanosomes of Rodents in Forested Uganda

Trypanosome diversity in small mammals in Uganda and the spread of Trypanosoma lewisi to native species

Uganda's diverse small mammalian fauna thrives due to its rich habitat diversity, which hosts a wide range of blood parasites, including trypanosomes, particularly the subgenus Herpetosoma typical for rodent hosts. We screened a total of 711 small mammals from various habitats for trypanosomes, with 253 microscopically examined blood smears and 458 tissue samples tested by nested PCR of the 18S rRNA gene. Of 51 rodent and 12 shrew species tested, microscopic screening reaches 7% overall prevalence (with four rodent species positive out of 15 and none of the shrew species out of four), while nested PCR indicated a prevalence of 13% (17 rodent and five shrew species positive out of 49 and 10, respectively). We identified 27 genotypes representing 11 trypanosome species, of which the majority (24 genotypes/9 species) belong to the Herpetosoma subgenus. Among these, we detected 15 new genotypes and two putative new species, labeled AF24 (found in Lophuromys woosnami) and AF25 (in Graphiurus murinus). Our finding of three new genotypes of the previously detected species AF01 belonging to the subgenus Ornithotrypanum in two Grammomys species and Oenomys hypoxanthus clearly indicates the consistent occurrence of this avian trypanosome in African small mammals. Additionally, in Aethomys hindei, we detected the putative new species of the subgenus Aneza. Within the T. lewisi subclade, we detected eleven genotypes, including six new; however, only the genotype AF05b from Mus and Rattus represents the invasive T. lewisi. Our study has improved our understanding of trypanosome diversity in African small mammals. The detection of T. lewisi in native small mammals expands the range of host species and highlighting the need for a broader approach to the epidemiology of T. lewisi.

Unexpectedly high diversity of trypanosomes in small sub-saharan mammals

The extremely species-rich genus Trypanosoma has recently been divided into 16 subgenera, most of which show fairly high host specificity, including the subgenus Herpetosoma parasitizing mainly rodents. Although most Herpetosoma spp. are highly host-specific, the best-known representative, Trypanosoma lewisi, has a cosmopolitan distribution and low host specificity. The present study investigates the general diversity of small mammal trypanosomes in East and Central Africa and the penetration of invasive T. lewisi into communities of native rodents. An extensive study of blood and tissue samples from Afrotropical micromammals (1,528 rodents, 135 shrews, and five sengis belonging to 37 genera and 133 species) captured in the Central African Republic, Ethiopia, Kenya, Malawi, Mozambique, Tanzania, and Zambia revealed 187 (11.2%) trypanosome-positive individuals. The prevalence of trypanosomes in host genera ranged from 2.1% in Aethomys to 37.1% in Lemniscomys. The only previously known trypanosome detected in our dataset was T. lewisi, newly found in Ethiopia, Kenya, and Tanzania in a wide range of native rodent hosts. Besides T. lewisi, 18S rRNA sequencing revealed 48 additional unique Herpetosoma genotypes representing at least 15 putative new species, which doubles the known sequence-based diversity of this subgenus, and approaches the true species richness in the study area. The other two genotypes represent two new species belonging to the subgenera Ornithotrypanum and Squamatrypanum. The trypanosomes of white-toothed shrews (Crocidura spp.) form a new phylogroup of Herpetosoma, unrelated to flagellates previously detected in insectivores. With 13 documented species, Ethiopia was the richest region for trypanosome diversity, which corresponds to the very diverse environments and generally high biodiversity of this country. We conclude that besides T. lewisi, the subgenus Herpetosoma is highly host-specific (e.g., species parasitizing the rodent genera Acomys and Gerbilliscus). Furthermore, several newly detected trypanosome species are specific to their endemic hosts, such as brush-furred mice (Lophuromys), dormice (Graphiurus), and white-toothed shrews (Crocidura).

Native and Introduced Trypanosome Parasites in Endemic and Introduced Murine Rodents of Sulawesi

The Indonesian island of Sulawesi is a globally significant biodiversity hotspot with substantial undescribed biota, particularly blood-borne parasites of endemic wildlife. Documenting the blood parasites of Sulawesi's murine rodents is the first fundamental step towards the discovery of pathogens likely to be of concern for the health and conservation of Sulawesi's endemic murines. We screened liver samples from 441 specimens belonging to 20 different species of murine rodents from 2 mountain ranges on Sulawesi, using polymerase chin reaction (PCR) primers targeting the conserved 18S rDNA region across the protozoan class Kinetoplastea. We detected infections in 156 specimens (10 host species) with a mean prevalence of 35.4% (95% confidence interval [CI] = 30.9-39.8%). Sequences from these samples identified 4 infections to the genus Parabodo, 1 to Blechomonas, and the remaining 151 to the genus Trypanosoma. Within Trypanosoma, we recovered 17 haplotypes nested within the Trypanosoma theileri clade infecting 117 specimens (8 host species) and 4 haplotypes nested within the Trypanosoma lewisi clade infecting 34 specimens (6 host species). Haplotypes within the T. theileri clade were related to regional Indo-Australian endemic trypanosomes, displayed geographic structuring but with evidence of long-term connectivity between mountains, and had substantial phylogenetic diversity. These results suggest T. theileri clade parasites are native to Sulawesi. Conversely, T. lewisi clade haplotypes were recovered from both endemic and introduced rodents, demonstrated complete geographic separation between clades, and had low genetic diversity. These results suggest that the T. lewisi clade parasites invaded Sulawesi recently and likely in 2 separate invasion events. Our results provide the first records of metakinetoplastids in Sulawesi's rodents and highlight the need for more extensive sampling for pathogens in this biodiversity hotspot.

Zoonotic Trypanosomes in Rats and Fleas of Venezuelan Slums

Rattus spp. are reservoirs of many human zoonoses, but their role in domestic transmission cycles of human trypanosomiasis is underestimated. In this study, we report trypanosome-infected Rattus norvegicus and Rattus rattus in human dwellings in slums neighboring Maracay, a large city near Caracas, the capital of Venezuela. Blood samples of R. norvegicus and R. rattus examined by PCR and FFLB (fluorescent fragment length barcoding) revealed a prevalence of 6.3% / 31.1% for Trypanosoma lewisi (agent of rat- and flea-borne human emergent zoonosis), and 10.5% / 24.6% for Trypanosoma cruzi (agent of Chagas disease). Detection in flea guts of T. lewisi (76%) and, unexpectedly, T. cruzi (21.3%) highlighted the role of fleas as carriers and vectors of these trypanosomes. A high prevalence of rats infected with T. lewisi and T. cruzi and respective flea and triatomine vectors poses a serious risk of human trypanosomiasis in Venezuelan slums. Anthropogenic activities responsible for growing rat and triatomine populations within human dwellings drastically increased human exposure to trypanosomes. This scenario has allowed for the reemergence of Chagas disease as an urban zoonosis in Venezuela and can propitiate the emergence of atypical T. lewisi infection in humans.

Spatio-temporal survey of small mammal-borne Trypanosoma lewisi in Cotonou, Benin, and the potential risk of human infection

Human trypanosomoses are the sleeping sickness in Africa and Chagas disease in Latin America. However, atypical human infections by animal trypanosomes have been described, but poorly investigated. Among them, the supposed rat-specific T. lewisi was shown to be responsible for a few severe cases. In Africa, the scarcity of data and the null awareness about the atypical human trypanosomoses suggest that the number of cases may be higher that currently thought. Furthermore, T. lewisi is resistant to normal human serum and therefore a potential human pathogen. In order to document T. lewisi distribution and ecology, a qPCR- and 16DNA sequencing-based survey was conducted in 369 rodents from three urban districts of Cotonou city, Benin, during three different periods of the same year. Our study demonstrated very high prevalence (57.2%) even when considering only individuals identified as positive through DNA sequencing (39.2%). Black rats represented the most dominant as well as the most T. lewisi-parasitized species. No difference was retrieved neither between seasons nor districts, suggesting a large infestation of rodents by trypanosomes throughout the year and the city. Our results suggest that conditions are gathered for rat to human transmission of T. lewisi in these socio-environmentally degraded urban areas, thus pointing towards the rapidly urbanizing Abidjan-Lagos corridor as a region at particular risk.

Uncovering Trypanosoma spp. diversity of wild mammals by the use of DNA from blood clots

Trypanosoma spp. infection in wild mammals is detected mainly through parasitological tests that usually display low sensitivity. We propose the use of DNA extracted directly from blood clots (BC), which are neglected sources of DNA for diagnosis and identification of Trypanosoma spp. This approach followed by nested PCR targeting the 18S SSU rDNA demonstrated to be sensitive and suitable to evaluate the diversity of trypanosomes infecting sylvatic mammals, including subpatent and mixed infections. Infection was detected in 95/120 (79.2%) samples from bats, carnivores and marsupials that included negative serological and hemoculture testing mammals. Thirteen Trypanosoma spp. or Molecular Operational Taxonomic Units (MOTUs) were identified, including two new MOTUs. The high diversity of trypanosomes species and MOTUs infecting bats and marsupials showed that these hosts can be considered as bio-accumulators of Trypanosoma spp., with specimens of Didelphis spp. displaying the highest trypanosome diversity. The use of blood clots allowed direct access to non-culturable parasites, mixed infections, besides bypassing the selective pressure on the parasites inherent to cultivation procedures. Trypanosoma cruzi was the species found infecting the highest number of individuals, followed by T. lainsoni. Positive PCR for T. cruzi was observed in 16 seronegative individuals and 30 individuals with negative hemocultures. Also, T. lainsoni, previously found only in rodents, showed to be capable of infecting bats and marsupials. This finding makes it clear that some species of Trypanosoma are more generalist than previously thought. Molecular diagnosis using nested PCR from DNA extracted from BC allowed the increase of the knowledge about host-spectrum and distribution of Trypanosoma spp. and allowed the identification of new MOTUs.

Diagnosis and genetic analysis of the worldwide distributed Rattus-borne Trypanosoma (Herpetosoma) lewisi and its allied species in blood and fleas of rodents

Trypanosoma (Herpetosoma) lewisi is a cosmopolitan parasite of rodents strongly linked to the human dispersal of Rattus spp. from Asia to the rest of the world. This species is highly phylogenetically related to trypanosomes from other rodents (T. lewisi-like), and sporadically infects other mammals. T. lewisi may opportunistically infect humans, and has been considered an emergent rat-borne zoonosis associated to poverty. We developed the THeCATL-PCR based on Cathepsin L (CATL) sequences to specifically detect T. (Herpetosoma) spp., and assess their genetic diversity. This method exhibited high sensitivity using blood samples, and is the first molecular method employed to search for T. lewisi in its flea vectors. THeCATL-PCR surveys using simple DNA preparation from blood preserved in ethanol or filter paper detected T. lewisi in Rattus spp. from human dwellings in South America (Brazil and Venezuela), East Africa (Mozambique), and Southeast Asia (Thailand, Cambodia and Lao PDR). In addition, native rodents captured in anthropogenic and nearby human settlements in natural habitats harbored T. (Herpetosoma) spp. PCR-amplified CATL gene fragments (253bp) distinguish T. lewisi and T. lewisi-like from other trypanosomes, and allow for assessment of genetic diversity and relationships among T. (Herpetosoma) spp. Our molecular surveys corroborated worldwide high prevalence of T. lewisi, incriminating Mastomys natalensis as an important carrier of this species in Africa, and supported its spillover from invader Rattus spp. to native rodents in Brazil and Mozambique. THeCATL-PCR provided new insights on the accurate diagnosis and genetic repertoire of T. (Herpetosoma) spp. in rodent and non-rodent hosts, revealing a novel species of this subgenus in an African gerbil. Phylogenetic analysis based on CATL sequences from T. (Herpetosoma) spp. and other trypanosomes (amplified using pan-trypanosome primers) uncovered rodents harboring, beyond mammal trypanosomes of different subgenera, some species that clustered in the lizard-snake clade of trypanosomes.