The first step in studying the epidemiology of a disease is the accurate identification of the pathogen. Traditional reliance on morphological identification has given way to the use of molecular methods for the detection and identification of pathogens, greatly improving our understanding of epidemiology. For the African tsetse-transmitted trypanosomes, the growth of PCR methods for identification of trypanosomes has led to increased appreciation of trypanosome genetic diversity and discovery of hitherto unknown trypanosome species, as well as greater knowledge about the number and type of trypanosome infections circulating in mammalian hosts and vectors. Sequence data and phylogenetic analysis have provided quantitative information on the relatedness of different trypanosome species and allowed the new trypanosome genotypes discovered through the use of species identification methods in the field to be accurately placed in the phylogenetic tree.

Restriction fragment length polymorphism (RFLP) analysis of both genomic and kinetoplast DNA from representative stocks from 3 Trypanosoma congolense subgroups (Savannah, Forest, and Kilifi), T. simiae and T. godfreyi, was used to investigate the relatedness of the different groups within subgenus Nannomonas, DNA probes for β-tubulin and the ribosomal DNA (rDNA) locus were isolated from a T. congolense Savannah genomic library; additional probes were generated by PCR amplification of mini-exon and glutamate and alanine rich protein (GARP) gene sequences. Our results provide evidence that at the molecular level the T. congolense Savannah and Forest groups are the most closely related groups within the subgenus Nannomonas: the Savannah and the Forest groups had mini-exon gene repeats of identical size, which shared homology, had mini-circles of the same size and had a high level of similarity (63%) when the banding patterns produced with a tubulin and rDNA probe were subjected to numerical analysis. All other pairwise combinations of groups have very low percentage similarities of < 10%, suggesting that the Kilifi group trypanosomes, are as distantly related to the T. congolense Savannah and Forest groups as they are to T. simiae or T. godfreyi. The conservation of the GARP gene between the Savannah, Forest and Kilifi groups provides the only evidence linking the Kilifi trypanosomes to the other groups in T. congolense. We find no evidence for the presence of the GARP gene in the T. simiae or T. godfreyi group trypanosomes.

African trypanosomes of the subgenera Nannomonas and Pycnomonas have been recorded from both wild and domestic suids. However, complete descriptions of some of these trypanosomes with regard to host range, pathogenicity, transmission and distribution are still lacking. Neither the recently described Trypanosoma (Nannomonas) godfreyi nor Trypanosoma (Nannomonas) congolense Tsavo have been isolated from mammalian hosts, while Trypanosoma (Pycnomonas) suis remains the rarest of the Salivarian trypanosomes. The only isolate presumed to be of the latter species is maintained at the Kenya Trypanosomiasis Research Institute, Nairobi. We present here the results of characterization of this isolate by morphology, tsetse transmission, the use of species-specific DNA probes and DNA sequence analysis. Morphology in stained blood smears revealed a small trypanosome with a free flagellum. Experimental transmission through Glossina morsitans morsitans showed a developmental cycle typical of subgenus Nannomonas. A positive identification was obtained with species-specific PCR primers for T. congolense Tsavo; moreover, the sequence of the SSU rRNA gene was almost identical to that of T. congolense Tsavo on database. In phylogenetic analysis of the SSU rRNA genes of Salivarian trypanosomes, T. congolense Tsavo grouped with T. simiae rather than T. congolense, suggesting that the name T. simiae Tsavo is more appropriate.