A review of the systematics, species identification and diagnostics of the Trypanosomatidae using the maxicircle kinetoplast DNA: from past to present

Molecular Detection of Kinetoplastid Species in Ticks and Fleas Associated with Dogs and Humans in Mexico

The Trypanosomatidae family encompasses around 24 genera of unicellular protozoans, many of which are transmitted by various hematophagous arthropods, particularly members of the Orders Diptera and Hemiptera. Fleas and ticks-an understudied group of ectoparasites-have been shown to be hosts of a wide and crescent variety of trypanosomatid species. Further, fleas and ticks of companion animals have been particularly neglected in trypanosomatid surveillance despite the proximity to human populations and the anthropophagous habits of many of these arthropods, which can potentially act as vectors of zoonotic trypanosomatids. We aimed to identify the presence, characterize the species, and establish the prevalence of Kinetoplastids, including members of the Trypanosomatidae family, in ectoparasites collected from dogs and humans from Mexico. A total of 537 ectoparasite specimens belonging to six ectoparasite taxa (Amblyomma mixtum, A. tenellum, Ctenocephalides felis felis, Pulex simulans, Rhipicephalus linnaei, and Rh. sanguineus s.s.) were collected from 15 States of Mexico. An 800 bp fragment of the 18S-rDNA gene from kinetoplastids was amplified and sequenced. The presence of two agents (Trypanosoma caninum and Parabodo sp.) was detected in R. linnaei ticks and one (Blechomonas lauriereadi) in the cat flea Ct. felis felis. This is the first record of genetic material of kinetoplastid species in ectoparasites from dogs and humans in Mexico.

A High Resolution Melting Analysis (HRM) PCR assay for the detection and identification of Old World Leishmania species

BACKGROUND

Cutaneous Leishmaniases (CL), highly endemic in Africa and Mediterranean region, are caused by different Leishmania parasite species. Accurate species identification is crucial for effective diagnosis, treatment, and control of these diseases, but traditionally relies on DNA-based methods. High Resolution Melting analysis PCR (HRM PCR) provides rapid results and precise differentiation based on nucleotide variations. We hypothesized that the Strumpellin gene of Leishmania could serve as an effective target for developing a HRM PCR method for the rapid and efficient detection and identification of Leishmania species in CL diagnosis.

METHODOLOGY

The Strumpellin gene was investigated in Trypanosomatidae family using bioinformatics and phylogenetic approaches to explore its evolutionary conservation and suitability for HRM PCR. HRM PCR target and primers were selected and validated on 73 different Leishmania DNAs. The analytical limit of detection was assessed, and the performance for detecting and identifying parasites in 38 cutaneous lesions aspirates was compared to Direct Examination (DE) and ITS1-PCR RFLP methods.

FINDINGS

The developed HRM PCR assay accurately identified promastigote DNAs of L. donovani/L. infantum, L. major, L. aethiopica, L. turanica, L. arabica, L. tarentolae and 3 genotypes of L. tropica. Differentiation was achievable with as little as a single nucleotide difference occurring within or between species. HRM profile interpretations were consistent with sequencing results of the HRM PCR target and identification by ITS1-PCR RFLP. The assay could detect the equivalent of 24 Leishmania parasites. In a small-scale sample, we brought proof of principle demonstration the HRM could detect and identify Leishmania in human cutaneous samples. In comparison to DE, the sensitivity and specificity of the HRM PCR assay on human cutaneous samples were 88% and 84.62%, respectively, while the ITS1-PCR assay evaluation parameters were 84% and 92.31%. Statistical analysis confirmed good correlation among the three tests, with both molecular methods providing congruent parasite identification. Notably, in three samples, only the HRM PCR assay was able to assign them to L. infantum or L. tropica.

CONCLUSIONS

The HRM PCR assay is a valuable tool for the detection and identification of Old World Leishmania species. Its integration into molecular diagnostic algorithms for CL or in eco-epidemiological studies holds promise for improving disease management and control.

Genetic characterization and description of Leishmania (Leishmania) ellisi sp. nov.: a new human-infecting species from the USA

In a 2018 report, an unusual case of cutaneous leishmaniasis was described in a 72-year-old female patient residing in Arizona, United States of America (USA). Preliminary analysis of the 18S rDNA and glyceraldehyde-3-phosphate dehydrogenase genes supported the conclusion that the Leishmania strain (strain 218-L139) isolated from this case was a novel species, though a complete taxonomic description was not provided. Identification of Leishmania at the species level is critical for clinical management and epidemiologic investigations so it is important that novel human-infecting species are characterized taxonomically and assigned a unique scientific name compliant with the ICZN code. Therefore, we sought to provide a complete taxonomic description of Leishmania strain 218-L139. Phylogenetic analysis of several nuclear loci and partial maxicircle genome sequences supported its position within the subgenus Leishmania and further clarified the distinctness of this new species. Morphological characterization of cultured promastigotes and amastigotes from the original case material is also provided. Thus, we conclude that Leishmania (Leishmania) ellisi is a new cause of autochthonous cutaneous leishmaniasis in the USA.

Genetic variability of Leishmania (Leishmania) infantum causing human visceral leishmaniasis in the Southeastern Brazil

Leishmania infantum is a protozoan that causes visceral leishmaniasis (VL) in the Americas and some regions of Europe. The disease is mainly characterized by hepatosplenomegaly and fever, and can be fatal. Factors related to the host and parasite can contribute to the transmission of Leishmania and the clinical outcome. The intraspecific genetic variability of L. infantum strains may be one of these factors. In this study, we evaluated the genetic variability of L. infantum obtained from bone marrow smear slides from patients in the Sao Paulo State, Brazil. For this, the minicircle of the kDNA hypervariable region was used as target by Sanger sequencing. By analyzing the similarity of the nucleotides and the maximum likelihood tree (Fasttree), we observed a high similarity (98%) among samples. Moreover, we identified four different profiles of L. infantum. In conclusion, L. infantum strains from Sao Paulo State, Brazil, showed low diversity measured by minicircle of the kDNA hypervariable region.

Nanopore-Based Direct RNA Sequencing of the Trypanosoma brucei Transcriptome Identifies Novel lncRNAs

Trypanosomatids are single-cell eukaryotic parasites. Unlike higher eukaryotes, they control gene expression post-transcriptionally and not at the level of transcription initiation. This involves all known cellular RNA circuits, from mRNA processing to mRNA decay, to translation, in addition to a large panel of RNA-interacting proteins that modulate mRNA abundance. However, other forms of gene regulation, for example by lncRNAs, cannot be excluded. LncRNAs are poorly studied in trypanosomatids, with only a single lncRNA characterized to date. Furthermore, it is not clear whether the complete inventory of trypanosomatid lncRNAs is known, because of the inherent cDNA-recoding and DNA-amplification limitations of short-read RNA sequencing. Here, we overcome these limitations by using long-read direct RNA sequencing (DRS) on nanopore arrays. We analyze the native RNA pool of the two main lifecycle stages of the African trypanosome Trypanosoma brucei, with a special emphasis on the inventory of lncRNAs. We identify 207 previously unknown lncRNAs, 32 of which are stage-specifically expressed. We also present insights into the complexity of the T. brucei transcriptome, including alternative transcriptional start and stop sites and potential transcript isoforms, to provide a bias-free understanding of the intricate RNA landscape in T. brucei.

Assembly of a Large Collection of Maxicircle Sequences and Their Usefulness for Leishmania Taxonomy and Strain Typing

Parasites of medical importance, such as Leishmania and Trypanosoma, are characterized by the presence of thousands of circular DNA molecules forming a structure known as kinetoplast, within the mitochondria. The maxicircles, which are equivalent to the mitochondrial genome in other eukaryotes, have been proposed as a promising phylogenetic marker. Using whole-DNA sequencing data, it is also possible to assemble maxicircle sequences as shown here and in previous works. In this study, based on data available in public databases and using a bioinformatics workflow previously reported by our group, we assembled the complete coding region of the maxicircles for 26 prototypical strains of trypanosomatid species. Phylogenetic analysis based on this dataset resulted in a robust tree showing an accurate taxonomy of kinetoplastids, which was also able to discern between closely related Leishmania species that are usually difficult to discriminate by classical methodologies. In addition, we provide a dataset of the maxicircle sequences of 60 Leishmania infantum field isolates from America, Western Europe, North Africa, and Eastern Europe. In agreement with previous studies, our data indicate that L. infantum parasites from Brazil are highly homogeneous and closely related to European strains, which were transferred there during the discovery of America. However, this study showed the existence of different L. infantum populations/clades within the Mediterranean region. A maxicircle signature for each clade has been established. Interestingly, two L. infantum clades were found coexisting in the same region of Spain, one similar to the American strains, represented by the Spanish JPCM5 reference strain, and the other, named “non-JPC like”, may be related to an important leishmaniasis outbreak that occurred in Madrid a few years ago. In conclusion, the maxicircle sequence emerges as a robust molecular marker for phylogenetic analysis and species typing within the kinetoplastids, which also has the potential to discriminate intraspecific variability.