Multilocus sequence analysis provides new insight into population structure and genetic diversity of Leishmania tropica in Morocco

Lesionia: a digital data management system to enhance collaborative management of epidemiological and clinical data of cutaneous leishmaniases patients

Digital Systems for Data Management (DSDM) have become a critical cornerstone in collaborative biomedical research and clinical trials involving multiple investigators, institutions, and populations. DSDM provide unique features that ensure that data meet the standards of FAIR (Findability, Accessibility, Interoperability and Reusability). We herein present Lesionia, a DSDM designed to support the PEER518 consortium that aimed at developing new cutaneous leishmaniases (CL) diagnostics using samples and data collected from patients suspected of having CL in countries in the MENA region and West Africa. The consortium involved nine institutions across five countries: Tunisia, Morocco, Lebanon, Mali, and the USA, and informally Scientists from Algeria and Nigeria. The guidelines on the data to be collected by the clinicians and biologists during the project were used for the development of a Questionnaire that served as a basis for the implementation of a dedicated web-based DSDM.Lesionia was developed and validated for the management and the analysis of clinical and epidemiological data in the diagnosis of CL. It consists of a relational database, a web-based user interface (WUI) and a tool for experimental data handling and analysis of clinical and epidemiological data of CL cases. The platform was deployed and validated during the PEER518 project using data collected across the involved teams. Lesionia is expandable to include further collaborators, partners, and projects. It is designed for data handling from the consented patient interview and sample collection to the samples' storage and investigation. The WUI permits data entry, fetching, visualization and analysis. Rigorous controls on data entry were implemented to reduce discrepancies. It also offers a set of analysis tools that range from descriptive statistics to variable correlation analysis. Lesionia is accessible in a secure manner to all users of the consortium through a web browser.Lesionia will be a valuable tool for collaborative and integrative management of clinical and epidemiological data. It is an open-source software that can broadly serve the scientific community interested in studying, controlling, reporting, and diagnosing CL and similar cutaneous diseases.

Wildlife as a Sentinel for Pathogen Introduction in Nonendemic Areas: First Detection of Leishmania tropica in Wildlife in Spain

Leishmaniasis is a chronic global arthropod-borne zoonotic disease produced by several species of Leishmania with cutaneous, mucocutaneous, and visceral clinical manifestations. In Spain, only Leishmania infantum has been reported so far, although other species of Leishmania, such as L. tropica and L. major, are present in surrounding countries. The aim of this work is to analyze the occurrence of Leishmania spp. infection in European wildcats (Felis silvestris) as sentinels, including their genotypic characterization. Necropsies of 18 road-killed wildcats were conducted. Samples of ear skin and spleen were taken for DNA isolation and PCR of the highly sensitive SSU-rDNA target. Subsequent PCR tests were performed using more specific targets for the determination of Leishmania species: hsp70 and ITS1. Positive samples were sequenced, and phylogenetic trees were constructed. Seven wildcats were found positive for Leishmania spp. Based on the hsp70 and ITS1 sequences, an animal was found to be infected only with L. tropica in ear skin samples, while two cats were found to be infected with L. infantum in both the ear skin and the spleen. In one animal, a clear sequence of L. infantum ITS1 and a sequence of L. tropica hsp70 were obtained from the ear skin. Since hsp70 and ITS1 sequencing was not possible in three cats, the species of Leishmania infecting them was not determined. This is the first report of autochthonous infection with L. tropica in the Iberian Peninsula. Health care professionals, including physicians, dermatologists, and veterinarians, must be aware of this for a correct diagnosis, treatment, and management of possible coinfections.

A comparative genomics approach reveals a local genetic signature of Leishmania tropica in Morocco

In Morocco, cutaneous leishmaniasis (CL) caused by Leishmania (L.) tropica is an important health problem. Despite the high incidence of CL in the country, the genomic heterogeneity of these parasites is still incompletely understood. In this study, we sequenced the genomes of 14 Moroccan isolates of L. tropica collected from confirmed cases of CL to investigate their genomic heterogeneity. Comparative genomics analyses were conducted by applying the recently established Genome Instability Pipeline (GIP), which allowed us to conduct phylogenomic and principal components analyses (PCA), and to assess genomic variations at the levels of the karyotype, gene copy number, single nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs) variants. Read-depth analyses revealed a mostly disomic karyotype, with the exception of the stable tetrasomy of chromosome 31. In contrast, we identified important gene copy number variations across all isolates, which affect known virulence genes and thus were probably selected in the field. SNP-based cluster analysis of the 14 isolates revealed a core group of 12 strains that formed a tight cluster and shared 45.1 % (87 751) of SNPs, as well as two strains (M3015, Ltr_16) that clustered separately from each other and the core group, suggesting the circulation of genetically highly diverse strains in Morocco. Phylogenetic analysis, which compared our 14 L. tropica isolates against 40 published genomes of L. tropica from a diverse array of locations, confirmed the genetic difference of our Moroccan isolates from all other isolates examined. In conclusion, our results indicate potential regional variations in SNP profiles that may differentiate Moroccan L. tropica from other L. tropica strains circulating in endemic countries in the Middle East. Our report paves the way for future research with a larger number of strains that will allow correlation of diverse phenotypes (resistance to treatments, virulence) and origins (geography, host species, year of isolation) to defined genomic signals such as gene copy number variations or SNP profiles that may represent interesting biomarker candidates.

Genetic Diversity and Population Structure of Leishmania infantum in Morocco as Revealed by Multilocus Sequence Typing (MLST) Approach

Leishmania infantum is endemic in Morocco, and it causes both visceral (VL) and cutaneous leishmaniasis (CL). In this study, the multilocus sequence typing (MLST) approach was used to investigate the phylogeny and population structure of Leishmania infantum strains isolated from CL and VL patients and the canine reservoir in different leishmaniasis endemic foci in Morocco. For this purpose, eight loci (pgm, alat, me, fh, g6pd, pgd, gpi and cytb) were amplified in 40 samples, out of which 31 were successfully sequenced. The genetic diversity analysis detected a high degree of intraspecific genetic variability among the studied strains. The phylogenetic and the haplotype analyses showed that most of the strains from the same geographical areas clustered together. The recombination among Leishmania infantum strains was revealed through a splits tree analysis and the number of recombination events. Moreover, the assessment of the gene flow between Leishmania infantum and Leishmania tropica through phylogenetic analysis and haplotype diversity in two endemic foci where the two species were sympatric showed no genetic exchange between the two species.

ITS1 and cpb genetic polymorphisms in Algerian and Tunisian Leishmania infantum isolates from humans and dogs

Leishmania (L.) infantum strains, isolated from varying hosts and clinical manifestations (cutaneous, visceral and canine leishmaniasis), were investigated in order to understand the genetic polymorphisms within this species in Algeria and Tunisia. Two DNA-based typing methods were tested in order to evaluate their effectiveness against Multilocus enzyme electrophoresis (MLEE), widely considered as the reference method for Leishmania parasite typing. On the other hand, MLEE is cumbersome, high-cost, time consuming and frequently does not detect intra-species genetic polymorphisms. In this work, we used two molecular target regions to discriminate L. infantum strains, Internal transcribed spacer 1 (ITS1) and the cysteine proteinase B (cpb). The ITS1 region offers good resolution for Leishmania discrimination but does not spotlight intra-species polymorphisms. In contrast, cpbE and cpbF PCR-Sequencing demonstrated a certain variability within CL and VL Algerian and Tunisian L. infantum isolates. Following phylogenetic analyses of 44 L. infantum isolates, two main groups were identified, a group with 39 bp deletion in the cpb sequence, composed of cutaneous, visceral and canine isolates from both countries with no significant clinical or geographic distribution; these samples were typed as MON-1, MON-24, and MON-80 zymodemes. A second group which presents a clear clusterization of Tunisian cutaneous strains belonging to the L. infantum MON-24. This group, with no deletion in the mature domain of the cpb gene sequence, should be further explored with a higher number of samples.

Environmental, Climatic, and Parasite Molecular Factors Impacting the Incidence of Cutaneous Leishmaniasis Due to Leishmania tropica in Three Moroccan Foci

Cutaneous leishmaniasis (CL) occurring due to Leishmania tropica is a public health problem in Morocco. The distribution and incidence of this form of leishmaniasis have increased in an unusual way in the last decade, and the control measures put in place are struggling to slow down the epidemic. This study was designed to assess the impact of climatic and environmental factors on CL in L. tropica foci. The data collected included CL incidence and climatic and environmental factors across three Moroccan foci (Foum Jemaa, Imintanout, and Ouazzane) from 2000 to 2019. Statistical analyses were performed using the linear regression model. An association was found between the occurrence of CL in Imintanout and temperature and humidity (r² = 0.6076, df = (1.18), p-value = 3.09 × 10⁻⁵; r² = 0.6306, df = (1.18), p-value = 1.77 × 10⁻⁵). As a second objective of our study, we investigated the population structure of L.tropica in these three foci, using the nuclear marker internal transcribed spacer 1 (ITS1). Our results showed a low-to-medium level of geographic differentiation among the L.tropica populations using pairwise differentiation. Molecular diversity indices showed a high genetic diversity in Foum Jemaa and Imintanout; indeed, 29 polymorphic sites were identified, leading to the definition of 13 haplotypes. Tajima’s D and Fu’s F test statistics in all populations were not statistically significant, and consistent with a population at drift–mutation equilibrium. Further analysis, including additional DNA markers and a larger sample size, could provide a more complete perspective of L. tropica’s population structure in these three regions. In addition, further research is needed to better understand the impact of climatic conditions on the transmission cycle of Leishmania, allowing both for the development of effective control measures, and for the development of a predictive model for this parasitosis.