Genomic polymorphism of Leishmania infantum: a relationship with clinical pleomorphism?

Colonization and genetic diversification processes of Leishmania infantum in the Americas

Leishmania infantum causes visceral leishmaniasis, a deadly vector-borne disease introduced to the Americas during the colonial era. This non-native trypanosomatid parasite has since established widespread transmission cycles using alternative vectors, and human infection has become a significant concern to public health, especially in Brazil. A multi-kilobase deletion was recently detected in Brazilian L. infantum genomes and is suggested to reduce susceptibility to the anti-leishmanial drug miltefosine. We show that deletion-carrying strains occur in at least 15 Brazilian states and describe diversity patterns suggesting that these derive from common ancestral mutants rather than from recurrent independent mutation events. We also show that the deleted locus and associated enzymatic activity is restored by hybridization with non-deletion type strains. Genetic exchange appears common in areas of secondary contact but also among closely related parasites. We examine demographic and ecological scenarios underlying this complex L. infantum population structure and discuss implications for disease control.

Philipp Schwabl, Mariana Boité, and colleagues analyze 126 Leishmania infantum genomes to determine how demographic and selective consequences of the parasite’s invasive history have contributed to intricate population genetic heterogeneity across Brazil. Their data suggest a complex interplay of population expansion, secondary contact and genetic exchange events underlying diversity patterns at short and long-distance scales. These processes also appear pivotal to the proliferation of a drug resistance-associated multi-gene deletion on chromosome 31.

Frequent Recombination Events in Leishmania donovani: Mining Population Data

The Leishmania donovani species complex consists of all L. donovani and L. infantum strains mainly responsible for visceral leishmaniasis (VL). It was suggested that genome rearrangements in Leishmania spp. occur very often, thus enabling parasites to adapt to the different environmental conditions. Some of these rearrangements may be directly linked to the virulence or explain the reduced efficacy of antimonial drugs in some isolates. In the current study, we focused on a large-scale analysis of putative gene conversion events using publicly available datasets. Previous population study of L. donovani suggested that population variability of L. donovani is relatively low, however the authors used masking procedures and strict read selection criteria. We decided to re-analyze DNA-seq data without masking sequences, because we were interested in the most dynamic fraction of the genome. The majority of samples have an excess of putative gene conversion/recombination events in the noncoding regions, however we found an overall excess of putative intrachromosomal gene conversion/recombination in the protein coding genes, compared to putative interchromosomal gene conversion/recombination events.

Global genome diversity of the Leishmania donovani complex

Protozoan parasites of the Leishmania donovani complex - L. donovani and L. infantum - cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. L. donovani isolates separated into five groups that largely coincide with geographical origin but vary greatly in diversity. In contrast, the majority of L. infantum samples fell into one globally-distributed group with little diversity. This picture is complicated by several hybrid lineages. Identified genetic groups vary in heterozygosity and levels of linkage, suggesting different recombination histories. We characterise chromosome-specific patterns of aneuploidy and identified extensive structural variation, including known and suspected drug resistance loci. This study reveals greater genetic diversity than suggested by geographically-focused studies, provides a resource of genomic variation for future work and sets the scene for a new understanding of the evolution and genetics of the Leishmania donovani complex.

Genetic diversity of Leishmania tropica in Morocco: does the dominance of one haplotype signify its fitness in both predominantly anthropophilic Phlebotomus sergenti and human beings?

In Morocco, cutaneous leishmaniasis (CL) caused by Leishmania tropica is endemic to locations where the predominantly anthropophilic blood-feeding Phlebotomus sergenti and humans co-perpetuate. The objective of this study was to explore whether the range of epidemiological features of CLcould be linked to the range of L. tropica genetic heterogeneity and to further explore the relationships between the genetic diversity of L. tropica in both P. sergenti and humans. L. tropica DNAwas extracted from dermal scarping smears of 125 CLpatients. Genetic polymorphisms were analyzed by sequencing the internal transcribed spacer (ITS) 1 and 5.8S rDNAgene. Nucleotide diversity (π), haplotype diversity (Hd) and Tajima's D test for neutrality, as well as overall and pairwise FSTvalues, were calculated using Arlequin ver 3.5 software. Out of the 125 amplified DNAsequences, 93 were completely sequenced and 13 L. tropica haplotypes were identified, which confirmed the significant genetic heterogeneity of L. tropica in Morocco. The most common haplotype included 74 out of 93 sequences; this haplotype is not only widely represented but was also detected in P. sergenti, which is known to be the most abundant species in the studied foci. Considering the negative value calculated using Tajima's D index, we briefly discussed the hypothesis that the L. tropica common haplotype propagation could be a sign of its fitness in P. sergenti and human hosts. Furthermore, analysis of molecular variance (AMOVA) shows significant correlations between intraspecific variants of L. tropica and patients' geographic origins. The long-term goals of the present pilot study are to further explore the relationships between the genetic diversity of L. tropica in human and P. sergenti populations.

Leishmania infections: Molecular targets and diagnosis

Progress in the diagnosis of leishmaniases depends on the development of effective methods and the discovery of suitable biomarkers. We propose firstly an update classification of Leishmania species and their synonymies. We demonstrate a global map highlighting the geography of known endemic Leishmania species pathogenic to humans. We summarize a complete list of techniques currently in use and discuss their advantages and limitations. The available data highlights the benefits of molecular markers in terms of their sensitivity and specificity to quantify variation from the subgeneric level to species complexes, (sub) species within complexes, and individual populations and infection foci. Each DNA-based detection method is supplied with a comprehensive description of markers and primers and proposal for a classification based on the role of each target and primer in the detection, identification and quantification of leishmaniasis infection. We outline a genome-wide map of genes informative for diagnosis that have been used for Leishmania genotyping. Furthermore, we propose a classification method based on the suitability of well-studied molecular markers for typing the 21 known Leishmania species pathogenic to humans. This can be applied to newly discovered species and to hybrid strains originating from inter-species crosses. Developing more effective and sensitive diagnostic methods and biomarkers is vital for enhancing Leishmania infection control programs.

Comparative expression profiling of Leishmania: modulation in gene expression between species and in different host genetic backgrounds

Background

Genome sequencing of Leishmania species that give rise to a range of disease phenotypes in the host has revealed highly conserved gene content and synteny across the genus. Only a small number of genes are differentially distributed between the three species sequenced to date, L. major, L. infantum and L. braziliensis. It is not yet known how many of these genes are expressed in the disease-promoting intracellular amastigotes of these species or whether genes conserved between the species are differentially expressed in the host.

Methods/Principal Findings

We have used customised oligonucleotide microarrays to confirm that all of the differentially distributed genes identified by genome comparisons are expressed in intracellular amastigotes, with only a few of these subject to regulation at the RNA level. In the first large-scale study of gene expression in L. braziliensis, we show that only ∼9% of the genes analysed are regulated in their RNA expression during the L. braziliensis life cycle, a figure consistent with that observed in other Leishmania species. Comparing amastigote gene expression profiles between species confirms the proposal that Leishmania transcriptomes undergo little regulation but also identifies conserved genes that are regulated differently between species in the host. We have also investigated whether host immune competence influences parasite gene expression, by comparing RNA expression profiles in L. major amastigotes derived from either wild-type (BALB/c) or immunologically compromised (Rag2^−/− γ_c^−/−) mice. While parasite dissemination from the site of infection is enhanced in the Rag2^−/− γ_c^−/− genetic background, parasite RNA expression profiles are unperturbed.

Conclusion/Significance

These findings support the hypothesis that Leishmania amastigotes are pre-adapted for intracellular survival and undergo little dynamic modulation of gene expression at the RNA level. Species-specific parasite factors contributing to virulence and pathogenicity in the host may be limited to the products of a small number of differentially distributed genes or the differential regulation of conserved genes, either of which are subject to translational and/or post-translational controls.

The single-celled parasite Leishmania, transmitted by sand flies in more than 88 tropical and sub-tropical countries globally, infects man and other mammals, causing a spectrum of diseases called the leishmaniases. Over 12 million people are currently infected worldwide with 2 million new cases reported each year. The type of leishmaniasis that develops in the mammalian host is dependent on the species of infecting parasite and the immune response to infection (that can be influenced by host genetic variation). Our research is focused on identifying parasite factors that contribute to pathogenicity in the host and understanding how these might differ between parasite species that give rise to the different clinical forms of leishmaniasis. Molecules of this type might lead to new therapeutic tools in the longer term. In this paper, we report a comparative analysis of gene expression profiles in three Leishmania species that give rise to different types of disease, focusing on the intracellular stages that reside in mammalian macrophages. Our results show that there are only a small number of differences between these parasite species, with host genetics playing only a minor role in influencing the parasites' response to their intracellular habitat. These small changes may be significant, however, in determining the clinical outcome of infection.

Cutaneous leishmaniasis (Leishmania tropica) in a German tourist after travel to Greece

We report on a German tourist returning from vacations in Southern Greece with cutaneous leishmaniasis (CL) presenting as multiple erythematosquamous lesions caused by Leishmania tropica (zymodeme MON-57). In spite of its endemicity, only few data are available on the incidence and current distribution of CL in Greece, which may allow for an assessment of the risk for travelers.

Cutaneous leishmaniasis

Cutaneous leishmaniasis is endemic in the tropics and neotropics. It is often referred to as a group of diseases because of the varied spectrum of clinical manifestations, which range from small cutaneous nodules to gross mucosal tissue destruction. Cutaneous leishmaniasis can be caused by several Leishmania spp and is transmitted to human beings and animals by sandflies. Despite its increasing worldwide incidence, but because it is rarely fatal, cutaneous leishmaniasis has become one of the so-called neglected diseases, with little interest by financial donors, public-health authorities, and professionals to implement activities to research, prevent, or control the disease. In endemic countries, diagnosis is often made clinically and, if possible, by microscopic examination of lesion biopsy smears to visually confirm leishmania parasites as the cause. The use of more sophisticated diagnostic techniques that allow for species identification is usually restricted to research or clinical settings in non-endemic countries. The mainstays of cutaneous leishmaniasis treatment are pentavalent antimonials, with new oral and topical treatment alternatives only becoming available within the past few years; a vaccine currently does not exist. Disease prevention and control are difficult because of the complexity of cutaneous leishmaniasis epizoology, and the few options available for effective vector control.

Leishmania and the leishmaniases: a parasite genetic update and advances in taxonomy, epidemiology and pathogenicity in humans

Leishmaniases remain a major public health problem today despite the vast amount of research conducted on Leishmania pathogens. The biological model is genetically and ecologically complex. This paper explores the advances in Leishmania genetics and reviews population structure, taxonomy, epidemiology and pathogenicity. Current knowledge of Leishmania genetics is placed in the context of natural populations. Various studies have described a clonal structure for Leishmania but recombination, pseudo-recombination and other genetic processes have also been reported. The impact of these different models on epidemiology and the medical aspects of leishmaniases is considered from an evolutionary point of view. The role of these parasites in the expression of pathogenicity in humans is also explored. It is important to ascertain whether genetic variability of the parasites is related to the different clinical expressions of leishmaniasis. The review aims to put current knowledge of Leishmania and the leishmaniases in perspective and to underline priority questions which 'leishmaniacs' must answer in various domains: epidemiology, population genetics, taxonomy and pathogenicity. It concludes by presenting a number of feasible ways of responding to these questions.

Comparative genomics: from genotype to disease phenotype in the leishmaniases

Recent progress in sequencing the genomes of several Leishmania species, causative agents of cutaneous, mucocutaneous and visceral leishmaniasis, is revealing unusual features of potential relevance to parasite virulence and pathogenesis in the host. While the genomes of Leishmania major, Leishmania braziliensis and Leishmania infantum are highly similar in content and organisation, species-specific genes and mechanisms distinguish one from another. In particular, the presence of retrotransposons and the components of a putative RNA interference machinery in L. braziliensis suggest the potential for both greater diversity and more tractable experimentation in this Leishmania Viannia species.

[Chronic lupoid leishmaniasis. A rare differential diagnosis in Germany for erythematous infiltrative facial plaques]

Lupoid leishmaniasis is a unique form of cutaneous leishmaniasis characterized by unusual clinical features and a chronic relapsing course. Clinically and histologically it is similar to lupus vulgaris, which is thus the most important differential diagnostic consideration. All patients with granulomatous facial lesions coming from endemic areas or with a positive travel history should be suspected of having leishmaniasis. We describe a 59-year-old woman with facial lupoid leishmaniasis.

Multilocus microsatellite typing as a new tool for discrimination of Leishmania infantum MON-1 strains

The Leishmania donovani complex, which consists of L. donovani, L. infantum-L. chagasi, and L. archibaldi, is responsible for visceral manifestations of leishmaniasis. Multilocus enzyme electrophoresis is the standard method for the characterization and identification of strains of Leishmania. For L. infantum, the predominance of zymodeme MON-1 significantly reduces the discriminative power of this approach. In the present study, we developed 17 independent polymorphic microsatellite markers for the typing of strains of L. infantum, with the main emphasis on zymodeme MON-1. The discriminative powers of 11 markers selected from among these markers were tested by using a panel of 63 isolates of the L. donovani complex. Unique multilocus genotypes were observed for the strains analyzed, with only three exceptions. Model-based and distance-based analyses of the data set showed comparable results. It was possible to discriminate between L. donovani sensu stricto, a non-MON-1 group of L. infantum isolates, and a MON-1 group of L. infantum isolates. Within MON-1, three clusters with geographical correlations became apparent. The frequency of heterozygosity in the alleles analyzed varied extremely between the different groups of isolates. The main clusters described are not consistent with species definitions based on isoenzyme analysis but confirm the results of former PCR-based investigations.

Molecular epidemiology of Leishmania (Viannia) guyanensis in French Guiana

Little information is available about the genetic variability of Leishmania populations and the possible correlations with ecoepidemiological features of leishmaniases. The present study was carried out in French Guiana, a country where cutaneous leishmaniases (CL) are endemic over the whole territory. The genetic polymorphism of a nuclear sequence encompassing the end of the ribosomal small subunit and the internal transcribed spacer 1 of 265 isolates from patients with CL was examined by restriction fragment length polymorphism analysis. Genotypes based on the fingerprinting phenetic integration were compared to epidemiological, clinical, and geographical data. In agreement with previous reports, five different Leishmania species were identified, but Leishmania (Viannia) guyanensis represented 95.8% of the samples. Two distinct L. (V.) guyanensis populations were found to originate in two ecologically characterized regions. Higher lesional parasite densities and the need for additional treatments were significantly linked to genotype group I. Parasites of genotype group II were more likely to cause chronic and disseminated cutaneous forms in patients. L. (V.) guyanensis was previously said not to be very polymorphic; however, the present analysis resulted in a significant degree of discrimination among L. (V.) guyanensis isolates from diverse ecological areas and with different clinical implications.

Atypical multifocal cutaneous leishmaniasis in an immunocompetent patient treated by liposomal amphotericin B

Multifocal cutaneous leishmaniasis (MCL) is an extremely rare disease in South Europe, and it mainly affects immunosuppressed patients. We report a case of MCL in an immunocompetent patient affected by type II diabetes mellitus that clinically presented with three large ulcers on the legs with a non-linear distribution and several months later with an erythematous-crusty lesion on the left cheek. Diagnosis of leishmaniasis due to Leishmania infantum was formulated by PCR analysis. Given the diffuse and wide lesions, the unresponsiveness to previous local and systemic treatments, a parenteral i.v. therapy with liposomal amphotericin B at a dosage of 3mg/kg/day for 5 days was started and then repeated on the 14th and 21st days, leading to a clear improvement in the clinical picture. The different clinical expression and the evolution of leishmaniasis depend on both the parasite subtype and the host's immunity status. L. infantum manifests with an atypical clinical feature more frequently than other species. The differential diagnosis for multiple ulcers must include several skin diseases, such as cutaneous TBC, bacterial ulcers, traumatic ulcers, deep mycoses, and sarcoidosis. However, an MCL should always be considered in subjects coming from endemic areas. In our case, the multifocality, the size of the lesions and the unresponsiveness to other treatment indicate a short course treatment with liposomal B amphotericin that proved to be a suitable alternative to traditional drugs used in MCL.

Genetic homogeneity within Leishmania (L.) infantum isolated from human and dogs: the relationship with the sandfly fauna distribution in endemic areas of Nueva Esparta State, Venezuela

Leishmania infantum has been described as a highly polymorphic group of parasites, responsible for visceral leishmaniasis and cutaneous leishmaniasis. In this paper we report the life-cycle of L. (L.) infantum in an endemic area of visceral leishmaniasis in Venezuela, by using molecular diagnosis and characterization of parasites isolated from dogs, humans with visceral leishmaniasis and sand flies. The molecular characterization was carried out by use of kDNA restriction analysis, dot-blot hybridization with species-specific probes and RFLP of the PCR products. The results demonstrated that L. (L.) infantum is the parasite responsible for VL in the island. The parasites were revealed to be genetically homogeneous with no intra-specific differences between isolates from different individuals. The highest homology of the isolates was with L. (L.) infantum from the Old World rather than with L. (L.) chagasi from the New World. Additionally, we report the geographical distribution of Lutzomyia longipalpis, and the relationship with the transmission of L. (L.) infantum in the studied area.

Leishmania (Viannia): genetic analysis of cutaneous and mucosal strains isolated from the same patient

Ten pairs of Leishmania (Viannia) strains isolated from mucosal and cutaneous lesions of the same patient were analyzed genotypically in order to determine whether populations that had metastasized to mucosal sites differed from those in the cutaneous lesion. The strains were previously characterized by multi locus enzyme electrophoresis and/or monoclonal antibodies reactivity, and, for this study, only isolates from the same patient which were identified as the same species were employed. PCR-RFLP of internal transcribed spacer (ITS) rDNA, random amplified polymorphic DNA (RAPD), and schizodeme analyses were conducted. All genotyping methods revealed microheterogeneity between cutaneous and mucosal isolates from the same patient. The PCR-RFLP of the ITS rDNA and RAPD analysis were numerically analyzed through similarity coefficients and dendrograms were generated. All phenograms clustered cutaneous and mucosal strains of the same patient in one branch with a high degree of similarity, and phenetic analysis matched between them. Schizodeme analysis revealed differences between strains that composed some pairs. Genetic analyses indicate that some populations that metastasize to mucosal sites are distinguishable from the population in cutaneous lesions, however, other approaches will be required to associate genetic polymorphisms with the cutaneous or mucosal phenotype of strains.

Epidemiological and clinical features of Leishmania (Viannia) braziliensis American cutaneous and mucocutaneous leishmaniasis in the State of Espírito Santo, Brazil

Between 1985 and 2000, epidemiological surveys of the American tegumentary leishmaniasis (ATL) were carried out in several rural and urban communities in Espírito Santo, Brazil. A total of 100 stocks of Leishmania (comprising isolates from both human and canine hosts with ATL) were identified by two methods of molecular characterization, using specific monoclonal antibodies and multilocus enzyme electrophoresis. Parasite isolates from 19 municipalities were found to belong to the same zymodeme and serodeme type as of the Leishmania (Viannia) braziliensis reference strain. In contrast, our genotyping studies have shown intra-specific variation among these parasites (comparisons of the variability of the internal transcribed spacers between the small and large subunits of the rRNA genes of the 22 stocks studied revealed at least 11 genotypes). Two main clusters of L. (V.) braziliensis genotypes were observed, representing parasites collected from different endemic regions in the state, where transmission reflects distinct eco-epidemiological features. Infection with this pathogen was associated with the characteristic disease forms, but neither the clinical outcome nor the response to treatment could be related to the genetic polymorphism of the isolates, as defined by using the proposed methodology.

Genetic polymorphism and molecular epidemiology of Leishmania (Viannia) braziliensis from different hosts and geographic areas in Brazil

Numerical zymotaxonomy and variability of the internal transcribed spacers (ITS) between the small and large subunits of the rRNA genes were used to examine strain variation and relationships in natural populations of Leishmania (Viannia) braziliensis. A total of 101 strains from distinct hosts and Brazilian geographic regions were assigned to 15 zymodemes clustered in two major genetic groups. The great number of isolates (48.5%) placed in zymodeme IOC/Z-27 were collected on the Atlantic coast. The high molecular diversity found in populations in the Amazon Basin was related to the great number of sandfly vector(s) in that region. The results of the restriction fragment length polymorphism analysis of the ITS depicted considerable intraspecific variation. Genotypic groups A, B, and C contained 39, 40, and 22 isolates, which were divided into 16, 10, and 15 genotypes, respectively. The genetic polymorphism observed demonstrates the degree of diversity of L. (V.) braziliensis strains from different regions where they are endemic. The results reinforce the clonal theory for Leishmania parasites showing the genetic diversity of this pathogen and an association of L. (V.) braziliensis genotypes with specific transmission cycles, probably reflecting an adaptation of different clones to the vector species involved.