Intraspecific genetic variability in a population of Moroccan Leishmania infantum revealed by PCR-RFLP of kDNA minicircles

Genetic Variability in Leishmaniasis-Causing Leishmania infantum in Humans and Dogs from North-East Spain

Leishmania infantum is the primary cause of visceral and cutaneous leishmaniasis in the European Mediterranean region. Subspecies-level characterization of L. infantum aids epidemiological studies by offering insights into the evolution and geographical distribution of the parasite and reservoir identity. In this study, conducted in north-east Spain, 26 DNA samples of L. infantum were analyzed, comprising 21 from 10 humans and 5 from 5 dogs. Minicircle kinetoplast DNA (kDNA) polymerase chain reaction assays using primers MC1 and MC2, followed by sequencing, were employed to assess intraspecific genetic variability. Single-nucleotide polymorphism (SNP) analysis detected seven genotypes (G1, G2, G12*-G15*, and G17*), with five being reported for the first time (*). The most prevalent was the newly described G13 (54%), while the other currently identified genotypes were predominantly found in single samples. The in silico restriction fragment length polymorphism (RFLP) method revealed five genotypes (B, F, N, P, and W), one of them previously unreported (W). Genotype B was the most prevalent (85%), comprising three SNP genotypes (G1, G2, and G13), whereas the other RFLP genotypes were associated with single SNP genotypes. These kDNA genotyping methods revealed significant intraspecific genetic diversity in L. infantum, demonstrating their suitability for fingerprinting and strain monitoring.

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.

High-resolution melting (HRM)-based detection of polymorphisms in the malic enzyme and glucose-6-phosphate isomerase genes for Leishmania infantum genotyping

BACKGROUND

Leishmaniasis is a zoonotic disease endemic in the Mediterranean region where Leishmania infantum is the causative agent of human and canine infection. Characterization of this parasite at the subspecies level can be useful in epidemiological studies, to evaluate the clinical course of the disease (e.g. resistant strains, visceral and cutaneous forms of leishmaniasis) as well as to identify infection reservoirs. Multilocus enzyme electrophoresis (MLEE), a method currently recognized as the reference method for characterizing and identifying strains of Leishmania, is cumbersome and time-consuming and requires cultured parasites. These disadvantages have led to the development of other methods, such as multilocus microsatellite typing (MLMT) and multilocus sequence typing (MLST), for typing Leishmania parasites; however, these methods have not yet been applied for routine use. In this study, we first used MLST to identify informative polymorphisms on single-copy genes coding for metabolic enzymes, following which we developed two rapid genotyping assays based on high-resolution melting (HRM) analysis to explore these polymorphisms in L. infantum parasites.

METHODS

A customized sequencing panel targeting 14 housekeeping genes was designed and MLST analysis was performed on nine L. infantum canine and human strains/isolates. Two quantitative real-time PCR-HRM assays were designed to analyze two informative polymorphisms on malic enzyme (ME) and glucose-6-phosphate isomerase (GPI) genes (390T/G and 1831A/G, respectively). The two assays were applied to 73 clinical samples/isolates from central/southern Italy and Pantelleria island, and the results were confirmed by DNA sequencing in a subset of samples.

RESULTS

The MLST analysis, together with sequences available in the Genbank database, enabled the identification of two informative polymorphisms on the genes coding for ME and GPI. The fast screening of these polymorphisms using two HRM-based assays in 73 clinical samples/isolates resulted in the identification of seven genotypes. Overall, genotype 1 (sequence type 390T/1831G) was the most highly represented (45.2%) in the overall sample and correlated with the most common L. infantum zymodemes (MON-1, MON-72). Interestingly, in Pantelleria island, the most prevalent genotype (70.6%) was genotype 6 (sequence type 390T/1831A).

CONCLUSIONS

Applying our HRM assays on clinical samples allowed us to identify seven different genotypes without the need for parasite isolation and cultivation. We have demonstrated that these assays could be used as fast, routine and inexpensive tools for epidemiological surveillance of L. infantum or for the identification of new infection reservoirs.

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.

The Sporadic cutaneous leishmaniasis due to Leishmania infantum in Morocco: A presumably trend towards endemicity

In Morocco, cutaneous leishmaniasis (CL) is an endemic disease; it is considered a major public health problem caused by three species Leishmaniamajor, Leishmaniatropica, and the dermotropic variant MON-24 of Leishmaniainfantum. This species has three incriminated vectors named; Phlebotomus ariasi, Phlebotomus longicuspis and Phlebotomus perniciosus, with the dog as reservoir.The main aim of this review is to elucidate the current epidemiological pattern of CL due to L.infantum and to investigate the factors facilitating its propagation throughout the country. Therefore, the number of CL cases due to L.infantum, their repartition; the distribution of L.infantum vectors, as well as the factors affecting their abundance and spread were investigated. We showed a wide extension of this form of CL, from the north of Morocco to the Saharan areas, as well as an increase of reported cases. This extension of the disease has been accompanied by a juxtaposed spread and a high abundance of confirmed vectors of L. infantum, which are present in almost all bioclimatic zones. In this review, we have highlighted the impact of climate: temperature, humidity, precipitation; vegetation and human activities on the geographical expansion of L. infantum vectors. These abiotic and biotic factors constitute favorable conditions for the increase of vector populations, and their introduction into areas where they did not exist before, and subsequently raise the risk of introduction of this form of cutaneous leishmaniasis into previously free areas. To conclude, CL by L.infantum, traditionally evolving as a sporadic form, is changing to an endemic mode, which seeks more epidemiological studies, and more attention from the health authorities when implementing control programs.

Leishmaniasis: where are we and where are we heading?

Leishmaniasis is a zoonotic disease in humans caused by the bite of a parasite-infected sandfly. The disease, widely referred to as "poor man's disease," affects millions of people worldwide. The clinical manifestation of the disease depends upon the species of the parasite and ranges from physical disfigurement to death if left untreated. Here, we review the past, present, and future of leishmaniasis in detail. The life cycle of Leishmania sp., along with its epidemiology, is discussed, and in addition, the line of therapeutics available for treatment currently is examined. The current status of the disease is critically evaluated, keeping emerging threats like human immunodeficiency virus (HIV) coinfection and post kala-azar dermal leishmaniasis (PKDL) into consideration. In summary, the review proposes a dire need for new therapeutics and reassessment of the measures and policies concerning emerging threats. New strategies are essential to achieve the goal of leishmaniasis eradication in the next few decades.

The role of sampling by cotton swab in the molecular diagnosis of cutaneous leishmaniasis

An appreciated sampling technique is essential for achieving optimum results from diagnostic tests of cutaneous leishmaniasis (CL); conventional sampling methods, such as skin biopsy and dermal scrapping, are painful for the patients and require qualified staff and hospital facilities, while swabbing is patient-friendly more comfortable than invasive traditional techniques and can be carried out under field conditions. The aim of this study is to evaluate a non-invasive sampling method (swab) in the cutaneous leishmaniasis diagnosis, compared to microscopic examination. The recruitment of 205 patients was done during 3 years in six regions known as endemic CL foci in the south-east, the centre, the south-west and the north of Morocco. The results showed that molecular detection of the nuclear marker ITS1 on swab materials is to be less sensitive than microscopic examination, and the difference was statistically significant (p-value = .036). Thereafter, 55 patients were randomly selected to compare the results of two molecular techniques (ITS1-PCR and nested KDNA-PCR), performed both on swab and on stained smears used for microscopic examination; ITS1-PCR results from stained smears reached 87% positivity against 65,2% for cotton swab; and it was statistically significant (p-value = .019); on the other hand for the KDNA marker, results from cotton swab reached 93% of positivity against 91% for stained smears; and statistically the difference was not significant (p-value = .5113). One can presume that rubbing over the lesion with cotton swab implies a low parasitic load collection, but the choice of the amplification target greatly influences the results obtained from cotton swab; on top of that swab remains useful in the cases of patients with multiples lesions or the latter are located in sensitive places difficult to reach with an invasive method such as the eyelids, the lips or other mucous areas.

Emerging and Re-Emerging Leishmaniases in the Mediterranean Area: What Can Be Learned from a Retrospective Review Analysis of the Situation in Morocco during 1990 to 2010?

In Morocco, cutaneous and visceral leishmaniases represent a public health concern. In this opinion paper, we propose to highlight chosen elements that have governed the drastic increase in the incidence of leishmaniases recorded in Morocco during the period between 1990 to 2010 in order to guide the prediction of the expansion of diseases and epidemic events. We highlight that the dispersion of the zoonotic cutaneous leishmaniasis (ZCL) form, caused by the Leishmania major parasite, appears to be closely related to that of its arthropod vector density, which is sensitive to changes in climate. The dissemination of anthroponotic cutaneous leishmaniasis (ACL) was related to an increase in human travel and local tourism during the studied decades. These are linked to economic expansion and infrastructure development. Interestingly, the main ACL foci are spatially aligned with the highways, and their occurrence was synchronized with the building of transportation infrastructure. During the above-mentioned decades, the zoonotic visceral leishmaniasis (ZVL) caused by Leishmania infantum has expanded from its historical northern territories, dispersing outwards in all directions. This spread follows the emergence of hamlets and villages connecting with major cities.

Genetic diversity and phylogenetic relationships between Leishmania infantum from dogs, humans and wildlife in south-east Spain

Leishmania infantum causes human and canine leishmaniosis. The parasite, transmitted by phlebotomine sand flies, infects species other than dogs and people, including wildlife, although their role as reservoirs of infection remains unknown for most species. Molecular typing of parasites to investigate genetic variability and evolutionary proximity can help understand transmission cycles and designing control strategies. We investigated Leishmania DNA variability in kinetoplast (kDNA) and internal transcribed spacer 2 (ITS2) sequences in asymptomatically infected wildlife (n = 58) and symptomatically and asymptomatically infected humans (n = 38) and dogs (n = 15) from south-east Spain, using single nucleotide polymorphisms (SNPs) and in silico restriction fragment length polymorphism (RFLP) analyses. All ITS2 sequences (n = 76) displayed a 99%-100% nucleotide identity with a L. infantum reference sequence, except one with a 98% identity to a reference Leishmania panamensis sequence, from an Ecuadorian patient. No heterogeneity was recorded in the 73 L. infantum ITS2 sequences except for one SNP in a human parasite sequence. In contrast, kDNA analysis of 44 L. infantum sequences revealed 11 SNP genotypes (nucleotide variability up to 4.3%) and four RFLP genotypes including B, F and newly described S and T genotypes. Genotype frequency was significantly greater in symptomatic compared to asymptomatic individuals. Both methods similarly grouped parasites as predominantly or exclusively found in humans, in dogs, in wildlife or in all three of them. Accordingly, the phylogenetic analysis of kDNA sequences revealed three main clusters, two as a paraphyletic human parasites clade and a third including dogs, people and wildlife parasites. Results suggest that Leishmania infantum genetics is complex even in small geographical areas and that, probably, several independent transmission cycles take place simultaneously including some connecting animals and humans. Investigating these transmission networks may be useful in understanding the transmission dynamics, infection risk and therefore in planning L. infantum control strategies.

Leishmaniasis in Northern Morocco: Predominance of Leishmania infantum Compared to Leishmania tropica

In Morocco, Leishmania infantum species is the main causative agents of visceral leishmaniasis (VL). However, cutaneous leishmaniasis (CL) due to L. infantum has been reported sporadically. Moreover, the recent geographical expansion of L. infantum in the Mediterranean subregion leads us to suggest whether the nonsporadic cases of CL due to this species are present. In this context, this review is written to establish a retrospective study of cutaneous and visceral leishmaniasis in northern Morocco between 1997 and 2018 and also to conduct a molecular study to identify the circulating species responsible for the recent cases of leishmaniases in this region. Data concerning leishmaniases cases were collected from the Epidemiology and Disease Control Directorate from 1997 to 2018. Human samples obtained from peripheral laboratories were examined using PCR-ITS1 method. The ITS1 products were subjected to digestion with the restriction endonuclease Mn1-I. Between 1997 and 2018, a total of 1,255 cases of cutaneous and visceral leishmaniasis were recorded in Tangier-Tetouan-Al Hoceima Region, i.e., 1.56% of the reported cases in Morocco (1,255/80,299). Concerning the geographical study covering the period 2007-2018, 79.5% (105/132) of the sectors were affected by leishmaniases. The molecular results showed that Humans were found to be infected with the L. infantum species with a high infection rate compared to L. tropica infection. Moreover, molecular characterization using ITS1 PCR-RFLP showed that the density of L. infantum was significantly higher (n = 68/81; 84%) than that of L. tropica (n = 13/81; 16%) (P-value 9.894e-10). While regarding visceral leishmaniasis, L. infantum was the only species responsible of this form. These findings of this study showed the emergence of L. infantum in Morocco and suggest that this species might be more prevalent than previously thought. Furthermore, the molecular determination of L. infantum will be helpful for control strategies by taking into consideration the reservoir of this species.

Genetic polymorphism in Leishmania infantum isolates from human and animals determined by nagt PCR-RFLP

BACKGROUND

Leishmania infantum is the causative agent of human visceral leishmaniasis (VL) and sporadic human cutaneous leishmaniasis (CL) in the Mediterranean region. The genetic variation of the Leishmania parasites may result in different phenotypes that can be associated with the geographical distribution and diversity of the clinical manifestations. The main objective of this study was to explore the genetic polymorphism in L. infantum isolates from human and animal hosts in different regions of Morocco.

METHODS

The intraspecific genetic variability of 40 Moroccan L. infantum MON-1 strains isolated from patients with VL (n = 31) and CL (n = 2) and from dogs (n = 7) was evaluated by PCR-RFLP of nagt, a single-copy gene encoding N-acetylglucosamine-1-phosphate transferase. For a more complete analysis of L. infantum polymorphism, we included the restriction patterns of nagt from 17 strains available in the literature and patterns determined by in-silico digestion of three sequences from the GenBank database.

RESULTS

Moroccan L. infantum strains presented a certain level of genetic diversity and six distinct nagt-RFLP genotypes were identified. Three of the six genotypes were exclusively identified in the Moroccan population of L. infantum: variant M1 (15%), variant M2 (7.5%), and variant M3 (2.5%). The most common genotype (65%), variant 2 (2.5%), and variant 4 (7.5%), were previously described in several countries with endemic leishmaniasis. Phylogenetic analysis segregated our L. infantum population into two distinct clusters, whereas variant M2 was clearly distinguished from both cluster I and cluster II. This distribution highlights the degree of genetic variability among the Moroccan L. infantum population.

CONCLUSION

The nagt PCR-RFLP method presented here showed an important genetic heterogeneity among Moroccan L. infantum strains isolated from human and canine reservoirs with 6 genotypes identified. Three of the six Moroccan nagt genotypes, have not been previously described and support the particular genetic diversity of the Moroccan L. infantum population reported in other studies.

Epidemiological and genetic studies suggest a common Leishmania infantum transmission cycle in wildlife, dogs and humans associated to vector abundance in Southeast Spain

Leishmania infantum infection was investigated in 202 wild carnivores, rodents and lagomorphs in Southeast Spain using a real-time PCR (rtPCR) in skin and organ samples, mostly spleen. Lesions compatible with leishmaniosis were not observed in any of the animals. Prevalence defined as the percentage of rtPCR-positive animals was 32% overall, and 45% in foxes (n = 69), 30% in rabbits (n = 80) and stone martens (n = 10), 19% in wood mice (n = 16), 0% in black rats (n = 10) and ranged between 0% and 100% in other minoritarian species including badgers, wild cats, wolves, raccoons, genets and hares. Most infected rabbits were rtPCR-positive in skin and not in spleen samples and the opposite was the case for foxes (p < 0.05). L. infantum prevalence was lowest in spring following months of non-exposure to phlebotomine sand fly vectors, and spatially matched recently estimated Phlebotomus perniciosus vector abundance and the prevalence of subclinical infection in dogs and humans. Prevalence increased with altitude and was greater in drier and less windy South and West compared to the coastal Southeast of the study area (p < 0.05). Genetic diversity of L. infantum from foxes, investigated by PCR-restriction fragment length polymorphisms of kinetoplast DNA, revealed B genotype in all animals, which is frequent in people and dogs in the Iberian Peninsula and Morocco. The study provides further evidence that subclinical L. infantum infection is widespread in wildlife with prevalence depending on environmental factors and that parasite tissue tropism may vary according to host species. Moreover, it suggests that sylvatic and domestic transmission cycles are closely interconnected.

[Molecular typing of Leishmania (Leishmania) amazonensis and species of the subgenus Viannia associated with cutaneous and mucosal leishmaniasis in Colombia: A concordance study]

INTRODUCTION

Multilocus enzyme electrophoresis (MLEE) is the reference standard for the characterization of Leishmania species. The test is restricted to specialized laboratories due to its technical complexity, cost, and time required to obtain results. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is used to identify Leishmania species.

OBJECTIVE

To establish the concordance between the two tests as identifying methods for circulating species in Colombia.

MATERIALS AND METHODS

A total of 96 isolates from patients with cutaneous or mucosal leishmaniasis were selected and identified by MLEE and PCR-RFLP with miniexon and hsp70 as the molecular targets, which were used sequentially. Restriction enzymes HaeIII and BccI were similarly applied. Cohen's kappa coefficient and the 95% confidence interval (CI) were calculated.

RESULTS

The kappa coefficient and the 95% CI between MLEE and PCR-RFLP displayed "very good" concordance with a coefficient of 0.98 (CI95%: 0.98 to 1.00). The identified species were Leishmania Viannia braziliensis, Leishmania Viannia panamensis, Leishmania Viannia guyanensis and Leishmania Leishmania amazonensis. A total of 80 of the 96 isolates were sequenced and the results obtained by PCR-RFLP were confirmed.

CONCLUSION

Due to the concordance obtained between tests results with the amplification of the genes miniexon and hsp70, PCR-RFLP is proposed as an alternative for identifying circulating Leishmania species in Colombia.