Evaluation of a Multilocus Sequence Typing (MLST) scheme for Leishmania (Viannia) braziliensis and Leishmania (Viannia) panamensis in Colombia

Herrera, Giovanny; Hernández, Carolina; Ayala, Martha S.; Flórez, Carolina; Teherán, Aníbal A.; Ramírez, Juan David

doi:10.1186/s13071-017-2175-8

Cited by 34 publications

(32 citation statements)

References 38 publications

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“…Likewise, the great diversity of circulating Leishmania species in Colombia plays a fundamental role in the permanence and propagation of the disease, given that neither epidemiological surveillance, nor treatment, take this variable into account. This assumes that all species are equally susceptible to treatment, which has been refuted in multiple studies [ 4 , 11 , 33 – 35 ]. The presence of some vectors in over half of the departments in Colombia ( Fig 5 ) shows the importance of this factor in the perpetuation of the epidemiological cycle.…”

Section: Discussionmentioning

confidence: 99%

“…equatoriensis , L . naiffi ), and that the most prevalent species exhibit high genetic diversity [ 9 – 11 ]. This set of conditions conspires to produce an incidence of 33.6 per 100,000 inhabitants in 2015, leading to the categorization of the country as one of Intense Transmission by the Panamerican Health Organization (PAHO) according to its Leishmaniasis Compound Index [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

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Geospatial-temporal distribution of Tegumentary Leishmaniasis in Colombia (2007–2016)

et al. 2018

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BackgroundTegumentary Leishmaniasis (TL) is a neglected disease with worldwide distribution and considered a public health problem, especially in Latin America. In Colombia, the governmental epidemiological surveillance system (SIVIGILA) is responsible for collecting information on the presentation of cases of TL from each of the municipalities and departments. In absence of a study compiling and analyzing currently available metadata of TL in Colombia, this study describes the geospatial-temporal distribution of TL and identifies the regions of the country on which prevention measures should be established in order to control the disease.Methodology/Principal findingsThis is an exploratory descriptive analysis of the distribution of TL in Colombia. Information was collected on new cases of the disease during the years 2007–2016 from the Colombian reporting system (SIVIGILA). Incidence calculations were made based on population estimates by departments and biogeographical regions. Time evolution is shown in biennial maps. A 10-year series was analyzed, showing that the Amazon region is the most affected in terms of incidence, while the Andean region has the highest number of cases with a high variability among the departments that make it up. In those departments where there is a greater reported diversity of vector species, a large number of cases was observed.Conclusions/SignificanceTransmission dynamics of TL in Colombia in the past 10 years have been variable, with a greater concentration of cases in the central and southern departments. The present study contributes to improve the understanding of the patterns of distribution of TL in Colombia and can be a basis for future studies of impact evaluation of Health policies in the country and the region.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Geospatial-temporal distribution of Tegumentary Leishmaniasis in Colombia (2007–2016)

et al. 2018

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“…The reported studies so far have focused on L. braziliensis, where the majority report consistent findings in describing its high intraspecific genetic diversity [16,26,43] even in cell populations isolated from a single L. braziliensis strain ("sub-strain") [44], while in L. panamensis the results are not yet concordant, probably for the molecular approaches used. While studies using MLST reveal extreme genetic homogeneity within L. panamensis [10], others using MLEE [5], sequencing of specific genes (Cytb/HSP70) [6], AFLP [13], or microsatellites [14], have reported a high intraspecific genetic diversity in this species. Considering that DNA high-throughput sequencing has the potential to identify changes in the whole genome structure, we used this approach to reveal the intraspecific genomic variability of L. panamensis from Colombian clinical isolates and Panamanian genomes retrieved from databases.…”

Section: Discussionmentioning

confidence: 94%

“…Several nuclear and mitochondrial DNA markers (cytochrome b, COII, gp63, 18S-rRNA, mini-exon, HSP-70, and ribosomal internal transcribed spacer regions (ITS-rDNA)) as well as different molecular techniques such as polymerase chain reaction (PCR) [9], multilocus sequence typing (MLST) [10], multilocus enzyme electrophoresis (MLEE) [5,11], random amplified polymorphism (RAPD) [12], amplified fragment length polymorphisms (AFLP) [13] and microsatellites [14], have been used to evaluate the inter and intraspecific genetic variability of different Leishmania species (L. tropica, L. major, L. donovani, L. braziliensis, L. peruviana, L. guyanensis, and L. panamensis) [13][14][15][16][17][18][19]. However, the identification of such genetic variants across the whole genome has become possible only with the arrival of DNA-seq.…”

Section: Introductionmentioning

confidence: 99%

Intraspecific Genomic Divergence and Minor Structural Variations in Leishmania (Viannia) panamensis

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Muñoz

Muskus

et al. 2020

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Leishmania (Viannia) panamensis is one of the most important Leishmania species associated with cutaneous leishmaniasis (CL) in Latin America. Despite its wide geographic distribution and pathogenic potential in humans and animals, the genomic variability of this species is low compared with other Leishmania species circulating in the same geographical area. No studies have reported a detailed analysis of the whole genome of L. panamensis from clinical isolates using DNA high-throughput sequencing to clarify its intraspecific genomic variability or plausible divergence. Therefore, this study aimed to evaluate the intraspecific genomic variability of L. panamensis from Colombia and Panama. A total of 22 genomes were analyzed, 19 from Colombian patients with CL and three genomes from Panama obtained from public databases. The phylogenomic analysis revealed the potential existence of three well-supported clades as evidence of intraspecific divergence. Additionally, the whole-genome analysis showed low structural variations in terms of ploidy, copy number variations, and single-nucleotide polymorphisms (SNPs). SNPs shared among all clades were identified, revealing their importance in different biological processes of L. panamensis. The findings not only expand our knowledge of intraspecific genomic variability of one of the most important Leishmania species in South America but also highlights the possible existence of different clades/lineages/subpopulations across a geographic scale.

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“…On the other hand, it was also shown that strains classified as different zymodemes can present the same genotype [ 18 , 20 ]. However, the low number of typed strains and the lack of consensus on the marker genes, as well as the lack of MLST database for Leishmania , have hindered the implementation of MLST as a reference typing method [ 22 ]. Until now, most of the epidemiological data available in the literature is based on MLEE classification, and many DNA-based typing methods correlate data with existing MLEE classification [ 23 , 24 ].…”

Section: Introductionmentioning

confidence: 99%

Exploiting genetic polymorphisms in metabolic enzymes for rapid screening of Leishmania infantum genotypes

et al. 2018

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BackgroundLeishmania infantum is the aetiological agent of visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL). Numerous strains and/or zymodemes have been identified and characterized by multilocus enzyme electrophoresis (MLEE). MLEE is considered the reference method for L. infantum parasite typing and it is based upon enzyme electrophoretic mobility analysis from promastigote cultures. However, the MLEE technique is cumbersome, time-consuming and does not detect silent genetic mutations or nucleotide changes that give rise to amino acid changes that do not alter electrophoretic mobility. As a result of these difficulties, many DNA-based typing methods have been developed over the past few years. However, relative to the enzymes utilized in MLEE analysis, we observed a shortage of DNA sequences available in the GenBank database or an absolute lack of sequences belonging to specific zymodemes. The aims of the present study were to (i) implement the number of sequences coding for metabolic enzymes used in MLEE; (ii) identify polymorphisms that characterize L. infantum zymodemes most prevalent in the Mediterranean basin; and (iii) exploit these polymorphisms to develop a rapid screening test that would give results comparable with existing MLEE typing.ResultsPartial sequences of seven metabolic enzyme genes (malic enzyme, 6-phosphogluconate dehydrogenase, mitochondrial isocitrate dehydrogenase, glucose-6-phosphate isomerase, glucose-6-phosphate dehydrogenase, phosphoglucomutase and mannose phosphate isomerase) were obtained from 11 L. infantum strains. The comparison of these sequences with those obtained from GenBank allowed for the identification of a few polymorphisms that could distinguish several zymodemes. In particular, the polymorphism 390T>G in the malic enzyme gene has been exploited to develop a high-resolution melt (HRM)-based assay to rapidly differentiate the genotype 390T, associated with zymodemes MON-1, MON-72 and MON-201, evidencing a partial agreement between genotyping results and MLEE. The assay has been successfully applied to L. infantum clinical isolates and clinical samples.ConclusionsA HRM-based assay for rapid identification of genotypes associated with the most common L. infantum zymodemes in the Mediterranean basin has been developed and its potential application in epidemiological research for L. infantum population screening, without parasite isolation and culturing, has been demonstrated.Electronic supplementary materialThe online version of this article (10.1186/s13071-018-3143-7) contains supplementary material, which is available to authorized users.

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Evaluation of a Multilocus Sequence Typing (MLST) scheme for Leishmania (Viannia) braziliensis and Leishmania (Viannia) panamensis in Colombia

Cited by 34 publications

References 38 publications

Geospatial-temporal distribution of Tegumentary Leishmaniasis in Colombia (2007–2016)

Geospatial-temporal distribution of Tegumentary Leishmaniasis in Colombia (2007–2016)

Intraspecific Genomic Divergence and Minor Structural Variations in Leishmania (Viannia) panamensis

Exploiting genetic polymorphisms in metabolic enzymes for rapid screening of Leishmania infantum genotypes

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