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Mendieta D, Vásquez V, Jaén L, Pineda V, Saldaña A, Calzada JE, Samudio F. Insights into the Genetic Diversity of Leishmania (Viannia) panamensis in Panama, Inferred via Multilocus Sequence Typing (MLST). Pathogens 2023; 12:pathogens12050747. [PMID: 37242417 DOI: 10.3390/pathogens12050747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/26/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Leishmaniasis is a disease caused by parasites of the genus Leishmania and transmitted by sand fly vectors. Tegumentary leishmaniasis is the most prevalent clinical outcome in Latin America, afflicting people from 18 countries. In Panama, the annual incidence rate of leishmaniasis is as high as 3000 cases, representing a major public health problem. In endemic regions, L. panamensis is responsible for almost eighty percent of human cases that present different clinical outcomes. These differences in disease outcomes could be the result of the local interplay between L. panamensis variants and human hosts with different genetic backgrounds. The genetic diversity of L. panamensis in Panama has only been partially explored, and the variability reported for this species is based on few studies restricted to small populations and/or with poor resolutive markers at low taxonomic levels. Accordingly, in this study, we explored the genetic diversity of sixty-nine L. panamensis isolates from different endemic regions of Panama, using an MLST approach based on four housekeeping genes (Aconitase, ALAT, GPI and HSP70). Two to seven haplotypes per locus were identified, and regional differences in the genetic diversity of L. panamensis were observed. A genotype analysis evidenced the circulation of thirteen L. panamensis genotypes, a fact that might have important implications for the local control of the disease.
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Affiliation(s)
- Daniel Mendieta
- Facultad de Ciencias Naturales Exactas y Tecnología, Universidad de Panamá, Panama City P.O. Box 0824-00073, Panama
| | - Vanessa Vásquez
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Avenida Justo Arosemena, Panama City P.O. Box 0816-02593, Panama
| | - Luis Jaén
- Facultad de Ciencias Naturales Exactas y Tecnología, Universidad de Panamá, Panama City P.O. Box 0824-00073, Panama
| | - Vanessa Pineda
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Avenida Justo Arosemena, Panama City P.O. Box 0816-02593, Panama
| | - Azael Saldaña
- Facultad de Ciencias Naturales Exactas y Tecnología, Universidad de Panamá, Panama City P.O. Box 0824-00073, Panama
- Centro de Investigación y Diagnóstico de Enfermedades Parasitarias (CIDEP), Universidad de Panamá, Panama City P.O. Box 0824-00073, Panama
- Sistema Nacional de Investigación, Panama City P.O. Box 0816-02852, Panama
| | - José Eduardo Calzada
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Avenida Justo Arosemena, Panama City P.O. Box 0816-02593, Panama
- Sistema Nacional de Investigación, Panama City P.O. Box 0816-02852, Panama
| | - Franklyn Samudio
- Facultad de Ciencias Naturales Exactas y Tecnología, Universidad de Panamá, Panama City P.O. Box 0824-00073, Panama
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Avenida Justo Arosemena, Panama City P.O. Box 0816-02593, Panama
- Sistema Nacional de Investigación, Panama City P.O. Box 0816-02852, Panama
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Llanes A, Cruz G, Morán M, Vega C, Pineda VJ, Ríos M, Penagos H, Suárez JA, Saldaña A, Lleonart R, Restrepo CM. Genomic diversity and genetic variation of Leishmania panamensis within its endemic range. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105342. [PMID: 35878820 DOI: 10.1016/j.meegid.2022.105342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Species belonging to the Leishmania (Viannia) subgenus are important causative agents of cutaneous and mucocutaneous leishmaniasis in Central and South America. These parasites possess several distinctive biological features that are influenced by their genetics, population structure, and genome instability. To date, several studies have revealed varying degrees of genetic diversity within Leishmania species. Particularly, in species of the L. (Viannia) subgenus, a generalized high intraspecific genetic diversity has been reported, although, conflicting conclusions have been drawn using different molecular techniques. Despite being the most common Leishmania species circulating in Panama and Colombia, few studies have analyzed clinical samples of Leishmania panamensis using whole-genome sequencing, and their restricted number of samples has limited the information they can provide to understand the population structure of L. panamensis. Here, we used next generation sequencing (NGS) to explore the genetic diversity of L. panamensis within its endemic range, analyzing data from 43 isolates of Colombian and Panamanian origin. Our results show the occurrence of three well-defined geographically correlated groups, and suggests the possible occurrence of additional phylogeographic groups. Furthermore, these results support the existence of a mixed mode of reproduction in L. panamensis, with varying frequencies of events of genetic recombination occurring primarily within subpopulations of closely related strains. This study offers important insights into the population genetics and reproduction mode of L. panamensis, paving the way to better understand their population structure and the emergence and maintenance of key eco-epidemiological traits.
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Affiliation(s)
- Alejandro Llanes
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Panama
| | - Génesis Cruz
- Escuela de Biología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panama City, Panama, Panama
| | - Mitchelle Morán
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Panama
| | - Carlos Vega
- Escuela de Biología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panama City, Panama, Panama
| | - Vanessa J Pineda
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama, Panama
| | - Margarita Ríos
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama, Panama
| | - Homero Penagos
- Hospital Regional Dr. Rafael Hernández, Caja de Seguro Social, David, Chiriquí, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama
| | - José A Suárez
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama
| | - Azael Saldaña
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama
| | - Ricardo Lleonart
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama.
| | - Carlos M Restrepo
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama.
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Miranda ADC, González KA, Samudio F, Pineda VJ, Calzada JE, Capitan-Barrios Z, Jiménez A, Castillo J, Mendoza Y, Suárez JA, Ortiz B, Méndez J, Pascale JM, Grögl M, Sosa N, Saldaña A. Molecular Identification of Parasites Causing Cutaneous Leishmaniasis in Panama. Am J Trop Med Hyg 2021; 104:1326-1334. [PMID: 33432903 DOI: 10.4269/ajtmh.20-1336] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 11/27/2020] [Indexed: 02/03/2023] Open
Abstract
Isolates from 475 cutaneous leishmaniasis (CL) patients from three endemic regions were studied by three typing techniques. The molecular analysis from lesion scrapings based on hsp70 PCR-RFLP showed that 78.1% (371/475) restriction patterns corresponded to Leishmania (Viannia) panamensis, 19% (90/475) to Leishmania (Viannia) guyanensis, and 3.0% (14/475) to Leishmania (Viannia) braziliensis. Promastigotes isolated by culture from lesions of 228 patients (48.0%, 228/475) were identified by multi-locus enzyme electrophoresis. Of them, 95.2% (217/228) were typified as L. (V.) panamensis, 1.3% (3/228) as L. (V.) guyanensis, 2.2% (5/228) as L. (V.) braziliensis, and 1.3% (3/228) as hybrids (L. [V.] braziliensis/L. [V.] panamensis). However, a partial sequencing analysis of the hsp70 gene from 77 selected samples showed 16.9% (13/77) typified as L. (V.) panamensis, 68.8% (53/77) as Leishmania (V.) sp., 1, 3.9% (3/77) as L. (V.) guyanensis, 1.3% (1/77) as L. (V.) braziliensis outlier, 2.6% (2/77) as Leishmania (Viannia) naiffi, 2.6% as (2/77) Leishmania (V.) sp., and 2 and 3.9% (3/77) hybrid isolates of L. (V.) braziliensis/L. (V.) guyanensis. These results confirm L. (V.) panamensis as the predominant species and cause of CL lesions in Panama and that L. (V.) guyanensis, L. (V.) braziliensis, and L. (V.) naiffi are circulating to a lower degree. Furthermore, the determination of parasite isolates belonging to atypical clusters and hybrid isolates suggests the circulation of genetic variants with important implications for the epidemiology and clinical follow-up of CL in Panama. No evidence of the existence of parasites of the Leishmania (Leishmania) mexicana complex in Panamanian territory was found in this study.
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Affiliation(s)
| | - Kadir A González
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Franklyn Samudio
- Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panama, Panama.,Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Vanessa J Pineda
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - José E Calzada
- Facultad de Medicina Veterinaria, Universidad de Panamá, Panama, Panama.,Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | | | - Ana Jiménez
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Juan Castillo
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Yaxelis Mendoza
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - José A Suárez
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Betsi Ortiz
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Juan Méndez
- Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Juan M Pascale
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Max Grögl
- U.S. Naval Medical Research Unit No. 6, Lima, Peru
| | - Néstor Sosa
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Azael Saldaña
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama.,Centro de Investigación y Diagnóstico de Enfermedades Parasitarias (CIDEP), Facultad de Medicina, Universidad de Panamá, Panama, Panama
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Patino LH, Muñoz M, Cruz-Saavedra L, Muskus C, Ramírez JD. Genomic Diversification, Structural Plasticity, and Hybridization in Leishmania (Viannia) braziliensis. Front Cell Infect Microbiol 2020; 10:582192. [PMID: 33178631 PMCID: PMC7596589 DOI: 10.3389/fcimb.2020.582192] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/28/2020] [Indexed: 01/12/2023] Open
Abstract
Leishmania (Viannia) braziliensis is an important Leishmania species circulating in several Central and South American countries. Among Leishmania species circulating in Brazil, Argentina and Colombia, L. braziliensis has the highest genomic variability. However, genomic variability at the whole genome level has been only studied in Brazilian and Peruvian isolates; to date, no Colombian isolates have been studied. Considering that in Colombia, L. braziliensis is a species with great clinical and therapeutic relevance, as well as the role of genetic variability in the epidemiology of leishmaniasis, we analyzed and evaluated intraspecific genomic variability of L. braziliensis from Colombian and Bolivian isolates and compared them with Brazilian isolates. Twenty-one genomes were analyzed, six from Colombian patients, one from a Bolivian patient, and 14 Brazilian isolates downloaded from public databases. The results obtained of Phylogenomic analysis showed the existence of four well-supported clades, which evidenced intraspecific variability. The whole-genome analysis revealed structural variations in the somy, mainly in the Brazilian genomes (clade 1 and clade 3), low copy number variations, and a moderate number of single-nucleotide polymorphisms (SNPs) in all genomes analyzed. Interestingly, the genomes belonging to clades 2 and 3 from Colombia and Brazil, respectively, were characterized by low heterozygosity (~90% of SNP loci were homozygous) and regions suggestive of loss of heterozygosity (LOH). Additionally, we observed the drastic whole genome loss of heterozygosity and possible hybridization events in one genome belonging to clade 4. Unique/shared SNPs between and within the four clades were identified, revealing the importance of some of them in biological processes of L. braziliensis. Our analyses demonstrate high genomic variability of L. braziliensis in different regions of South America, mainly in Colombia and suggest that this species exhibits striking genomic diversity and a capacity of genomic hybridization; additionally, this is the first study to report whole-genome sequences of Colombian L. braziliensis isolates.
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Affiliation(s)
- Luz H Patino
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Lissa Cruz-Saavedra
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Carlos Muskus
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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Intraspecific Genomic Divergence and Minor Structural Variations in Leishmania (Viannia) panamensis. Genes (Basel) 2020; 11:genes11030252. [PMID: 32120946 PMCID: PMC7140786 DOI: 10.3390/genes11030252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/07/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
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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Mladineo I, Trumbić Ž, Radonić I, Vrbatović A, Hrabar J, Bušelić I. Anisakis simplex complex: ecological significance of recombinant genotypes in an allopatric area of the Adriatic Sea inferred by genome-derived simple sequence repeats. Int J Parasitol 2017; 47:215-223. [DOI: 10.1016/j.ijpara.2016.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/18/2016] [Accepted: 11/20/2016] [Indexed: 11/24/2022]
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