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Silva H, Ferreira TR, Muneeswaran K, Samarasinghe SR, Alves-Ferreira EVC, Grigg ME, Chandrasekharan NV, Sacks DL, Karunaweera ND. Autochthonous Leishmaniasis Caused by Leishmania tropica, Identified by Using Whole-Genome Sequencing, Sri Lanka. Emerg Infect Dis 2024; 30:1872-1883. [PMID: 39174018 PMCID: PMC11347009 DOI: 10.3201/eid3009.231238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024] Open
Abstract
Cutaneous leishmaniasis is atypical in Sri Lanka because Leishmania donovani, which typically causes visceral disease, is the causative agent. The origins of recently described hybrids between L. donovani and other Leishmania spp. usually responsible for cutaneous leishmaniasis remain unknown. Other endemic dermotropic Leishmania spp. have not been reported in Sri Lanka. Genome analysis of 27 clinical isolates from Sri Lanka and 32 Old World Leishmania spp. strains found 8 patient isolates clustered with L. tropica and 19 with L. donovani. The L. tropica isolates from Sri Lanka shared markers with strain LtK26 reported decades ago in India, indicating they were not products of recent interspecies hybridization. Because L. tropica was isolated from patients with leishmaniasis in Sri Lanka, our findings indicate L. donovani is not the only cause of cutaneous leishmaniasis in Sri Lanka and potentially explains a haplotype that led to interspecies dermotropic L. donovani hybrids.
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de Paula Baptista R, Tucker MS, Valente MJ, Srivastava SK, Chehab N, Li A, Shaik JS, Ramirez JD, Rosenthal BM, Khan A. Comparative genomics of Giardia duodenalis sub-assemblage AI beaver (Be-2) and human (WB-C6) strains show remarkable homozygosity, sequence similarity, and conservation of VSP genes. Sci Rep 2024; 14:13582. [PMID: 38866814 PMCID: PMC11169602 DOI: 10.1038/s41598-024-63783-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
Giardia duodenalis, a major cause of waterborne infection, infects a wide range of mammalian hosts and is subdivided into eight genetically well-defined assemblages named A through H. However, fragmented genomes and a lack of comparative analysis within and between the assemblages render unclear the molecular mechanisms controlling host specificity and differential disease outcomes. To address this, we generated a near-complete de novo genome of AI assemblage using the Oxford Nanopore platform by sequencing the Be-2 genome. We generated 148,144 long-reads with quality scores of > 7. The final genome assembly consists of only nine contigs with an N50 of 3,045,186 bp. This assembly agrees closely with the assembly of another strain in the AI assemblage (WB-C6). However, a critical difference is that a region previously placed in the five-prime region of Chr5 belongs to Chr4 of Be-2. We find a high degree of conservation in the ploidy, homozygosity, and the presence of cysteine-rich variant-specific surface proteins (VSPs) within the AI assemblage. Our assembly provides a nearly complete genome of a member of the AI assemblage of G. duodenalis, aiding population genomic studies capable of elucidating Giardia transmission, host range, and pathogenicity.
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Affiliation(s)
- Rodrigo de Paula Baptista
- Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Medicine, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Matthew S Tucker
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Matthew J Valente
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Subodh K Srivastava
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Nadya Chehab
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Alison Li
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Jahangheer S Shaik
- Insights and Analytics, Applied Data Science and Learning, Data Science Institute, Takeda, Cambridge, MA, 02142, USA
| | - Juan David Ramirez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Benjamin M Rosenthal
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Asis Khan
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA.
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Khan A, Alves-Ferreira EVC, Vogel H, Botchie S, Ayi I, Pawlowic MC, Robinson G, Chalmers RM, Lorenzi H, Grigg ME. Phylogenomic reconstruction of Cryptosporidium spp. captured directly from clinical samples reveals extensive genetic diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589752. [PMID: 38659886 PMCID: PMC11042339 DOI: 10.1101/2024.04.17.589752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Cryptosporidium is a leading cause of severe diarrhea and mortality in young children and infants in Africa and southern Asia. More than twenty Cryptosporidium species infect humans, of which C. parvum and C. hominis are the major agents causing moderate to severe diarrhea. Relatively few genetic markers are typically applied to genotype and/or diagnose Cryptosporidium. Most infections produce limited oocysts making it difficult to perform whole genome sequencing (WGS) directly from stool samples. Hence, there is an immediate need to apply WGS strategies to 1) develop high-resolution genetic markers to genotype these parasites more precisely, 2) to investigate endemic regions and detect the prevalence of different genotypes, and the role of mixed infections in generating genetic diversity, and 3) to investigate zoonotic transmission and evolution. To understand Cryptosporidium global population genetic structure, we applied Capture Enrichment Sequencing (CES-Seq) using 74,973 RNA-based 120 nucleotide baits that cover ~92% of the genome of C. parvum. CES-Seq is sensitive and successfully sequenced Cryptosporidium genomic DNA diluted up to 0.005% in human stool DNA. It also resolved mixed strain infections and captured new species of Cryptosporidium directly from clinical/field samples to promote genome-wide phylogenomic analyses and prospective GWAS studies.
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Affiliation(s)
- A Khan
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - E V C Alves-Ferreira
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - H Vogel
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Comparative Biomedical Scientist Training Program, National Institutes of Health, Bethesda, MD, 20892, USA
| | - S Botchie
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - I Ayi
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - M C Pawlowic
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - G Robinson
- Cryptosporidium Reference Unit, Public Health Wales, Microbiology and Health Protection, Singleton Hospital, Swansea, SA2 8QA, UK
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK
| | - R M Chalmers
- Cryptosporidium Reference Unit, Public Health Wales, Microbiology and Health Protection, Singleton Hospital, Swansea, SA2 8QA, UK
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK
| | - H Lorenzi
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - M E Grigg
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Mezhzherin SV, Morozov-Leonov SY, Rostovska OV. Nuclear gene introgressions in hybrid populations of water frog Pelophylax esculentus complex: geographical analysis of the phenomenon and its interpretation. Genetica 2024; 152:31-42. [PMID: 38361120 DOI: 10.1007/s10709-024-00203-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/31/2024] [Indexed: 02/17/2024]
Abstract
Reproduction of water frog hybrids Pelophylax esculentus (Pelophylax ridibundus x Pelophylax lessonae) is associated with hemiclonal reproduction and backcrossing. The hemiclonal mode of reproduction occurs within P. esculentus allodiploids. In this case, the unrecombined genome of one parental species is transmitted to the offspring after premeiotic elimination of the chromosome set of the second parental species. Usually, the chromosome set of P. lessonae is eliminated, and the altered genome of P. ridibundus is passed on to the progeny. The hemiclonal inheritance within diploid Pelophylax esculentus hybrids may be accompanied by certain aberrations of premeiotic elimination. As a result, the formation of P. ridibundus specimens with introgressions of the P. lessonae genetic material, or the formation of recombinant hybrids occurs, depending on which of the parental species backcrossing takes place. The aim of our study is to describe the aberration of premeiotic elimination within the water frog P. esculentus complex detected by the nuclear gene Ldh-B inheritance, with an attempt to find out the causes of this phenomenon. It has been established that aberrations of premeiotic elimination are widespread, but only within populations of water frog from the river system of Upper Dnieper within Ukraine. The highest level of introgression takes place in the water frog populations within Kiev metropolis under conditions of expressed anthropogenization, while the maximum frequency of recombinants was detected within populations from the basin of Desna River, that has preserved native ecosystems. It was demonstrated that the frequency of premeiotic aberrations does not correlate with the intensity of interspecific water frog hybridization. Populations with introgressions are more common than populations with recombinants, however, within the latter, the frequency of recombination events is higher. The primary factor of gametogenesis aberrations, most likely, is the genetic characteristics of the local populations of parental species, since unambiguous explanations of this phenomenon based on the action of environmental stress (pollution of water systems) are not obvious.
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Affiliation(s)
- Sergey V Mezhzherin
- Department of Evolutionary Genetic and Fundamentals of Systematics, I.I. Schmalhausen Institute of Zoology, B. Khmel'nitskogo Str., Kiev-30, 01601, Ukraine
| | - Svyatoslav Yu Morozov-Leonov
- Department of Evolutionary Genetic and Fundamentals of Systematics, I.I. Schmalhausen Institute of Zoology, B. Khmel'nitskogo Str., Kiev-30, 01601, Ukraine.
| | - Olga V Rostovska
- Department of Evolutionary Genetic and Fundamentals of Systematics, I.I. Schmalhausen Institute of Zoology, B. Khmel'nitskogo Str., Kiev-30, 01601, Ukraine
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5
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Sádlová J, Yeo M, Mateus DS, Phelan J, Hai LA, Bhattacharyya T, Kurtev S, Sebesta O, Myskova J, Seblova V, Andersson B, Florez de Sessions P, Volf P, Miles MA. Comparative genomics of Leishmania donovani progeny from genetic crosses in two sand fly species and impact on the diversity of diagnostic and vaccine candidates. PLoS Negl Trop Dis 2024; 18:e0011920. [PMID: 38295092 PMCID: PMC10830044 DOI: 10.1371/journal.pntd.0011920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
Sand fly transmitted Leishmania species are responsible for severe, wide ranging, visceral and cutaneous leishmaniases. Genetic exchange can occur among natural Leishmania populations and hybrids can now be produced experimentally, with limitations. Feeding Phlebotomus orientalis or Phlebotomus argentipes on two strains of Leishmania donovani yielded hybrid progeny, selected using double drug resistance and fluorescence markers. Fluorescence activated cell sorting of cultured clones derived from these hybrids indicated diploid progeny. Multilocus sequence typing of the clones showed hybridisation and nuclear heterozygosity, although with inheritance of single haplotypes in a kinetoplastid target. Comparative genomics showed diversity of clonal progeny between single chromosomes, and extraordinary heterozygosity across all 36 chromosomes. Diversity between progeny was seen for the HASPB antigen, which has been noted previously as having implications for design of a therapeutic vaccine. Genomic diversity seen among Leishmania strains and hybrid progeny is of great importance in understanding the epidemiology and control of leishmaniasis. As an outcome of this study we strongly recommend that wider biological archives of different Leishmania species from endemic regions should be established and made available for comparative genomics. However, in parallel, performance of genetic crosses and genomic comparisons should give fundamental insight into the specificity, diversity and limitations of candidate diagnostics, vaccines and drugs, for targeted control of leishmaniasis.
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Affiliation(s)
- Jovana Sádlová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - David S. Mateus
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Le Anh Hai
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Tapan Bhattacharyya
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Stefan Kurtev
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Ondrej Sebesta
- Laboratory of Confocal and Fluorescence Microscopy, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jitka Myskova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Veronika Seblova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Paola Florez de Sessions
- Genome Institute of Singapore, Biomedical Sciences Institutes, Agency for Science, Technology and Research, Singapore
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michael A. Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
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6
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Srivastava SK, Parker C, O'Brien CN, Tucker MS, Thompson PC, Rosenthal BM, Dubey JP, Khan A, Jenkins MC. Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella. Sci Rep 2023; 13:22802. [PMID: 38129566 PMCID: PMC10739835 DOI: 10.1038/s41598-023-50117-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Eimeria tenella is a major cause of caecal coccidiosis in commercial poultry chickens worldwide. Here, we report chromosomal scale assembly of Eimeria tenella strain APU2, a strain isolated from commercial broiler chickens in the U.S. We obtained 100× sequencing Oxford Nanopore Technology (ONT) and more than 800× Coverage of Illumina Next-Seq. We created the assembly using the hybrid approach implemented in MaSuRCA, achieving a contiguous 51.34 Mb chromosomal-scale scaffolding enabling identification of structural variations. The AUGUSTUS pipeline predicted 8060 genes, and BUSCO deemed the genomes 99% complete; 6278 (78%) genes were annotated with Pfam domains, and 1395 genes were assigned GO-terms. Comparing E. tenella strains (APU2, US isolate and Houghton, UK isolate) derived Houghton strain of E. tenella revealed 62,905 high stringency differences, of which 45,322 are single nucleotide polymorphisms (SNPs) (0.088%). The rate of transitions/transversions among the SNPs are 1.63 ts/tv. The strains possess conserved gene order but have profound sequence heterogeneity in a several chromosomal segments (chr 2, 11 and 15). Genic and intergenic variation in defined gene families was evaluated between the two strains to possibly identify sequences under selection. The average genic nucleotide diversity of 2.8 with average 2 kb gene length (0.145%) at genic level. We examined population structure using available E. tenella sequences in NCBI, revealing that the two E. tenella isolates from the U.S. (E. tenella APU2 and Wisconsin, "ERR296879") share a common maternal inheritance with the E. tenella Houghton. Our chromosomal level assembly promotes insight into Eimeria biology and evolution, hastening drug discovery and vaccine development.
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Affiliation(s)
- Subodh K Srivastava
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA.
| | - Carolyn Parker
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Celia N O'Brien
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Matthew S Tucker
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Peter C Thompson
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Benjamin M Rosenthal
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Jitender P Dubey
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Asis Khan
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Mark C Jenkins
- USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA.
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Catta-Preta CMC, Ferreira TR, Ghosh K, Paun A, Sacks D. HOP1 and HAP2 are conserved components of the meiosis-related machinery required for successful mating in Leishmania. Nat Commun 2023; 14:7159. [PMID: 37935664 PMCID: PMC10630298 DOI: 10.1038/s41467-023-42789-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/21/2023] [Indexed: 11/09/2023] Open
Abstract
Whole genome analysis of Leishmania hybrids generated experimentally in sand flies supports a meiotic mechanism of genetic exchange, with Mendelian segregation of the nuclear genome. Here, we perform functional analyses through the generation of double drug-resistant hybrids in vitro and in vivo (during sand fly infections) to assess the importance of conserved meiosis-related genes in recombination and plasmogamy. We report that HOP1 and a HAP2-paralog (HAP2-2) are essential components of the Leishmania meiosis machinery and cell-to-cell fusion mechanism, respectively, since deletion of either gene in one or both parents significantly reduces or completely abrogates mating competence. These findings significantly advance our understanding of sexual reproduction in Leishmania, with likely relevance to other trypanosomatids, by formally demonstrating the involvement of a meiotic protein homolog and a distinct fusogen that mediates non-canonical, bilateral fusion in the hybridizing cells.
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Affiliation(s)
- Carolina Moura Costa Catta-Preta
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tiago Rodrigues Ferreira
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kashinath Ghosh
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrea Paun
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Sacks
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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8
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Serafim TD, Iniguez E, Barletta ABF, Cecilio P, Doehl JSP, Short M, Lack J, Nair V, Disotuar M, Wilson T, Coutinho-Abreu IV, Meneses C, Andersen J, Alves E Silva TL, Oliveira F, Vega-Rodriguez J, Barillas-Mury C, Ribeiro JMC, Beverley SM, Kamhawi S, Valenzuela JG. Leishmania genetic exchange is mediated by IgM natural antibodies. Nature 2023; 623:149-156. [PMID: 37880367 DOI: 10.1038/s41586-023-06655-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/19/2023] [Indexed: 10/27/2023]
Abstract
Host factors that mediate Leishmania genetic exchange are not well defined. Here we demonstrate that natural IgM (IgMn)1-4 antibodies mediate parasite genetic exchange by inducing the transient formation of a spherical parasite clump that promotes parasite fusion and hybrid formation. We establish that IgMn from Leishmania-free animals binds to the surface of Leishmania parasites to induce significant changes in the expression of parasite transcripts and proteins. Leishmania binding to IgMn is partially lost after glycosidase treatment, although parasite surface phosphoglycans, including lipophosphoglycan, are not required for IgMn-induced parasite clumping. Notably, the transient formation of parasite clumps is essential for Leishmania hybridization in vitro. In vivo, we observed a 12-fold increase in hybrid formation in sand flies provided a second blood meal containing IgMn compared with controls. Furthermore, the generation of recombinant progeny from mating hybrids and parental lines were only observed in sand flies provided with IgMn. Both in vitro and in vivo IgM-induced Leishmania crosses resulted in full genome hybrids that show equal patterns of biparental contribution. Leishmania co-option of a host natural antibody to facilitate mating in the insect vector establishes a new paradigm of parasite-host-vector interdependence that contributes to parasite diversity and fitness by promoting genetic exchange.
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Affiliation(s)
- Tiago D Serafim
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
| | - Eva Iniguez
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Ana Beatriz F Barletta
- Mosquito Immunity and Vector Competence Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Pedro Cecilio
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Johannes S P Doehl
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Mara Short
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vinod Nair
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Maria Disotuar
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Timothy Wilson
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Iliano V Coutinho-Abreu
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Claudio Meneses
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - John Andersen
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Thiago Luiz Alves E Silva
- Molecular Parasitology and Entomology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Fabiano Oliveira
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Joel Vega-Rodriguez
- Molecular Parasitology and Entomology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Carolina Barillas-Mury
- Mosquito Immunity and Vector Competence Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - José M C Ribeiro
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Stephen M Beverley
- Department of Molecular Microbiology, School of Medicine, Washington University, St Louis, MO, USA.
| | - Shaden Kamhawi
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
| | - Jesus G Valenzuela
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
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9
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Al-Ghafli H, Barribeau SM. Double trouble: trypanosomatids with two hosts have lower infection prevalence than single host trypanosomatids. Evol Med Public Health 2023; 11:202-218. [PMID: 37404250 PMCID: PMC10317189 DOI: 10.1093/emph/eoad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 04/21/2023] [Indexed: 07/06/2023] Open
Abstract
Trypanosomatids are a diverse family of protozoan parasites, some of which cause devastating human and livestock diseases. There are two distinct infection life cycles in trypanosomatids; some species complete their entire life cycle in a single host (monoxenous) while others infect two hosts (dixenous). Dixenous trypanosomatids are mostly vectored by insects, and the human trypanosomatid diseases are caused mainly by vectored parasites. While infection prevalence has been described for subsets of hosts and trypanosomatids, little is known about whether monoxenous and dixenous trypanosomatids differ in infection prevalence. Here, we use meta-analyses to synthesise all published evidence of trypanosomatid infection prevalence for the last two decades, encompassing 931 unique host-trypansomatid systems. In examining 584 studies that describe infection prevalence, we find, strikingly, that monoxenous species are two-fold more prevalent than dixenous species across all hosts. We also find that dixenous trypanosomatids have significantly lower infection prevalence in insects than their non-insect hosts. To our knowledge, these results reveal for the first time, a fundamental difference in infection prevalence according to host specificity where vectored species might have lower infection prevalence as a result of a potential 'jack of all trades, master of none' style trade-off between the vector and subsequent hosts.
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Affiliation(s)
- Hawra Al-Ghafli
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Seth M Barribeau
- Corresponding author. Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool, UK. E-mail:
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10
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Leishmania allelic selection during experimental sand fly infection correlates with mutational signatures of oxidative DNA damage. Proc Natl Acad Sci U S A 2023; 120:e2220828120. [PMID: 36848551 PMCID: PMC10013807 DOI: 10.1073/pnas.2220828120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Trypanosomatid pathogens are transmitted by blood-feeding insects, causing devastating human infections. These parasites show important phenotypic shifts that often impact parasite pathogenicity, tissue tropism, or drug susceptibility. The evolutionary mechanisms that allow for the selection of such adaptive phenotypes remain only poorly investigated. Here, we use Leishmania donovani as a trypanosomatid model pathogen to assess parasite evolutionary adaptation during experimental sand fly infection. Comparing the genome of the parasites before and after sand fly infection revealed a strong population bottleneck effect as judged by allele frequency analysis. Apart from random genetic drift caused by the bottleneck effect, our analyses revealed haplotype and allelic changes during sand fly infection that seem under natural selection given their convergence between independent biological replicates. Our analyses further uncovered signature mutations of oxidative DNA damage in the parasite genomes after sand fly infection, suggesting that Leishmania suffers from oxidative stress inside the insect digestive tract. Our results propose a model of Leishmania genomic adaptation during sand fly infection, with oxidative DNA damage and DNA repair processes likely driving haplotype and allelic selection. The experimental and computational framework presented here provides a useful blueprint to assess evolutionary adaptation of other eukaryotic pathogens inside their insect vectors, such as Plasmodium spp, Trypanosoma brucei, and Trypanosoma cruzi.
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11
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Black JA, Reis-Cunha JL, Cruz AK, Tosi LR. Life in plastic, it's fantastic! How Leishmania exploit genome instability to shape gene expression. Front Cell Infect Microbiol 2023; 13:1102462. [PMID: 36779182 PMCID: PMC9910336 DOI: 10.3389/fcimb.2023.1102462] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023] Open
Abstract
Leishmania are kinetoplastid pathogens that cause leishmaniasis, a debilitating and potentially life-threatening infection if untreated. Unusually, Leishmania regulate their gene expression largely post-transcriptionally due to the arrangement of their coding genes into polycistronic transcription units that may contain 100s of functionally unrelated genes. Yet, Leishmania are capable of rapid and responsive changes in gene expression to challenging environments, often instead correlating with dynamic changes in their genome composition, ranging from chromosome and gene copy number variations to the generation of extrachromosomal DNA and the accumulation of point mutations. Typically, such events indicate genome instability in other eukaryotes, coinciding with genetic abnormalities, but for Leishmania, exploiting these products of genome instability can provide selectable substrates to catalyse necessary gene expression changes by modifying gene copy number. Unorthodox DNA replication, DNA repair, replication stress factors and DNA repeats are recognised in Leishmania as contributors to this intrinsic instability, but how Leishmania regulate genome plasticity to enhance fitness whilst limiting toxic under- or over-expression of co-amplified and co-transcribed genes is unclear. Herein, we focus on fresh, and detailed insights that improve our understanding of genome plasticity in Leishmania. Furthermore, we discuss emerging models and factors that potentially circumvent regulatory issues arising from polycistronic transcription. Lastly, we highlight key gaps in our understanding of Leishmania genome plasticity and discuss future studies to define, in higher resolution, these complex regulatory interactions.
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Affiliation(s)
- Jennifer A. Black
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil,The Wellcome Centre for Integrative Parasitology, School of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom,*Correspondence: Luiz. R.O. Tosi, ; Jennifer A. Black,
| | | | - Angela. K. Cruz
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz. R.O. Tosi
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil,*Correspondence: Luiz. R.O. Tosi, ; Jennifer A. Black,
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12
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Cofre J, Saalfeld K. The first embryo, the origin of cancer and animal phylogeny. I. A presentation of the neoplastic process and its connection with cell fusion and germline formation. Front Cell Dev Biol 2023; 10:1067248. [PMID: 36684435 PMCID: PMC9846517 DOI: 10.3389/fcell.2022.1067248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/16/2022] [Indexed: 01/05/2023] Open
Abstract
The decisive role of Embryology in understanding the evolution of animal forms is founded and deeply rooted in the history of science. It is recognized that the emergence of multicellularity would not have been possible without the formation of the first embryo. We speculate that biophysical phenomena and the surrounding environment of the Ediacaran ocean were instrumental in co-opting a neoplastic functional module (NFM) within the nucleus of the first zygote. Thus, the neoplastic process, understood here as a biological phenomenon with profound embryologic implications, served as the evolutionary engine that favored the formation of the first embryo and cancerous diseases and allowed to coherently create and recreate body shapes in different animal groups during evolution. In this article, we provide a deep reflection on the Physics of the first embryogenesis and its contribution to the exaptation of additional NFM components, such as the extracellular matrix. Knowledge of NFM components, structure, dynamics, and origin advances our understanding of the numerous possibilities and different innovations that embryos have undergone to create animal forms via Neoplasia during evolutionary radiation. The developmental pathways of Neoplasia have their origins in ctenophores and were consolidated in mammals and other apical groups.
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Affiliation(s)
- Jaime Cofre
- Laboratório de Embriologia Molecular e Câncer, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil,*Correspondence: Jaime Cofre,
| | - Kay Saalfeld
- Laboratório de Filogenia Animal, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
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13
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Hadermann A, Heeren S, Maes I, Dujardin JC, Domagalska MA, Van den Broeck F. Genome diversity of Leishmania aethiopica. Front Cell Infect Microbiol 2023; 13:1147998. [PMID: 37153154 PMCID: PMC10157169 DOI: 10.3389/fcimb.2023.1147998] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Leishmania aethiopica is a zoonotic Old World parasite transmitted by Phlebotomine sand flies and causing cutaneous leishmaniasis in Ethiopia and Kenya. Despite a range of clinical manifestations and a high prevalence of treatment failure, L. aethiopica is one of the most neglected species of the Leishmania genus in terms of scientific attention. Here, we explored the genome diversity of L. aethiopica by analyzing the genomes of twenty isolates from Ethiopia. Phylogenomic analyses identified two strains as interspecific hybrids involving L. aethiopica as one parent and L. donovani and L. tropica respectively as the other parent. High levels of genome-wide heterozygosity suggest that these two hybrids are equivalent to F1 progeny that propagated mitotically since the initial hybridization event. Analyses of allelic read depths further revealed that the L. aethiopica - L. tropica hybrid was diploid and the L. aethiopica - L. donovani hybrid was triploid, as has been described for other interspecific Leishmania hybrids. When focusing on L. aethiopica, we show that this species is genetically highly diverse and consists of both asexually evolving strains and groups of recombining parasites. A remarkable observation is that some L. aethiopica strains showed an extensive loss of heterozygosity across large regions of the nuclear genome, which likely arose from gene conversion/mitotic recombination. Hence, our prospection of L. aethiopica genomics revealed new insights into the genomic consequences of both meiotic and mitotic recombination in Leishmania.
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Affiliation(s)
- Amber Hadermann
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Senne Heeren
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Malgorzata Anna Domagalska
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- *Correspondence: Frederik Van den Broeck, ; Malgorzata Anna Domagalska,
| | - Frederik Van den Broeck
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- *Correspondence: Frederik Van den Broeck, ; Malgorzata Anna Domagalska,
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Abstract
Genetic exchange between different Leishmania strains in the sand fly vector has been experimentally demonstrated and is supported by population genetic studies. In nature, opportunities for Leishmania interstrain mating are restricted to flies biting multiply infected hosts or through multiple bites of different hosts. In contrast, self-mating could occur in any infected sand fly. By crossing two recombinant lines derived from the same Leishmania major strain, each expressing a different drug-resistance marker, self-hybridization in L. major was confirmed in a natural sand fly vector, Phlebotomus duboscqi, and in frequencies comparable to interstrain crosses. We provide the first high resolution, whole-genome sequencing analysis of large numbers of selfing progeny, their parents, and parental subclones. Genetic exchange consistent with classical meiosis is supported by the biallelic inheritance of the rare homozygous single nucleotide polymorphisms (SNPs) that arose by mutation during the generation of the parental clones. In contrast, heterozygous SNPs largely failed to be transmitted in Mendelian ratios for reasons not understood. SNPs that were heterozygous in both parents, however, recombined to produce homozygous alleles in some hybrids. For trisomic chromosomes present in both parents, transmittal to the progeny was only altered by self-hybridization, involving a gain or loss of somy in frequencies predicted by a meiotic process. Whole-genome polyploidization was also observed in the selfing progeny. Thus, self-hybridization in Leishmania, with its potential to occur in any infected sand fly, may be an important source of karyotype variation, loss of heterozygosity, and functional diversity. IMPORTANCE Leishmania are parasitic protozoa that cause a wide spectrum of diseases collectively known as the leishmaniases. Sexual reproduction in Leishmania has been proposed as an important source of genetic diversity and has been formally demonstrated to occur inside the sand fly vector midgut. Nevertheless, in the wild, opportunities for genetic exchange between different Leishmania species or strains are restricted by the capacity of different Leishmania strains to colonize the same sand fly. In this work, we report the first high resolution, whole-genome sequence analysis of intraclonal genetic exchange as a type of self-mating in Leishmania. Our data reveal that self-hybridization can occur with comparable frequency as interstrain mating under experimental lab conditions, leading to important genomic alterations that can potentially take place within every naturally infected sand fly.
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15
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da Silva VS, Machado CR. Sex in protists: A new perspective on the reproduction mechanisms of trypanosomatids. Genet Mol Biol 2022; 45:e20220065. [PMID: 36218381 PMCID: PMC9552303 DOI: 10.1590/1678-4685-gmb-2022-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/07/2022] [Indexed: 11/04/2022] Open
Abstract
The Protist kingdom individuals are the most ancestral representatives of eukaryotes. They have inhabited Earth since ancient times and are currently found in the most diverse environments presenting a great heterogeneity of life forms. The unicellular and multicellular algae, photosynthetic and heterotrophic organisms, as well as free-living and pathogenic protozoa represents the protist group. The evolution of sex is directly associated with the origin of eukaryotes being protists the earliest protagonists of sexual reproduction on earth. In eukaryotes, the recombination through genetic exchange is a ubiquitous mechanism that can be stimulated by DNA damage. Scientific evidences support the hypothesis that reactive oxygen species (ROS) induced DNA damage can promote sexual recombination in eukaryotes which might have been a decisive factor for the origin of sex. The fact that some recombination enzymes also participate in meiotic sex in modern eukaryotes reinforces the idea that sexual reproduction emerged as consequence of specific mechanisms to cope with mutations and alterations in genetic material. In this review we will discuss about origin of sex and different strategies of evolve sexual reproduction in some protists such that cause human diseases like malaria, toxoplasmosis, sleeping sickness, Chagas disease, and leishmaniasis.
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Affiliation(s)
- Verônica Santana da Silva
- Universidade Federal de Minas Gerais, Departamento de Genética,
Ecologia e Evolução, Belo Horizonte, MG, Brazil
| | - Carlos Renato Machado
- Universidade Federal de Minas Gerais, Departamento de Bioquímica e
Imunologia, Belo Horizonte, MG, Brazil
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16
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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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17
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Silva JA, Pinheiro AI, Dourado ML, Medina L, Queiroz A, Guimarães LH, Lessa MM, Lago EL, Machado PRL, Wilson ME, Carvalho EM, Schriefer A. Leishmania braziliensis causing human disease in Northeast Brazil presents loci with genotypes in long-term equilibrium. PLoS Negl Trop Dis 2022; 16:e0010390. [PMID: 35704664 PMCID: PMC9239440 DOI: 10.1371/journal.pntd.0010390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/28/2022] [Accepted: 04/03/2022] [Indexed: 11/23/2022] Open
Abstract
Background Leishmaniases are neglected tropical diseases that inflict great burden to poor areas of the globe. Intense research has aimed to identify parasite genetic signatures predictive of infection outcomes. Consistency of diagnostic tools based on these markers would greatly benefit from accurate understanding of Leishmania spp. population genetics. We explored two chromosomal loci to characterize a population of L. braziliensis causing human disease in Northeast Brazil. Methodology/Principal findings Two temporally distinct samples of L. braziliensis were obtained from patients attending the leishmaniasis clinic at the village of Corte de Pedra: (2008–2011) primary sample, N = 120; (1999–2001) validation sample, N = 35. Parasites were genotyped by Sanger’s sequencing of two 600 base pairs loci starting at nucleotide positions 3,074 and 425,451 of chromosomes 24 and 28, respectively. Genotypes based on haplotypes of biallelic positions in each locus were tested for several population genetic parameters as well as for geographic clustering within the region. Ample geographic overlap of genotypes at the two loci was observed as indicated by non-significant Cusick and Edward’s comparisons. No linkage disequilibrium was detected among combinations of haplotypes for both parasite samples. Homozygous and heterozygous genotypes displayed Hardy-Weinberg equilibrium (HWE) at both loci in the two samples when straight observed and expected counts were compared by Chi-square (p>0.5). However, Bayesian statistics using one million Monte-Carlo randomizations disclosed a less robust HWE for chromosome 24 genotypes, particularly in the primary sample (p = 0.04). Fixation indices (Fst) were consistently lower than 0.05 among individuals of the two samples at both tested loci, and no intra-populational structuralization could be detected using STRUCTURE software. Conclusions/Significance These findings suggest that L. braziliensis can maintain stable populations in foci of human leishmaniasis and are capable of robust genetic recombination possibly due to events of sexual reproduction during the parasite’s lifecycle. Leishmania braziliensis affects poor human populations in the tropics, may cause face disfiguring lesions and may also resist treatment. There has been intense research for markers in these parasites genetic contents for helping predict if an infected human being would be of greater chance of severe disease or treatment failure. The consistent identification of such markers requires a deep understanding of how genes circulate within these parasites’ natural populations. We explored two small segments of DNA (i.e. loci), one on chromosome 24, the other on chromosome 28 of L. braziliensis to characterize a population that causes human disease in Northeast Brazil. We employed two samples of parasites obtained from lesions of patients diagnosed from 1999 to 2001, and from 2008 to 2011. We sequenced the DNA of those loci in each parasite of the two samples. Then, we evaluated the status of several population genetics parameters among them. Based on our findings to that region, we concluded that L. braziliensis can maintain populations that are genetically stable for several years in foci of human leishmaniasis and are capable of robust recombination of their genetic contents, probably due to events of sexual reproduction during its lifecycle.
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Affiliation(s)
- Juliana A. Silva
- Serviço de Imunologia, Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia (UFBA), Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, UFBA, Salvador, Brazil
| | - Ana Isabelle Pinheiro
- Serviço de Imunologia, Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia (UFBA), Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, UFBA, Salvador, Brazil
| | - Maria Luiza Dourado
- Serviço de Imunologia, Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia (UFBA), Salvador, Brazil
| | - Lilian Medina
- Serviço de Imunologia, Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia (UFBA), Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, UFBA, Salvador, Brazil
| | - Adriano Queiroz
- Instituto Gonçalo Moniz, Fundação Instituto Oswaldo Cruz, Salvador, Brazil
| | - Luiz Henrique Guimarães
- Serviço de Imunologia, Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia (UFBA), Salvador, Brazil
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais (INCT-DT), Salvador, Brazil
- Universidade Federal do Sul da Bahia, Teixeira de Freitas, Brazil
| | - Marcus Miranda Lessa
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, UFBA, Salvador, Brazil
| | - Ednaldo L. Lago
- Serviço de Imunologia, Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia (UFBA), Salvador, Brazil
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais (INCT-DT), Salvador, Brazil
| | - Paulo Roberto L. Machado
- Serviço de Imunologia, Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia (UFBA), Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, UFBA, Salvador, Brazil
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais (INCT-DT), Salvador, Brazil
| | - Mary E. Wilson
- Departments of Internal Medicine and Microbiology, University of Iowa and the VA Medical Center, Iowa City, Iowa, United States of America
| | - Edgar M. Carvalho
- Serviço de Imunologia, Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia (UFBA), Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, UFBA, Salvador, Brazil
- Instituto Gonçalo Moniz, Fundação Instituto Oswaldo Cruz, Salvador, Brazil
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais (INCT-DT), Salvador, Brazil
| | - Albert Schriefer
- Serviço de Imunologia, Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia (UFBA), Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, UFBA, Salvador, Brazil
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais (INCT-DT), Salvador, Brazil
- Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, UFBA, Salvador, Brazil
- * E-mail:
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Cruz-Saavedra L, Schwabl P, Vallejo GA, Carranza JC, Muñoz M, Patino LH, Paniz-Mondolfi A, Llewellyn MS, Ramírez JD. Genome plasticity driven by aneuploidy and loss of heterozygosity in Trypanosoma cruzi. Microb Genom 2022; 8. [PMID: 35748878 PMCID: PMC9455712 DOI: 10.1099/mgen.0.000843] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trypanosoma cruzi the causative agent of Chagas disease shows a marked genetic diversity and divided into at least six Discrete Typing Units (DTUs). High intra genetic variability has been observed in the TcI DTU, the most widely distributed DTU, where patterns of genomic diversity can provide information on ecological and evolutionary processes driving parasite population structure and genome organization. Chromosomal aneuploidies and rearrangements across multigene families represent an evidence of T. cruzi genome plasticity. We explored genomic diversity among 18 Colombian T. cruzi I clones and 15 T. cruzi I South American strains. Our results confirm high genomic variability, heterozygosity and presence of a clade compatible with the TcIdom genotype, described for strains from humans in Colombia and Venezuela. TcI showed high structural plasticity across the geographical region studied. Differential events of whole and segmental aneuploidy (SA) along chromosomes even between clones from the same strain were found and corroborated by the depth and allelic frequency. We detected loss of heterozygosity (LOH) events in different chromosomes, however, the size and location of segments under LOH varied between clones. Genes adjacent to breakpoints were evaluated, and retrotransposon hot spot genes flanked the beginning of segmental aneuploidies. Our results suggest that T. cruzi genomes, like those of Leishmania, may have a highly unstable structure and there is now an urgent need to design experiments to explore any potential adaptive role for the plasticity observed.
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Affiliation(s)
- Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Philipp Schwabl
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Gustavo A Vallejo
- Laboratorio de Investigación en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Julio C Carranza
- Laboratorio de Investigación en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz Helena Patino
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Alberto Paniz-Mondolfi
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin S Llewellyn
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.,Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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19
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Franssen SU, Sanders MJ, Berriman M, Petersen CA, Cotton JA. Geographic Origin and Vertical Transmission of Leishmania infantum Parasites in Hunting Hounds, United States. Emerg Infect Dis 2022; 28:1211-1223. [PMID: 35608628 PMCID: PMC9155895 DOI: 10.3201/eid2806.211746] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Vertical transmission of leishmaniasis is common but is difficult to study against the background of pervasive vector transmission. We present genomic data from dogs in the United States infected with Leishmania infantum parasites; these infections have persisted in the apparent absence of vector transmission. We demonstrate that these parasites were introduced from the Old World separately and more recently than L. infantum from South America. The parasite population shows unusual genetics consistent with a lack of meiosis: a high level of heterozygous sites shared across all isolates and no decrease in linkage with genomic distance between variants. Our data confirm that this parasite population has been evolving with little or no sexual reproduction. This demonstration of vertical transmission has profound implications for the population genetics of Leishmania parasites. When investigating transmission in complex natural settings, considering vertical transmission alongside vector transmission is vital.
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Ferreira TR, Sacks DL. Experimental Hybridization in Leishmania: Tools for the Study of Genetic Exchange. Pathogens 2022; 11:pathogens11050580. [PMID: 35631101 PMCID: PMC9144296 DOI: 10.3390/pathogens11050580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 02/06/2023] Open
Abstract
Despite major advances over the last decade in our understanding of Leishmania reproductive strategies, the sexual cycle in Leishmania has defied direct observation and remains poorly investigated due to experimental constraints. Here, we summarize the findings and conclusions drawn from genetic analysis of experimental hybrids generated in sand flies and highlight the recent advances in generating hybrids in vitro. The ability to hybridize between culture forms of different species and strains of Leishmania should invite more intensive investigation of the mechanisms underlying genetic exchange and provide a rich source of recombinant parasites for future genetic analyses.
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21
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Matos GM, Lewis MD, Talavera-López C, Yeo M, Grisard EC, Messenger LA, Miles MA, Andersson B. Microevolution of Trypanosoma cruzi reveals hybridization and clonal mechanisms driving rapid genome diversification. eLife 2022; 11:75237. [PMID: 35535495 PMCID: PMC9098224 DOI: 10.7554/elife.75237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/22/2022] [Indexed: 12/11/2022] Open
Abstract
Protozoa and fungi are known to have extraordinarily diverse mechanisms of genetic exchange. However, the presence and epidemiological relevance of genetic exchange in Trypanosoma cruzi, the agent of Chagas disease, has been controversial and debated for many years. Field studies have identified both predominantly clonal and sexually recombining natural populations. Two of six natural T. cruzi lineages (TcV and TcVI) show hybrid mosaicism, using analysis of single-gene locus markers. The formation of hybrid strains in vitro has been achieved and this provides a framework to study the mechanisms and adaptive significance of genetic exchange. Using whole genome sequencing of a set of experimental hybrids strains, we have confirmed that hybrid formation initially results in tetraploid parasites. The hybrid progeny showed novel mutations that were not attributable to either (diploid) parent showing an increase in amino acid changes. In long-term culture, up to 800 generations, there was a variable but gradual erosion of progeny genomes towards triploidy, yet retention of elevated copy number was observed at several core housekeeping loci. Our findings indicate hybrid formation by fusion of diploid T. cruzi, followed by sporadic genome erosion, but with substantial potential for adaptive evolution, as has been described as a genetic feature of other organisms, such as some fungi.
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Affiliation(s)
- Gabriel Machado Matos
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianopolis, Brazil.,Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Michael D Lewis
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Carlos Talavera-López
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden.,Institute of Computational Biology, Computational Health Centre, Helmholtz Munich, Munich, Germany
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Edmundo C Grisard
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianopolis, Brazil
| | - Louisa A Messenger
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael A Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
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22
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Silveira KRD, Nogueira PM, Soares RP. Effect of hybridization on Lipophosphoglycan expression in Leishmania major. Cell Biol Int 2022; 46:1169-1174. [PMID: 35312138 DOI: 10.1002/cbin.11798] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/07/2022]
Abstract
Leishmania major is the causative agent of cutaneous leishmaniasis (CL). It is one of the most studied Leishmania species not only during vector interaction, but also in the vertebrate host. Lipophosphoglycan (LPG) is the Leishmania multifunctional virulence factor during host-parasite interaction, whose polymorphisms are involved in the immunopathology of leishmaniasis. Although natural hybrids occur in nature, hybridization of L. major strains in the laboratory was successfully demonstrated. However, LPG expression in the hybrids remains unknown. LPGs from parental (Friedlin-Fn and Seidman-Sd) and hybrids (FnSd3, FnSd4A, FnSd4B and FnSd6F) were extracted, purified and their repeat units analyzed by immunoblotting and fluorophore-assisted carbohydrate electrophoresis (FACE). Parental strains have distinct profiles in LPG expression, and a mixed profile was observed for all hybrids. Variable levels of NO production by macrophages were detected after LPG exposure (parental and hybrids) and were strain specific. This article is protected by copyright. All rights reserved.
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23
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Kajuluri LP, Gargvanshi S, Sahasrabuddhe AA. Intracellular localization of MyosinXXI discriminates Leishmania spp and Leptomonasseymouri. Biochem Biophys Res Commun 2022; 604:70-75. [PMID: 35299073 DOI: 10.1016/j.bbrc.2022.02.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 11/29/2022]
Abstract
The patients with the most dreaded Leishmania donovani infections are now regularly been detected with co-infecting monoxenous trypanosomatid, Leptomonas seymouri, of which pathological consequence is obscure. Due to high degree of morphological similarity, its presence remains unmarked in the culture which leads to anomalous research outcomes. The available methods to detect Leptomonas in cultures are cumbersome and are not quantitative. We report here that MyosinXXI serves as a distinguishing biomarker that can be used to mark the presence of L. seymouri in Leishmania cultures. The method uses Leishmania MyosinXXI antibodies employed in immunofluorescence microscopy that shows a specialized localization pattern in Leishmania but not in Leptomonas (Patent application No. IN201711014439). This method is not only qualitative, but can also quantify the L. seymouri load in the cultured field isolates and serves as a remarkable tool to ascertain laboratory strains of Leishmania.
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Affiliation(s)
| | - Shivani Gargvanshi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Amogh A Sahasrabuddhe
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India.
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24
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Lypaczewski P, Thakur L, Jain A, Kumari S, Paulini K, Matlashewski G, Jain M. An intraspecies Leishmania donovani hybrid from the Indian subcontinent is associated with an atypical phenotype of cutaneous disease. iScience 2022; 25:103802. [PMID: 35198868 PMCID: PMC8841885 DOI: 10.1016/j.isci.2022.103802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/11/2022] [Accepted: 01/20/2022] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is a neglected tropical disease endemic in over 90 countries. The disease has two main pathologies; cutaneous leishmaniasis (CL) that generally self-heals, and visceral leishmaniasis (VL) that is fatal if untreated. The majority of VL cases, concentrated on the Indian subcontinent (ISC) and East Africa, are caused by Leishmania donovani. However, recent foci of CL on the ISC have been attributed as an atypical phenotype of L. donovani including a recent outbreak in Himachal Pradesh, India. Whole genome sequencing and phylogenetic analysis was undertaken to investigate the origins and genetic factors leading to this pathology atypical of L. donovani. Here we demonstrate the isolate from Himachal Pradesh is derived from a genetic hybridization between two independent L. donovani parents from the 'Yeti' ISC1 divergent clade of parasites, identified in the Nepalese highlands. This reveals that intraspecies L. donovani hybrids can give rise to a novel strain associated with CL.
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Affiliation(s)
- Patrick Lypaczewski
- Department of Microbiology and Immunology, McGill University, 3775 University St, Montreal H3A 2B4, Canada
| | - Lovlesh Thakur
- Department of Zoology, Central University of Punjab, Bathinda, Punjab, India
| | - Aklank Jain
- Department of Zoology, Central University of Punjab, Bathinda, Punjab, India
| | - Sandhya Kumari
- Indira Gandhi Medical College, Shimla, Himachal Pradesh, India
| | - Kayla Paulini
- Department of Microbiology and Immunology, McGill University, 3775 University St, Montreal H3A 2B4, Canada
| | - Greg Matlashewski
- Department of Microbiology and Immunology, McGill University, 3775 University St, Montreal H3A 2B4, Canada
| | - Manju Jain
- Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
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25
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Kay C, Peacock L, Williams TA, Gibson W. Signatures of hybridization in Trypanosoma brucei. PLoS Pathog 2022; 18:e1010300. [PMID: 35139131 PMCID: PMC8863249 DOI: 10.1371/journal.ppat.1010300] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 02/22/2022] [Accepted: 01/22/2022] [Indexed: 11/19/2022] Open
Abstract
Genetic exchange among disease-causing micro-organisms can generate progeny that combine different pathogenic traits. Though sexual reproduction has been described in trypanosomes, its impact on the epidemiology of Human African Trypanosomiasis (HAT) remains controversial. However, human infective and non-human infective strains of Trypanosoma brucei circulate in the same transmission cycles in HAT endemic areas in subsaharan Africa, providing the opportunity for mating during the developmental cycle in the tsetse fly vector. Here we investigated inheritance among progeny from a laboratory cross of T. brucei and then applied these insights to genomic analysis of field-collected isolates to identify signatures of past genetic exchange. Genomes of two parental and four hybrid progeny clones with a range of DNA contents were assembled and analysed by k-mer and single nucleotide polymorphism (SNP) frequencies to determine heterozygosity and chromosomal inheritance. Variant surface glycoprotein (VSG) genes and kinetoplast (mitochondrial) DNA maxi- and minicircles were extracted from each genome to examine how each of these components was inherited in the hybrid progeny. The same bioinformatic approaches were applied to an additional 37 genomes representing the diversity of T. brucei in subsaharan Africa and T. evansi. SNP analysis provided evidence of crossover events affecting all 11 pairs of megabase chromosomes and demonstrated that polyploid hybrids were formed post-meiotically and not by fusion of the parental diploid cells. VSGs and kinetoplast DNA minicircles were inherited biparentally, with approximately equal numbers from each parent, whereas maxicircles were inherited uniparentally. Extrapolation of these findings to field isolates allowed us to distinguish clonal descent from hybridization by comparing maxicircle genotype to VSG and minicircle repertoires. Discordance between maxicircle genotype and VSG and minicircle repertoires indicated inter-lineage hybridization. Significantly, some of the hybridization events we identified involved human infective and non-human infective trypanosomes circulating in the same geographic areas.
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Affiliation(s)
- Christopher Kay
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Lori Peacock
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
- Bristol Veterinary School, University of Bristol, Bristol, United Kingdom
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Wendy Gibson
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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26
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Gutiérrez-Corbo C, Domínguez-Asenjo B, Pérez-Pertejo Y, García-Estrada C, Bello FJ, Balaña-Fouce R, Reguera RM. Axenic interspecies and intraclonal hybrid formation in Leishmania: Successful crossings between visceral and cutaneous strains. PLoS Negl Trop Dis 2022; 16:e0010170. [PMID: 35139072 PMCID: PMC8827483 DOI: 10.1371/journal.pntd.0010170] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/13/2022] [Indexed: 12/29/2022] Open
Abstract
Diseases caused by trypanosomatids are serious public health concerns in low-income endemic countries. Leishmaniasis is presented in two main clinical forms, visceral leishmaniasis-caused by L. infantum and L. donovani-and cutaneous leishmaniasis-caused by many species, including L. major, L. tropica and L. braziliensis. As for certain other trypanosomatids, sexual reproduction has been confirmed in these parasites, and formation of hybrids can contribute to virulence, drug resistance or adaptation to the host immune system. In the present work, the capability of intraclonal and interspecies genetic exchange has been investigated using three parental strains: L. donovani, L. tropica and L. major, which have been engineered to express different fluorescent proteins and antibiotic resistance markers in order to facilitate the phenotypic selection of hybrid parasites after mating events. Stationary and exponential-phase promastigotes of each species were used, in in vitro experiments, some of them containing LULO cells (an embryonic cell line derived from Lutzomyia longipalpis). Several intraclonal hybrids were obtained with L. tropica as crossing progenitor, but not with L. donovani or L. major. In interspecies crossings, three L. donovani x L. major hybrids and two L. donovani x L. tropica hybrids were isolated, thereby demonstrating the feasibility to obtain in vitro hybrids of parental lines causing different tropism of leishmaniasis. Ploidy analysis revealed an increase in DNA content in all hybrids compared to the parental strains, and nuclear analysis showed that interspecies hybrids are complete hybrids, i.e. each of them showing at least one chromosomal set from each parental. Regarding kDNA inheritance, discrepancies were observed between maxi and minicircle heritage. Finally, phenotypic studies showed either intermediate phenotypes in terms of growth profiles, or a decreased in vitro infection capacity compared to the parental cells. To the best of our knowledge, this is the first time that in vitro interspecies outcrossing has been demonstrated between Leishmania species with different tropism, thus contributing to shed light on the mechanisms underlying sexual reproduction in these parasites.
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Affiliation(s)
- Camino Gutiérrez-Corbo
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain
| | | | - Yolanda Pérez-Pertejo
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Carlos García-Estrada
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Felio J Bello
- Facultad de Ciencias Agropecuarias, Programa de Medicina Veterinaria, Universidad de la Salle, Bogotá, Colombia
| | - Rafael Balaña-Fouce
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain
- * E-mail: (RB-F); (RMR)
| | - Rosa M. Reguera
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain
- * E-mail: (RB-F); (RMR)
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27
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Negreira GH, Monsieurs P, Imamura H, Maes I, Kuk N, Yagoubat A, Van den Broeck F, Sterkers Y, Dujardin JC, Domagalska M. High throughput single-cell genome sequencing gives insights into the generation and evolution of mosaic aneuploidy in Leishmania donovani. Nucleic Acids Res 2022; 50:293-305. [PMID: 34893872 PMCID: PMC8886908 DOI: 10.1093/nar/gkab1203] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/17/2021] [Accepted: 11/23/2021] [Indexed: 11/14/2022] Open
Abstract
Leishmania, a unicellular eukaryotic parasite, is a unique model for aneuploidy and cellular heterogeneity, along with their potential role in adaptation to environmental stresses. Somy variation within clonal populations was previously explored in a small subset of chromosomes using fluorescence hybridization methods. This phenomenon, termed mosaic aneuploidy (MA), might have important evolutionary and functional implications but remains under-explored due to technological limitations. Here, we applied and validated a high throughput single-cell genome sequencing method to study for the first time the extent and dynamics of whole karyotype heterogeneity in two clonal populations of Leishmania promastigotes representing different stages of MA evolution in vitro. We found that drastic changes in karyotypes quickly emerge in a population stemming from an almost euploid founder cell. This possibly involves polyploidization/hybridization at an early stage of population expansion, followed by assorted ploidy reduction. During further stages of expansion, MA increases by moderate and gradual karyotypic alterations, affecting a defined subset of chromosomes. Our data provide the first complete characterization of MA in Leishmania and pave the way for further functional studies.
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Affiliation(s)
- Gabriel H Negreira
- Molecular Parasitology Unit, Institute of Tropical
Medicine, Antwerp, Belgium
| | - Pieter Monsieurs
- Molecular Parasitology Unit, Institute of Tropical
Medicine, Antwerp, Belgium
| | - Hideo Imamura
- Molecular Parasitology Unit, Institute of Tropical
Medicine, Antwerp, Belgium
| | - Ilse Maes
- Molecular Parasitology Unit, Institute of Tropical
Medicine, Antwerp, Belgium
| | - Nada Kuk
- MiVEGEC, University of Montpellier, CNRS, IRD,
Montpellier, France
| | - Akila Yagoubat
- MiVEGEC, University of Montpellier, CNRS, IRD,
Montpellier, France
| | - Frederik Van den Broeck
- Molecular Parasitology Unit, Institute of Tropical
Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation,
Rega Institute for Medical Research, Katholieke Universiteit
Leuven, 3000 Leuven, Belgium
| | - Yvon Sterkers
- MiVEGEC, University of Montpellier, CNRS, IRD,
Montpellier, France
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Institute of Tropical
Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of
Antwerp, Belgium
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28
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Pinello JF, Clark TG. HAP2-Mediated Gamete Fusion: Lessons From the World of Unicellular Eukaryotes. Front Cell Dev Biol 2022; 9:807313. [PMID: 35071241 PMCID: PMC8777248 DOI: 10.3389/fcell.2021.807313] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 01/29/2023] Open
Abstract
Most, if not all the cellular requirements for fertilization and sexual reproduction arose early in evolution and are retained in extant lineages of single-celled organisms including a number of important model organism species. In recent years, work in two such species, the green alga, Chlamydomonas reinhardtii, and the free-living ciliate, Tetrahymena thermophila, have lent important new insights into the role of HAP2/GCS1 as a catalyst for gamete fusion in organisms ranging from protists to flowering plants and insects. Here we summarize the current state of knowledge around how mating types from these algal and ciliate systems recognize, adhere and fuse to one another, current gaps in our understanding of HAP2-mediated gamete fusion, and opportunities for applying what we know in practical terms, especially for the control of protozoan parasites.
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Affiliation(s)
- Jennifer F. Pinello
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Theodore G. Clark
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
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29
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Louradour I, Ferreira TR, Duge E, Karunaweera N, Paun A, Sacks D. Stress conditions promote Leishmania hybridization in vitro marked by expression of the ancestral gamete fusogen HAP2 as revealed by single-cell RNA-seq. eLife 2022; 11:73488. [PMID: 34994687 PMCID: PMC8794473 DOI: 10.7554/elife.73488] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/06/2022] [Indexed: 12/18/2022] Open
Abstract
Leishmania are protozoan parasites transmitted by the bite of sand fly vectors producing a wide spectrum of diseases in their mammalian hosts. These diverse clinical outcomes are directly associated with parasite strain and species diversity. Although Leishmania reproduction is mainly clonal, a cryptic sexual cycle capable of producing hybrid genotypes has been inferred from population genetic studies and directly demonstrated by laboratory crosses. Experimentally, mating competence has been largely confined to promastigotes developing in the sand fly midgut. The ability to hybridize culture promastigotes in vitro has been limited so far to low-efficiency crosses between two Leishmania tropica strains, L747 and MA37, that mate with high efficiency in flies. Here, we show that exposure of promastigote cultures to DNA damage stress produces a remarkably enhanced efficiency of in vitro hybridization of the L. tropica strains and extends to other species, including Leishmania donovani, Leishmania infantum, and Leishmania braziliensis, a capacity to generate intra- and interspecific hybrids. Whole-genome sequencing and total DNA content analyses indicate that the hybrids are in each case full genome, mostly tetraploid hybrids. Single-cell RNA sequencing of the L747 and MA37 parental lines highlights the transcriptome heterogeneity of culture promastigotes and reveals discrete clusters that emerge post-irradiation in which genes potentially involved in genetic exchange are expressed, including the ancestral gamete fusogen HAP2. By generating reporter constructs for HAP2, we could select for promastigotes that could either hybridize or not in vitro. Overall, this work reveals that there are specific populations involved in Leishmania hybridization associated with a discernible transcriptomic signature, and that stress facilitated in vitro hybridization can be a transformative approach to generate large numbers of hybrid genotypes between diverse species and strains.
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Affiliation(s)
- Isabelle Louradour
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, United States
| | - Tiago Rodrigues Ferreira
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, United States
| | - Emma Duge
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, United States
| | - Nadira Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Andrea Paun
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, United States
| | - David Sacks
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, United States
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30
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Glans H, Lind Karlberg M, Advani R, Bradley M, Alm E, Andersson B, Downing T. High genome plasticity and frequent genetic exchange in Leishmania tropica isolates from Afghanistan, Iran and Syria. PLoS Negl Trop Dis 2021; 15:e0010110. [PMID: 34968388 PMCID: PMC8754299 DOI: 10.1371/journal.pntd.0010110] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/12/2022] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Background The kinetoplastid protozoan Leishmania tropica mainly causes cutaneous leishmaniasis in humans in the Middle East, and relapse or treatment failure after treatment are common in this area. L. tropica’s digenic life cycle includes distinct stages in the vector sandfly and the mammalian host. Sexual reproduction and genetic exchange appear to occur more frequently than in other Leishmania species. Understanding these processes is complicated by chromosome instability during cell division that yields aneuploidy, recombination and heterozygosity. This combination of rare recombination and aneuploid permits may reveal signs of hypothetical parasexual mating, where diploid cells fuse to form a transient tetraploid that undergoes chromosomal recombination and gradual chromosomal loss. Methodology/principal findings The genome-wide SNP diversity from 22 L. tropica isolates showed chromosome-specific runs of patchy heterozygosity and extensive chromosome copy number variation. All these isolates were collected during 2007–2017 in Sweden from patients infected in the Middle East and included isolates from a patient possessing two genetically distinct leishmaniasis infections three years apart with no evidence of re-infection. We found differing ancestries on the same chromosome (chr36) across multiple samples: matching the reference genome with few derived alleles, followed by blocks of heterozygous SNPs, and then by clusters of homozygous SNPs with specific recombination breakpoints at an inferred origin of replication. Other chromosomes had similar marked changes in heterozygosity at strand-switch regions separating polycistronic transcriptional units. Conclusion/significance These large-scale intra- and inter-chromosomal changes in diversity driven by recombination and aneuploidy suggest multiple mechanisms of cell reproduction and diversification in L. tropica, including mitotic, meiotic and parasexual processes. It underpins the need for more genomic surveillance of Leishmania, to detect emerging hybrids that could spread more widely and to better understand the association between genetic variation and treatment outcome. Furthering our understanding of Leishmania genome evolution and ancestry will aid better diagnostics and treatment for cutaneous leishmaniasis caused by L.tropica in the Middle East. Cutaneous leishmaniasis is mainly caused by Leishmania tropica in the Middle East, where it is known for treatment failure and a need for prolonged and/or multiple treatments. Several factors affect the clinical presentation and treatment outcome, such as host genetic variability and specific immune response, as well as environmental factors and the vector species. Little is known about the parasite genome and its influence on treatment response. By analysing the genome of 22 isolates of L. tropica, we have revealed extensive genomic variation and a complex population structure with evidence of genetic exchange within and among the isolates, indicating a possible presence of sexual or parasexual mechanisms. Understanding the Leishmania genome better may improve future treatment and better understanding of treatment failure and relapse.
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Affiliation(s)
- Hedvig Glans
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Dermatology & Venerology, Dept of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Maria Lind Karlberg
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Reza Advani
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Maria Bradley
- Division of Dermatology & Venerology, Dept of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Dermatology and Venerology, Karolinska University Hospital, Stockholm, Sweden
| | - Erik Alm
- The European Center for Disease Prevention and Control, Stockholm, Sweden
| | - Björn Andersson
- Department of Cell & Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland
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31
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Leishmania and the Model of Predominant Clonal Evolution. Microorganisms 2021; 9:microorganisms9112409. [PMID: 34835534 PMCID: PMC8620605 DOI: 10.3390/microorganisms9112409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 01/23/2023] Open
Abstract
As it is the case for other pathogenic microorganisms, the respective impact of clonality and genetic exchange on Leishmania natural populations has been the object of lively debates since the early 1980s. The predominant clonal evolution (PCE) model states that genetic exchange in these parasites’ natural populations may have a high relevance on an evolutionary scale, but is not sufficient to erase a persistent phylogenetic signal and the existence of bifurcating trees. Recent data based on high-resolution markers and genomic polymorphisms fully confirm the PCE model down to a microevolutionary level.
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Medina-Rincón GJ, Gallo-Bernal S, Jiménez PA, Cruz-Saavedra L, Ramírez JD, Rodríguez MJ, Medina-Mur R, Díaz-Nassif G, Valderrama-Achury MD, Medina HM. Molecular and Clinical Aspects of Chronic Manifestations in Chagas Disease: A State-of-the-Art Review. Pathogens 2021; 10:pathogens10111493. [PMID: 34832648 PMCID: PMC8619182 DOI: 10.3390/pathogens10111493] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/11/2022] Open
Abstract
Chronic manifestations of Chagas disease present as disabling and life-threatening conditions affecting mainly the cardiovascular and gastrointestinal systems. Although meaningful research has outlined the different molecular mechanisms underlying Trypanosoma cruzi’s infection and the host-parasite interactions that follow, prompt diagnosis and treatment remain a challenge, particularly in developing countries and also in those where the disease is considered non-endemic. This review intends to present an up-to-date review of the parasite’s life cycle, genetic diversity, virulence factors, and infective mechanisms, as well as the epidemiology, clinical presentation, diagnosis, and treatment options of the main chronic complications of Chagas disease.
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Affiliation(s)
- Germán J. Medina-Rincón
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia; (S.G.-B.); (M.D.V.-A.); (H.M.M.)
- Correspondence: ; Tel.: +57-310-817-2369
| | - Sebastián Gallo-Bernal
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia; (S.G.-B.); (M.D.V.-A.); (H.M.M.)
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Radiology, Harvard Medical School, Boston, MA 02114, USA
| | - Paula A. Jiménez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (P.A.J.); (L.C.-S.); (J.D.R.)
| | - Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (P.A.J.); (L.C.-S.); (J.D.R.)
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111221, Colombia; (P.A.J.); (L.C.-S.); (J.D.R.)
| | - María Juliana Rodríguez
- Division of Cardiology, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá 110131, Colombia; (M.J.R.); (R.M.-M.)
| | - Ramón Medina-Mur
- Division of Cardiology, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá 110131, Colombia; (M.J.R.); (R.M.-M.)
| | - Gustavo Díaz-Nassif
- Division of Gastroenterology and Liver Diseases, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá 111221, Colombia;
| | | | - Héctor M. Medina
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia; (S.G.-B.); (M.D.V.-A.); (H.M.M.)
- Division of Cardiology, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá 110131, Colombia; (M.J.R.); (R.M.-M.)
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Development of an Amplicon-Based Next-Generation Sequencing Protocol to Identify Leishmania Species and Other Trypanosomatids in Leishmaniasis Endemic Areas. Microbiol Spectr 2021; 9:e0065221. [PMID: 34643453 PMCID: PMC8515931 DOI: 10.1128/spectrum.00652-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Trypanosomatid infections are an important public health threat affecting many low-income countries across the tropics, particularly in the Americas. Trypanosomatids can infect many vertebrate, invertebrate, and plant species and play an important role as human pathogens. Among these clinically relevant pathogens are species from the genera Leishmania and Trypanosoma. Mixed trypanosomatid infections remain a largely unexplored phenomenon. Herein, we describe the application of an amplicon-based next-generation sequencing (NGS) assay to detect and identify trypanosomatid species in mammalian reservoirs, human patients, and sand fly vectors throughout regions of Leishmania endemicity. Sixty-five samples from different departments of Colombia, including two samples from Venezuela, were analyzed: 49 samples from cutaneous leishmaniasis (CL) patients, 8 from sand flies, 2 from domestic reservoirs (Canis familiaris), and 6 from wild reservoirs (Phyllostomus hastatus). DNA from each sample served to identify the presence of trypanosomatids through conventional PCR using heat shock protein 70 (HSP70) gene as the target. PCR products underwent sequencing by Sanger sequencing and NGS, and trypanosomatid species were identified by using BLASTn against a reference database built from trypanosomatid-derived HSP70 sequences. The alpha and beta diversity indexes of amplicon sequence variants were calculated for each group. The results revealed the presence of mixed infections with more than two Leishmania species in 34% of CL samples analyzed. Trypanosoma cruzi was identified in samples from wild reservoirs, as well as in sand fly vectors. Coinfection events with three different Leishmania species were identified in domestic reservoirs. These findings depose the traditional paradigm of leishmaniasis as being a single-species-driven infection and redraw the choreography of host-pathogen interaction in the context of multiparasitism. Further research is needed to decipher how coinfections may influence disease progression. This knowledge is key to developing an integrated approach for diagnosis and treatment. IMPORTANCE Traditionally, there has been a frequent, yet incorrect assumption that phlebotomine vectors, animal reservoirs, and human hosts are susceptible to Leishmania infection by a single parasite species. However, current evidence supports that these new vector-parasite-reservoir associations lend vectors and reservoirs greater permissiveness to certain Leishmania species, thus promoting the appearance of coinfection events, particularly in disease-endemic regions. The present study describes the application of an amplicon-based next-generation sequencing (NGS) assay to detect and identify trypanosomatid species in mammalian reservoirs, human patients, and sand fly vectors from regions of endemicity for leishmaniasis. This changes our understanding of the clinical course of leishmaniasis in areas of endemicity.
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Geerts M, Schnaufer A, Van den Broeck F. rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects. BMC Bioinformatics 2021; 22:468. [PMID: 34583651 PMCID: PMC8479924 DOI: 10.1186/s12859-021-04384-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 09/20/2021] [Indexed: 12/28/2022] Open
Abstract
Background The advent of population-scale genome projects has revolutionized our biological understanding of parasitic protozoa. However, while hundreds to thousands of nuclear genomes of parasitic protozoa have been generated and analyzed, information about the diversity, structure and evolution of their mitochondrial genomes remains fragmentary, mainly because of their extraordinary complexity. Indeed, unicellular flagellates of the order Kinetoplastida contain structurally the most complex mitochondrial genome of all eukaryotes, organized as a giant network of homogeneous maxicircles and heterogeneous minicircles. We recently developed KOMICS, an analysis toolkit that automates the assembly and circularization of the mitochondrial genomes of Kinetoplastid parasites. While this tool overcomes the limitation of extracting mitochondrial assemblies from Next-Generation Sequencing datasets, interpreting and visualizing the genetic (dis)similarity within and between samples remains a time-consuming process. Results Here, we present a new analysis toolkit—rKOMICS—to streamline the analyses of minicircle sequence diversity in population-scale genome projects. rKOMICS is a user-friendly R package that has simple installation requirements and that is applicable to all 27 trypanosomatid genera. Once minicircle sequence alignments are generated, rKOMICS allows to examine, summarize and visualize minicircle sequence diversity within and between samples through the analyses of minicircle sequence clusters. We showcase the functionalities of the (r)KOMICS tool suite using a whole-genome sequencing dataset from a recently published study on the history of diversification of the Leishmania braziliensis species complex in Peru. Analyses of population diversity and structure highlighted differences in minicircle sequence richness and composition between Leishmania subspecies, and between subpopulations within subspecies. Conclusion The rKOMICS package establishes a critical framework to manipulate, explore and extract biologically relevant information from mitochondrial minicircle assemblies in tens to hundreds of samples simultaneously and efficiently. This should facilitate research that aims to develop new molecular markers for identifying species-specific minicircles, or to study the ancestry of parasites for complementary insights into their evolutionary history.
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Affiliation(s)
- Manon Geerts
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Frederik Van den Broeck
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium. .,Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, 3000, Leuven, Belgium.
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Reproduction in Trypanosomatids: Past and Present. BIOLOGY 2021; 10:biology10060471. [PMID: 34071741 PMCID: PMC8230138 DOI: 10.3390/biology10060471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 01/07/2023]
Abstract
Simple Summary The reproduction of trypanosomatids is a fundamental issue for host–parasite interaction, and its biological importance lies in knowing how these species acquire new defense mechanisms against the countermeasures imposed by the host, which is consistent with the theory of the endless race or the Red Queen hypothesis for the existence of meiotic sex. Moreover, the way these species re-produce may also be at the origin of novel and more virulent clades and is relevant from a thera-peutic or vaccination point of view, as sex may contribute to increased tolerance and even to the rapid acquisition of drug resistance mechanisms. Kinetoplastids are single-celled organisms, many of them being responsible for important parasitic diseases, globally termed neglected diseases, which are endemic in low-income countries. Leishmaniasis, African (sleeping sickness) and American trypanosomiasis (Chagas disease) caused by trypanosomatids are among the most ne-glected tropical scourges related to poverty and poor health systems. The reproduction of these microorganisms has long been considered to be clonal due to population genetic observations. However, there is increasing evidence of true sex and genetic exchange events under laboratory conditions. We would like to highlight the importance of this topic in the field of host/parasite in-terplay, virulence, and drug resistance. Abstract Diseases caused by trypanosomatids (Sleeping sickness, Chagas disease, and leishmaniasis) are a serious public health concern in low-income endemic countries. These diseases are produced by single-celled parasites with a diploid genome (although aneuploidy is frequent) organized in pairs of non-condensable chromosomes. To explain the way they reproduce through the analysis of natural populations, the theory of strict clonal propagation of these microorganisms was taken as a rule at the beginning of the studies, since it partially justified their genomic stability. However, numerous experimental works provide evidence of sexual reproduction, thus explaining certain naturally occurring events that link the number of meiosis per mitosis and the frequency of mating. Recent techniques have demonstrated genetic exchange between individuals of the same species under laboratory conditions, as well as the expression of meiosis specific genes. The current debate focuses on the frequency of genomic recombination events and its impact on the natural parasite population structure. This paper reviews the results and techniques used to demonstrate the existence of sex in trypanosomatids, the inheritance of kinetoplast DNA (maxi- and minicircles), the impact of genetic exchange in these parasites, and how it can contribute to the phenotypic diversity of natural populations.
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Peacock L, Kay C, Farren C, Bailey M, Carrington M, Gibson W. Sequential production of gametes during meiosis in trypanosomes. Commun Biol 2021; 4:555. [PMID: 33976359 PMCID: PMC8113336 DOI: 10.1038/s42003-021-02058-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 03/24/2021] [Indexed: 02/03/2023] Open
Abstract
Meiosis is a core feature of eukaryotes that occurs in all major groups, including the early diverging excavates. In this group, meiosis and production of haploid gametes have been described in the pathogenic protist, Trypanosoma brucei, and mating occurs in the salivary glands of the insect vector, the tsetse fly. Here, we searched for intermediate meiotic stages among trypanosomes from tsetse salivary glands. Many different cell types were recovered, including trypanosomes in Meiosis I and gametes. Significantly, we found trypanosomes containing three nuclei with a 1:2:1 ratio of DNA contents. Some of these cells were undergoing cytokinesis, yielding a mononucleate gamete and a binucleate cell with a nuclear DNA content ratio of 1:2. This cell subsequently produced three more gametes in two further rounds of division. Expression of the cell fusion protein HAP2 (GCS1) was not confined to gametes, but also extended to meiotic intermediates. We propose a model whereby the two nuclei resulting from Meiosis I undergo asynchronous Meiosis II divisions with sequential production of haploid gametes.
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Affiliation(s)
- Lori Peacock
- School of Biological Sciences University of Bristol, Bristol, UK
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Chris Kay
- School of Biological Sciences University of Bristol, Bristol, UK
| | - Chloe Farren
- School of Biological Sciences University of Bristol, Bristol, UK
| | - Mick Bailey
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Wendy Gibson
- School of Biological Sciences University of Bristol, Bristol, UK.
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Lima ACS, Gomes CMC, Tomokane TY, Campos MB, Zampieri RA, Jorge CL, Laurenti MD, Silveira FT, Corbett CEP, Floeter-Winter LM. Molecular tools confirm natural Leishmania (Viannia) guyanensis/L. (V.) shawi hybrids causing cutaneous leishmaniasis in the Amazon region of Brazil. Genet Mol Biol 2021; 44:e20200123. [PMID: 33949621 PMCID: PMC8108439 DOI: 10.1590/1678-4685-gmb-2020-0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 03/03/2021] [Indexed: 11/22/2022] Open
Abstract
Seven isolates from patients with American cutaneous leishmaniasis in the Amazon region of Brazil were phenotypically suggestive of Leishmania (Viannia) guyanensis/L. (V.) shawi hybrids. In this work, two molecular targets were employed to check the hybrid identity of the putative hybrids. Heat shock protein 70 (hsp70) gene sequences were analyzed by three different polymerase chain reaction (PCR) approaches, and two different patterns of inherited hsp70 alleles were found. Three isolates presented heterozygous L. (V.) guyanensis/L. (V.) shawi patterns, and four presented homozygous hsp70 patterns involving only L. (V.) shawi alleles. The amplicon sequences confirmed the RFLP patterns. The high-resolution melting method detected variant heterozygous and homozygous profiles. Single-nucleotide polymorphism genotyping/cleaved amplified polymorphic site analysis suggested a higher contribution from L. (V.) guyanensis in hsp70 heterozygous hybrids. Additionally, PCR-RFLP analysis targeting the enzyme mannose phosphate isomerase (mpi) gene indicated heterozygous and homozygous cleavage patterns for L. (V.) shawi and L. (V.) guyanensis, corroborating the hsp70 findings. In this communication, we present molecular findings based on partial informative regions of the coding sequences of hsp70 and mpi as markers confirming that some of the parasite strains from the Brazilian Amazon region are indeed hybrids between L. (V.) guyanensis and L. (V.) shawi.
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Affiliation(s)
- Ana Carolina S Lima
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, SP, Brazil.,Ministério da Saúde, Secretaria de Vigilância em Saúde, Instituto Evandro Chagas, Belém, PA, Brazil
| | - Claudia Maria C Gomes
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, SP, Brazil
| | - Thaise Y Tomokane
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, SP, Brazil
| | - Marliane Batista Campos
- Ministério da Saúde, Secretaria de Vigilância em Saúde, Instituto Evandro Chagas, Belém, PA, Brazil
| | - Ricardo A Zampieri
- Universidade de São Paulo, Instituto de Biociências, Departamento de Fisiologia, São Paulo, SP, Brazil
| | - Carolina L Jorge
- Universidade de São Paulo, Instituto de Biociências, Departamento de Fisiologia, São Paulo, SP, Brazil
| | - Marcia D Laurenti
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, SP, Brazil
| | - Fernando T Silveira
- Ministério da Saúde, Secretaria de Vigilância em Saúde, Instituto Evandro Chagas, Belém, PA, Brazil
| | - Carlos Eduardo P Corbett
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, São Paulo, SP, Brazil
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Louradour I, Ferreira TR, Ghosh K, Shaik J, Sacks D. In Vitro Generation of Leishmania Hybrids. Cell Rep 2021; 31:107507. [PMID: 32294444 DOI: 10.1016/j.celrep.2020.03.071] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 01/21/2020] [Accepted: 03/20/2020] [Indexed: 01/01/2023] Open
Abstract
Protozoan parasites in the genus Leishmania produce a broad spectrum of diseases in their human hosts. The strain and species-specific genes controlling these diverse clinical outcomes have remained poorly tractable using reverse genetics approaches. A cryptic sexual cycle involving a meiotic-like process has been described in Leishmania but is so far confined to parasites growing in the sand fly vector. Here, we describe the reproducible in vitro generation of hybrid clones using axenic culture forms of Leishmania tropica promastigotes. Analysis of SNPs marker inheritance and whole-genome sequencing data indicate that the progeny clones are full genomic hybrids. The demonstration that mating-competent forms arise in culture should facilitate experimental study of the mating biology of Leishmania and the generation of large numbers of recombinant parasites for positional cloning of important genes.
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Affiliation(s)
- Isabelle Louradour
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tiago Rodrigues Ferreira
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kashinath Ghosh
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - David Sacks
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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Gibson W. The sexual side of parasitic protists. Mol Biochem Parasitol 2021; 243:111371. [PMID: 33872659 DOI: 10.1016/j.molbiopara.2021.111371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/26/2021] [Accepted: 04/13/2021] [Indexed: 01/09/2023]
Abstract
Much of the vast evolutionary landscape occupied by Eukaryotes is dominated by protists. Though parasitism has arisen in many lineages, there are three main groups of parasitic protists of relevance to human and livestock health: the Apicomplexa, including the malaria parasite Plasmodium and coccidian pathogens of livestock such as Eimeria; the excavate flagellates, encompassing a diverse range of protist pathogens including trypanosomes, Leishmania, Giardia and Trichomonas; and the Amoebozoa, including pathogenic amoebae such as Entamoeba. These three groups represent separate, deep branches of the eukaryote tree, underlining their divergent evolutionary histories. Here, I explore what is known about sex in these three main groups of parasitic protists.
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Affiliation(s)
- Wendy Gibson
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, United Kingdom.
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Lypaczewski P, Matlashewski G. Leishmania donovani hybridisation and introgression in nature: a comparative genomic investigation. THE LANCET MICROBE 2021; 2:e250-e258. [DOI: 10.1016/s2666-5247(21)00028-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 01/17/2023] Open
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Leishmania Sexual Reproductive Strategies as Resolved through Computational Methods Designed for Aneuploid Genomes. Genes (Basel) 2021; 12:genes12020167. [PMID: 33530584 PMCID: PMC7912377 DOI: 10.3390/genes12020167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/21/2021] [Accepted: 01/21/2021] [Indexed: 11/23/2022] Open
Abstract
A cryptic sexual reproductive cycle in Leishmania has been inferred through population genetic studies revealing the presence of hybrid genotypes in natural isolates, with attempts made to decipher sexual strategies by studying complex chromosomal inheritance patterns. A more informative approach is to study the products of controlled, laboratory-based experiments where known strains or species are crossed in the sand fly vector to generate hybrid progeny. These hybrids can be subsequently studied through high resolution sequencing technologies and software suites such as PAINT that disclose inheritance patterns including ploidies, parental chromosome contributions and recombinations, all of which can inform the sexual strategy. In this work, we discuss the computational methods in PAINT that can be used to interpret the sexual strategies adopted specifically by aneuploid organisms and summarize how PAINT has been applied to the analysis of experimental hybrids to reveal meiosis-like sexual recombination in Leishmania.
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Telittchenko R, Descoteaux A. Study on the Occurrence of Genetic Exchange Among Parasites of the Leishmania mexicana Complex. Front Cell Infect Microbiol 2020; 10:607253. [PMID: 33365278 PMCID: PMC7750183 DOI: 10.3389/fcimb.2020.607253] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/10/2020] [Indexed: 12/24/2022] Open
Abstract
In Leishmania, genetic exchange has been experimentally demonstrated to occur in the sand fly vector and in promastigote axenic cultures through a meiotic-like process. No evidence of genetic exchange in mammalian hosts have been reported so far, possibly due to the fact that the Leishmania species used in previous studies replicate within individual parasitophorous vacuoles. In the present work, we explored the possibility that residing in communal vacuoles may provide conditions favorable for genetic exchange for L. mexicana and L. amazonensis. Using promastigote lines of both species harboring integrated or episomal drug-resistance markers, we assessed whether genetic exchange can occur in axenic cultures, in infected macrophages as well as in infected mice. We obtained evidence of genetic exchange for L. amazonensis in both axenic promastigote cultures and infected macrophages. However, the resulting products of those putative genetic events were unstable as they did not sustain growth in subsequent sub-cultures, precluding further characterization.
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Affiliation(s)
- Roman Telittchenko
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
| | - Albert Descoteaux
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada
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43
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Kelly FD, Yates PA, Landfear SM. Nutrient sensing in Leishmania: Flagellum and cytosol. Mol Microbiol 2020; 115:849-859. [PMID: 33112443 DOI: 10.1111/mmi.14635] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/18/2022]
Abstract
Parasites are by definition organisms that utilize resources from a host to support their existence, thus, promoting their ability to establish long-term infections and disease. Hence, sensing and acquiring nutrients for which the parasite and host compete is central to the parasitic mode of existence. Leishmania are flagellated kinetoplastid parasites that parasitize phagocytic cells, principally macrophages, of vertebrate hosts and the alimentary tract of sand fly vectors. Because nutritional supplies vary over time within both these hosts and are often restricted in availability, these parasites must sense a plethora of nutrients and respond accordingly. The flagellum has been recognized as an "antenna" that plays a core role in sensing environmental conditions, and various flagellar proteins have been implicated in sensing roles. In addition, these parasites exhibit non-flagellar intracellular mechanisms of nutrient sensing, several of which have been explored. Nonetheless, mechanistic details of these sensory pathways are still sparse and represent a challenging frontier for further experimental exploration.
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Affiliation(s)
- Felice D Kelly
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Phillip A Yates
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Scott M Landfear
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
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Easton A, Gao S, Lawton SP, Bennuru S, Khan A, Dahlstrom E, Oliveira RG, Kepha S, Porcella SF, Webster J, Anderson R, Grigg ME, Davis RE, Wang J, Nutman TB. Molecular evidence of hybridization between pig and human Ascaris indicates an interbred species complex infecting humans. eLife 2020; 9:e61562. [PMID: 33155980 PMCID: PMC7647404 DOI: 10.7554/elife.61562] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
Human ascariasis is a major neglected tropical disease caused by the nematode Ascaris lumbricoides. We report a 296 megabase (Mb) reference-quality genome comprised of 17,902 protein-coding genes derived from a single, representative Ascaris worm. An additional 68 worms were collected from 60 human hosts in Kenyan villages where pig husbandry is rare. Notably, the majority of these worms (63/68) possessed mitochondrial genomes that clustered closer to the pig parasite Ascaris suum than to A. lumbricoides. Comparative phylogenomic analyses identified over 11 million nuclear-encoded SNPs but just two distinct genetic types that had recombined across the genomes analyzed. The nuclear genomes had extensive heterozygosity, and all samples existed as genetic mosaics with either A. suum-like or A. lumbricoides-like inheritance patterns supporting a highly interbred Ascaris species genetic complex. As no barriers appear to exist for anthroponotic transmission of these 'hybrid' worms, a one-health approach to control the spread of human ascariasis will be necessary.
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Affiliation(s)
- Alice Easton
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
- Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Shenghan Gao
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
- Beijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
| | - Scott P Lawton
- Epidemiology Research Unit (ERU) Department of Veterinary and Animal Sciences, Northern Faculty, Scotland’s Rural College (SRUC)InvernessUnited Kingdom
| | - Sasisekhar Bennuru
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
| | - Asis Khan
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
| | - Eric Dahlstrom
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Rita G Oliveira
- Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Stella Kepha
- London School of Tropical Medicine and HygieneLondonUnited Kingdom
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Joanne Webster
- Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
- Royal Veterinary College, University of London, Department of Pathobiology and Population SciencesHertfordshireUnited Kingdom
| | - Roy Anderson
- Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Michael E Grigg
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
| | - Jianbin Wang
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
- Department of Biochemistry and Cellular and Molecular Biology, University of TennesseeKnoxvilleUnited States
| | - Thomas B Nutman
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
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Succinate dehydrogenase gene as a marker for studying Blastocystis genetic diversity. Heliyon 2020; 6:e05387. [PMID: 33163680 PMCID: PMC7609450 DOI: 10.1016/j.heliyon.2020.e05387] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/01/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022] Open
Abstract
Blastocystis has been reported as the most common eukaryotic microorganism residing in the intestines of both humans and animals, with a prevalence of up to 100% in some populations. Since this is a cryptic species, sequence polymorphism are the single strategy to analyses its genetic diversity, being traditionally used the analysis of ssu rRNA gene sequence to determine alleles and subtypes (STs) for this species. This multicopy gene has shown high diversity among different STs, making necessary to explore other genes to assess intraspecific diversity. This study evaluated the use of a novel genetic marker, succinate dehydrogenase (SDHA), for the typing and evaluation of the genetic diversity and genetic population structure of Blastocystis. In total, 375 human fecal samples were collected and subjected to PCR, subtyped using the ssu rRNA marker, and then the SDHA gene was amplified via PCR for 117 samples. We found some incongruences between tree topologies for both molecular markers. However, the clustering by ST previously established for Blastocystis was congruent in the concatenated sequence. SDHA showed lower reticulation (The origination of a lineage through the partial merging of two ancestor lineages) signals and better intra ST clustering ability. Clusters with geographical associations were observed intra ST. The genetic diversity was lower in the marker evaluated compared to that of the ssu rRNA gene (nucleotide diversity = 0.03344 and 0.16986, respectively) and the sequences analyzed showed population expansion with genetic differentiation principally among STs. The ssu rRNA gene was useful to explore interspecific diversity but together with the SDHA gene the resolution power to evaluate intra ST diversity was higher. These results showed the potential of the SDHA marker for studying the intra ST genetic diversity of Blastocystis related with geographical location and the inter ST diversity using the concatenated sequences.
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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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Abstract
Parasites are interesting models for studying speciation processes because they have a high potential for specialization, thanks to the intimate ecological association with their hosts and vectors. Yet little is known about the circumstances under which new parasite lineages emerge. Here we studied the genome diversity of parasites of the Leishmania braziliensis species complex that inhabit both Amazonian and Andean biotas in Peru. We identify three major parasite lineages that occupy particular ecological niches and show that these emerged during forestation changes over the past 150,000 y. We furthermore discovered that meiotic recombination between Amazonian and Andean lineages resulted in full-genome hybrids presenting mixed mitochondrial genomes, providing insights into the genetic consequences of hybridization in parasitic protozoa. The tropical Andes are an important natural laboratory to understand speciation in many taxa. Here we examined the evolutionary history of parasites of the Leishmania braziliensis species complex based on whole-genome sequencing of 67 isolates from 47 localities in Peru. We first show the origin of Andean Leishmania as a clade of near-clonal lineages that diverged from admixed Amazonian ancestors, accompanied by a significant reduction in genome diversity and large structural variations implicated in host–parasite interactions. Within the Andean species, patterns of population structure were strongly associated with biogeographical origin. Molecular clock and ecological niche modeling suggested that the history of diversification of the Andean lineages is limited to the Late Pleistocene and intimately associated with habitat contractions driven by climate change. These results suggest that changes in forestation over the past 150,000 y have influenced speciation and diversity of these Neotropical parasites. Second, genome-scale analyses provided evidence of meiotic-like recombination between Andean and Amazonian Leishmania species, resulting in full-genome hybrids. The mitochondrial genome of these hybrids consisted of homogeneous uniparental maxicircles, but minicircles originated from both parental species. We further show that mitochondrial minicircles—but not maxicircles—show a similar evolutionary pattern to the nuclear genome, suggesting that compatibility between nuclear-encoded mitochondrial genes and minicircle-encoded guide RNA genes is essential to maintain efficient respiration. By comparing full nuclear and mitochondrial genome ancestries, our data expand our appreciation on the genetic consequences of diversification and hybridization in parasitic protozoa.
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Cotton JA, Franssen SU. A Way Straight-Forward for Leishmania Genetics. Trends Parasitol 2020; 36:719-721. [PMID: 32741600 DOI: 10.1016/j.pt.2020.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 11/29/2022]
Abstract
Genetic exchange between Leishmania parasites was demonstrated in sandflies over 10 years ago. Louradour et al. have shown in vitro hybridization of two Leishmania tropica isolates, with the potential to remove a major roadblock to using forward genetics in Leishmania, understanding Leishmania reproductive biology, and analyzing gene flow in natural populations.
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Affiliation(s)
- James A Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Susanne U Franssen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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49
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Touching the Surface: Diverse Roles for the Flagellar Membrane in Kinetoplastid Parasites. Microbiol Mol Biol Rev 2020; 84:84/2/e00079-19. [PMID: 32238446 DOI: 10.1128/mmbr.00079-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
While flagella have been studied extensively as motility organelles, with a focus on internal structures such as the axoneme, more recent research has illuminated the roles of the flagellar surface in a variety of biological processes. Parasitic protists of the order Kinetoplastida, which include trypanosomes and Leishmania species, provide a paradigm for probing the role of flagella in host-microbe interactions and illustrate that this interface between the flagellar surface and the host is of paramount importance. An increasing body of knowledge indicates that the flagellar membrane serves a multitude of functions at this interface: attachment of parasites to tissues within insect vectors, close interactions with intracellular organelles of vertebrate cells, transactions between flagella from different parasites, junctions between the flagella and the parasite cell body, emergence of nanotubes and exosomes from the parasite directed to either host or microbial targets, immune evasion, and sensing of the extracellular milieu. Recent whole-organelle or genome-wide studies have begun to identify protein components of the flagellar surface that must mediate these diverse host-parasite interactions. The increasing corpus of knowledge on kinetoplastid flagella will likely prove illuminating for other flagellated or ciliated pathogens as well.
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50
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Franssen SU, Durrant C, Stark O, Moser B, Downing T, Imamura H, Dujardin JC, Sanders MJ, Mauricio I, Miles MA, Schnur LF, Jaffe CL, Nasereddin A, Schallig H, Yeo M, Bhattacharyya T, Alam MZ, Berriman M, Wirth T, Schönian G, Cotton JA. Global genome diversity of the Leishmania donovani complex. eLife 2020; 9:e51243. [PMID: 32209228 PMCID: PMC7105377 DOI: 10.7554/elife.51243] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/27/2020] [Indexed: 12/30/2022] Open
Abstract
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.
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Affiliation(s)
| | - Caroline Durrant
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | | | | | - Tim Downing
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Dublin City UniversityDublinIreland
| | | | - Jean-Claude Dujardin
- Institute of Tropical MedicineAntwerpBelgium
- Department of Biomedical Sciences, University of AntwerpAntwerpBelgium
| | - Mandy J Sanders
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Isabel Mauricio
- Universidade Nova de Lisboa Instituto de Higiene e MedicinaLisboaPortugal
| | - Michael A Miles
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Lionel F Schnur
- Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical SchoolJerusalemIsrael
| | - Charles L Jaffe
- Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical SchoolJerusalemIsrael
| | - Abdelmajeed Nasereddin
- Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical SchoolJerusalemIsrael
| | - Henk Schallig
- Amsterdam University Medical Centres – Academic Medical Centre at the University of Amsterdam, Department of Medical Microbiology – Experimental ParasitologyAmsterdamNetherlands
| | - Matthew Yeo
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | | | - Mohammad Z Alam
- Department of Parasitology, Bangladesh Agricultural UniversityMymensinghBangladesh
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Thierry Wirth
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des AntillesParisFrance
- École Pratique des Hautes Études (EPHE)Paris Sciences & Lettres (PSL)ParisFrance
| | | | - James A Cotton
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
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