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Heeren S, Maes I, Sanders M, Lye LF, Adaui V, Arevalo J, Llanos-Cuentas A, Garcia L, Lemey P, Beverley SM, Cotton JA, Dujardin JC, Van den Broeck F. Diversity and dissemination of viruses in pathogenic protozoa. Nat Commun 2023; 14:8343. [PMID: 38102141 PMCID: PMC10724245 DOI: 10.1038/s41467-023-44085-2] [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: 05/03/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses are the most abundant biological entities on Earth and play a significant role in the evolution of many organisms and ecosystems. In pathogenic protozoa, the presence of viruses has been linked to an increased risk of treatment failure and severe clinical outcome. Here, we studied the molecular epidemiology of the zoonotic disease cutaneous leishmaniasis in Peru and Bolivia through a joint evolutionary analysis of Leishmania braziliensis and their dsRNA Leishmania virus 1. We show that parasite populations circulate in tropical rainforests and are associated with single viral lineages that appear in low prevalence. In contrast, groups of hybrid parasites are geographically and ecologically more dispersed and associated with an increased prevalence, diversity and spread of viruses. Our results suggest that parasite gene flow and hybridization increased the frequency of parasite-virus symbioses, a process that may change the epidemiology of leishmaniasis in the region.
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Affiliation(s)
- 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
| | | | - Lon-Fye Lye
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Vanessa Adaui
- Laboratory of Biomolecules, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Jorge Arevalo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Lineth Garcia
- Instituto de Investigación Biomédicas e Investigación Social, Universidad Mayor de San Simon, Cochabamba, Bolivia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Stephen M Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - James A Cotton
- Welcome Sanger Institute, Hinxton, UK
- School of Biodiversity, One Health and Comparative Medicine, Wellcome Centre for Integrative Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - 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.
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2
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Mendieta D, Vásquez V, Jaén L, Pineda V, Saldaña A, Calzada JE, Samudio F. Insights into the Genetic Diversity of Leishmania (Viannia) panamensis in Panama, Inferred via Multilocus Sequence Typing (MLST). Pathogens 2023; 12:pathogens12050747. [PMID: 37242417 DOI: 10.3390/pathogens12050747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/26/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Leishmaniasis is a disease caused by parasites of the genus Leishmania and transmitted by sand fly vectors. Tegumentary leishmaniasis is the most prevalent clinical outcome in Latin America, afflicting people from 18 countries. In Panama, the annual incidence rate of leishmaniasis is as high as 3000 cases, representing a major public health problem. In endemic regions, L. panamensis is responsible for almost eighty percent of human cases that present different clinical outcomes. These differences in disease outcomes could be the result of the local interplay between L. panamensis variants and human hosts with different genetic backgrounds. The genetic diversity of L. panamensis in Panama has only been partially explored, and the variability reported for this species is based on few studies restricted to small populations and/or with poor resolutive markers at low taxonomic levels. Accordingly, in this study, we explored the genetic diversity of sixty-nine L. panamensis isolates from different endemic regions of Panama, using an MLST approach based on four housekeeping genes (Aconitase, ALAT, GPI and HSP70). Two to seven haplotypes per locus were identified, and regional differences in the genetic diversity of L. panamensis were observed. A genotype analysis evidenced the circulation of thirteen L. panamensis genotypes, a fact that might have important implications for the local control of the disease.
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Affiliation(s)
- Daniel Mendieta
- Facultad de Ciencias Naturales Exactas y Tecnología, Universidad de Panamá, Panama City P.O. Box 0824-00073, Panama
| | - Vanessa Vásquez
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Avenida Justo Arosemena, Panama City P.O. Box 0816-02593, Panama
| | - Luis Jaén
- Facultad de Ciencias Naturales Exactas y Tecnología, Universidad de Panamá, Panama City P.O. Box 0824-00073, Panama
| | - Vanessa Pineda
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Avenida Justo Arosemena, Panama City P.O. Box 0816-02593, Panama
| | - Azael Saldaña
- Facultad de Ciencias Naturales Exactas y Tecnología, Universidad de Panamá, Panama City P.O. Box 0824-00073, Panama
- Centro de Investigación y Diagnóstico de Enfermedades Parasitarias (CIDEP), Universidad de Panamá, Panama City P.O. Box 0824-00073, Panama
- Sistema Nacional de Investigación, Panama City P.O. Box 0816-02852, Panama
| | - José Eduardo Calzada
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Avenida Justo Arosemena, Panama City P.O. Box 0816-02593, Panama
- Sistema Nacional de Investigación, Panama City P.O. Box 0816-02852, Panama
| | - Franklyn Samudio
- Facultad de Ciencias Naturales Exactas y Tecnología, Universidad de Panamá, Panama City P.O. Box 0824-00073, Panama
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Avenida Justo Arosemena, Panama City P.O. Box 0816-02593, Panama
- Sistema Nacional de Investigación, Panama City P.O. Box 0816-02852, Panama
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3
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Heeren S, Maes I, Sanders M, Lye LF, Arevalo J, Llanos-Cuentas A, Garcia L, Lemey P, Beverley SM, Cotton JA, Dujardin JC, den Broeck FV. Parasite hybridization promotes spreading of endosymbiotic viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534103. [PMID: 36993291 PMCID: PMC10055345 DOI: 10.1101/2023.03.24.534103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Viruses are the most abundant biological entities on Earth and play a significant role in the evolution of many organisms and ecosystems. In pathogenic protozoa, the presence of endosymbiotic viruses has been linked to an increased risk of treatment failure and severe clinical outcome. Here, we studied the molecular epidemiology of the zoonotic disease cutaneous leishmaniasis in Peru and Bolivia through a joint evolutionary analysis of Leishmania braziliensis parasites and their endosymbiotic Leishmania RNA virus. We show that parasite populations circulate in isolated pockets of suitable habitat and are associated with single viral lineages that appear in low prevalence. In contrast, groups of hybrid parasites were geographically and ecologically dispersed, and commonly infected from a pool of genetically diverse viruses. Our results suggest that parasite hybridization, likely due to increased human migration and ecological perturbations, increased the frequency of endosymbiotic interactions known to play a key role in disease severity.
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Affiliation(s)
- 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
| | - Mandy Sanders
- Parasite Genomics Group, Welcome Sanger Institute, Hinxton, United Kingdom
| | - Lon-Fye Lye
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, United States
| | - Jorge Arevalo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Lineth Garcia
- Instituto de Investigación Biomédicas e Investigación Social, Universidad Mayor de San Simon, Cochabamba, Bolivia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Stephen M Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, United States
| | - James A Cotton
- Parasite Genomics Group, Welcome Sanger Institute, Hinxton, United Kingdom
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - 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
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Pilling OA, Reis-Cunha JL, Grace CA, Berry ASF, Mitchell MW, Yu JA, Malekshahi CR, Krespan E, Go CK, Lombana C, Song YS, Amorim CF, Lago AS, Carvalho LP, Carvalho EM, Brisson D, Scott P, Jeffares DC, Beiting DP. Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies. PLoS Pathog 2023; 19:e1011230. [PMID: 36940219 PMCID: PMC10063166 DOI: 10.1371/journal.ppat.1011230] [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: 09/03/2022] [Revised: 03/30/2023] [Accepted: 02/22/2023] [Indexed: 03/21/2023] Open
Abstract
In Brazil, Leishmania braziliensis is the main causative agent of the neglected tropical disease, cutaneous leishmaniasis (CL). CL presents on a spectrum of disease severity with a high rate of treatment failure. Yet the parasite factors that contribute to disease presentation and treatment outcome are not well understood, in part because successfully isolating and culturing parasites from patient lesions remains a major technical challenge. Here we describe the development of selective whole genome amplification (SWGA) for Leishmania and show that this method enables culture-independent analysis of parasite genomes obtained directly from primary patient skin samples, allowing us to circumvent artifacts associated with adaptation to culture. We show that SWGA can be applied to multiple Leishmania species residing in different host species, suggesting that this method is broadly useful in both experimental infection models and clinical studies. SWGA carried out directly on skin biopsies collected from patients in Corte de Pedra, Bahia, Brazil, showed extensive genomic diversity. Finally, as a proof-of-concept, we demonstrated that SWGA data can be integrated with published whole genome data from cultured parasite isolates to identify variants unique to specific geographic regions in Brazil where treatment failure rates are known to be high. SWGA provides a relatively simple method to generate Leishmania genomes directly from patient samples, unlocking the potential to link parasite genetics with host clinical phenotypes.
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Affiliation(s)
- Olivia A. Pilling
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - João L. Reis-Cunha
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Cooper A. Grace
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Alexander S. F. Berry
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew W. Mitchell
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jane A. Yu
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
| | - Clara R. Malekshahi
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Elise Krespan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Christina K. Go
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Cláudia Lombana
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yun S. Song
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Camila F. Amorim
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alexsandro S. Lago
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, Brazil
| | - Lucas P. Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, Brazil
| | - Edgar M. Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, Brazil
| | - Dustin Brisson
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Phillip Scott
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Daniel C. Jeffares
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Daniel P. Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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5
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Higuera A, Salas-Leiva DE, Curtis B, Patiño LH, Zhao D, Jerlström-Hultqvist J, Dlutek M, Muñoz M, Roger AJ, Ramírez JD. Draft genomes of Blastocystis subtypes from human samples of Colombia. Parasit Vectors 2023; 16:52. [PMID: 36732768 PMCID: PMC9896827 DOI: 10.1186/s13071-022-05619-7] [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: 09/05/2022] [Accepted: 12/14/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Blastocystis is one of the most common eukaryotic microorganisms colonizing the intestines of both humans and animals, but the conditions under which it may be a pathogen are unclear. METHODS To study the genomic characteristics of circulating subtypes (ST) in Colombia, we established nine xenic cultures from Blastocystis isolated from human fecal samples, we identified 10 different subtypes, since one sample had a mixed infection. Thus, the genomes of the subtypes ST1 (n = 3), ST2 (n = 1), ST3 (n = 2), ST6 (n = 1), ST7 (n = 1), and ST8 (n = 2) were sequenced using Illumina and Oxford Nanopore Technologies (ONT). RESULTS Analyses of these draft nuclear genomes indicated remarkable diversity in terms of genome size and guanine-cytosine (GC) content among the compared STs. Illumina sequencing-only draft genomes contained 824 to 2077 scaffolds, with total genome size ranging from 12 to 13.2 Mb and N50 values ranging from 10,585 to 29,404 base pairs (bp). The genome of one ST1 isolate was sequenced using ONT. This assembly was more contiguous, with a size of 20 million base pairs (Mb) spread over 116 scaffolds, and an N50 of 248,997 bp. CONCLUSION This work represents one of the few large-scale comparative genomic analyses of Blastocystis isolates, providing an additional glimpse into its genomic diversity.
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Affiliation(s)
- Adriana Higuera
- grid.412191.e0000 0001 2205 5940Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Dayana E. Salas-Leiva
- grid.5335.00000000121885934Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW United Kingdom
| | - Bruce Curtis
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Luz H. Patiño
- grid.412191.e0000 0001 2205 5940Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Dandan Zhao
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Jon Jerlström-Hultqvist
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, BMC, Uppsala Universitet, Box 596, 751 24 Uppsala, Sweden
| | - Marlena Dlutek
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Marina Muñoz
- grid.412191.e0000 0001 2205 5940Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Andrew J. Roger
- grid.55602.340000 0004 1936 8200Institute for Comparative Genomics (ICG), Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2 Canada
| | - Juan David Ramírez
- grid.412191.e0000 0001 2205 5940Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia ,grid.59734.3c0000 0001 0670 2351Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY USA
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6
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de Albuquerque-Melo BC, Cysne-Finkelstein L, Gonçalves-Oliveira LF, Cascabulho CM, Henriques-Pons A, Pereira MCDS, Alves CR, Dias-Lopes G. Impact of collaborative actions of Leishmania (Viannia) braziliensis subpopulations on the infection profile. Parasitology 2022; 149:1526-1535. [PMID: 35822537 PMCID: PMC11010534 DOI: 10.1017/s003118202200097x] [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: 04/11/2022] [Revised: 06/02/2022] [Accepted: 07/01/2022] [Indexed: 11/06/2022]
Abstract
This study focuses on the role of the population structure of Leishmania spp. on the adaptive capacity of the parasite. Herein, we investigate the contribution of subpopulations of the L. (V.) braziliensis Thor strain (Thor03, Thor10 and Thor22) in the profile of murine macrophages infection. Infection assays were performed with binary combinations of these subpopulations at stationary phases. The initial interaction time showed major effects on the combination assays, as demonstrated by the significant increase in the infection rate at 5 h. Based on the endocytic index (EI), Thor10 (EI = 563.6) and Thor03 (EI = 497) showed a higher infection load compared to Thor22 (EI = 227.3). However, the EI decreased in Thor03 after 48 h (EI = 447) and 72 h (EI = 388.3) of infection, and showed changes in the infection level in all Thor10/Thor22 combinations. Assays with CellTrace CFSE-labelled Thor22 promastigotes indicated an increase (~1.5 fold) in infection by this subpopulation in the presence of Thor10 when compared to the infection profile of Thor03/Thor22 combinations in the same proportions. In addition, the potential of these subpopulations, alone or in binary combinations, to modulate the expression of cytokines and nitric oxide (NO) in vitro was investigated. Lower NO and tumour necrosis factor-α production levels were observed for all Thor10/Thor22 combinations at 24 h compared to these subpopulations alone. In contrast, Thor03/Thor22 combination assays increased IL-10 production at this time. Collectively, these results provide in vitro evidence on the potential of L. (V.) braziliensis population structure to play a relevant role in a host infection by this parasite.
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Affiliation(s)
| | - Léa Cysne-Finkelstein
- Laboratório de Imunoparasitologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil
| | - Luiz Filipe Gonçalves-Oliveira
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil
| | - Cynthia Machado Cascabulho
- Laboratório de Inovação em Terapias, Ensino e Bioprodutos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil
| | - Andrea Henriques-Pons
- Laboratório de Inovação em Terapias, Ensino e Bioprodutos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil
| | | | - Carlos Roberto Alves
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil
| | - Geovane Dias-Lopes
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil
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7
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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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8
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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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9
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Zabala-Peñafiel A, Cysne-Finkelstein L, Conceição-Silva F, Fagundes A, Miranda LDFC, Souza-Silva F, Brandt AAML, Dias-Lopes G, Alves CR. Novel Insights Into Leishmania (Viannia) braziliensis In Vitro Fitness Guided by Temperature Changes Along With Its Subtilisins and Oligopeptidase B. Front Cell Infect Microbiol 2022; 12:805106. [PMID: 35531337 PMCID: PMC9069558 DOI: 10.3389/fcimb.2022.805106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
Proteases are virulence factors with a recognized impact on the Leishmania spp. life cycle. This study considers a set of analyses measuring phenotypic factors of L. (V.) braziliensis clinical isolates as promastigotes growth curves, murine peritoneal macrophages infection, inflammatory mediators production, and serine proteases gene expression (subtilisin 13: S13, subtilisin 28: S28, oligopeptidase B: OPB) assessing these isolates’ fitness on in vitro conditions. Parasites had different behavior during the early growth phase from day zero to day three, and all isolates reached the stationary growth phase between days four and seven. Macrophages infection showed two tendencies, one of decreased infection rate and number of parasites per macrophage (Infection Index <1000) and another with a constant infection index (≥1400). TNF-α (≥10 pg/mL) detected in infections by 75% of isolates, IL-6 (≥80 pg/mL) by 30% of isolates and low levels of NO (≥0.01µM) in almost all infections. Gene expression showed higher values of S13 (≥2RQ) in the intracellular amastigotes of all the isolates evaluated. On the contrary, S28 expression was low (≤1RQ) in all isolates. OPB expression was different between promastigotes and intracellular amastigotes, being significantly higher (≥2RQ) in the latter form of 58% of the isolates. Predictive structural assays of S13 and OPB were performed to explore temperature influence on gene expression and the encoded proteases. Gene expression data is discussed based on in silico predictions of regulatory regions that show plasticity in the linearity index of secondary structures of S13 and OPB 3’-untranslated regions of mRNA, dependent on temperature changes. While hairpin structures suggest an active region of mRNA for both genes above 26°C, pseudoknot structure found in S13 is an indication of a particular profile of this gene at mammalian host temperatures (37°C). Furthermore, the predicted 3D structures are in accordance with the influence of these temperatures on the catalytic site stability of both enzymes, favoring their action over peptide substrates. Data gathered here suggest that L. (V.) braziliensis serine proteases can be influenced by the temperature conditions affecting parasite fitness throughout its life cycle.
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Affiliation(s)
- Anabel Zabala-Peñafiel
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lea Cysne-Finkelstein
- Laboratório de Imunoparasitologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fatima Conceição-Silva
- Laboratório de Imunoparasitologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Aline Fagundes
- Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Luciana de Freitas Campos Miranda
- Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Franklin Souza-Silva
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Universidade Iguaçu, Dom Rodrigo, Nova Iguaçu, Rio de Janeiro, Brazil
| | - Artur A. M. L. Brandt
- Departamento de Computação e Sistemas, Faculdade de Educação Tecnológica do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Ciência da Computação, Univeritas-Rio, Rio de Janeiro, Brazil
| | - Geovane Dias-Lopes
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- *Correspondence: Geovane Dias-Lopes, ; Carlos Roberto Alves,
| | - Carlos Roberto Alves
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- *Correspondence: Geovane Dias-Lopes, ; Carlos Roberto Alves,
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10
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Monte-Neto RL, Fernandez-Prada C, Moretti NS. Sex under pressure: stress facilitates Leishmania in vitro hybridization. Trends Parasitol 2022; 38:274-276. [PMID: 35181250 DOI: 10.1016/j.pt.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 10/19/2022]
Abstract
The selection of Leishmania hybrids in axenic culture was considered rare until recently, when Louradour and Ferreira et al., demonstrated that induced DNA damage facilitates genetic exchange, resulting in full genome tetraploid progenies in vitro. Meiosis-related gene homologues HAP2, GEX1, and RAD51 were found to be involved, opening new avenues for functional genomic studies.
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Affiliation(s)
- Rubens L Monte-Neto
- Biotecnologia Aplicada ao Estudo de Patógenos (BAP) - Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brasil.
| | - Christopher Fernandez-Prada
- Faculté de Médecine Vétérinaire, Département de Pathologie et Microbiologie, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Nilmar S Moretti
- Laboratório de Biologia Molecular de Patógenos (LBMP) - Departamento de Microbiologia, Imunologia e Parasitologia - Universidade Federal de São Paulo, São Paulo, SP, Brasil
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11
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Patiño LH, Muñoz M, Pavia P, Muskus C, Shaban M, Paniz-Mondolfi A, Ramírez JD. Filling the gaps in Leishmania naiffi and Leishmania guyanensis genome plasticity. G3-GENES GENOMES GENETICS 2021; 12:6427546. [PMID: 34791158 PMCID: PMC8727957 DOI: 10.1093/g3journal/jkab377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/15/2021] [Indexed: 11/22/2022]
Abstract
Insufficient and irregular data reports on Leishmaniasis, issuing from the developing world, have left much to be desired in terms of understanding the molecular signatures producing distinct infectious phenotypes of the disease. Herein, we report on the complete genome sequencing of Leishmania naiffi and Leishmania guyanensis, sampled from patients in regions of Colombia and Venezuela. In this study, the isolates of cutaneous lesions from both species presented limited structural variation at the chromosomal level, low gene copy number variation, and high genetic heterogeneity. We compared these sequences to the reference genomes hitherto related from Brazil and French Guyana. Although of the same species, we note a consequential genomic disparity between the Venezuelan and French Guyanese isolates of L. guyanensis. Although less significant on the global schema of cutaneous and mucosal disease, such genomic studies of L. naiffi and L. guyanensis substantiate the gaps in understanding of the molecular architecture and multivariate clinical pictures of Leishmaniasis, on an international scale.
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Affiliation(s)
- Luz H Patiño
- Facultad de Ciencias Naturales, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Facultad de Ciencias Naturales, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá, Colombia
| | | | - Carlos Muskus
- Programa de Estudios y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, Medellín, Colombia
| | - Maryia Shaban
- Incubadora Venezolana de la Ciencia/Instituto de Investigaciones Biomédicas IDB, Barquisimeto, Venezuela
| | - Alberto Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan David Ramírez
- Facultad de Ciencias Naturales, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá, Colombia.,Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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12
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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: 11] [Impact Index Per Article: 3.7] [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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13
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Antonia AL, Barnes AB, Martin AT, Wang L, Ko DC. Variation in Leishmania chemokine suppression driven by diversification of the GP63 virulence factor. PLoS Negl Trop Dis 2021; 15:e0009224. [PMID: 34710089 PMCID: PMC8577781 DOI: 10.1371/journal.pntd.0009224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 11/09/2021] [Accepted: 10/17/2021] [Indexed: 11/18/2022] Open
Abstract
Leishmaniasis is a neglected tropical disease with diverse outcomes ranging from self-healing lesions, to progressive non-healing lesions, to metastatic spread and destruction of mucous membranes. Although resolution of cutaneous leishmaniasis is a classic example of type-1 immunity leading to self-healing lesions, an excess of type-1 related inflammation can contribute to immunopathology and metastatic spread. Leishmania genetic diversity can contribute to variation in polarization and robustness of the immune response through differences in both pathogen sensing by the host and immune evasion by the parasite. In this study, we observed a difference in parasite chemokine suppression between the Leishmania (L.) subgenus and the Viannia (V.) subgenus, which is associated with severe immune-mediated pathology such as mucocutaneous leishmaniasis. While Leishmania (L.) subgenus parasites utilize the virulence factor and metalloprotease glycoprotein-63 (gp63) to suppress the type-1 associated host chemokine CXCL10, L. (V.) panamensis did not suppress CXCL10. To understand the molecular basis for the inter-species variation in chemokine suppression, we used in silico modeling to identify a putative CXCL10-binding site on GP63. The putative CXCL10 binding site is in a region of gp63 under significant positive selection, and it varies from the L. major wild-type sequence in all gp63 alleles identified in the L. (V.) panamensis reference genome. Mutating wild-type L. (L.) major gp63 to the L. (V.) panamensis sequence at the putative binding site impaired cleavage of CXCL10 but not a non-specific protease substrate. Notably, Viannia clinical isolates confirmed that L. (V.) panamensis primarily encodes non-CXCL10-cleaving gp63 alleles. In contrast, L. (V.) braziliensis has an intermediate level of activity, consistent with this species having more equal proportions of both alleles. Our results demonstrate how parasite genetic diversity can contribute to variation in immune responses to Leishmania spp. infection that may play critical roles in the outcome of infection. Leishmaniasis is a neglected tropical disease caused by Leishmania parasites and spread by the bites of infected sand flies. Most cases of leishmaniasis present as self-healing sores that are resolved by a balanced immune response. Other cases of leishmaniasis involve spread to sites distant from the original bite, including damage of the inner surfaces of the mouth and nose. These cases of leishmaniasis involve an excessive immune response. Leishmania parasites produce virulence factor proteins, such as GP63, to trick the immune system into mounting a weaker response. GP63 specifically degrades signaling proteins that attract and activate certain immune cells. Here, we demonstrate that Leishmania parasite species have evolved to differ in their ability to degrade signaling proteins. In Leishmania species known to cause more immune-mediated tissue damage, the GP63 virulence factor has evolved to not degrade specific immune signaling proteins, thus attracting, and activating more immune cells. Our results demonstrate how diversity among Leishmania parasite species can contribute to variation in immune responses that may play critical roles in the outcome of infection.
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Affiliation(s)
- Alejandro L. Antonia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Alyson B. Barnes
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Amelia T. Martin
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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14
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De Martin A, Lütge M, Stanossek Y, Engetschwiler C, Cupovic J, Brown K, Demmer I, Broglie MA, Geuking MB, Jochum W, McCoy KD, Stoeckli SJ, Ludewig B. Distinct microbial communities colonize tonsillar squamous cell carcinoma. Oncoimmunology 2021; 10:1945202. [PMID: 34367729 PMCID: PMC8312615 DOI: 10.1080/2162402x.2021.1945202] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Squamous cell carcinoma of the tonsil is one of the most frequent cancers of the oropharynx. The escalating rate of tonsil cancer during the last decades is associated with the increase of high risk-human papilloma virus (HR-HPV) infections. While the microbiome in oropharyngeal malignant diseases has been characterized to some extent, the microbial colonization of HR-HPV-associated tonsil cancer remains largely unknown. Using 16S rRNA gene amplicon sequencing, we have characterized the microbiome of human palatine tonsil crypts in patients suffering from HR-HPV-associated tonsil cancer in comparison to a control cohort of adult sleep apnea patients. We found an increased abundance of the phyla Firmicutes and Actinobacteria in tumor patients, whereas the abundance of Spirochetes and Synergistetes was significantly higher in the control cohort. Furthermore, the accumulation of several genera such as Veillonella, Streptococcus and Prevotella_7 in tonsillar crypts was associated with tonsil cancer. In contrast, Fusobacterium, Prevotella and Treponema_2 were enriched in sleep apnea patients. Machine learning-based bacterial species analysis indicated that a particular bacterial composition in tonsillar crypts is tumor-predictive. Species-specific PCR-based validation in extended patient cohorts confirmed that differential abundance of Filifactor alocis and Prevotella melaninogenica is a distinct trait of tonsil cancer. This study shows that tonsil cancer patients harbor a characteristic microbiome in the crypt environment that differs from the microbiome of sleep apnea patients on all phylogenetic levels. Moreover, our analysis indicates that profiling of microbial communities in distinct tonsillar niches provides microbiome-based avenues for the diagnosis of tonsil cancer.
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Affiliation(s)
- Angelina De Martin
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Mechthild Lütge
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Yves Stanossek
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland.,Department of Otorhinolaryngology, Head and Neck Surgery, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | | | - Jovana Cupovic
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Kirsty Brown
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Izadora Demmer
- Institute of Pathology, Kantonsspital Sankt Gallen, St. Gallen, Switzerland
| | - Martina A Broglie
- Department of Otorhinolaryngology - Head and Neck Surgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Markus B Geuking
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute of Chronic Diseases; Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Wolfram Jochum
- Institute of Pathology, Kantonsspital Sankt Gallen, St. Gallen, Switzerland
| | - Kathy D McCoy
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Sandro J Stoeckli
- Department of Otorhinolaryngology, Head and Neck Surgery, Kantonsspital St.Gallen, St. Gallen, Switzerland
| | - Burkhard Ludewig
- Institute of Immunobiology, Kantonsspital St.Gallen, St. Gallen, Switzerland.,Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
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15
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Dos Santos AGA, da Silva MGL, Carneiro EL, de Lima LL, Fernandes ACBS, Silveira TGV, Sant'Ana DDMG, Nogueira-Melo GDA. A New Target Organ of Leishmania (Viannia) braziliensis Chronic Infection: The Intestine. Front Cell Infect Microbiol 2021; 11:687499. [PMID: 34336715 PMCID: PMC8317265 DOI: 10.3389/fcimb.2021.687499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/22/2021] [Indexed: 01/22/2023] Open
Abstract
Leishmania (Viannia) braziliensis is one of the main causes of cutaneous leishmaniasis in the Americas. This species presents genetic polymorphism that can cause destructive lesions in oral, nasal, and oropharyngeal tracts. In a previous study, the parasite caused several histopathological changes to hamster ileums. Our study evaluates immune response components, morphological changes, and effects on neurons in the ileums of hamsters infected by three different strains of L. (V.) braziliensis in two infection periods. For the experiment, we separated hamsters into four groups: a control group and three infected groups. Infected hamsters were euthanized 90- or 120-days post infection. We used three strains of L. (V.) braziliensis: the reference MHOM/BR/1975/M2903 and two strains isolated from patients who had different responses to Glucantime® treatment (MHOM/BR/2003/2314 and MHOM/BR/2000/1655). After laparotomy, ileums were collected for histological processing, biochemical analysis, and evaluation of neurons in the myenteric and submucosal plexuses of the enteric nervous system (ENS). The results demonstrated the increase of blood leukocytes after the infection. Optical microscopy analysis showed histopathological changes with inflammatory infiltrates, edemas, ganglionitis, and Leishmania amastigotes in the ileums of infected hamsters. We observed changes in the organ histoarchitecture of infected hamsters when compared to control groups, such as thicker muscular and submucosa layers, deeper and wider crypts, and taller and broader villi. The number of intraepithelial lymphocytes and TGF-β-immunoreactive cells increased in all infected groups when compared to the control groups. Mast cells increased with longer infection periods. The infection also caused remodeling of intestinal collagen and morphometry of myenteric and submucosal plexus neurons; but this effect was dependent on infection duration. Our results show that L. (V.) braziliensis infection caused time-dependent alterations in hamster ileums. This was demonstrated by the reduction of inflammatory cells and the increase of tissue regeneration factors at 120 days of infection. The infected groups demonstrated different profiles in organ histoarchitecture, migration of immune cells, and morphometry of ENS neurons. These findings suggest that the small intestine (or at least the ileum) is a target organ for L. (V.) braziliensis infection, as the infection caused changes that were dependent on duration and strain.
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Affiliation(s)
| | | | - Erick Lincoln Carneiro
- Department of Clinical Analysis and Biomedicine, Universidade Estadual de Maringá, Maringá, Brazil
| | - Lainy Leiny de Lima
- Department of Morphological Sciences, Universidade Estadual de Maringá, Maringá, Brazil
| | | | | | - Debora de Mello Gonçales Sant'Ana
- Biosciences and Physiopathology Program, Universidade Estadual de Maringá, Maringá, Brazil.,Department of Morphological Sciences, Universidade Estadual de Maringá, Maringá, Brazil
| | - Gessilda de Alcantara Nogueira-Melo
- Biosciences and Physiopathology Program, Universidade Estadual de Maringá, Maringá, Brazil.,Department of Clinical Analysis and Biomedicine, Universidade Estadual de Maringá, Maringá, Brazil
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16
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Serine proteases profiles of Leishmania (Viannia) braziliensis clinical isolates with distinct susceptibilities to antimony. Sci Rep 2021; 11:14234. [PMID: 34244581 PMCID: PMC8271011 DOI: 10.1038/s41598-021-93665-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/29/2021] [Indexed: 11/10/2022] Open
Abstract
Glucantime (SbV) is the first-line treatment against American Tegumentary Leishmaniasis. Resistance cases to this drug have been reported and related to host characteristics and parasite phenotypes. In this study, 12 Leishmania (Viannia) braziliensis isolates from patients that presented clinical cure (Responders—R) and relapse or therapeutic failure (Non-responders—NR) after treatment with antimony, were analyzed. These parasites were assessed by in vitro susceptibility to SbIII and SbV, serine proteases activity measured with substrate (z-FR-AMC) and specific inhibitors (TLCK, AEBSF and PMSF). In vitro susceptibility of axenic amastigotes to SbIII showed a significant difference between R and NR groups. The protease assays showed that TLCK inhibited almost 100% of activity in both axenic amastigotes and promastigotes while AEBSF inhibited around 70%, and PMSF showed lower inhibition of some isolates. Principal component and clustering analysis performed with these data yielded one homogeneous cluster with only NR isolates and three heterogeneous clusters with R and NR isolates. Additionally, differential expression of subtilisins (LbrM.13.0860 and LbrM.28.2570) and TXNPx (LbrM.15.1080) was evaluated in promastigotes and axenic amastigotes from both groups. The results showed a higher expression of LbrM.13.0860 and LbrM.15.1080 genes in axenic amastigotes, while LbrM.28.2570 gene had the lowest expression in all isolates, regardless of the parasite form. The data presented here show a phenotypic heterogeneity among the parasites, suggesting that exploration of in vitro phenotypes based on SbIII and serine proteases profiles can aid in the characterization of L. (V.) braziliensis clinical isolates.
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