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Murphy M, Greenhouse B. MOIRE: A software package for the estimation of allele frequencies and effective multiplicity of infection from polyallelic data. bioRxiv 2023:2023.10.03.560769. [PMID: 37873322 PMCID: PMC10592951 DOI: 10.1101/2023.10.03.560769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Malaria parasite genetic data can provide insight into parasite phenotypes, evolution, and transmission. However, estimating key parameters such as allele frequencies, multiplicity of infection (MOI), and within-host relatedness from genetic data has been challenging, particularly in the presence of multiple related coinfecting strains. Existing methods often rely on single nucleotide polymorphism (SNP) data and do not account for within-host relatedness. In this study, we introduce a Bayesian approach called MOIRE (Multiplicity Of Infection and allele frequency REcovery), designed to estimate allele frequencies, MOI, and within-host relatedness from genetic data subject to experimental error. Importantly, MOIRE is flexible in accommodating both polyallelic and SNP data, making it adaptable to diverse genotyping panels. We also introduce a novel metric, the effective MOI ( e M O I ) , which integrates MOI and within-host relatedness, providing a robust and interpretable measure of genetic diversity. Using extensive simulations and real-world data from a malaria study in Namibia, we demonstrate the superior performance of MOIRE over naive estimation methods, accurately estimating MOI up to 7 with moderate sized panels of diverse loci (e.g. microhaplotypes). MOIRE also revealed substantial heterogeneity in population mean MOI and mean relatedness across health districts in Namibia, suggesting detectable differences in transmission dynamics. Notably, e M O I emerges as a portable metric of within-host diversity, facilitating meaningful comparisons across settings, even when allele frequencies or genotyping panels are different. MOIRE represents an important addition to the analysis toolkit for malaria population dynamics. Compared to existing software, MOIRE enhances the accuracy of parameter estimation and enables more comprehensive insights into within-host diversity and population structure. Additionally, MOIRE's adaptability to diverse data sources and potential for future improvements make it a valuable asset for research on malaria and other organisms, such as other eukaryotic pathogens. MOIRE is available as an R package at https://eppicenter.github.io/moire/.
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Affiliation(s)
- Maxwell Murphy
- Department of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
- EPPIcenter program, Division of HIV, ID and Global Medicine, University of California, San Francisco, CA, USA
| | - Bryan Greenhouse
- EPPIcenter program, Division of HIV, ID and Global Medicine, University of California, San Francisco, CA, USA
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Roeb E. Interleukin-13 (IL-13)-A Pleiotropic Cytokine Involved in Wound Healing and Fibrosis. Int J Mol Sci 2023; 24:12884. [PMID: 37629063 PMCID: PMC10454844 DOI: 10.3390/ijms241612884] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
The liver, as a central metabolic organ, is systemically linked to metabolic-inflammatory diseases. In the pathogenesis of the metabolic syndrome, inflammatory and metabolic interactions between the intestine, liver, and adipose tissue lead to the progression of hepatic steatosis to metabolic-dysfunction-associated steatohepatitis (MASH) and consecutive MASH-induced fibrosis. Clinical and animal studies revealed that IL-13 might be protective in the development of MASH through both the preservation of metabolic functions and Th2-polarized inflammation in the liver and the adipose tissue. In contrast, IL-13-associated loss of mucosal gut barrier function and IL-13-associated enhanced hepatic fibrosis may contribute to the progression of MASH. However, there are only a few publications on the effect of IL-13 on metabolic diseases and possible therapies to influence them. In this review article, different aspects of IL-13-associated effects on the liver and metabolic liver diseases, which are partly contradictory, are summarized and discussed on the basis of the recent literature.
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Affiliation(s)
- Elke Roeb
- Department of Gastroenterology, Justus Liebig University Giessen, Klinikstr. 33, 35392 Giessen, Germany
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Reguera-gómez M, Valero MA, Artigas P, De Elías-escribano A, Fantozzi MC, Luzón-garcía MP, Salas-coronas J, Boissier J, Mas-coma S, Bargues MD. Geographical Influence on Morphometric Variability of Genetically “Pure” Schistosoma haematobium Eggs from Sub-Saharan Migrants in Spain. Trop Med Infect Dis 2023; 8:144. [PMID: 36977146 PMCID: PMC10054267 DOI: 10.3390/tropicalmed8030144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/14/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
Schistosome eggs play a key role in schistosomiasis diagnosis and research. The aim of this work is to morphogenetically study the eggs of Schistosoma haematobium found in sub-Saharan migrants present in Spain, analyzing their morphometric variation in relation to the geographical origin of the parasite (Mali, Mauritania and Senegal). Only eggs considered “pure” S. haematobium by genetic characterization (rDNA ITS-2 and mtDNA cox1) have been used. A total of 162 eggs obtained from 20 migrants from Mali, Mauritania and Senegal were included in the study. Analyses were made by the Computer Image Analysis System (CIAS). Following a previously standardized methodology, seventeen measurements were carried out on each egg. The morphometric analysis of the three morphotypes detected (round, elongated and spindle) and the biometric variations in relation to the country of origin of the parasite on the egg phenotype were carried out by canonical variate analysis. Mahalanobis distances, when all egg measurements were analyzed, showed differences between: (i) Mali-Mauritania, Mali-Senegal and Mauritania-Senegal in the round morphotype; (ii) Mali-Mauritania and Mauritania-Senegal in the elongated morphotype; and (iii) Mauritania-Senegal in the spindle morphotype. Mahalanobis distances, when spine variables were analyzed, showed differences between Mali-Senegal in the round morphotype. In conclusion, this is the first phenotypic study performed on individually genotyped “pure” S. haematobium eggs, allowing the assessment of the intraspecific morphological variations associated with the geographical origin of the schistosome eggs.
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Angora EK, Vangraefschepe A, Allienne JF, Menan H, Coulibaly JT, Meïté A, Raso G, Winkler MS, Yavo W, Touré AO, N'Goran EK, Zinsstag J, Utzinger J, Balmer O, Boissier J. Population genetic structure of Schistosoma haematobium and Schistosoma haematobium × Schistosoma bovis hybrids among school-aged children in Côte d'Ivoire. Parasite 2022; 29:23. [PMID: 35522066 PMCID: PMC9074780 DOI: 10.1051/parasite/2022023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 04/04/2022] [Indexed: 11/29/2022] Open
Abstract
While population genetics of Schistosoma haematobium have been investigated in West Africa, only scant data are available from Côte d’Ivoire. The purpose of this study was to analyze both genetic variability and genetic structure among S. haematobium populations and to quantify the frequency of S. haematobium × S. bovis hybrids in school-aged children in different parts of Côte d’Ivoire. Urine samples were subjected to a filtration method and examined microscopically for Schistosoma eggs in four sites in the western and southern parts of Côte d’Ivoire. A total of 2692 miracidia were collected individually and stored on Whatman® FTA cards. Of these, 2561 miracidia were successfully genotyped for species and hybrid identification using rapid diagnostic multiplex mitochondrial cox1 PCR and PCR Restriction Fragment Length Polymorphism (PCR-RFLP) analysis of the nuclear ITS2 region. From 2164 miracidia, 1966 (90.9%) were successfully genotyped using at least 10 nuclear microsatellite loci to investigate genetic diversity and population structure. Significant differences were found between sites in all genetic diversity indices and genotypic differentiation was observed between the site in the West and the three sites in the East. Analysis at the infrapopulation level revealed clustering of parasite genotypes within individual children, particularly in Duekoué (West) and Sikensi (East). Of the six possible cox1-ITS2 genetic profiles obtained from miracidia, S. bovis cox1 × S. haematobium ITS2 (42.0%) was the most commonly observed in the populations. We identified only 15 miracidia (0.7%) with an S. bovis cox1 × S. bovis ITS2 genotype. Our study provides new insights into the population genetics of S. haematobium and S. haematobium × S. bovis hybrids in humans in Côte d’Ivoire and we advocate for researching hybrid schistosomes in animals such as rodents and cattle in Côte d’Ivoire.
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Affiliation(s)
- Etienne K Angora
- Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel, Switzerland - University of Basel, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland - Unité de Formation et de Recherche Sciences Pharmaceutiques et Biologiques, Université Félix Houphouët-Boigny, BPV 34 Abidjan, Côte d'Ivoire
| | - Alexane Vangraefschepe
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, 66860 Perpignan, France
| | - Jean-François Allienne
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, 66860 Perpignan, France
| | - Hervé Menan
- Unité de Formation et de Recherche Sciences Pharmaceutiques et Biologiques, Université Félix Houphouët-Boigny, BPV 34 Abidjan, Côte d'Ivoire
| | - Jean T Coulibaly
- Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel, Switzerland - University of Basel, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland - Unité de Formation et de Recherche Biosciences, Université Félix Houphouët-Boigny, 22 BP 770, Abidjan 22, Côte d'Ivoire - Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, 01 BP 1303, Abidjan 01, Côte d'Ivoire
| | - Aboulaye Meïté
- Programme National de Lutte contre les Maladies Tropicales Négligées à Chimiothérapie Préventive, 06 BP 6394, Abidjan 06, Côte d'Ivoire
| | - Giovanna Raso
- Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel, Switzerland - University of Basel, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
| | - Mirko S Winkler
- Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel, Switzerland - University of Basel, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
| | - William Yavo
- Unité de Formation et de Recherche Sciences Pharmaceutiques et Biologiques, Université Félix Houphouët-Boigny, BPV 34 Abidjan, Côte d'Ivoire
| | - André O Touré
- Institut Pasteur de Côte d'Ivoire, BPV 490 Abidjan, Côte d'Ivoire
| | - Eliézer K N'Goran
- Unité de Formation et de Recherche Biosciences, Université Félix Houphouët-Boigny, 22 BP 770, Abidjan 22, Côte d'Ivoire - Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, 01 BP 1303, Abidjan 01, Côte d'Ivoire
| | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel, Switzerland - University of Basel, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel, Switzerland - University of Basel, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
| | - Oliver Balmer
- Swiss Tropical and Public Health Institute, P.O. Box, CH-4002 Basel, Switzerland - University of Basel, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
| | - Jérôme Boissier
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, 66860 Perpignan, France
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Onyekwere AM, Rey O, Allienne JF, Nwanchor MC, Alo M, Uwa C, Boissier J. Population Genetic Structure and Hybridization of Schistosoma haematobium in Nigeria. Pathogens 2022; 11:pathogens11040425. [PMID: 35456103 PMCID: PMC9026724 DOI: 10.3390/pathogens11040425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 11/21/2022] Open
Abstract
Background: Schistosomiasis is a major poverty-related disease caused by dioecious parasitic flatworms of the genus Schistosoma with a health impact on both humans and animals. Hybrids of human urogenital schistosome and bovine intestinal schistosome have been reported in humans in several of Nigeria’s neighboring West African countries. No empirical studies have been carried out on the genomic diversity of Schistosoma haematobium in Nigeria. Here, we present novel data on the presence and prevalence of hybrids and the population genetic structure of S. haematobium. Methods: 165 Schistosoma-positive urine samples were obtained from 12 sampling sites in Nigeria. Schistosoma haematobium eggs from each sample were hatched and each individual miracidium was picked and preserved in Whatman® FTA cards for genomic analysis. Approximately 1364 parasites were molecularly characterized by rapid diagnostic multiplex polymerase chain reaction (RD-PCR) for mitochondrial DNA gene (Cox1 mtDNA) and a subset of 1136 miracidia were genotyped using a panel of 18 microsatellite markers. Results: No significant difference was observed in the population genetic diversity (p > 0.05), though a significant difference was observed in the allelic richness of the sites except sites 7, 8, and 9 (p < 0.05). Moreover, we observed two clusters of populations: west (populations 1−4) and east (populations 7−12). Of the 1364 miracidia genotyped, 1212 (89%) showed an S. bovis Cox1 profile and 152 (11%) showed an S. haematobium cox1 profile. All parasites showed an S. bovis Cox1 profile except for some at sites 3 and 4. Schistosoma miracidia full genotyping showed 59.3% of the S. bovis ITS2 allele. Conclusions: This study provides novel insight into hybridization and population genetic structure of S. haematobium in Nigeria. Our findings suggest that S. haematobium x S. bovis hybrids are common in Nigeria. More genomic studies on both human- and animal-infecting parasites are needed to ascertain the role of animals in schistosome transmission.
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Affiliation(s)
- Amos Mathias Onyekwere
- Department of Biology, Alex Ekwueme Federal University, Ndufu-Alike, Abakaliki PMB 1010, Nigeria; (A.M.O.); (C.U.)
- IHPE, University Montpellier, CNRS, Ifremer, University Perpignan Via Domitia, F-66000 Perpignan, France; (O.R.); (J.-F.A.)
| | - Olivier Rey
- IHPE, University Montpellier, CNRS, Ifremer, University Perpignan Via Domitia, F-66000 Perpignan, France; (O.R.); (J.-F.A.)
| | - Jean-François Allienne
- IHPE, University Montpellier, CNRS, Ifremer, University Perpignan Via Domitia, F-66000 Perpignan, France; (O.R.); (J.-F.A.)
| | | | - Moses Alo
- Department of Microbiology, Alex Ekwueme Federal University, Ndufu-Alike, Abakaliki PMB 1010, Nigeria;
| | - Clementina Uwa
- Department of Biology, Alex Ekwueme Federal University, Ndufu-Alike, Abakaliki PMB 1010, Nigeria; (A.M.O.); (C.U.)
| | - Jerome Boissier
- IHPE, University Montpellier, CNRS, Ifremer, University Perpignan Via Domitia, F-66000 Perpignan, France; (O.R.); (J.-F.A.)
- Correspondence: ; Tel.: +33-430-192-312
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Long JC, Taylor SE, Barbosa LM, Silva LK, Reis MG, Blanton RE. Cryptic population structure and transmission dynamics uncovered for Schistosoma mansoni populations by genetic analyses. Sci Rep 2022; 12:1059. [PMID: 35058485 PMCID: PMC8776789 DOI: 10.1038/s41598-022-04776-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/23/2021] [Indexed: 11/18/2022] Open
Abstract
Patterns of diversity in pathogen genomes provide a window into the spatiotemporal spread of disease. In this study, we tested the hypothesis that Schistosoma mansoni parasites form genetic clusters that coincide with the communities of their human hosts. We also looked for genetic clustering of parasites at the sub-community level. Our data consists of 14 microsatellite DNA markers, typed from pooled DNA samples from [Formula: see text] infected individuals living in three Brazilian communities. We found a one-to-one correspondence between genetic clusters found by K-means cluster analysis and communities when [Formula: see text]. These clusters are also easily identified in a neighbor-joining tree and principal coordinates plots. K-means analysis with [Formula: see text] also reveals genetic clusters of parasites at the sub-community level. These sub-clusters also appear on the neighbor-joining tree and principal coordinates plots. A surprising finding is a genetic relationship between subgroups in widely separated human communities. This connection suggests the existence of common transmission sites that have wide influence. In summary, the genetic structure of S. mansoni in Brazil juxtaposes local isolation that is occasionally broken by long-range migration. Permanent eradication of schistosomes will require both local efforts and the identification of regional infection reservoirs.
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Affiliation(s)
- Jeffrey C Long
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA.
| | - Sarah E Taylor
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Lucio M Barbosa
- Bahiana School of Medicine and Public Health, Av. Silveira Martins, n 3386, Salvador, Bahia, 41150-100, Brazil
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Ministry of Health, Waldemar Falcão Street, 121, Salvador, Bahia, Brazil
| | - Luciano K Silva
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Ministry of Health, Waldemar Falcão Street, 121, Salvador, Bahia, Brazil
| | - Mitermayer G Reis
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Ministry of Health, Waldemar Falcão Street, 121, Salvador, Bahia, Brazil
- Faculty of Medicine of Bahia, Federal University of Bahia, Praça Conselheiro Almeida Couto, s/n - Largo do Terreiro de Jesus, Salvador, BA, 40025-010, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, 60 College Street, P.O. Box 208034, New Haven, CT, USA
| | - Ronald E Blanton
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2306, New Orleans, LA, 70112, USA
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Kovach JD, Long JC, Barbosa LM, Moura ARSS, Silva LK, Reis MG, Blanton RE. A Schistosoma mansoni tri- and tetramer microsatellite catalog for genetic population diversity and differentiation. Int J Parasitol 2021; 51:1007-1014. [PMID: 34022195 DOI: 10.1016/j.ijpara.2021.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 02/08/2023]
Abstract
All Schistosoma mansoni tri- and tetranucleotide repeat microsatellites published as of December 2018 were identified. All 52 were evaluated for autosomal location, strength of amplification, scorability and behavior as single-copy loci by polyacrylamide and capillary gel electrophoresis. Of these, 27 were unique, autosomal, polymorphic, easily scored and single copy as assessed on pooled adult worm DNA from two different continental origins and adult worm clones. These microsatellites were distributed across all seven autosomal chromosomes. On laboratory strains their heterozygosity ranged from 0.22 to 0.77. Individual markers had 5-13 alleles, allelic richness of 2-10 and an effective allele number of 1.3-8.14. Those infected by Schistosoma mansoni carry many genetically distinct, sexually reproducing parasites, therefore, for an individual infection the complete allele frequency profile of their progeny consists of a pool of DNA from multiple diploid eggs. Using a set of 25 microsatellites, we calculated allele frequency profiles of eggs in fecal samples from people in two Brazilian communities separated by 6 km: Jenipapo (n = 80) and Volta do Rio (n = 38). There were no a priori characteristics that could predict the performance of markers in natural infections based on their performance with laboratory strains. Increasing marker number did not change accuracy for differentiation and diversity but did improve precision. Our data suggest that using a random set of 10-20 microsatellites appears to result in values that exhibit low standard deviations for diversity and differentiation indices. All identified microsatellites as well as PCR conditions, allele size, primer sequences and references for all tri- and tetramer microsatellites markers presented in this work are available at: https://sites.google.com/case.edu/cwru-and-fiocruz-wdrc/home.
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Affiliation(s)
- Jeffrey D Kovach
- Center for Global Health and Diseases, Case Western Reserve University, Biomedical Research Building, 2109 Adelbert Rd., Cleveland, OH 44106, USA
| | - Jeffrey C Long
- University of New Mexico, Department of Anthropology, Albuquerque, 1 University of New Mexico, NM 87131, USA
| | - Lúcio M Barbosa
- Bahiana School of Medicine and Public Health, Av. Silveira Martins, n° 3386, Salvador, Bahia 41150-100, Brazil; Gonçalo Moniz Research Centre, Oswaldo Cruz Foundation, Rua Waldemar Falcão, 121 Brotas, Salvador, Bahia 40296-710, Brazil
| | - Ana Rafaela Silva Simões Moura
- Gonçalo Moniz Research Centre, Oswaldo Cruz Foundation, Rua Waldemar Falcão, 121 Brotas, Salvador, Bahia 40296-710, Brazil
| | - Luciano K Silva
- Gonçalo Moniz Research Centre, Oswaldo Cruz Foundation, Rua Waldemar Falcão, 121 Brotas, Salvador, Bahia 40296-710, Brazil
| | - Mitermayer G Reis
- Gonçalo Moniz Research Centre, Oswaldo Cruz Foundation, Rua Waldemar Falcão, 121 Brotas, Salvador, Bahia 40296-710, Brazil; School of Medicine, Federal University of Bahia, Salvador, Bahia, Brazil; Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Ronald E Blanton
- Department of Tropical Medicine, Tulane School of Public Health and Tropical Medicine, Tidewater Building, 1440 Canal Street, New Orleans, LA 70112, USA.
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Berger DJ, Crellen T, Lamberton PHL, Allan F, Tracey A, Noonan JD, Kabatereine NB, Tukahebwa EM, Adriko M, Holroyd N, Webster JP, Berriman M, Cotton JA. Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration. Nat Commun 2021; 12:4776. [PMID: 34362894 PMCID: PMC8346512 DOI: 10.1038/s41467-021-24958-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 07/06/2021] [Indexed: 02/07/2023] Open
Abstract
Control and elimination of the parasitic disease schistosomiasis relies on mass administration of praziquantel. Whilst these programmes reduce infection prevalence and intensity, their impact on parasite transmission and evolution is poorly understood. Here we examine the genomic impact of repeated mass drug administration on Schistosoma mansoni populations with documented reduced praziquantel efficacy. We sequenced whole-genomes of 198 S. mansoni larvae from 34 Ugandan children from regions with contrasting praziquantel exposure. Parasites infecting children from Lake Victoria, a transmission hotspot, form a diverse panmictic population. A single round of treatment did not reduce this diversity with no apparent population contraction caused by long-term praziquantel use. We find evidence of positive selection acting on members of gene families previously implicated in praziquantel action, but detect no high frequency functionally impactful variants. As efforts to eliminate schistosomiasis intensify, our study provides a foundation for genomic surveillance of this major human parasite.
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Affiliation(s)
- Duncan J Berger
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
- Department of Pathology and Pathogen Biology, Centre for Emerging, Endemic and Exotic Diseases, Royal Veterinary College, University of London, Herts, UK.
| | - Thomas Crellen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Poppy H L Lamberton
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK
- Institute for Biodiversity, Animal Health, and Comparative Medicine, and Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Fiona Allan
- The Natural History Museum, Department of Life Sciences, London, UK
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jennifer D Noonan
- Institute of Parasitology, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Narcis B Kabatereine
- Vector Borne & Neglected Tropical Disease Control Division, Ministry of Health, Kampala, Uganda
| | - Edridah M Tukahebwa
- Vector Borne & Neglected Tropical Disease Control Division, Ministry of Health, Kampala, Uganda
| | - Moses Adriko
- Vector Borne & Neglected Tropical Disease Control Division, Ministry of Health, Kampala, Uganda
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Joanne P Webster
- Department of Pathology and Pathogen Biology, Centre for Emerging, Endemic and Exotic Diseases, Royal Veterinary College, University of London, Herts, UK.
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK.
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
| | - James A Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
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Neves MI, Gower CM, Webster JP, Walker M. Revisiting density-dependent fecundity in schistosomes using sibship reconstruction. PLoS Negl Trop Dis 2021; 15:e0009396. [PMID: 33983965 DOI: 10.1371/journal.pntd.0009396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 05/25/2021] [Accepted: 04/19/2021] [Indexed: 11/19/2022] Open
Abstract
The stability of parasite populations is regulated by density-dependent processes occurring at different stages of their life cycle. In dioecious helminth infections, density-dependent fecundity is one such regulatory process that describes the reduction in egg production by female worms in high worm burden within-host environments. In human schistosomiasis, the operation of density-dependent fecundity is equivocal and investigation is hampered by the inaccessibility of adult worms that are located intravascularly. Current understanding is almost exclusively limited to data collected from two human autopsy studies conducted over 40 years ago, with subsequent analyses having reached conflicting conclusions. Whether egg production is regulated in a density-dependent manner is key to predicting the effectiveness of interventions targeting the elimination of schistosomiasis and to the interpretation of parasitological data collected during monitoring and evaluation activities. Here, we revisit density-dependent fecundity in the two most globally important human Schistosoma spp. using a statistical modelling approach that combines molecular inference on the number of parents/adult worms in individual human hosts with parasitological egg count data from mainland Tanzania and Zanzibar. We find a non-proportional relationship between S. haematobium egg counts and inferred numbers of female worms, providing the first clear evidence of density-dependent fecundity in this schistosome species. We do not find robust evidence for density-dependent fecundity in S. mansoni because of high sensitivity to some modelling assumptions and the lower statistical power of the available data. We discuss the strengths and limitations of our model-based analytical approach and its potential for improving our understanding of density dependence in schistosomiasis and other human helminthiases earmarked for elimination. Schistosomiasis is a devastating disease of poverty currently estimated to infect over 220 million people. It is caused by parasitic worms (blood flukes) that live for, on average, 5–7 years inside the blood vessels of infected hosts and produce hundreds of eggs daily. Whether egg production is regulated in a density-dependent manner, and if so under what conditions, has been controversial for schistosomiasis, and investigation is hampered due to the inaccessible location of adult worms. Resolving this fundamental question is important because density dependencies determine the resilience of helminthiases to interventions. Here, we have revisited this longstanding and unresolved question of density-dependent fecundity in human schistosomes using a novel statistical modelling approach that combines information from molecular and parasitological data. We report the first clear evidence of density-dependent fecundity in S. haematobium, the causative agent of millions of cases of urogenital schistosomiasis. Our findings are of critical importance both to mathematical modellers predicting the impact of interventions and to public health policy makers striving to meet the 2030 elimination targets for schistosomiasis. This study also serves to illustrate a new biostatistical approach that could be applied to investigate density dependencies in other helminthiases where adult parasites are inaccessible.
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Mawa PA, Kincaid-Smith J, Tukahebwa EM, Webster JP, Wilson S. Schistosomiasis Morbidity Hotspots: Roles of the Human Host, the Parasite and Their Interface in the Development of Severe Morbidity. Front Immunol 2021; 12:635869. [PMID: 33790908 PMCID: PMC8005546 DOI: 10.3389/fimmu.2021.635869] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/25/2021] [Indexed: 12/14/2022] Open
Abstract
Schistosomiasis is the second most important human parasitic disease in terms of socioeconomic impact, causing great morbidity and mortality, predominantly across the African continent. For intestinal schistosomiasis, severe morbidity manifests as periportal fibrosis (PPF) in which large tracts of macro-fibrosis of the liver, visible by ultrasound, can occlude the main portal vein leading to portal hypertension (PHT), sequelae such as ascites and collateral vasculature, and ultimately fatalities. For urogenital schistosomiasis, severe morbidity manifests as pathology throughout the urinary system and genitals, and is a definitive cause of squamous cell bladder carcinoma. Preventative chemotherapy (PC) programmes, delivered through mass drug administration (MDA) of praziquantel (PZQ), have been at the forefront of schistosomiasis control programmes in sub-Saharan Africa since their commencement in Uganda in 2003. However, despite many successes, 'biological hotspots' (as distinct from 'operational hotspots') of both persistent high transmission and morbidity remain. In some areas, this failure to gain control of schistosomiasis has devastating consequences, with not only persistently high infection intensities, but both "subtle" and severe morbidity remaining prevalent. These hotspots highlight the requirement to revisit research into severe morbidity and its mechanisms, a topic that has been out of favor during times of PC implementation. Indeed, the focality and spatially-structured epidemiology of schistosomiasis, its transmission persistence and the morbidity induced, has long suggested that gene-environmental-interactions playing out at the host-parasite interface are crucial. Here we review evidence of potential unique parasite factors, host factors, and their gene-environmental interactions in terms of explaining differential morbidity profiles in the human host. We then take the situation of schistosomiasis mansoni within the Albertine region of Uganda as a case study in terms of elucidating the factors behind the severe morbidity observed and the avenues and directions for future research currently underway within a new research and clinical trial programme (FibroScHot).
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Affiliation(s)
- Patrice A. Mawa
- Immunomodulation and Vaccines Programme, Medical Research Council-Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine (MRC/UVRI and LSHTM) Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Julien Kincaid-Smith
- Centre for Emerging, Endemic and Exotic Diseases (CEEED), Department of Pathobiology and Population Sciences (PPS), Royal Veterinary College, University of London, Herts, United Kingdom
| | | | - Joanne P. Webster
- Centre for Emerging, Endemic and Exotic Diseases (CEEED), Department of Pathobiology and Population Sciences (PPS), Royal Veterinary College, University of London, Herts, United Kingdom
| | - Shona Wilson
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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Rey O, Webster BL, Huyse T, Rollinson D, Van den Broeck F, Kincaid-Smith J, Onyekwere A, Boissier J. Population genetics of African Schistosoma species. Infect Genet Evol 2021; 89:104727. [PMID: 33486128 DOI: 10.1016/j.meegid.2021.104727] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/09/2021] [Accepted: 01/13/2021] [Indexed: 02/06/2023]
Abstract
Blood flukes within the genus Schistosoma (schistosomes) are responsible for the major disease, schistosomiasis, in tropical and sub-tropical areas. This disease is predominantly present on the African continent with more than 85% of the human cases. Schistosomes are also parasites of veterinary importance infecting livestock and wildlife. Schistosoma population genetic structure and diversity are important characteristics that may reflect variations in selection pressures such as those induced by host (mammalian and snail) environments, habitat change, migration and also treatment/control interventions, all of which also shape speciation and evolution of the whole Schistosoma genus. Investigations into schistosome population genetic structure, diversity and evolution has been an area of important debate and research. Supported by advances in molecular techniques with capabilities for multi-locus genetic analyses for single larvae schistosome genetic investigations have greatly progressed in the last decade. This paper aims to review the genetic studies of both animal and human infecting schistosome. Population genetic structures are reviewed at different spatial scales: local, regional or continental (i.e. phylogeography). Within species genetic diversities are discussed compared and the compounding factors discussed, including the effect of mass drug administration. Finally, the ability for intra-species hybridisation questions species integrities and poses many questions in relation to the natural epidemiology of co-endemic species. Here we review molecularly confirmed hybridisation events (in relation to human disease) and discuss the possible impact for ongoing and future control and elimination.
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Affiliation(s)
- O Rey
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan, France
| | - B L Webster
- Wolfson Wellcome Biomedical Laboratories, Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom; London Centre for Neglected Tropical Disease Research, Imperial College London School of Public Health, London W2 1PG, United Kingdom
| | - T Huyse
- Department of Biology, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium; Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
| | - D Rollinson
- Wolfson Wellcome Biomedical Laboratories, Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom; London Centre for Neglected Tropical Disease Research, Imperial College London School of Public Health, London W2 1PG, United Kingdom
| | - F Van den Broeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium; Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - J Kincaid-Smith
- Centre for Emerging, Endemic and Exotic Diseases (CEEED), Department of Pathobiology and Population Sciences (PPS), Royal Veterinary College, University of London, Hawkshead Campus, Herts AL9 7TA, United Kingdom
| | - A Onyekwere
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan, France
| | - J Boissier
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan, France.
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Kebede T, Bech N, Allienne JF, Olivier R, Erko B, Boissier J. Genetic evidence for the role of non-human primates as reservoir hosts for human schistosomiasis. PLoS Negl Trop Dis 2020; 14:e0008538. [PMID: 32898147 PMCID: PMC7500647 DOI: 10.1371/journal.pntd.0008538] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 09/18/2020] [Accepted: 06/29/2020] [Indexed: 12/20/2022] Open
Abstract
Background Schistosomiasis is a chronic parasitic disease, that affects over 207 million people and causes over 200,000 deaths annually, mainly in sub-Saharan Africa. Although many health measures have been carried out to limit parasite transmission, significant numbers of non-human primates such as Chlorocebus aethiops (Ch. aethiops) (vervet) and Papio anubis (baboon) are infected with S. mansoni, notably in Ethiopia, where they are expected to have potentially significant implications for transmission and control efforts. Objective The objective of this study was to assess and compare the genetic diversity and population structure of S. mansoni isolates from human and non-human primates free-ranging in close proximity to villages in selected endemic areas of Ethiopia. Methods A cross-sectional study was conducted in three transmission sites: Bochesa, Kime and Fincha. A total of 2,356 S. mansoni miracidia were directly isolated from fecal specimens of 104 hosts (i.e. 60 human hosts and 44 non-human primates). We performed DNA extraction and PCR amplification using fourteen microsatellite loci. Results At population scale we showed strong genetic structure between the three sample sites. At the definitive host scale, we observed that host factors can shape the genetic composition of parasite infra-populations. First, in male patients, we observed a positive link between parasite genetic diversity and the age of the patients. Second, we observed a difference in genetic diversity which was high in human males, medium in human females and low in non-human primates (NHPs). Finally, whatever the transmission site no genetic structure was observed between human and non-human primates, however, there appears to be little barriers, if any, host specificity of the S. mansoni populations with cross-host infections. Conclusion Occurrence of infection of a single host with multiple S. mansoni strains and inter- and intra-host genetic variations was observed. Substantial genetic diversity and gene flow across the S. mansoni population occurred at each site and non-human primates likely play a role in local transmission and maintenance of infection. Therefore, public health and wildlife professionals should work together to improve disease control and elimination strategies. Schistosomiasis is a chronic disease caused by flukes (trematodes). The definitive host spectrum of schistosomes, whether human, non-human primates (NHPs) or other mammals, is highly dependent on the schistosome species concerned. Genetic diversity and population structure studies of S. mansoni have provided insights into the variation of natural populations. Understanding S. mansoni genetic diversity and population structure of isolates from human and non-human primate hosts living in close proximity showed the occurrence of infection of a single host with multiple S. mansoni strains and inter- and intra-host genetic variations. In this article, the researchers assert the fact that genetic approach reveals that parasites from the three different sites are independent. Thus, we could consider the three sites as geographical replicates showing the influence of NHPs in parasitic transmission in Ethiopia. This study provides insights into the epidemiology, genetic diversity and population structure of S. mansoni in human and non-human primates in Ethiopia, all of which are crucial for the control of schistosomiasis.
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Affiliation(s)
- Tadesse Kebede
- Department of Microbiology, Immunology and Parasitology, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Laboratoire Interactions Hôtes-Pathogènes-Environnements (IHPE), UMR 5244 CNRS, University of Perpignan, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
- * E-mail:
| | - Nicolas Bech
- Laboratory of Ecologie et Biologie des Interactions (EBI), UMR CNRS 7267, Poitiers University, Poitiers, France
| | - Jean-François Allienne
- Laboratoire Interactions Hôtes-Pathogènes-Environnements (IHPE), UMR 5244 CNRS, University of Perpignan, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Rey Olivier
- Laboratoire Interactions Hôtes-Pathogènes-Environnements (IHPE), UMR 5244 CNRS, University of Perpignan, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jerome Boissier
- Laboratoire Interactions Hôtes-Pathogènes-Environnements (IHPE), UMR 5244 CNRS, University of Perpignan, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
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Abstract
While disease and outbreaks are mainly clonal for bacteria and other asexually reproducing organisms, sexual reproduction in schistosomes and other helminths usually results in unique individuals. For sexually reproducing organisms, the traits conserved in clones will instead be conserved in the group of organisms that tends to breed together, the population. While the same tools are applied to characterize DNA, how results are interpreted can be quite different at times (see another article in this collection, http://www.asmscience.org/content/journal/microbiolspec/10.1128/microbiolspec.AME-0002-2018). It is difficult to know what the real effect any control program has on the parasite population without assessing the health of this population, how they respond to the control measure, and how they recover, if they do. This review, part of the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases, concentrates on one approach using pooled samples to study schistosome populations and shows how this and other approaches have contributed to our understanding of this parasite family's biology and epidemiology. *This article is part of a curated collection.
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Faust CL, Crotti M, Moses A, Oguttu D, Wamboko A, Adriko M, Adekanle EK, Kabatereine N, Tukahebwa EM, Norton AJ, Gower CM, Webster JP, Lamberton PHL. Two-year longitudinal survey reveals high genetic diversity of Schistosoma mansoni with adult worms surviving praziquantel treatment at the start of mass drug administration in Uganda. Parasit Vectors 2019; 12:607. [PMID: 31881923 PMCID: PMC6935072 DOI: 10.1186/s13071-019-3860-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 12/17/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND A key component of schistosomiasis control is mass drug administration with praziquantel. While control interventions have been successful in several endemic regions, mass drug administration has been less effective in others. Here we focus on the impact of repeated praziquantel treatment on the population structure and genetic diversity of Schistosoma mansoni. METHODS We examined S. mansoni epidemiology, population genetics, and variation in praziquantel susceptibility in parasites isolated from children across three primary schools in a high endemicity region at the onset of the Ugandan National Control Programme. Children were sampled at 11 timepoints over two years, including one week and four weeks post-praziquantel treatment to evaluate short-term impacts on clearance and evidence of natural variation in susceptibility to praziquantel. RESULTS Prevalence of S. mansoni was 85% at baseline. A total of 3576 miracidia larval parasites, isolated from 203 individual children, were genotyped at seven loci. Overall, genetic diversity was high and there was low genetic differentiation, indicating high rates of parasite gene flow. Schistosome siblings were found both pre-treatment and four weeks post-treatment, demonstrating adult worms surviving treatment and natural praziquantel susceptibility variation in these populations at the beginning of mass drug administration. However, we did not find evidence for selection on these parasites. While genetic diversity decreased in the short-term (four weeks post-treatment), diversity did not decrease over the entire period despite four rounds of mass treatment. Furthermore, within-host genetic diversity was affected by host age, host sex, infection intensity and recent praziquantel treatment. CONCLUSIONS Our findings suggest that praziquantel treatments have short-term impacts on these parasite populations but impacts were transient and no long-term reduction in genetic diversity was observed. High gene flow reduces the likelihood of local adaptation, so even though parasites surviving treatment were observed, these were likely to be diluted at the beginning of the Ugandan National Control Programme. Together, these results suggest that MDA in isolation may be insufficient to reduce schistosome populations in regions with high genetic diversity and gene flow.
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Affiliation(s)
- Christina L. Faust
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Marco Crotti
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Arinaitwe Moses
- Vector Control Division, Ministry of Health, Kampala, Uganda
| | - David Oguttu
- Vector Control Division, Ministry of Health, Kampala, Uganda
| | - Aidah Wamboko
- Vector Control Division, Ministry of Health, Kampala, Uganda
| | - Moses Adriko
- Vector Control Division, Ministry of Health, Kampala, Uganda
| | - Elizabeth K. Adekanle
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | | | | | - Alice J. Norton
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Charlotte M. Gower
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Joanne P. Webster
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead, UK
| | - Poppy H. L. Lamberton
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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15
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Abstract
BACKGROUND Sibship reconstruction is a form of parentage analysis that can be used to identify the number of helminth parental genotypes infecting individual hosts using genetic data on only their offspring. This has the potential to be used for estimating individual worm burdens when adult parasites are otherwise inaccessible, the case for many of the most globally important human helminthiases and neglected tropical diseases. Yet methods of inferring worm burdens from sibship reconstruction data on numbers of unique parental genotypes are lacking, limiting the method's scope of application. RESULTS We developed a novel statistical method for estimating female worm burdens from data on the number of unique female parental genotypes derived from sibship reconstruction. We illustrate the approach using genotypic data on Schistosoma mansoni (miracidial) offspring collected from schoolchildren in Tanzania. We show how the bias and precision of worm burden estimates critically depends on the number of sampled offspring and we discuss strategies for obtaining sufficient sample sizes and for incorporating judiciously formulated prior information to improve the accuracy of estimates. CONCLUSIONS This work provides a novel approach for estimating individual-level worm burdens using genetic data on helminth offspring. This represents a step towards a wider scope of application of parentage analysis techniques. We discuss how the method could be used to assist in the interpretation of monitoring and evaluation data collected during mass drug administration programmes targeting human helminthiases and to help resolve outstanding questions on key population biological processes that govern the transmission dynamics of these neglected tropical diseases.
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Affiliation(s)
- M Inês Neves
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hawkshead Lane, Hatfield, UK. .,London Centre for Neglected Tropical Disease Research, London, UK.
| | - Joanne P Webster
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hawkshead Lane, Hatfield, UK.,London Centre for Neglected Tropical Disease Research, London, UK
| | - Martin Walker
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hawkshead Lane, Hatfield, UK.,London Centre for Neglected Tropical Disease Research, London, UK
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Djuikwo-Teukeng FF, Kouam Simo A, Allienne JF, Rey O, Njayou Ngapagna A, Tchuem-Tchuente LA, Boissier J. Population genetic structure of Schistosoma bovis in Cameroon. Parasit Vectors 2019; 12:56. [PMID: 30678712 PMCID: PMC6346511 DOI: 10.1186/s13071-019-3307-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/08/2019] [Indexed: 11/24/2022] Open
Abstract
Background Schistosomiasis is neglected tropical parasitic disease affecting both humans and animals. Due to the human health impact, population genetic studies have focused on the three main human-infecting schistosome species: Schistosoma mansoni, S. haematobium and S. japonicum. Here we present novel data on the population genetic structure of Schistosoma bovis, a highly widespread and prevalent schistosome infecting ruminants, and therefore of veterinary importance. Methods Adult S. bovis were sampled in the two main abattoirs of Cameroon (Yaoundé and Douala). Twenty-two cows originating from four distinct localities were sampled and a total of 218 parasites were recovered. All parasites were genotyped using a panel of 14 microsatellite markers and a sub-sample of 91 parasites were sequenced and characterized with the mitochondrial (cox1) and nuclear (ITS) genetic markers. Results No significant difference in allelic richness, heterozygosity, nucleotide diversity and haplotype diversity was observed between the populations. Additionally, no strong genetic structure was observed at the country scale. Our data also show that S. bovis is more polymorphic than its sister species, S. haematobium, and that the haplotype diversity is similar to that of S. mansoni while the nucleotide diversity does not significantly differ from that of S. haematobium. The resulting negative Tajima’s D* and Fu and Li’s D* indices could be a signature of population demographic expansion. No S. haematobium/S. bovis hybrids were observed in our populations, thus all samples were considered as pure S. bovis. Conclusions This study provides novel insights into genetic diversity and population genetic structure of S. bovis. No strong genetic structure was observed at the country scale but some genetic indices could be associated as a signature of population demographic expansion. Electronic supplementary material The online version of this article (10.1186/s13071-019-3307-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Alain Kouam Simo
- Université des Montagnes, Faculty of Heath Science, PO Box: 208, Bangangté, Cameroon
| | - Jean-François Allienne
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, F-66860, Perpignan, France
| | - Olivier Rey
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, F-66860, Perpignan, France
| | | | - Louis Albert Tchuem-Tchuente
- Centre for Schistosomiasis and Parasitology, Yaoundé, Cameroon.,Laboratory of Parasitology and Ecology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Jérôme Boissier
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, F-66860, Perpignan, France.
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17
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Le Clec'h W, Chevalier FD, McDew-White M, Allan F, Webster BL, Gouvras AN, Kinunghi S, Tchuem Tchuenté LA, Garba A, Mohammed KA, Ame SM, Webster JP, Rollinson D, Emery AM, Anderson TJC. Whole genome amplification and exome sequencing of archived schistosome miracidia. Parasitology 2018; 145:1739-47. [PMID: 29806576 DOI: 10.1017/S0031182018000811] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Adult schistosomes live in the blood vessels and cannot easily be sampled from humans, so archived miracidia larvae hatched from eggs expelled in feces or urine are commonly used for population genetic studies. Large collections of archived miracidia on FTA cards are now available through the Schistosomiasis Collection at the Natural History Museum (SCAN). Here we describe protocols for whole genome amplification of Schistosoma mansoni and Schistosome haematobium miracidia from these cards, as well as real time PCR quantification of amplified schistosome DNA. We used microgram quantities of DNA obtained for exome capture and sequencing of single miracidia, generating dense polymorphism data across the exome. These methods will facilitate the transition from population genetics, using limited numbers of markers to population genomics using genome-wide marker information, maximising the value of collections such as SCAN.
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Gower CM, Gehre F, Marques SR, Lamberton PHL, Lwambo NJ, Webster JP. Phenotypic and genotypic monitoring of Schistosoma mansoni in Tanzanian schoolchildren five years into a preventative chemotherapy national control programme. Parasit Vectors 2017; 10:593. [PMID: 29197426 PMCID: PMC5712074 DOI: 10.1186/s13071-017-2533-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 11/13/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Schistosoma mansoni is a parasite of profound medical importance. Current control focusses on mass praziquantel (PZQ) treatment of populations in endemic areas, termed Preventative Chemotherapy (PC). Large-scale PC programmes exert prolonged selection pressures on parasites with the potential for, direct and/or indirect, emergence of drug resistance. Molecular methods can help monitor genetic changes of schistosome populations over time and in response to drug treatment, as well as estimate adult worm burdens through parentage analysis. Furthermore, methods such as in vitro drug sensitivity assays help phenotype in vivo parasite genotypic drug efficacy. METHODS We conducted combined in vitro PZQ efficacy testing with population genetic analyses of S. mansoni collected from children from two schools in 2010, five years after the introduction of a National Control Programme. Children at one school had received four annual PZQ treatments and the other school had received two mass treatments in total. We compared genetic differentiation, indices of genetic diversity, and estimated adult worm burden from parasites collected in 2010 with samples collected in 2005 (before the control programme began) and in 2006 (six months after the first PZQ treatment). Using 2010 larval samples, we also compared the genetic similarity of those with high and low in vitro sensitivity to PZQ. RESULTS We demonstrated that there were individual parasites with reduced PZQ susceptibility in the 2010 collections, as evidenced by our in vitro larval behavioural phenotypic assay. There was no evidence, however, that miracidia showing phenotypically reduced susceptibility clustered together genetically. Molecular analysis also demonstrated a significant reduction of adult worm load over time, despite little evidence of reduction in parasite infection intensity, as measured by egg output. Genetic diversity of infections did not reduce over time, despite changes in the genetic composition of the parasite populations. CONCLUSIONS Genotypic and phenotypic monitoring did not indicate a selective sweep, as may be expected if PZQ treatment was selecting a small number of related "resistant" parasites, but there was evidence of genetic changes at the population level over time. Genetic data were used to estimate adult worm burdens, which unlike parasite infection intensity, showed reductions over time, suggesting the relaxation of negative density-dependent constraints on parasite fecundity with PZQ treatment. We thereby demonstrated that density-dependence in schistosome populations may complicate evaluation and monitoring of control programmes.
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Affiliation(s)
- Charlotte M. Gower
- Centre for Endemic, Emerging and Exotic Diseases, The Royal Veterinary College, University of London, London, AL9 7TA UK
- Department of Infectious Disease Epidemiology, Imperial College, Faculty of Medicine, W2 1PG, London, UK
| | - Florian Gehre
- Department of Infectious Disease Epidemiology, Imperial College, Faculty of Medicine, W2 1PG, London, UK
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sara R. Marques
- Department of Life Sciences, Imperial College, Faculty of Medicine, London, UK
| | - Poppy H. L. Lamberton
- Department of Infectious Disease Epidemiology, Imperial College, Faculty of Medicine, W2 1PG, London, UK
- Institute of Biodiversity, Animal Health & Comparative Medicine & Wellcome Centre for Molecular Parasitology, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Nicholas J. Lwambo
- Mwanza Research Centre, National Institute for Medical Research, Mwanza, Tanzania
| | - Joanne P. Webster
- Centre for Endemic, Emerging and Exotic Diseases, The Royal Veterinary College, University of London, London, AL9 7TA UK
- Department of Infectious Disease Epidemiology, Imperial College, Faculty of Medicine, W2 1PG, London, UK
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Moendeg KJ, Angeles JMM, Nakao R, Leonardo LR, Fontanilla IKC, Goto Y, Kirinoki M, Villacorte EA, Rivera PT, Inoue N, Chigusa Y, Kawazu SI. Geographic strain differentiation of Schistosoma japonicum in the Philippines using microsatellite markers. PLoS Negl Trop Dis 2017; 11:e0005749. [PMID: 28692692 PMCID: PMC5519200 DOI: 10.1371/journal.pntd.0005749] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 07/20/2017] [Accepted: 06/25/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Microsatellites have been found to be useful in determining genetic diversities of various medically-important parasites which can be used as basis for an effective disease management and control program. In Asia and Africa, the identification of different geographical strains of Schistosoma japonicum, S. haematobium and S. mansoni as determined through microsatellites could pave the way for a better understanding of the transmission epidemiology of the parasite. Thus, the present study aims to apply microsatellite markers in analyzing the populations of S. japonicum from different endemic areas in the Philippines for possible strain differentiation. METHODOLOGY/ PRINCIPAL FINDINGS Experimental mice were infected using the cercariae of S. japonicum collected from infected Oncomelania hupensis quadrasi snails in seven endemic municipalities. Adult worms were harvested from infected mice after 45 days of infection and their DNA analyzed against ten previously characterized microsatellite loci. High genetic diversity was observed in areas with high endemicity. The degree of genetic differentiation of the parasite population between endemic areas varies. Geographical separation was considered as one of the factors accounting for the observed difference between populations. Two subgroups have been observed in one of the study sites, suggesting that co-infection with several genotypes of the parasite might be present in the population. Clustering analysis showed no particular spatial structuring between parasite populations from different endemic areas. This result could possibly suggest varying degrees of effects of the ongoing control programs and the existing gene flow in the populations, which might be attributed to migration and active movement of infected hosts from one endemic area to another. CONCLUSIONS/ SIGNIFICANCE Based on the results of the study, it is reasonable to conclude that genetic diversity could be one possible criterion to assess the infection status in highly endemic areas. Genetic surveillance using microsatellites is therefore important to predict the ongoing gene flow and degree of genetic diversity, which indirectly reflects the success of the control program in schistosomiasis-endemic areas.
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Affiliation(s)
- Kharleezelle J. Moendeg
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
- Department of Biology, School of Science and Engineering, Ateneo de Manila University, Quezon City, Manila, Philippines
| | - Jose Ma M. Angeles
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Lydia R. Leonardo
- Department of Parasitology, College of Public Health, University of the Philippines Manila, Philippines
| | | | - Yasuyuki Goto
- Laboratory of Molecular Immunology, Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masashi Kirinoki
- Department of Tropical Medicine and Parasitology, Dokkyo Medical University School of Medicine, Tochigi, Japan
| | - Elena A. Villacorte
- Department of Parasitology, College of Public Health, University of the Philippines Manila, Philippines
| | - Pilarita T. Rivera
- Department of Parasitology, College of Public Health, University of the Philippines Manila, Philippines
| | - Noboru Inoue
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Yuichi Chigusa
- Department of Tropical Medicine and Parasitology, Dokkyo Medical University School of Medicine, Tochigi, Japan
| | - Shin-ichiro Kawazu
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
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20
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Thaenkham U, Phuphisut O, Nuamtanong S, Yoonuan T, Sa-Nguankiat S, Vonghachack Y, Belizario VY, Dung DT, Dekumyoy P, Waikagul J. Genetic differences among Haplorchis taichui populations in Indochina revealed by mitochondrial COX1 sequences. J Helminthol 2017; 91:597-604. [PMID: 27411962 DOI: 10.1017/S0022149X1600050X] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Haplorchis taichui is an intestinal heterophyid fluke that is pathogenic to humans. It is widely distributed in Asia, with a particularly high prevalence in Indochina. Previous work revealed that the lack of gene flow between three distinct populations of Vietnamese H. taichui can be attributed to their geographic isolation with no interconnected river basins. To test the hypothesis that interconnected river basins allow gene flow between otherwise isolated populations of H. taichui, as previously demonstrated for another trematode, Opisthorchis viverrini, we compared the genetic structures of seven populations of H. taichui from various localities in the lower Mekong Basin, in Thailand and Laos, with those in Vietnam, using the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene. To determine the gene flow between these H. taichui populations, we calculated their phylogenetic relationships, genetic distances and haplotype diversity. Each population showed very low nucleotide diversity at this locus. However, high levels of genetic differentiation between the populations indicated very little gene flow. A phylogenetic analysis divided the populations into four clusters that correlated with the country of origin. The negligible gene flow between the Thai and Laos populations, despite sharing the Mekong Basin, caused us to reject our hypothesis. Our data suggest that the distribution of H. taichui populations was incidentally associated with national borders.
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