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Pennance T, Calvelo J, Tennessen JA, Burd R, Cayton J, Bollmann SR, Blouin MS, Spaan JM, Hoffmann FG, Ogara G, Rawago F, Andiego K, Mulonga B, Odhiambo M, Loker ES, Laidemitt MR, Lu L, Iriarte A, Odiere MR, Steinauer ML. The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni. BMC Genomics 2024; 25:192. [PMID: 38373909 PMCID: PMC10875847 DOI: 10.1186/s12864-024-10103-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Control and elimination of schistosomiasis is an arduous task, with current strategies proving inadequate to break transmission. Exploration of genetic approaches to interrupt Schistosoma mansoni transmission, the causative agent for human intestinal schistosomiasis in sub-Saharan Africa and South America, has led to genomic research of the snail vector hosts of the genus Biomphalaria. Few complete genomic resources exist, with African Biomphalaria species being particularly underrepresented despite this being where the majority of S. mansoni infections occur. Here we generate and annotate the first genome assembly of Biomphalaria sudanica sensu lato, a species responsible for S. mansoni transmission in lake and marsh habitats of the African Rift Valley. Supported by whole-genome diversity data among five inbred lines, we describe orthologs of immune-relevant gene regions in the South American vector B. glabrata and present a bioinformatic pipeline to identify candidate novel pathogen recognition receptors (PRRs). RESULTS De novo genome and transcriptome assembly of inbred B. sudanica originating from the shoreline of Lake Victoria (Kisumu, Kenya) resulted in a haploid genome size of ~ 944.2 Mb (6,728 fragments, N50 = 1.067 Mb), comprising 23,598 genes (BUSCO = 93.6% complete). The B. sudanica genome contains orthologues to all described immune genes/regions tied to protection against S. mansoni in B. glabrata, including the polymorphic transmembrane clusters (PTC1 and PTC2), RADres, and other loci. The B. sudanica PTC2 candidate immune genomic region contained many PRR-like genes across a much wider genomic region than has been shown in B. glabrata, as well as a large inversion between species. High levels of intra-species nucleotide diversity were seen in PTC2, as well as in regions linked to PTC1 and RADres orthologues. Immune related and putative PRR gene families were significantly over-represented in the sub-set of B. sudanica genes determined as hyperdiverse, including high extracellular diversity in transmembrane genes, which could be under pathogen-mediated balancing selection. However, no overall expansion in immunity related genes was seen in African compared to South American lineages. CONCLUSIONS The B. sudanica genome and analyses presented here will facilitate future research in vector immune defense mechanisms against pathogens. This genomic/transcriptomic resource provides necessary data for the future development of molecular snail vector control/surveillance tools, facilitating schistosome transmission interruption mechanisms in Africa.
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Affiliation(s)
- Tom Pennance
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon, OR, USA.
| | - Javier Calvelo
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Universidad de La República, Montevideo, 11600, Uruguay
| | | | - Ryan Burd
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon, OR, USA
| | - Jared Cayton
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon, OR, USA
| | | | | | - Johannie M Spaan
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon, OR, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, USA
| | - George Ogara
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Fredrick Rawago
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Kennedy Andiego
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Boaz Mulonga
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Meredith Odhiambo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Eric S Loker
- Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Martina R Laidemitt
- Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Lijun Lu
- Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Universidad de La República, Montevideo, 11600, Uruguay
| | - Maurice R Odiere
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Michelle L Steinauer
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon, OR, USA.
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Pennance T, Calvelo J, Tennessen JA, Burd R, Cayton J, Bollmann SR, Blouin MS, Spaan JM, Hoffmann FG, Ogara G, Rawago F, Andiego K, Mulonga B, Odhiambo M, Loker ES, Laidemitt MR, Lu L, Iriarte A, Odiere M, Steinauer ML. The genome and transcriptome of the snail Biomphalaria sudanica s.l.: Immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni. bioRxiv 2023:2023.11.01.565203. [PMID: 37961413 PMCID: PMC10635097 DOI: 10.1101/2023.11.01.565203] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background Control and elimination of schistosomiasis is an arduous task, with current strategies proving inadequate to break transmission. Exploration of genetic approaches to interrupt Schistosoma mansoni transmission, the causative agent for human intestinal schistosomiasis in sub-Saharan Africa and South America, has led to genomic research of the snail vector hosts of the genus Biomphalaria. Few complete genomic resources exist, with African Biomphalaria species being particularly underrepresented despite this being where the majority of S. mansoni infections occur. Here we generate and annotate the first genome assembly of Biomphalaria sudanica sensu lato, a species responsible for S. mansoni transmission in lake and marsh habitats of the African Rift Valley. Supported by whole-genome diversity data among five inbred lines, we describe orthologs of immune-relevant gene regions in the South American vector B. glabrata and present a bioinformatic pipeline to identify candidate novel pathogen recognition receptors (PRRs). Results De novo genome and transcriptome assembly of inbred B. sudanica originating from the shoreline of Lake Victoria (Kisumu, Kenya) resulted in a haploid genome size of ~944.2 Mb (6732 fragments, N50=1.067 Mb), comprising 23,598 genes (BUSCO=93.6% complete). The B. sudanica genome contains orthologues to all described immune genes/regions tied to protection against S. mansoni in B. glabrata. The B. sudanica PTC2 candidate immune genomic region contained many PRR-like genes across a much wider genomic region than has been shown in B. glabrata, as well as a large inversion between species. High levels of intra-species nucleotide diversity were seen in PTC2, as well as in regions linked to PTC1 and RADres orthologues. Immune related and putative PRR gene families were significantly over-represented in the sub-set of B. sudanica genes determined as hyperdiverse, including high extracellular diversity in transmembrane genes, which could be under pathogen-mediated balancing selection. However, no overall expansion in immunity related genes were seen in African compared to South American lineages. Conclusions The B. sudanica genome and analyses presented here will facilitate future research in vector immune defense mechanisms against pathogens. This genomic/transcriptomic resource provides necessary data for the future development of molecular snail vector control/surveillance tools, facilitating schistosome transmission interruption mechanisms in Africa.
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Affiliation(s)
- Tom Pennance
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon OR, USA
| | - Javier Calvelo
- Laboratorio Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo 11600, Uruguay
| | | | - Ryan Burd
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon OR, USA
| | - Jared Cayton
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon OR, USA
| | | | | | - Johannie M Spaan
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon OR, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS USA
| | - George Ogara
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Fredrick Rawago
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Kennedy Andiego
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Boaz Mulonga
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Meredith Odhiambo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), P. O. Box 1578-40100, Kisumu, Kenya
| | - Eric S Loker
- Department of Biology, Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131, U.S.A
| | - Martina R Laidemitt
- Department of Biology, Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131, U.S.A
| | - Lijun Lu
- Department of Biology, Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131, U.S.A
| | - Andrés Iriarte
- Laboratorio Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo 11600, Uruguay
| | - Maurice Odiere
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS USA
| | - Michelle L Steinauer
- College of Osteopathic Medicine of the Pacific - Northwest, Western University of Health Sciences, Lebanon OR, USA
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Wiegand RE, Mwinzi PNM, Montgomery SP, Chan YL, Andiego K, Omedo M, Muchiri G, Ogutu MO, Rawago F, Odiere MR, Karanja DMS, Secor WE. A Persistent Hotspot of Schistosoma mansoni Infection in a Five-Year Randomized Trial of Praziquantel Preventative Chemotherapy Strategies. J Infect Dis 2017; 216:1425-1433. [PMID: 28968877 PMCID: PMC5913648 DOI: 10.1093/infdis/jix496] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [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: 07/21/2017] [Accepted: 09/13/2017] [Indexed: 12/28/2022] Open
Abstract
Background Persistent hotspots have been described after mass drug administration (MDA) for the control of schistosomiasis, but they have not been studied during the course of a multiyear MDA program. Methods In data from a 5-year study of school-based and village-wide preventive chemotherapy strategies for Schistosoma mansoni, spatial scan statistics were used to find infection hotspots in 3 populations: 5- to 8-year-olds, 9- to 12-year-olds, and adults. Negative binomial regression was used to analyze changes from baseline, and receiver operating characteristic analyses were used to predict which villages would reach prevalence and intensity endpoints. Results We identified a persistent hotspot, not associated with study arm, where S. mansoni infection prevalence and intensity did not decrease as much as in villages outside the hotspot. Significant differences from baseline were realized after 1 year of MDA: we did not identify factors that moderated this relationship. Villages meeting specified endpoints at year 5 were predicted from prior year data with moderately high sensitivity and specificity. Conclusions The MDA strategies were less effective at reducing prevalence and intensity in the hotspot compared with other villages. Villages that reached year 5 endpoints could be detected earlier, which may provide the opportunity to amend intervention strategies.
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Affiliation(s)
- Ryan E Wiegand
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Pauline N M Mwinzi
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Susan P Montgomery
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Kennedy Andiego
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Martin Omedo
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Geoffrey Muchiri
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Michael O Ogutu
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Fredrick Rawago
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Maurice R Odiere
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Diana M S Karanja
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - W Evan Secor
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
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Onkanga IO, Mwinzi PNM, Muchiri G, Andiego K, Omedo M, Karanja DMS, Wiegand RE, Secor WE, Montgomery SP. Impact of two rounds of praziquantel mass drug administration on Schistosoma mansoni infection prevalence and intensity: a comparison between community wide treatment and school based treatment in western Kenya. Int J Parasitol 2016; 46:439-45. [PMID: 26940547 PMCID: PMC4920687 DOI: 10.1016/j.ijpara.2016.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 11/30/2015] [Revised: 01/21/2016] [Accepted: 01/22/2016] [Indexed: 11/16/2022]
Abstract
Comparison of mass drug administration approaches for schistosomiasis was performed. The study presents results of a mid-term analysis of a 5 year study. School-based and community-wide distribution yielded a similar prevalence decrease. School-based distribution had a greater impact on intensity of infection.
This study compared the effectiveness of the community-wide treatment and school-based treatment approaches in the control of Schistosoma mansoni infections in villages with ⩾25% prevalence in western Kenya. Stool samples from first year students, 9–12 year olds and adults (20–55 years) were analyzed by the Kato–Katz technique for S. mansoni eggs. After two rounds of treatment, S. mansoni prevalence and intensity levels significantly declined in both treatment approaches. Prevalence comparisons between the two approaches did not show any significant differences following treatment. However, infection intensity levels in the 9–12 year old school-attending pupils were significantly higher in the community-wide treatment arm than in the school-based treatment arm. Nevertheless, significant reductions in S. mansoni infection prevalence and intensity levels were achieved among school-age children regardless of the treatment approach used.
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Affiliation(s)
- Isaac O Onkanga
- Center for Global Health Research, Kenya Medical Research Institute, P.O. Box 1578-40100, Kisumu, Kenya
| | - Pauline N M Mwinzi
- Center for Global Health Research, Kenya Medical Research Institute, P.O. Box 1578-40100, Kisumu, Kenya
| | - Geoffrey Muchiri
- Center for Global Health Research, Kenya Medical Research Institute, P.O. Box 1578-40100, Kisumu, Kenya
| | - Kennedy Andiego
- Center for Global Health Research, Kenya Medical Research Institute, P.O. Box 1578-40100, Kisumu, Kenya
| | - Martin Omedo
- Center for Global Health Research, Kenya Medical Research Institute, P.O. Box 1578-40100, Kisumu, Kenya
| | - Diana M S Karanja
- Center for Global Health Research, Kenya Medical Research Institute, P.O. Box 1578-40100, Kisumu, Kenya
| | - Ryan E Wiegand
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Rd, N.E., Atlanta, GA 30329, USA
| | - W Evan Secor
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Rd, N.E., Atlanta, GA 30329, USA.
| | - Susan P Montgomery
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, 1600 Clifton Rd, N.E., Atlanta, GA 30329, USA
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