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Ihara F, Kyan H, Takashima Y, Ono F, Hayashi K, Matsuo T, Igarashi M, Nishikawa Y, Hikosaka K, Sakamoto H, Nakamura S, Motooka D, Yamauchi K, Ichikawa-Seki M, Fukumoto S, Sasaki M, Ikadai H, Kusakisako K, Ohari Y, Yoshida A, Sasai M, Grigg ME, Yamamoto M. Far-East Asian Toxoplasma isolates share ancestry with North and South/Central American recombinant lineages. Nat Commun 2024; 15:4278. [PMID: 38778039 PMCID: PMC11111807 DOI: 10.1038/s41467-024-47625-6] [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: 08/16/2023] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
Toxoplasma gondii is a global protozoan pathogen. Clonal lineages predominate in Europe, North America, Africa, and China, whereas highly recombinant parasites are endemic in South/Central America. Far East Asian T. gondii isolates are not included in current global population genetic structure analyses at WGS resolution. Here we report a genome-wide population study that compared eight Japanese and two Chinese isolates against representative worldwide T. gondii genomes using POPSICLE, a novel population structure analyzing software. Also included were 7 genomes resurrected from non-viable isolates by target enrichment sequencing. Visualization of the genome structure by POPSICLE shows a mixture of Chinese haplogroup (HG) 13 haploblocks introgressed within the genomes of Japanese HG2 and North American HG12. Furthermore, two ancestral lineages were identified in the Japanese strains; one lineage shares a common ancestor with HG11 found in both Japanese strains and North American HG12. The other ancestral lineage, found in T. gondii isolates from a small island in Japan, is admixed with genetically diversified South/Central American strains. Taken together, this study suggests multiple ancestral links between Far East Asian and American T. gondii strains and provides insight into the transmission history of this cosmopolitan organism.
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Affiliation(s)
- Fumiaki Ihara
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
- Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Immunoparasitology, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hisako Kyan
- Okinawa Prefectural Institute of Health and Environment, Uruma, Okinawa, 904-2241, Japan
| | - Yasuhiro Takashima
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1112, Japan
- Center for One Medicine Translational Research, COMIT, Gifu University, Gifu, 501-1112, Japan
| | - Fumiko Ono
- Department of Veterinary Associated Science, Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime, 794-8555, Japan
| | - Kei Hayashi
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime, 794-8555, Japan
| | - Tomohide Matsuo
- Joint Faculty of Veterinary Medicine Kagoshima University, Kagoshima, 890-0065, Japan
| | - Makoto Igarashi
- National Research Center for Protozoan Diseases, University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Yoshifumi Nishikawa
- National Research Center for Protozoan Diseases, University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Kenji Hikosaka
- Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, Chiba, 260-0856, Japan
| | - Hirokazu Sakamoto
- Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, Chiba, 260-0856, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kiyoshi Yamauchi
- Laboratory of Wildlife Management, Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Madoka Ichikawa-Seki
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Shinya Fukumoto
- National Research Center for Protozoan Diseases, University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Motoki Sasaki
- Laboratory of Veterinary Anatomy, University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Hiromi Ikadai
- Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Aomori, 034-8628, Japan
| | - Kodai Kusakisako
- Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Aomori, 034-8628, Japan
| | - Yuma Ohari
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, 001-0020, Japan
| | - Ayako Yoshida
- Laboratory of Veterinary Parasitic Diseases, Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2155, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, 889-2155, Japan
| | - Miwa Sasai
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
- Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Immunoparasitology, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Michael E Grigg
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institutes of Health, National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, MD, 20892, USA
| | - Masahiro Yamamoto
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
- Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan.
- Department of Immunoparasitology, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, 565-0871, Japan.
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Maboko BB, Sibeko-Matjila KP, Pierneef R, Chan WY, Josemans A, Marumo RD, Mbizeni S, Latif AA, Mans BJ. South African Buffalo-Derived Theileria parva Is Distinct From Other Buffalo and Cattle-Derived T. parva. Front Genet 2021; 12:666096. [PMID: 34249088 PMCID: PMC8269612 DOI: 10.3389/fgene.2021.666096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Theileria parva is a protozoan parasite transmitted by the brown-eared ticks, Rhipicephalus appendiculatus and Rhipicephalus zambeziensis. Buffaloes are the parasite's ancestral host, with cattle being the most recent host. The parasite has two transmission modes namely, cattle-cattle and buffalo-cattle transmission. Cattle-cattle T. parva transmission causes East Coast fever (ECF) and January disease syndromes. Buffalo to cattle transmission causes Corridor disease. Knowledge on the genetic diversity of South African T. parva populations will assist in determining its origin, evolution and identify any cattle-cattle transmitted strains. To achieve this, genomic DNA of blood and in vitro culture material infected with South African isolates (8160, 8301, 8200, 9620, 9656, 9679, Johnston, KNP2, HL3, KNP102, 9574, and 9581) were extracted and paired-end whole genome sequencing using Illumina HiSeq 2500 was performed. East and southern African sample data (Chitongo Z2, Katete B2, Kiambu Z464/C12, Mandali Z22H10, Entebbe, Nyakizu, Katumba, Buffalo LAWR, and Buffalo Z5E5) was also added for comparative purposes. Data was analyzed using BWA and SAMtools variant calling with the T. parva Muguga genome sequence used as a reference. Buffalo-derived strains had higher genetic diversity, with twice the number of variants compared to cattle-derived strains, confirming that buffaloes are ancestral reservoir hosts of T. parva. Host specific SNPs, however, could not be identified among the selected 74 gene sequences. Phylogenetically, strains tended to cluster by host with South African buffalo-derived strains clustering with buffalo-derived strains. Among the buffalo-derived strains, South African strains were genetically divergent from other buffalo-derived strains indicating possible geographic sub-structuring. Geographic sub- structuring was also observed within South Africa strains. The knowledge generated from this study indicates that to date, ECF is not circulating in buffalo from South Africa. It also shows that T. parva has historically been present in buffalo from South Africa before the introduction of ECF and was not introduced into buffalo during the ECF epidemic.
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Affiliation(s)
- Boitumelo B Maboko
- Agricultural Research Council, Onderstepoort Veterinary Research, Pretoria, South Africa.,Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
| | | | - Rian Pierneef
- Agricultural Research Council, Biotechnology Platform, Pretoria, South Africa
| | - Wai Y Chan
- Agricultural Research Council, Biotechnology Platform, Pretoria, South Africa
| | - Antoinette Josemans
- Agricultural Research Council, Onderstepoort Veterinary Research, Pretoria, South Africa
| | - Ratselane D Marumo
- Agricultural Research Council, Onderstepoort Veterinary Research, Pretoria, South Africa
| | - Sikhumbuzo Mbizeni
- Agricultural Research Council, Onderstepoort Veterinary Research, Pretoria, South Africa.,Department of Agriculture and Animal Health, University of South Africa, Pretoria, South Africa
| | - Abdalla A Latif
- School of Life Sciences, University of KwaZulu Natal, Durban, South Africa
| | - Ben J Mans
- Agricultural Research Council, Onderstepoort Veterinary Research, Pretoria, South Africa.,Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa.,Department of Life and Consumer Sciences, University of South Africa, Pretoria, South Africa
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