Bovine Piroplasma Populations in the Philippines Characterized Using Targeted Amplicon Deep Sequencing
Molecular assays and capillary electrophoresis sequencing have been used to identify parasites in livestock. The low sample capacity, which increases labor and processing time, is one drawback. Targeted amplicon sequencing (Ampliseq) uses the fast and large sample capacity platform to identify paras...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-10-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/10/2584 |
| _version_ | 1797572819371950080 |
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| author | Eloiza May Galon Adrian Miki Macalanda Tatsuki Sugi Kyoko Hayashida Naoko Kawai Taishi Kidaka Rochelle Haidee Ybañez Paul Franck Adjou Moumouni Aaron Edmond Ringo Hang Li Shengwei Ji Junya Yamagishi Adrian Ybañez Xuenan Xuan |
| author_facet | Eloiza May Galon Adrian Miki Macalanda Tatsuki Sugi Kyoko Hayashida Naoko Kawai Taishi Kidaka Rochelle Haidee Ybañez Paul Franck Adjou Moumouni Aaron Edmond Ringo Hang Li Shengwei Ji Junya Yamagishi Adrian Ybañez Xuenan Xuan |
| author_sort | Eloiza May Galon |
| collection | DOAJ |
| description | Molecular assays and capillary electrophoresis sequencing have been used to identify parasites in livestock. The low sample capacity, which increases labor and processing time, is one drawback. Targeted amplicon sequencing (Ampliseq) uses the fast and large sample capacity platform to identify parasites in the target host, overcoming this limitation. DNA was extracted from 162 whole blood samples collected from cattle in three provinces in the Philippines. Using Illumina’s Miseq platform, the V4 hypervariable region of the piroplasma 18S rRNA gene was amplified and sequenced. The AMPtk pipeline was used to obtain distinct amplicon sequence variants (ASVs) and the NCBI BLAST non-redundant database was used to assign taxonomy. In total, 95 (58.64%) samples were positive for piroplasma. Using the AMPTk pipeline, 2179 ASVs were obtained. A total of 79 distinct ASVs were obtained after clustering and filtering, which belonged to genera <i>Babesia</i> (n = 58), <i>Theileria</i> (n = 17), <i>Hepatozoon</i> (n = 2), and <i>Sarcocystis</i> (n = 2). The ASV top hits were composed of 10 species: <i>Babesia bovis</i>, <i>B. bigemina</i>, <i>Theileria orientalis</i>, <i>Babesia</i> sp., <i>Hepatozoon canis</i>, <i>Sarcocystis cruzi</i>, <i>T. annulata</i>, <i>T. equi</i>, <i>T. mutans</i>, and <i>Theileria</i> sp. Thung Song. The results generated in this study demonstrated the applicability of Ampliseq in detecting piroplasmid parasites infecting cattle in the Philippines. |
| first_indexed | 2024-03-10T21:01:19Z |
| format | Article |
| id | doaj.art-1f3c2c9f47c045baa0ccfcda9dafd38c |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T21:01:19Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-1f3c2c9f47c045baa0ccfcda9dafd38c2023-11-19T17:28:59ZengMDPI AGMicroorganisms2076-26072023-10-011110258410.3390/microorganisms11102584Bovine Piroplasma Populations in the Philippines Characterized Using Targeted Amplicon Deep SequencingEloiza May Galon0Adrian Miki Macalanda1Tatsuki Sugi2Kyoko Hayashida3Naoko Kawai4Taishi Kidaka5Rochelle Haidee Ybañez6Paul Franck Adjou Moumouni7Aaron Edmond Ringo8Hang Li9Shengwei Ji10Junya Yamagishi11Adrian Ybañez12Xuenan Xuan13National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, JapanCollege of Veterinary Medicine and Biomedical Sciences, Cavite State University, Indang 4122, PhilippinesInternational Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, JapanInternational Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, JapanInternational Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, JapanInternational Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, JapanNational Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, JapanNational Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, JapanNational Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, JapanNational Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, JapanNational Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, JapanInternational Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, JapanInstitute of Molecular Genetics, Parasitology, and Vector-Borne Diseases—Main Campus, Cebu Technological University, Cebu City 6000, PhilippinesNational Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, JapanMolecular assays and capillary electrophoresis sequencing have been used to identify parasites in livestock. The low sample capacity, which increases labor and processing time, is one drawback. Targeted amplicon sequencing (Ampliseq) uses the fast and large sample capacity platform to identify parasites in the target host, overcoming this limitation. DNA was extracted from 162 whole blood samples collected from cattle in three provinces in the Philippines. Using Illumina’s Miseq platform, the V4 hypervariable region of the piroplasma 18S rRNA gene was amplified and sequenced. The AMPtk pipeline was used to obtain distinct amplicon sequence variants (ASVs) and the NCBI BLAST non-redundant database was used to assign taxonomy. In total, 95 (58.64%) samples were positive for piroplasma. Using the AMPTk pipeline, 2179 ASVs were obtained. A total of 79 distinct ASVs were obtained after clustering and filtering, which belonged to genera <i>Babesia</i> (n = 58), <i>Theileria</i> (n = 17), <i>Hepatozoon</i> (n = 2), and <i>Sarcocystis</i> (n = 2). The ASV top hits were composed of 10 species: <i>Babesia bovis</i>, <i>B. bigemina</i>, <i>Theileria orientalis</i>, <i>Babesia</i> sp., <i>Hepatozoon canis</i>, <i>Sarcocystis cruzi</i>, <i>T. annulata</i>, <i>T. equi</i>, <i>T. mutans</i>, and <i>Theileria</i> sp. Thung Song. The results generated in this study demonstrated the applicability of Ampliseq in detecting piroplasmid parasites infecting cattle in the Philippines.https://www.mdpi.com/2076-2607/11/10/2584piroplasmaamplicon sequencingNGScattlePhilippines |
| spellingShingle | Eloiza May Galon Adrian Miki Macalanda Tatsuki Sugi Kyoko Hayashida Naoko Kawai Taishi Kidaka Rochelle Haidee Ybañez Paul Franck Adjou Moumouni Aaron Edmond Ringo Hang Li Shengwei Ji Junya Yamagishi Adrian Ybañez Xuenan Xuan Bovine Piroplasma Populations in the Philippines Characterized Using Targeted Amplicon Deep Sequencing Microorganisms piroplasma amplicon sequencing NGS cattle Philippines |
| title | Bovine Piroplasma Populations in the Philippines Characterized Using Targeted Amplicon Deep Sequencing |
| title_full | Bovine Piroplasma Populations in the Philippines Characterized Using Targeted Amplicon Deep Sequencing |
| title_fullStr | Bovine Piroplasma Populations in the Philippines Characterized Using Targeted Amplicon Deep Sequencing |
| title_full_unstemmed | Bovine Piroplasma Populations in the Philippines Characterized Using Targeted Amplicon Deep Sequencing |
| title_short | Bovine Piroplasma Populations in the Philippines Characterized Using Targeted Amplicon Deep Sequencing |
| title_sort | bovine piroplasma populations in the philippines characterized using targeted amplicon deep sequencing |
| topic | piroplasma amplicon sequencing NGS cattle Philippines |
| url | https://www.mdpi.com/2076-2607/11/10/2584 |
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