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Li M, Liu T, Wang Y, Zhang L, Lu F, Xia J, Zheng M, Zhang M, Wang B, Xu Y. Immunogenic and diagnostic potential of recombinant apical membrane antigen-1 from Plasmodium malariae. Diagn Microbiol Infect Dis 2024; 110:116480. [PMID: 39163788 DOI: 10.1016/j.diagmicrobio.2024.116480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/22/2024]
Abstract
The apical membrane antigen-1 (AMA-1) is a crucial target for malaria management and prevention strategies. While the immunogenicity of AMA-1 has been extensively studied for Plasmodium falciparum and Plasmodium vivax, there is a notable scarcity of information for Plasmodium malariae. In this study, recombinant PmAMA-1 was expressed in Escherichia coli, and its integrity was confirmed via western blotting and indirect immunofluorescence assays. Immunization of BALB/c mice with rPmAMA-1 emulsified in Freund's adjuvant resulted in significantly elevated specific IgG antibodies, predominantly IgG1. The immune response exhibited Th1, Th2, and Th17 phenotypes, with a notable Th1 bias. Antisera from immunized mice effectively recognized native PmAMA-1 on P. malariae. These results suggest that PmAMA-1 is a promising target for both vaccine development and diagnostic applications for P. malariae infections, offering dual preventive and diagnostic benefits in malaria control.
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Affiliation(s)
- Moyan Li
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Tingting Liu
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Yuerong Wang
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Anhui, China; Institute of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Luwen Zhang
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Anhui, China; Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, Anhui, China
| | - Fanbo Lu
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Anhui, China; Department of Clinical laboratory, the Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jinxing Xia
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Meijuan Zheng
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Min Zhang
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Bo Wang
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Anhui, China.
| | - Yuanhong Xu
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Anhui, China.
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Zhang T, Li H, Jiang M, Hou H, Gao Y, Li Y, Wang F, Wang J, Peng K, Liu YX. Nanopore sequencing: flourishing in its teenage years. J Genet Genomics 2024:S1673-8527(24)00244-3. [PMID: 39293510 DOI: 10.1016/j.jgg.2024.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 09/20/2024]
Abstract
Over the past decade, nanopore sequencing has experienced significant advancements and changes, transitioning from an initially emerging technology to a significant instrument in the field of genomic sequencing. However, as advancements in next-generation sequencing technology persist, nanopore sequencing also improves. This paper reviews the developments, applications, and outlook on nanopore sequencing technology. Currently, nanopore sequencing supports both DNA and RNA sequencing, making it widely applicable in areas such as telomere-to-telomere (T2T) genome assembly, direct RNA sequencing (DRS), and metagenomics. The openness and versatility of nanopore sequencing have established it as a preferred option for an increasing number of research teams, signaling a transformative influence on life science research. As nanopore sequencing technology advances, it provides a faster, more cost-effective approach with extended read lengths, demonstrating the significant potential for complex genome assembly, pathogen detection, environmental monitoring, and human disease research, offering a fresh perspective in sequencing technologies.
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Affiliation(s)
- Tianyuan Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China; Wuhan Benagen Technology Co., Ltd, Wuhan, 430000, China
| | - Hanzhou Li
- Wuhan Benagen Technology Co., Ltd, Wuhan, 430000, China
| | - Mian Jiang
- Wuhan Benagen Technology Co., Ltd, Wuhan, 430000, China
| | - Huiyu Hou
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yunyun Gao
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yali Li
- Wuhan Benagen Technology Co., Ltd, Wuhan, 430000, China
| | - Fuhao Wang
- Wuhan Benagen Technology Co., Ltd, Wuhan, 430000, China
| | - Jun Wang
- Wuhan Benagen Technology Co., Ltd, Wuhan, 430000, China
| | - Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
| | - Yong-Xin Liu
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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3
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de Cesare M, Mwenda M, Jeffreys AE, Chirwa J, Drakeley C, Schneider K, Mambwe B, Glanz K, Ntalla C, Carrasquilla M, Portugal S, Verity RJ, Bailey JA, Ghinai I, Busby GB, Hamainza B, Hawela M, Bridges DJ, Hendry JA. Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing. Nat Commun 2024; 15:1413. [PMID: 38360754 PMCID: PMC10869361 DOI: 10.1038/s41467-024-45688-z] [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: 03/06/2023] [Accepted: 01/31/2024] [Indexed: 02/17/2024] Open
Abstract
Genomic surveillance of Plasmodium falciparum malaria can provide policy-relevant information about antimalarial drug resistance, diagnostic test failure, and the evolution of vaccine targets. Yet the large and low complexity genome of P. falciparum complicates the development of genomic methods, while resource constraints in malaria endemic regions can limit their deployment. Here, we demonstrate an approach for targeted nanopore sequencing of P. falciparum from dried blood spots (DBS) that enables cost-effective genomic surveillance of malaria in low-resource settings. We release software that facilitates flexible design of amplicon sequencing panels and use this software to design two target panels for P. falciparum. The panels generate 3-4 kbp reads for eight and sixteen targets respectively, covering key drug-resistance associated genes, diagnostic test antigens, polymorphic markers and the vaccine target csp. We validate our approach on mock and field samples, demonstrating robust sequencing coverage, accurate variant calls within coding sequences, the ability to explore P. falciparum within-sample diversity and to detect deletions underlying rapid diagnostic test failure.
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Affiliation(s)
- Mariateresa de Cesare
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | | | - Anna E Jeffreys
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | - Jacob Chirwa
- National Malaria Elimination Centre, Chainama, Lusaka, Zambia
| | | | | | | | - Karolina Glanz
- Max Planck Institute for Infection Biology, Berlin, Germany
| | | | | | | | | | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine and Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Isaac Ghinai
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | - George B Busby
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | - Busiku Hamainza
- National Malaria Elimination Centre, Chainama, Lusaka, Zambia
| | - Moonga Hawela
- National Malaria Elimination Centre, Chainama, Lusaka, Zambia
| | | | - Jason A Hendry
- Nuffield Department of Medicine, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK.
- Max Planck Institute for Infection Biology, Berlin, Germany.
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Delandre O, Lamer O, Loreau JM, Papa Mze N, Fonta I, Mosnier J, Gomez N, Javelle E, Pradines B. Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones ( Pf3D7, PfW2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification. BIOLOGY 2024; 13:89. [PMID: 38392307 PMCID: PMC10886359 DOI: 10.3390/biology13020089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024]
Abstract
Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technology from Oxford Nanopore Technologies can produce long-read sequences, in contrast to previous short-read technologies used as the gold standard to sequence Plasmodium. Two clones of P. falciparum (Pf3D7 and PfW2) were sequenced in long-read using the PromethION sequencer from Oxford Nanopore Technologies without genomic amplification. This made it possible to create a processing analysis pipeline for human Plasmodium with ONT Fastq only. De novo assembly revealed N50 lengths of 18,488 kb and 17,502 kb for the Pf3D7 and PfW2, respectively. The genome size was estimated at 23,235,407 base pairs for the Pf3D7 clone and 21,712,038 base pairs for the PfW2 clone. The average genome coverage depth was estimated at 787X and 653X for the Pf3D7 and PfW2 clones, respectively. This study proposes an assembly processing pipeline for the human Plasmodium genome using software adapted to large ONT data and the high AT percentage of Plasmodium. This search provides all the parameters which were optimized for use with the software selected in the pipeline.
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Affiliation(s)
- Océane Delandre
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Ombeline Lamer
- Unité Bactériologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France
- Aix-Marseille Univ, INSERM, SSA, IRBA, MCT, 13005 Marseille, France
| | - Jean-Marie Loreau
- French Armed Forces Center for Epidemiology and Public Health (CESPA), 13014 Marseille, France
| | - Nasserdine Papa Mze
- Service de Biologie, Unité de Microbiologie, Hôpital Mignot, Centre Hospitalier de Versailles, 78150 Versailles, France
| | - Isabelle Fonta
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Joel Mosnier
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Nicolas Gomez
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Emilie Javelle
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
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