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Choi JW, Ha SO, Kim YJ, Shin JS, Choi MJ, Yu SE, Han J, Park EJ, Park KS, Kang JH. Characterization of Escherichia coli Strains for Novel Production of Plasmodium ovale Lactate Dehydrogenase. Microorganisms 2024; 12:876. [PMID: 38792706 PMCID: PMC11123484 DOI: 10.3390/microorganisms12050876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Malaria is one of the most prevalent diseases worldwide with high incidence and mortality. Among the five species that can infect humans, Plasmodium ovale morphologically resembles Plasmodium vivax, resulting in misidentification and confusion in diagnosis, and is responsible for malarial disease relapse due to the formation of hypnozoites. P. ovale receives relatively less attention compared to other major parasites, such as P. falciparum and P. vivax, primarily due to its lower pathogenicity, mortality rates, and prevalence rates. To efficiently produce lactate dehydrogenase (LDH), a major target for diagnosing malaria, this study used three Escherichia coli strains, BL21(DE3), BL21(DE3)pLysS, and Rosetta(DE3), commonly used for recombinant protein production. These strains were characterized to select the optimal strain for P. ovale LDH (PoLDH) production. Gene cloning for recombinant PoLDH production and transformation of the three strains for protein expression were performed. The optimal PoLDH overexpression and washing buffer conditions in nickel-based affinity chromatography were established to ensure high-purity PoLDH. The yields of PoLDH expressed by the three strains were as follows: BL21(DE3), 7.6 mg/L; BL21(DE3)pLysS, 7.4 mg/L; and Rosetta(DE3), 9.5 mg/L. These findings are expected to be highly useful for PoLDH-specific diagnosis and development of antimalarial therapeutics.
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Affiliation(s)
- Jae-Won Choi
- Department of Biopharmaceutical Sciences, Cheongju University, Cheongju 28160, Republic of Korea
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
- Department of Pharmaceutical and Biopharmaceutical Sciences, Cheongju University, Cheongju 28160, Republic of Korea
| | - Sang-Oh Ha
- Department of Pharmaceutical and Biopharmaceutical Sciences, Cheongju University, Cheongju 28160, Republic of Korea
| | - Yeon-Jun Kim
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
| | - Jun-Seop Shin
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
| | - Min-Ji Choi
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
| | - Si-Eun Yu
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
| | - Junghun Han
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
| | - Eun-Ji Park
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
| | - Kyoung Sik Park
- Department of Biopharmaceutical Sciences, Cheongju University, Cheongju 28160, Republic of Korea
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
- Department of Pharmaceutical and Biopharmaceutical Sciences, Cheongju University, Cheongju 28160, Republic of Korea
| | - Jung Hoon Kang
- Department of Biopharmaceutical Sciences, Cheongju University, Cheongju 28160, Republic of Korea
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
- Department of Pharmaceutical and Biopharmaceutical Sciences, Cheongju University, Cheongju 28160, Republic of Korea
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2
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Sun Y, Xin J, Xu Y, Wang X, Zhao F, Niu C, Liu S. Research Progress on Sesquiterpene Compounds from Artabotrys Plants of Annonaceae. Molecules 2024; 29:1648. [PMID: 38611927 PMCID: PMC11013193 DOI: 10.3390/molecules29071648] [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: 02/29/2024] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
Artabotrys, a pivotal genus within the Annonaceae family, is renowned for its extensive biological significance and medicinal potential. The genus's sesquiterpene compounds have attracted considerable interest from the scientific community due to their structural complexity and diverse biological activities. These compounds exhibit a range of biological activities, including antimalarial, antibacterial, anti-inflammatory analgesic, and anti-tumor properties, positioning them as promising candidates for medical applications. This review aims to summarize the current knowledge on the variety, species, and structural characteristics of sesquiterpene compounds isolated from Artabotrys plants. Furthermore, it delves into their pharmacological activities and underlying mechanisms, offering a comprehensive foundation for future research.
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Affiliation(s)
- Yupei Sun
- School of Pharmacy, Yantai University, Yantai 264005, China; (Y.S.); (Y.X.); (X.W.)
| | - Jianzeng Xin
- School of Life Sciences, Yantai University, Yantai 264005, China;
| | - Yaxi Xu
- School of Pharmacy, Yantai University, Yantai 264005, China; (Y.S.); (Y.X.); (X.W.)
| | - Xuyan Wang
- School of Pharmacy, Yantai University, Yantai 264005, China; (Y.S.); (Y.X.); (X.W.)
| | - Feng Zhao
- School of Pharmacy, Yantai University, Yantai 264005, China; (Y.S.); (Y.X.); (X.W.)
| | - Changshan Niu
- College of Pharmacy, University of Utah, Salt Lake City, UT 84108, USA
| | - Sheng Liu
- School of Pharmacy, Yantai University, Yantai 264005, China; (Y.S.); (Y.X.); (X.W.)
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3
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Higgins M, Manko E, Ward D, Phelan JE, Nolder D, Sutherland CJ, Clark TG, Campino S. New reference genomes to distinguish the sympatric malaria parasites, Plasmodium ovale curtisi and Plasmodium ovale wallikeri. Sci Rep 2024; 14:3843. [PMID: 38360879 PMCID: PMC10869833 DOI: 10.1038/s41598-024-54382-5] [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: 11/03/2023] [Accepted: 02/12/2024] [Indexed: 02/17/2024] Open
Abstract
Despite Plasmodium ovale curtisi (Poc) and wallikeri (Pow) being important human-infecting malaria parasites that are widespread across Africa and Asia, little is known about their genome diversity. Morphologically identical, Poc and Pow are indistinguishable and commonly misidentified. Recent rises in the incidence of Poc/Pow infections have renewed efforts to address fundamental knowledge gaps in their biology, and to develop diagnostic tools to understand their epidemiological dynamics and malaria burden. A major roadblock has been the incompleteness of available reference assemblies (PocGH01, PowCR01; ~ 33.5 Mbp). Here, we applied multiple sequencing platforms and advanced bioinformatics tools to generate new reference genomes, Poc221 (South Sudan; 36.0 Mbp) and Pow222 (Nigeria; 34.3 Mbp), with improved nuclear genome contiguity (> 4.2 Mbp), annotation and completeness (> 99% Plasmodium spp., single copy orthologs). Subsequent sequencing of 6 Poc and 15 Pow isolates from Africa revealed a total of 22,517 and 43,855 high-quality core genome SNPs, respectively. Genome-wide levels of nucleotide diversity were determined to be 2.98 × 10-4 (Poc) and 3.43 × 10-4 (Pow), comparable to estimates for other Plasmodium species. Overall, the new reference genomes provide a robust foundation for dissecting the biology of Poc/Pow, their population structure and evolution, and will contribute to uncovering the recombination barrier separating these species.
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Affiliation(s)
- Matthew Higgins
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Emilia Manko
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Daniel Ward
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jody E Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Debbie Nolder
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- UK Health Security Agency, Malaria Reference Laboratory, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Colin J Sutherland
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- UK Health Security Agency, Malaria Reference Laboratory, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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de Freitas BS, Fernandes GH, Pereira ACEDS, Peixoto HM. Artesunate-mefloquine therapy for uncomplicated Plasmodium falciparum malaria: an updated systematic review and meta-analysis of efficacy and safety. Trans R Soc Trop Med Hyg 2024; 118:84-94. [PMID: 37772768 DOI: 10.1093/trstmh/trad069] [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: 03/21/2023] [Revised: 07/28/2023] [Accepted: 09/03/2023] [Indexed: 09/30/2023] Open
Abstract
To provide a continuous update on the safety and efficacy of artesunate-mefloquine (ASMQ) compared with other artemisinin combination therapy (ACT) schemes used in the treatment of uncomplicated malaria caused by Plasmodium falciparum, this study updated and expanded the results of the systematic literature review published in 2016. Only randomised controlled clinical trials published from 1 January 2001 to 12 June 2023 from five databases were included in this study. The results related to efficacy, expressed through RR, were summarized in meta-analyses, performed according to the compared ACTs and with the intention-to-treat and per-protocol analyses. The results related to safety were synthesized in a descriptive manner. Thirty-two studies were included, of which 24 had been analysed in the 2016 review and eight new ones were added. Although the methodological quality of most studies was considered moderate, the body of evidence gathered indicates that ASMQ continues to be safe and effective for the treatment of uncomplicated infections caused by P. falciparum compared with other ACTs. However, the inclusion of two new studies, which identified failure rates exceeding 10%, suggests a possible reduction in the efficacy of ASMQ in the analysed locations. The incidence of serious adverse effects, such as seizure, encephalopathy and cardiac arrhythmia, was infrequent in both the ASMQ group and the comparison groups. After including new evidence, ASMQ is still recommended as a first-line treatment of uncomplicated malaria caused by P. falciparum, although local aspects need to be considered.
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Affiliation(s)
- Beatriz Sales de Freitas
- Faculty of Medicine, University of Brasilia (UnB), Brasilia, University Campus Darcy Ribeiro, Asa Norte, Brasília, DF 70910-900, Brazil
| | - Gabriel Haiek Fernandes
- Faculty of Medicine, University of Brasilia (UnB), Brasilia, University Campus Darcy Ribeiro, Asa Norte, Brasília, DF 70910-900, Brazil
| | | | - Henry Maia Peixoto
- Faculty of Medicine, University of Brasilia (UnB), Brasilia, University Campus Darcy Ribeiro, Asa Norte, Brasília, DF 70910-900, Brazil
- Centre for Tropical Medicine, University of Brasília (UnB), University Campus Darcy Ribeiro, Asa Norte, Brasília, DF 70904970 Brazil
- National Institute for Science and Technology for Health Technology Assessment (IATS/CNPq), Porto Alegre, Rio Grande do Sul 90035-903, Brazil
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5
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Cepeda AS, Mello B, Pacheco MA, Luo Z, Sullivan SA, Carlton JM, Escalante AA. The Genome of Plasmodium gonderi: Insights into the Evolution of Human Malaria Parasites. Genome Biol Evol 2024; 16:evae027. [PMID: 38376987 PMCID: PMC10901558 DOI: 10.1093/gbe/evae027] [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: 08/30/2023] [Revised: 12/21/2023] [Accepted: 02/03/2024] [Indexed: 02/22/2024] Open
Abstract
Plasmodium species causing malaria in humans are not monophyletic, sharing common ancestors with nonhuman primate parasites. Plasmodium gonderi is one of the few known Plasmodium species infecting African old-world monkeys that are not found in apes. This study reports a de novo assembled P. gonderi genome with complete chromosomes. The P. gonderi genome shares codon usage, syntenic blocks, and other characteristics with the human parasites Plasmodium ovale s.l. and Plasmodium malariae, also of African origin, and the human parasite Plasmodium vivax and species found in nonhuman primates from Southeast Asia. Using phylogenetically aware methods, newly identified syntenic blocks were found enriched with conserved metabolic genes. Regions outside those blocks harbored genes encoding proteins involved in the vertebrate host-Plasmodium relationship undergoing faster evolution. Such genome architecture may have facilitated colonizing vertebrate hosts. Phylogenomic analyses estimated the common ancestor between P. vivax and an African ape parasite P. vivax-like, within the Asian nonhuman primates parasites clade. Time estimates incorporating P. gonderi placed the P. vivax and P. vivax-like common ancestor in the late Pleistocene, a time of active migration of hominids between Africa and Asia. Thus, phylogenomic and time-tree analyses are consistent with an Asian origin for P. vivax and an introduction of P. vivax-like into Africa. Unlike other studies, time estimates for the clade with Plasmodium falciparum, the most lethal human malaria parasite, coincide with their host species radiation, African hominids. Overall, the newly assembled genome presented here has the quality to support comparative genomic investigations in Plasmodium.
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Affiliation(s)
- Axl S Cepeda
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA
| | - Beatriz Mello
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA
| | - Zunping Luo
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Steven A Sullivan
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Jane M Carlton
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA
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6
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Poespoprodjo JR, Douglas NM, Ansong D, Kho S, Anstey NM. Malaria. Lancet 2023; 402:2328-2345. [PMID: 37924827 DOI: 10.1016/s0140-6736(23)01249-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 05/22/2023] [Accepted: 06/16/2023] [Indexed: 11/06/2023]
Abstract
Malaria is resurging in many African and South American countries, exacerbated by COVID-19-related health service disruption. In 2021, there were an estimated 247 million malaria cases and 619 000 deaths in 84 endemic countries. Plasmodium falciparum strains partly resistant to artemisinins are entrenched in the Greater Mekong region and have emerged in Africa, while Anopheles mosquito vectors continue to evolve physiological and behavioural resistance to insecticides. Elimination of Plasmodium vivax malaria is hindered by impractical and potentially toxic antirelapse regimens. Parasitological diagnosis and treatment with oral or parenteral artemisinin-based therapy is the mainstay of patient management. Timely blood transfusion, renal replacement therapy, and restrictive fluid therapy can improve survival in severe malaria. Rigorous use of intermittent preventive treatment in pregnancy and infancy and seasonal chemoprevention, potentially combined with pre-erythrocytic vaccines endorsed by WHO in 2021 and 2023, can substantially reduce malaria morbidity. Improved surveillance, better access to effective treatment, more labour-efficient vector control, continued drug development, targeted mass drug administration, and sustained political commitment are required to achieve targets for malaria reduction by the end of this decade.
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Affiliation(s)
- Jeanne Rini Poespoprodjo
- Centre for Child Health and Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Timika Malaria Research Facility, Papuan Health and Community Development Foundation, Timika, Indonesia; Mimika District Hospital and District Health Authority, Timika, Indonesia; Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
| | - Nicholas M Douglas
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Department of Infectious Diseases, Christchurch Hospital, Te Whatu Ora Waitaha, Christchurch, New Zealand; Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Daniel Ansong
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Steven Kho
- Timika Malaria Research Facility, Papuan Health and Community Development Foundation, Timika, Indonesia; Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Department of Infectious Diseases, Royal Darwin Hospital, Darwin, NT, Australia
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7
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Potlapalli VR, Muller MS, Ngasala B, Ali IM, Na YB, Williams DR, Kharabora O, Chhetri S, Liu MS, Carey-Ewend K, Lin FC, Mathias D, Tarimo BB, Juliano JJ, Parr JB, Lin JT. Real-time PCR detection of mixed Plasmodium ovale curtisi and wallikeri infections in human and mosquito hosts. PLoS Negl Trop Dis 2023; 17:e0011274. [PMID: 38064489 PMCID: PMC10732364 DOI: 10.1371/journal.pntd.0011274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/20/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023] Open
Abstract
Plasmodium ovale curtisi (Poc) and Plasmodium ovale wallikeri (Pow) represent distinct non-recombining Plasmodium species that are increasing in prevalence in sub-Saharan Africa. Though they circulate sympatrically, co-infection within human and mosquito hosts has rarely been described. Separate 18S rRNA real-time PCR assays that detect Poc and Pow were modified to allow species determination in parallel under identical cycling conditions. The lower limit of detection was 0.6 plasmid copies/μL (95% CI 0.4-1.6) for Poc and 4.5 plasmid copies/μL (95% CI 2.7-18) for Pow, or 0.1 and 0.8 parasites/μL, respectively, assuming 6 copies of 18s rRNA per genome. However, the assays showed cross-reactivity at concentrations greater than 103 plasmid copies/μL (roughly 200 parasites/μL). Mock mixtures were used to establish criteria for classifying mixed Poc/Pow infections that prevented false-positive detection while maintaining sensitive detection of the minority ovale species down to 100 copies/μL (<1 parasite/μL). When the modified real-time PCR assays were applied to field-collected blood samples from Tanzania and Cameroon, species identification by real-time PCR was concordant with nested PCR in 19 samples, but additionally detected two mixed Poc/Pow infections where nested PCR detected a single Po species. When real-time PCR was applied to oocyst-positive Anopheles midguts saved from mosquitoes fed on P. ovale-infected persons, mixed Poc/Pow infections were detected in 11/14 (79%). Based on these results, 8/9 P. ovale carriers transmitted both P. ovale species to mosquitoes, though both Po species could only be detected in the blood of two carriers. The described real-time PCR approach can be used to identify the natural occurrence of mixed Poc/Pow infections in human and mosquito hosts and reveals that such co-infections and co-transmission are likely more common than appreciated.
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Affiliation(s)
- Varun R. Potlapalli
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Meredith S. Muller
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Billy Ngasala
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Innocent Mbulli Ali
- Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Yu Bin Na
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Danielle R. Williams
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Oksana Kharabora
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Srijana Chhetri
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Mei S. Liu
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Kelly Carey-Ewend
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Feng-Chang Lin
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Derrick Mathias
- Florida Medical Entomology Laboratory, Institute of Food & Agricultural Sciences, University of Florida, Vero Beach, Florida United States of America
| | - Brian B. Tarimo
- Vector Immunity and Transmission Biology Unit, Department of Environmental Health and Ecological Sciences, Ifakara Health Institute-Bagamoyo Office, Bagamoyo, Tanzania
| | - Jonathan J. Juliano
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jonathan B. Parr
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Jessica T. Lin
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
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8
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Phelan JE, Turkiewicz A, Manko E, Thorpe J, Vanheer LN, van de Vegte-Bolmer M, Ngoc NTH, Binh NTH, Thieu NQ, Gitaka J, Nolder D, Beshir KB, Dombrowski JG, Di Santi SM, Bousema T, Sutherland CJ, Campino S, Clark TG. Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control. Genome Med 2023; 15:96. [PMID: 37950308 PMCID: PMC10636944 DOI: 10.1186/s13073-023-01247-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Malaria continues to be a major threat to global public health. Whole genome sequencing (WGS) of the underlying Plasmodium parasites has provided insights into the genomic epidemiology of malaria. Genome sequencing is rapidly gaining traction as a diagnostic and surveillance tool for clinical settings, where the profiling of co-infections, identification of imported malaria parasites, and detection of drug resistance are crucial for infection control and disease elimination. To support this informatically, we have developed the Malaria-Profiler tool, which rapidly (within minutes) predicts Plasmodium species, geographical source, and resistance to antimalarial drugs directly from WGS data. RESULTS The online and command line versions of Malaria-Profiler detect ~ 250 markers from genome sequences covering Plasmodium speciation, likely geographical source, and resistance to chloroquine, sulfadoxine-pyrimethamine (SP), and other anti-malarial drugs for P. falciparum, but also providing mutations for orthologous resistance genes in other species. The predictive performance of the mutation library was assessed using 9321 clinical isolates with WGS and geographical data, with most being single-species infections (P. falciparum 7152/7462, P. vivax 1502/1661, P. knowlesi 143/151, P. malariae 18/18, P. ovale ssp. 5/5), but co-infections were identified (456/9321; 4.8%). The accuracy of the predicted geographical profiles was high to both continental (96.1%) and regional levels (94.6%). For P. falciparum, markers were identified for resistance to chloroquine (49.2%; regional range: 24.5% to 100%), sulfadoxine (83.3%; 35.4- 90.5%), pyrimethamine (85.4%; 80.0-100%) and combined SP (77.4%). Markers associated with the partial resistance of artemisinin were found in WGS from isolates sourced from Southeast Asia (30.6%). CONCLUSIONS Malaria-Profiler is a user-friendly tool that can rapidly and accurately predict the geographical regional source and anti-malarial drug resistance profiles across large numbers of samples with WGS data. The software is flexible with modifiable bioinformatic pipelines. For example, it is possible to select the sequencing platform, display specific variants, and customise the format of outputs. With the increasing application of next-generation sequencing platforms on Plasmodium DNA, Malaria-Profiler has the potential to be integrated into point-of-care and surveillance settings, thereby assisting malaria control. Malaria-Profiler is available online (bioinformatics.lshtm.ac.uk/malaria-profiler) and as standalone software ( https://github.com/jodyphelan/malaria-profiler ).
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Affiliation(s)
- Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK.
| | - Anna Turkiewicz
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Emilia Manko
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Joseph Thorpe
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Leen N Vanheer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Marga van de Vegte-Bolmer
- Department of Medical Microbiology and Radboud Center for Infectious Diseases, Radboud University Medical Center, University of Nijmegen, Nijmegen, The Netherlands
| | - Nguyen Thi Hong Ngoc
- Molecular Biology Department, Parasitology and Entomology, Vietnam National Institute of Malariology, Hanoi, Vietnam
| | - Nguyen Thi Huong Binh
- Molecular Biology Department, Parasitology and Entomology, Vietnam National Institute of Malariology, Hanoi, Vietnam
| | - Nguyen Quang Thieu
- Molecular Biology Department, Parasitology and Entomology, Vietnam National Institute of Malariology, Hanoi, Vietnam
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Gen. Kago Rd, Thika, Kenya
| | - Debbie Nolder
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
- UK Health Security Agency Malaria Reference Laboratory, LSHTM, London, WC1E 7HT, UK
| | - Khalid B Beshir
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Jamille G Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, Univ. of São Paulo, São Paulo, Brazil
| | - Silvia Maria Di Santi
- School of Medicine, Instituto de Medicina Tropical, University of São Paulo, São Paulo, Brazil
| | - Teun Bousema
- Department of Medical Microbiology and Radboud Center for Infectious Diseases, Radboud University Medical Center, University of Nijmegen, Nijmegen, The Netherlands
| | - Colin J Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
- UK Health Security Agency Malaria Reference Laboratory, LSHTM, London, WC1E 7HT, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK.
- Faculty of Epidemiology and Population Health, LSHTM, London, WC1E 7HT, UK.
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9
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Potlapalli V, Muller MS, Ngasala B, Ali IM, Na YB, Williams DR, Kharabora O, Chhetri S, Liu MS, Carey-Ewend K, Lin FC, Mathias D, Tarimo BB, Juliano JJ, Parr J, Lin JT. Real-time PCR detection of mixed Plasmodium ovale curtisi and wallikeri species infections in human and mosquito hosts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535020. [PMID: 37034766 PMCID: PMC10081274 DOI: 10.1101/2023.03.31.535020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Plasmodium ovale curtisi (Poc) and Plasmodium ovale wallikeri (Pow) represent distinct non-recombining malaria species that are increasing in prevalence in sub-Saharan Africa. Though they circulate sympatrically, co-infection within human and mosquito hosts has rarely been described. Separate 18S rRNA real-time PCR assays that detect Poc and Pow were modified to allow species determination in parallel under identical cycling conditions. The lower limit of detection was 0.6 plasmid copies/μL (95% CI 0.4-1.6) for Poc and 4.5 plasmid copies/μL (95% CI( 2.7- 18) for Pow, or 0.1 and 0.8 parasites/μL, respectively, assuming 6 copies of 18s rRNA per genome. However, the assays showed cross-reactivity at concentrations greater than 103 plasmid copies/μL (roughly 200 parasites/μL). Mock mixtures were used to establish criteria for classifying mixed Poc/Pow infections that prevented false-positive detection while maintaining sensitive detection of the minority ovale species down to 10° copies/μL (<1 parasite/μL). When the modified real-time PCR assays were applied to field-collected blood samples from Tanzania and Cameroon, species identification by real-time PCR was concordant with nested PCR, but additionally detected two mixed Poc/Pow infections where nested PCR detected a single Po species. When real-time PCR was applied to 14 oocyst-positive Anopheles midguts saved from mosquitoes fed on P. ovate-infected persons, mixed Poc/Pow infections were detected in 11 (79%). Based on these results, 8/9 P. ovate carriers transmitted both P. ovate species to mosquitoes, though both Po species could only be detected in the blood of two carriers. The described real-time PCR approach can be used to identify the natural occurrence of mixed Poc/Pow infections in human and mosquito hosts and reveals that such co-infections and co-transmission are likely more common than appreciated.
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Affiliation(s)
- Varun Potlapalli
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - Meredith S Muller
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - Billy Ngasala
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Innocent Mbulli Ali
- Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Yu Bin Na
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - Danielle R Williams
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC USA
| | - Oksana Kharabora
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - Srijana Chhetri
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - Mei S Liu
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - Kelly Carey-Ewend
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA
| | - Feng-Chang Lin
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA
| | - Derrick Mathias
- Florida Medical Entomology Laboratory, Institute of Food & Agricultural Sciences, University of Florida, Vero Beach, FL USA
| | - Brian B Tarimo
- Vector Immunity and Transmission Biology Unit, Department of Environmental Health and Ecological Sciences, Ifakara Health Institute-Bagamoyo Office, Bagamoyo, Tanzania
| | - Jonathan J Juliano
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA
| | - Jonathan Parr
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - Jessica T Lin
- Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA
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10
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Johora FT, Kibria MG, Fuehrer HP, Alam MS. A Case of Plasmodium malariae in Bangladesh: A Representation of the Suboptimal Performance of Rapid Diagnostic Approaches in Malaria Elimination Settings. Pathogens 2022; 11:pathogens11101072. [PMID: 36297130 PMCID: PMC9607251 DOI: 10.3390/pathogens11101072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/07/2022] [Accepted: 09/16/2022] [Indexed: 11/29/2022] Open
Abstract
Plasmodium malariae is a neglected human malaria parasite with low parasitemia that often results in the misdiagnosis and underestimation of the actual disease burden of this pathogen. Microscopy is the best diagnostic tool, despite the fact that rapid diagnostic tests (RDTs) are the best surveillance tool for malaria diagnosis in many rural areas for their ease of use in elimination settings. For parasite antigen detection other than P. falciparum, RDTs depend on essential glycolytic Plasmodium proteins, i.e., Plasmodium lactate dehydrogenase (pLDH) and Plasmodium aldolase (pAldo) antigens. There is a lack of species-specific test kits for P. malariae, and overall, its rapid antigenic test accuracy is questionable. False negative results can accelerate the burden of asymptomatic malaria infection and transmission. Here, we report a case of a malaria patient in Bangladesh infected with P. malariae who tested negative on pLDH and pAldo based RDTs. This case provides useful information for health providers to be aware of possible RDT failure and also for the future development of analytically sensitive test kits for P. malariae.
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Affiliation(s)
- Fatema Tuj Johora
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Mohammad Golam Kibria
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
- Department of Medical Biochemistry, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hans-Peter Fuehrer
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Mohammad Shafiul Alam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
- Correspondence:
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