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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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Akafity G, Kumi N, Ashong J. Diagnosis and management of malaria in the intensive care unit. JOURNAL OF INTENSIVE MEDICINE 2024; 4:3-15. [PMID: 38263976 PMCID: PMC10800773 DOI: 10.1016/j.jointm.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/17/2023] [Accepted: 09/02/2023] [Indexed: 01/25/2024]
Abstract
Malaria is responsible for approximately three-quarters of a million deaths in humans globally each year. Most of the morbidity and mortality reported are from Sub-Saharan Africa and Asia, where the disease is endemic. In non-endemic areas, malaria is the most common cause of imported infection and is associated with significant mortality despite recent advancements and investments in elimination programs. Severe malaria often requires intensive care unit admission and can be complicated by cerebral malaria, respiratory distress, acute kidney injury, bleeding complications, and co-infection. Intensive care management includes prompt diagnosis and early initiation of effective antimalarial therapy, recognition of complications, and appropriate supportive care. However, the lack of diagnostic capacities due to limited advances in equipment, personnel, and infrastructure presents a challenge to the effective diagnosis and management of malaria. This article reviews the clinical classification, diagnosis, and management of malaria as relevant to critical care clinicians, highlighting the role of diagnostic capacity, treatment options, and supportive care.
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Affiliation(s)
- George Akafity
- Department of Research, Monitoring, and Evaluation, Cape Coast Teaching Hospital, Cape Coast, Ghana
| | - Nicholas Kumi
- Intensive Care Unit, Department of Critical Care and Anesthesia, Cape Coast Teaching Hospital, Cape Coast, Ghana
| | - Joyce Ashong
- Department of Paediatrics and Child Health, Cape Coast Teaching Hospital, Cape Coast, Ghana
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Yigezu E, Wondale B, Abebe D, Tamiru G, Eligo N, Lindtjørn B, Gadisa E, Tadesse FG, Massebo F. Malaria misdiagnosis in the routine health system in Arba Minch area district in southwest Ethiopia: an implication for malaria control and elimination. Malar J 2023; 22:273. [PMID: 37710252 PMCID: PMC10503053 DOI: 10.1186/s12936-023-04711-2] [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: 02/28/2023] [Accepted: 09/10/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Plasmodium falciparum and Plasmodium vivax are coendemic in Ethiopia, with different proportion in different settings. Microscopy is the diagnostic tool in Ethiopian health centres. Accurate species-specific diagnosis is vital for appropriate treatment of cases to interrupt its transmission. Therefore, this study assessed the status of species-specific misdiagnosis by microscope compared with polymerase chain reaction (PCR). METHODS A health facility based cross-sectional study was conducted from November 2019 to January 2020 in Kolla Shelle Health centre, Arba Minch Zuria district. The study population were suspected malaria cases, who visited the health centre for a diagnosis and treatment. Consecutive microscopy positive cases as well as a sample of microscopically negative cases were included for molecular analysis by polymerase chain reaction (PCR). RESULTS 254 microscopically negative and 193 microscopically positive malaria suspects were included. Of the 193 malaria positive cases, 46.1% [95% confidence interval (CI) 38.9-53.4] (89/193) were P. falciparum infection, 52.3% (95% CI 45.0-59.5) (101/193) were P. vivax infection, and 1.6% (3/193) had mixed infection of P. falciparum and P. vivax. Of the microscopically positive cases of P. falciparum, 3.4% (3/89) were P. vivax and 11.2% (10/89) were mixed infections with P. falciparum and P. vivax and a single case was negative molecularly. Similarly, of the microscopically positive P. vivax cases, 5.9% (6/101) were P. falciparum and 1% (1/101) was mixed infection. Single case was negative by molecular technique. Of the 254 microscopically negative cases, 0.8% were tested positive for P. falciparum and 2% for P. vivax by PCR. Considering molecular technique as a reference, the sensitivity of microscopy for detecting P. falciparum was 89.2% and for P. vivax, it was 91.2%. The specificity of microscopy for detecting P. falciparum was 96.1% and for P. vivax, it was 97.7%. However, the sensitivity of microscopy in detecting mixed infection of P. falciparum and P. vivax was low (8.3%). CONCLUSION There were cases left untreated or inappropriately treated due to the species misidentification. Therefore, to minimize this problem, the gaps in the microscopic-based malaria diagnosis should be identified. It is recommended to regularly monitor the competency of malaria microscopists in the study area to improve species identification and diagnosis accuracy.
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Affiliation(s)
- Engida Yigezu
- Department of Biology, Arba Minch University, Arba Minch, Ethiopia
| | - Biniam Wondale
- Department of Biology, Arba Minch University, Arba Minch, Ethiopia
| | - Daniel Abebe
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Girum Tamiru
- Department of Biology, Arba Minch University, Arba Minch, Ethiopia
| | - Nigatu Eligo
- Department of Biology, Arba Minch University, Arba Minch, Ethiopia
| | - Bernt Lindtjørn
- Centre for International Health, University of Bergen, Bergen, Norway
| | | | | | - Fekadu Massebo
- Department of Biology, Arba Minch University, Arba Minch, Ethiopia
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Genetic Diversity and Phylogenetic Relatedness of Plasmodium ovale curtisi and Plasmodium ovale wallikeri in sub-Saharan Africa. Microorganisms 2022; 10:microorganisms10061147. [PMID: 35744665 PMCID: PMC9227610 DOI: 10.3390/microorganisms10061147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 12/14/2022] Open
Abstract
P. ovale was until recently thought to be a single unique species. However, the deployment of more sensitive tools has led to increased diagnostic sensitivity, including new evidence supporting the presence of two sympatric species: P. ovale curtisi (Poc) and P. ovale wallikeri (Pow). The increased reports and evolution of P. ovale subspecies are concerning for sub-Saharan Africa where the greatest burden of malaria is borne. Employing published sequence data, we set out to decipher the genetic diversity and phylogenetic relatedness of P. ovale curtisi and P. ovale wallikeri using the tryptophan-rich protein and small subunit ribosomal RNA genes from Gabon, Senegal, Ethiopia and Kenya. Higher number of segregating sites were recorded in Poc isolates from Gabon than from Ethiopia, with a similar trend in the number of haplotypes. With regards to Pow, the number of segregating sites and haplotypes from Ethiopia were higher than from those in Gabon. Poc from Kenya, had higher segregating sites (20), and haplotypes (4) than isolates from Senegal (8 and 3 respectively), while nucleotide from Senegal were more diverse (θw = 0.02159; π = 0.02159) than those from Kenya (θw = 0.01452; π = 0.01583). Phylogenetic tree construction reveal two large clades with Poc from Gabon and Ethiopia, and distinct Gabonese and Ethiopian clades on opposite ends. A similar observation was recorded for the phylogeny of Poc isolates from Kenya and Senegal. With such results, there is a high potential that ovale malaria control measures deployed in one country may be effective in the other since parasite from both countries show some degree of relatedness. How this translates to malaria control efforts throughout the continent would be next step deserving more studies.
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Fuehrer HP, Campino S, Sutherland CJ. The primate malaria parasites Plasmodium malariae, Plasmodium brasilianum and Plasmodium ovale spp.: genomic insights into distribution, dispersal and host transitions. Malar J 2022; 21:138. [PMID: 35505317 PMCID: PMC9066925 DOI: 10.1186/s12936-022-04151-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/05/2022] [Indexed: 01/04/2023] Open
Abstract
During the twentieth century, there was an explosion in understanding of the malaria parasites infecting humans and wild primates. This was built on three main data sources: from detailed descriptive morphology, from observational histories of induced infections in captive primates, syphilis patients, prison inmates and volunteers, and from clinical and epidemiological studies in the field. All three were wholly dependent on parasitological information from blood-film microscopy, and The Primate Malarias” by Coatney and colleagues (1971) provides an overview of this knowledge available at that time. Here, 50 years on, a perspective from the third decade of the twenty-first century is presented on two pairs of primate malaria parasite species. Included is a near-exhaustive summary of the recent and current geographical distribution for each of these four species, and of the underlying molecular and genomic evidence for each. The important role of host transitions in the radiation of Plasmodium spp. is discussed, as are any implications for the desired elimination of all malaria species in human populations. Two important questions are posed, requiring further work on these often ignored taxa. Is Plasmodium brasilianum, circulating among wild simian hosts in the Americas, a distinct species from Plasmodium malariae? Can new insights into the genomic differences between Plasmodium ovale curtisi and Plasmodium ovale wallikeri be linked to any important differences in parasite morphology, cell biology or clinical and epidemiological features?
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Affiliation(s)
- Hans-Peter Fuehrer
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Colin J Sutherland
- Department of Infection Biology, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
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Fitri LE, Widaningrum T, Endharti AT, Prabowo MH, Winaris N, Nugraha RYB. Malaria diagnostic update: From conventional to advanced method. J Clin Lab Anal 2022; 36:e24314. [PMID: 35247002 PMCID: PMC8993657 DOI: 10.1002/jcla.24314] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Update diagnostic methods play essential roles in dealing with the current global malaria situation and decreasing malaria incidence. AIM Global malaria control programs require the availability of adequate laboratory tests in the quick and convenient field. RESULTS There are several methods to find out the existence of parasites within the blood. The oldest one is by microscopy, which is still a gold standard, although rapid diagnostic tests (RDTs) have rapidly become a primary diagnostic test in many endemic areas. Because of microscopy and RDTs limitation, novel serological and molecular methods have been developed. Many kinds of polymerase chain reaction (PCR) provide rapid results and higher specificity and sensitivity. The loop-mediated isothermal amplification (LAMP) and biosensing-based molecular techniques as point of care tests (POCT) will become a cost-effective approach to advance diagnostic testing. CONCLUSION Despite conventional techniques are still being used in the field, the exploration and field implementation of advanced techniques for the diagnosis of malaria are still being developed rapidly.
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Affiliation(s)
- Loeki Enggar Fitri
- Department of Parasitology, Faculty of Medicine Universitas Brawijaya, Malang, Indonesia.,Malaria Research Group, Faculty of Medicine Universitas Brawijaya, Malang, Indonesia
| | - Tarina Widaningrum
- Malaria Research Group, Faculty of Medicine Universitas Brawijaya, Malang, Indonesia.,Department of Pharmacology, Faculty of Medicine Universitas Brawijaya, Malang, Indonesia
| | - Agustina Tri Endharti
- Department of Parasitology, Faculty of Medicine Universitas Brawijaya, Malang, Indonesia
| | - Muhammad Hatta Prabowo
- Department of Pharmacy, Faculty of Science Universitas Islam Indonesia, Sleman, Indonesia
| | - Nuning Winaris
- Department of Parasitology, Faculty of Medicine Universitas Brawijaya, Malang, Indonesia.,Malaria Research Group, Faculty of Medicine Universitas Brawijaya, Malang, Indonesia
| | - Rivo Yudhinata Brian Nugraha
- Department of Parasitology, Faculty of Medicine Universitas Brawijaya, Malang, Indonesia.,Malaria Research Group, Faculty of Medicine Universitas Brawijaya, Malang, Indonesia
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